Environmental and energy assessment of an aviary laying-hen housing system in the Midwestern United States

The laying-hen industry in the United States has been under pressure to change or modify the conventional housing systems. Traditionally, hens have been kept in conventional cages inside environmentally-controlled buildings. These cages are stacked wire mesh enclosures with mechanized egg collection, feed and water delivery systems. Over the past decade there has been much pressure to improve the welfare of the hens by replacing conventional cages with alternative housing systems. There are a number of alternative housing options under consideration or being used. In the cage free system the birds have access to the floor, but are limited to the inside of a barn. The aviary system monitored in this study is a subset of this cage-free system where a tiered structure is used to increase space allocation to the hen while accommodating more hens (than a single level barn). The aviary system also use mechanized egg collection, feed and water delivery systems similar to traditional barns. When the studies described in this dissertation were started, information on the aviary system seemed quite valuable, but the timeliness of the data has become even more apparent over the last few years. Where some states had previously been dealing with transitions to lower stocking densities (fewer hens per unit of area) or alternative systems, there is now an agreement on the table that may bring this transition to a national level. Because the aviary system is so different from conventional housing, there are questions about the impact and performance of such a system. The most obvious difference in all alternative housing, including aviaries, is the lower stocking density. With the lower stocking density, there are many questions about the correct management of houses, especially in winter. The potential issue with ventilation for indoor air quality at the lower stocking density is the possible need for supplemental heat and its proper distribution in the house. This dissertation looks at this issue from many different angles including ventilation rate, indoor air quality, heat and moisture production of the birds, fuel usage, and the birds\u27 preference for winter temperature-ammonia combinations. With the lower stocking density there is also a concern that the labor and utilities provided on a per bird basis will be higher. Another concern with the systems is that a portion of manure from the birds is held in the house on the floor as litter. The litter on the floor impacts indoor air quality. The ammonia and dust concentrations and emissions were two of the major concerns with regard to the litter. With the aviary system, the birds have the ability to be more active. There are questions about how this activity level impacts the heat and moisture production rates of these birds. Overall, there is very little information on the aviary system in the United States. This dissertation aims to address these questions and concerns

Projections for measuring the size of the solar core with neutrino-electron scattering

We quantify the amount of data needed in order to measure the size and position of the $^8$B neutrino production region within the solar core, for experiments looking at elastic scattering between electrons and solar neutrinos. The directions of the electrons immediately after scattering are strongly correlated with the incident directions of the neutrinos, however this is degraded significantly by the subsequent scattering of these electrons in the detector medium. We generate distributions of such electrons for different neutrino production profiles, and use a maximum likelihood analysis to make projections for future experimental sensitivity. We find that with approximately 20 years worth of data the Super Kamiokande experiment could constrain the central radius of the shell in which $^8$B neutrinos are produced to be less than 0.22 of the total solar radius at 95% confidence.Comment: 5 pages, 2 figures. Matches version accepted to PRL. Improved 2D analysis and results discussio

The radius and other fundamental parameters of the F9 V star beta Virginis

We have used the Sydney University Stellar Interferometer (SUSI) to measure the angular diameter of the F9 V star beta Virginis. After correcting for limb darkening and combining with the revised Hipparcos parallax, we derive a radius of 1.703 +/- 0.022 R_sun (1.3%). We have also calculated the bolometric flux from published measurements which, combined with the angular diameter, implies an effective temperature of 6059 +/- 49 K (0.8%). We also derived the luminosity of beta Vir to be L = 3.51 +/- 0.08 L_sun (2.1%). Solar-like oscillations were measured in this star by Carrier et al. (2005) and using their value for the large frequency separation yields the mean stellar density with an uncertainty of about 2%. Our constraints on the fundamental parameters of beta Vir will be important to test theoretical models of this star and its oscillations.Comment: accepted for publication in MNRAS. Updated reference

Evolutionary history of human colitis-associated colorectal cancer

Objective: IBD confers an increased lifetime risk of developing colorectal cancer (CRC), and colitis-associated CRC (CA-CRC) is molecularly distinct from sporadic CRC (S-CRC). Here we have dissected the evolutionary history of CA-CRC using multiregion sequencing. Design: Exome sequencing was performed on fresh-frozen multiple regions of carcinoma, adjacent non-cancerous mucosa and blood from 12 patients with CA-CRC (n=55 exomes), and key variants were validated with orthogonal methods. Genome-wide copy number profiling was performed using single nucleotide polymorphism arrays and low-pass whole genome sequencing on archival non-dysplastic mucosa (n=9), low-grade dysplasia (LGD; n=30), high-grade dysplasia (HGD; n=13), mixed LGD/HGD (n=7) and CA-CRC (n=19). Phylogenetic trees were reconstructed, and evolutionary analysis used to reveal the temporal sequence of events leading to CA-CRC. Results: 10/12 tumours were microsatellite stable with a median mutation burden of 3.0 single nucleotide alterations (SNA) per Mb, ~20% higher than S-CRC (2.5 SNAs/Mb), and consistent with elevated ageing-associated mutational processes. Non-dysplastic mucosa had considerable mutation burden (median 47 SNAs), including mutations shared with the neighbouring CA-CRC, indicating a precancer mutational field. CA-CRCs were often near triploid (40%) or near tetraploid (20%) and phylogenetic analysis revealed that copy number alterations (CNAs) began to accrue in non-dysplastic bowel, but the LGD/HGD transition often involved a punctuated ‘catastrophic’ CNA increase. Conclusions: Evolutionary genomic analysis revealed precancer clones bearing extensive SNAs and CNAs, with progression to cancer involving a dramatic accrual of CNAs at HGD. Detection of the cancerised field is an encouraging prospect for surveillance, but punctuated evolution may limit the window for early detection

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

An Integrated TCGA Pan-Cancer Clinical Data Resource to Drive High-Quality Survival Outcome Analytics

For a decade, The Cancer Genome Atlas (TCGA) program collected clinicopathologic annotation data along with multi-platform molecular profiles of more than 11,000 human tumors across 33 different cancer types. TCGA clinical data contain key features representing the democratized nature of the data collection process. To ensure proper use of this large clinical dataset associated with genomic features, we developed a standardized dataset named the TCGA Pan-Cancer Clinical Data Resource (TCGA-CDR), which includes four major clinical outcome endpoints. In addition to detailing major challenges and statistical limitations encountered during the effort of integrating the acquired clinical data, we present a summary that includes endpoint usage recommendations for each cancer type. These TCGA-CDR findings appear to be consistent with cancer genomics studies independent of the TCGA effort and provide opportunities for investigating cancer biology using clinical correlates at an unprecedented scale. Analysis of clinicopathologic annotations for over 11,000 cancer patients in the TCGA program leads to the generation of TCGA Clinical Data Resource, which provides recommendations of clinical outcome endpoint usage for 33 cancer types

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

Effects of antiplatelet therapy on stroke risk by brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases: subgroup analyses of the RESTART randomised, open-label trial

Background Findings from the RESTART trial suggest that starting antiplatelet therapy might reduce the risk of recurrent symptomatic intracerebral haemorrhage compared with avoiding antiplatelet therapy. Brain imaging features of intracerebral haemorrhage and cerebral small vessel diseases (such as cerebral microbleeds) are associated with greater risks of recurrent intracerebral haemorrhage. We did subgroup analyses of the RESTART trial to explore whether these brain imaging features modify the effects of antiplatelet therapy

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