Application of advanced techniques for the remote detection, modelling and spatial analysis of mesquite (prosopis spp.) invasion in Western Australia

Invasive plants pose serious threats to economic, social and environmental interests throughout the world. Developing strategies for their management requires a range of information that is often impractical to collect from ground based surveys. In other cases, such as retrospective analyses of historical invasion rates and patterns, data is rarely, if ever, available from such surveys. Instead, historical archives of remotely sensed imagery provides one of the only existing records, and are used in this research to determine invasion rates and reconstruct invasion patterns of a ca 70 year old exotic mesquite population (Leguminoseae: Prosopis spp.) in the Pilbara Region of Western Australia, thereby helping to identify ways to reduce spread and infill. A model was then developed using this, and other, information to predict which parts of the Pilbara are most a risk. This information can assist in identifying areas requiring the most vigilant intervention and pre-emptive measures. Precise information of the location and areal extent of an invasive species is also crucial for land managers and policy makers for crafting management strategies aimed at control, confinement or eradication of some or all of the population. Therefore, the third component of this research was to develop and test high spectral and spatial resolution airborne imagery as a potential monitoring tool for tracking changes at various intervals and quantifying the effectiveness of management strategies adopted. To this end, high spatial resolution digital multispectral imagery (4 channels, 1 m spatial resolution) and hyperspectral imagery (126 channels, 3 m spatial resolution) was acquired and compared for its potential for distinguishing mesquite from coexisting species and land covers.These three modules of research are summarised hereafter. To examine the rates and patterns of mesquite invasion through space and time, canopies were extracted from a temporal series of panchromatic aerial photography over an area of 450 ha using unsupervised classification. Non-mesquite trees and shrubs were not discernible from mesquite using this imagery (or technique) and so were masked out using an image acquired prior to invasion. The accuracy of the mesquite extractions were corroborated in the field and found to be high (R2 = 0.98, P36 m2 (66-94%) with both approaches and image types. However, both approaches used on the hyperspectral imagery were more reliable at capturing patches >36 m2 than the DMSI using either approach. The lowest omission and commission rates were obtained using pairwise separation on the hyperspectral imagery, which was significantly more accurate than DMSI using an overall separation approach (Z=2.78, P36 m2. However, hyperspectral imagery processed using pairwise separation appears to be superior, even though not statistically different to hyperspectral imagery processed using overall separation or DMSI processed using pairwise separation at the 95% confidence level. Mapping smaller patches may require the use of very high spatial resolution imagery, such as that achievable from unmanned airborne vehicles, coupled with a hyperspectral instrument. Alternatively, management may continue to rely on visual airborne surveys flown at low altitude and speed, which have proven to be capable at mapping small and isolated mesquite shrubs in the study area used in this research

Future Contingents and the Logic of Temporal Omniscience

At least since Aristotle’s famous 'sea-battle' passages in On Interpretation 9, some substantial minority of philosophers has been attracted to the doctrine of the open future--the doctrine that future contingent statements are not true. But, prima facie, such views seem inconsistent with the following intuition: if something has happened, then (looking back) it was the case that it would happen. How can it be that, looking forwards, it isn’t true that there will be a sea battle, while also being true that, looking backwards, it was the case that there would be a sea battle? This tension forms, in large part, what might be called the problem of future contingents. A dominant trend in temporal logic and semantic theorizing about future contingents seeks to validate both intuitions. Theorists in this tradition--including some interpretations of Aristotle, but paradigmatically, Thomason (1970), as well as more recent developments in Belnap, et. al (2001) and MacFarlane (2003, 2014)--have argued that the apparent tension between the intuitions is in fact merely apparent. In short, such theorists seek to maintain both of the following two theses: (i) the open future: Future contingents are not true, and (ii) retro-closure: From the fact that something is true, it follows that it was the case that it would be true. It is well-known that reflection on the problem of future contingents has in many ways been inspired by importantly parallel issues regarding divine foreknowledge and indeterminism. In this paper, we take up this perspective, and ask what accepting both the open future and retro-closure predicts about omniscience. When we theorize about a perfect knower, we are theorizing about what an ideal agent ought to believe. Our contention is that there isn’t an acceptable view of ideally rational belief given the assumptions of the open future and retro-closure, and thus this casts doubt on the conjunction of those assumptions

IR and UV Galaxies at z=0.6 -- Evolution of Dust Attenuation and Stellar Mass as Revealed by SWIRE and GALEX

We study dust attenuation and stellar mass of $\rm z\sim 0.6$ star-forming galaxies using new SWIRE observations in IR and GALEX observations in UV. Two samples are selected from the SWIRE and GALEX source catalogs in the SWIRE/GALEX field ELAIS-N1-00 ($\Omega = 0.8$ deg$^2$). The UV selected sample has 600 galaxies with photometric redshift (hereafter photo-z) $0.5 \leq z \leq 0.7$ and NUV$\leq 23.5$ (corresponding to \rm L_{FUV} \geq 10^{9.6} L_\sun). The IR selected sample contains 430 galaxies with $f_{24\mu m} \geq 0.2$ mJy (\rm L_{dust} \geq 10^{10.8} L_\sun) in the same photo-z range. It is found that the mean $\rm L_{dust}/L_{FUV}$ ratios of the z=0.6 UV galaxies are consistent with that of their z=0 counterparts of the same $\rm L_{FUV}$. For IR galaxies, the mean $\rm L_{dust}/L_{FUV}$ ratios of the z=0.6 LIRGs (\rm L_{dust} \sim 10^{11} L_\sun) are about a factor of 2 lower than local LIRGs, whereas z=0.6 ULIRGs (\rm L_{dust} \sim 10^{12} L_\sun) have the same mean $\rm L_{dust}/L_{FUV}$ ratios as their local counterparts. This is consistent with the hypothesis that the dominant component of LIRG population has changed from large, gas rich spirals at z$>0.5$ to major-mergers at z=0. The stellar mass of z=0.6 UV galaxies of \rm L_{FUV} \leq 10^{10.2} L_\sun is about a factor 2 less than their local counterparts of the same luminosity, indicating growth of these galaxies. The mass of z=0.6 UV lunmous galaxies (UVLGs: \rm L_{FUV} > 10^{10.2} L_\sun) and IR selected galaxies, which are nearly exclusively LIRGs and ULIRGs, is the same as their local counterparts.Comment: 27 pages, 8 figures, to be published in the Astrophysical Journal Supplement series dedicated to GALEX result

Dark sectors 2016 Workshop: community report

This report, based on the Dark Sectors workshop at SLAC in April 2016, summarizes the scientific importance of searches for dark sector dark matter and forces at masses beneath the weak-scale, the status of this broad international field, the important milestones motivating future exploration, and promising experimental opportunities to reach these milestones over the next 5-10 years

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

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

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

The Long-Baseline Neutrino Experiment: Exploring Fundamental Symmetries of the Universe

The preponderance of matter over antimatter in the early Universe, the dynamics of the supernova bursts that produced the heavy elements necessary for life and whether protons eventually decay --- these mysteries at the forefront of particle physics and astrophysics are key to understanding the early evolution of our Universe, its current state and its eventual fate. The Long-Baseline Neutrino Experiment (LBNE) represents an extensively developed plan for a world-class experiment dedicated to addressing these questions. LBNE is conceived around three central components: (1) a new, high-intensity neutrino source generated from a megawatt-class proton accelerator at Fermi National Accelerator Laboratory, (2) a near neutrino detector just downstream of the source, and (3) a massive liquid argon time-projection chamber deployed as a far detector deep underground at the Sanford Underground Research Facility. This facility, located at the site of the former Homestake Mine in Lead, South Dakota, is approximately 1,300 km from the neutrino source at Fermilab -- a distance (baseline) that delivers optimal sensitivity to neutrino charge-parity symmetry violation and mass ordering effects. This ambitious yet cost-effective design incorporates scalability and flexibility and can accommodate a variety of upgrades and contributions. With its exceptional combination of experimental configuration, technical capabilities, and potential for transformative discoveries, LBNE promises to be a vital facility for the field of particle physics worldwide, providing physicists from around the globe with opportunities to collaborate in a twenty to thirty year program of exciting science. In this document we provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess.Comment: Major update of previous version. This is the reference document for LBNE science program and current status. Chapters 1, 3, and 9 provide a comprehensive overview of LBNE's scientific objectives, its place in the landscape of neutrino physics worldwide, the technologies it will incorporate and the capabilities it will possess. 288 pages, 116 figure