The Redesign of a Reengineering Class

This paper reports on a redesign of an MBA Process Reengineering course from the traditional 16-week format to a weekend format. A survey was conducted to compare student learning of the educational objectives in the two formats. In addition, observations from both students and the instructor are discussed. The paper recommends such a format for additional intensive course opportunities

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

MAVEN Deliverable 7.2: Impact Assessment - Technical Report

This deliverable focuses on an important topic within the MAVEN project - evaluation of the project impact. This is an important step that will allow us to say what the results and impact of the different technologies, functionalities as well as assumptions are. It covers different dimensions of the impact assessment as stated in the Deliverable D7.1 - Impact assessment plan [10]. The field tests proved that the technology in the vehicle works together with the infrastructure and the solution is technically feasible. This was demonstrated also during particular events and is reported in the attached test protocols. At the same time, the emulation and simulation in Dominion software proved the functionality, for example with respect to the cooperative perception or safety indicators. The tests also proved that the key performance indicator "minimum time to the collision" decreases when applying the cooperative sensing. Also, the number of human interventions needed was zero in all the tests. This deliverable also discussed selected results of a detailed user survey aiming at understanding the expected impacts and transition of automated vehicles. The overall number of respondents reached 209. The responses have revealed some interesting facts. For example, over 80% of the respondents believe that CAVs will decrease the number of traffic accidents. Similarly, about 70% of the respondents expect improvements in traffic congestions. Over 82% of respondents declared that they would accept some detour when driving if it helps the overall traffic situation. The literature review, however, indicated that autonomous vehicles will have either a positive or a negative effect on the environment, depending on the policies. For example, opening cars as a mode of transport to new user groups (seniors, children etc.) together with improvements of the traffic, flow parameters can increase the traffic volume on roads. Policy makers shall focus on the integration of the CAVs into a broader policy concept including car or ride-sharing, electromobility and others. In order to evaluate the transition, for example, the influence of different penetration rates of CAVs on the performance, a microscopic traffic simulation was performed. Here the particular MAVEN use cases, as well as their combination, was addressed. The results of the simulation are rather promising. The potential for improvements in traffic performance is clearly there. It was demonstrated that a proper integration of CAVs into city traffic management can, for example, help with respect to the environmental goals (Climate Action of the European Commission) and reduce CO2 emissions by up to 12 % (a combination of GLOSA and signal optimization). On corridors with a green wave, a capacity increase of up to 34% was achieved. The conclusions from this project can be used not only by other researchers but mainly by traffic managers and decision-makers in cities. The findings can get a better idea about the real impacts of particular use cases (such as green wave, GLOSA and others) in the cities. An important added value is also the focus on the transition phase. It was demonstrated that already for lower penetration rates (even 20% penetration of automated vehicles), there are significant improvements in traffic performance. For example, the platooning leads to a decrease of CO2 emissions of 2,6% or the impact indicator by 17,7%

MR Imaging Radiomics Signatures for Predicting the Risk of Breast Cancer Recurrence as Given by Research Versions of MammaPrint, Oncotype DX, and PAM50 Gene Assays

To investigate relationships between computer-extracted breast magnetic resonance (MR) imaging phenotypes with multigene assays of MammaPrint, Oncotype DX, and PAM50 to assess the role of radiomics in evaluating the risk of breast cancer recurrence

LSST Science Book, Version 2.0

A survey that can cover the sky in optical bands over wide fields to faint magnitudes with a fast cadence will enable many of the exciting science opportunities of the next decade. The Large Synoptic Survey Telescope (LSST) will have an effective aperture of 6.7 meters and an imaging camera with field of view of 9.6 deg^2, and will be devoted to a ten-year imaging survey over 20,000 deg^2 south of +15 deg. Each pointing will be imaged 2000 times with fifteen second exposures in six broad bands from 0.35 to 1.1 microns, to a total point-source depth of r~27.5. The LSST Science Book describes the basic parameters of the LSST hardware, software, and observing plans. The book discusses educational and outreach opportunities, then goes on to describe a broad range of science that LSST will revolutionize: mapping the inner and outer Solar System, stellar populations in the Milky Way and nearby galaxies, the structure of the Milky Way disk and halo and other objects in the Local Volume, transient and variable objects both at low and high redshift, and the properties of normal and active galaxies at low and high redshift. It then turns to far-field cosmological topics, exploring properties of supernovae to z~1, strong and weak lensing, the large-scale distribution of galaxies and baryon oscillations, and how these different probes may be combined to constrain cosmological models and the physics of dark energy.Comment: 596 pages. Also available at full resolution at http://www.lsst.org/lsst/sciboo

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Copy number signatures and mutational processes in ovarian carcinoma.

The genomic complexity of profound copy number aberrations has prevented effective molecular stratification of ovarian cancers. Here, to decode this complexity, we derived copy number signatures from shallow whole-genome sequencing of 117 high-grade serous ovarian cancer (HGSOC) cases, which were validated on 527 independent cases. We show that HGSOC comprises a continuum of genomes shaped by multiple mutational processes that result in known patterns of genomic aberration. Copy number signature exposures at diagnosis predict both overall survival and the probability of platinum-resistant relapse. Measurement of signature exposures provides a rational framework to choose combination treatments that target multiple mutational processes.NIHR, Ovarian Cancer Action, Cancer Research UK Cambridge Centre, Cambridge Experimental Cancer Medicine Centr