Legislature’s Planning Committee 2015 Report

A message from Senator Tanya Cook, Chair of the Legislature’s Planning Committee 2015-2016 The Legislature’s Planning Committee serves a vital role in the Nebraska Unicameral. In an era of term limits, the Planning Committee provides future-focused, data-driven research for senators to use in crafting smart, effective policies. The 2015 Database Update continues to highlight nine key benchmarks – Economy, Agriculture, Natural Resources, State and Local Government, Education, Health and Human Services, Public Safety, Transportation, and Telecommunications – that give a well-rounded picture of the state’s strengths, struggles, and opportunities. The Planning Committee owes a debt of gratitude to Dr. John Bartle and Jerry Deichert, who have worked tirelessly since the Committee’s founding to ensure the best, most accurate data is provided to Nebraska’s policymakers. Thanks are also in order for the staffers and students at the University of Nebraska-Omaha’s College of Public Affairs and Community Service, as well as the other professors and researchers who have worked with the Committee over the years. I hope the data in this update will inform and inspire ever better policy decisions and discussions in Nebraska. The Planning Committee’s collection of studies and data resources will only continue to grow, and I trust that Nebraska’s policymakers will continue to utilize the information wisely. Sincerely,Senator Tanya CookLegislative District 1

Legislature’s Planning Committee 2013 Report

The Legislature’s Planning Committee was created in 2009, pursuant to LB 653, introduced by Senator John Harms, of Scottsbluff. The 2012-13 Committee is: Senator John Harms, ChairSenator Tanya Cook, Vice-ChairSenator Greg Adams, Speaker of the LegislatureSenator John Wightman, Chair, Executive BoardSenator Heath Mello, Chair, Appropriations CommitteeSenator Mike GloorSenator Kathy CampbellSenator Paul SchumacherSenator Kate Sullivan When the Committee was formed in 2009, it was decided that, in order to achieve their goals, they would be assisted by the Legislative Research Office and the College of Public Affairs at the University of Nebraska at Omaha. The Committee also formed three sub-committees: 1) Mission Statement and Goals; 2) Research Data Base; and 3) Special Funding. The Mission Statement was adopted and it was decided that there would be nine categories for data collection: Agriculture, Economy, Education, Health & Human Services, Natural Resources, Public Safety, State & Local Government, Telecommunications, and Transportation. The Goals for each category were adopted and it was decided that the Economy section would be completed first. The Research Data Base sub-committee chose benchmarks for the Economy category and Jerry Deichert and John Bartle, with the assistance of grad student Skiarn Issarachaiyos, began collecting data for each benchmark. The Mission Statement and Goals committee, having completed their task, then became a second research benchmarking committee. The remaining eight categories were divided up between the two sub-committees and benchmarks were picked for each category. Jerry, John, and Skairn then collected data for each category. They also prepared summaries of data and made note of policy considerations for each category. This report consists of the data, summaries, and policy considerations for each of the nine categories. During this time, the Legislative Research Office prepared for the committee binders, for each of the nine categories, which contain a history of legislation passed in Nebraska for each category during the last thirty years, as well as what is currently being done in other states – compiled from organizations such as the National Conference of State Legislatures. These binders are available to be checked out in the Legislative Research Office. The Planning Committee will also be in charge of updating the data and policy considerations each year for all benchmarks in each category. We are hopeful that this will be of great assistance to Legislators and staff as they craft and debate legislation each Session. This Report is the 2013 Update to the 2011 Report. Added this year is a section titled “Selected Characteristics for Nebraska Legislative Districts from the 2008-2012 American Community Survey”, and also an “At A Glance” summary of the trends of how Nebraska is doing in each area. This Report and the Executive Summary are available on the Legislature’s Website at http://www.nebraskalegislature.gov/reports/lpc.ph

Telomeric expression sites are highly conserved in trypanosoma brucei

Subtelomeric regions are often under-represented in genome sequences of eukaryotes. One of the best known examples of the use of telomere proximity for adaptive purposes are the bloodstream expression sites (BESs) of the African trypanosome Trypanosoma brucei. To enhance our understanding of BES structure and function in host adaptation and immune evasion, the BES repertoire from the Lister 427 strain of T. brucei were independently tagged and sequenced. BESs are polymorphic in size and structure but reveal a surprisingly conserved architecture in the context of extensive recombination. Very small BESs do exist and many functioning BESs do not contain the full complement of expression site associated genes (ESAGs). The consequences of duplicated or missing ESAGs, including ESAG9, a newly named ESAG12, and additional variant surface glycoprotein genes (VSGs) were evaluated by functional assays after BESs were tagged with a drug-resistance gene. Phylogenetic analysis of constituent ESAG families suggests that BESs are sequence mosaics and that extensive recombination has shaped the evolution of the BES repertoire. This work opens important perspectives in understanding the molecular mechanisms of antigenic variation, a widely used strategy for immune evasion in pathogens, and telomere biology

Multi-drug resistant Acinetobacter infections in critically injured Canadian forces soldiers

<p>Abstract</p> <p>Background</p> <p>Military members, injured in Afghanistan or Iraq, have returned home with multi-drug resistant <it>Acinetobacter baumannii </it>infections. The source of these infections is unknown.</p> <p>Methods</p> <p>Retrospective study of all Canadian soldiers who were injured in Afghanistan and who required mechanical ventilation from January 1 2006 to September 1 2006. Patients who developed <it>A. baumannii </it>ventilator associated pneumonia (VAP) were identified. All <it>A. baumannii </it>isolates were retrieved for study patients and compared with <it>A. baumannii </it>isolates from environmental sources from the Kandahar military hospital using pulsed-field gel electrophoresis (PFGE).</p> <p>Results</p> <p>During the study period, six Canadian Forces (CF) soldiers were injured in Afghanistan, required mechanical ventilation and were repatriated to Canadian hospitals. Four of these patients developed <it>A. baumannii </it>VAP. <it>A. baumannii </it>was also isolated from one environmental source in Kandahar – a ventilator air intake filter. Patient isolates were genetically indistinguishable from each other and from the isolates cultured from the ventilator filter. These isolates were resistant to numerous classes of antimicrobials including the carbapenems.</p> <p>Conclusion</p> <p>These results suggest that the source of <it>A. baumannii </it>infection for these four patients was an environmental source in the military field hospital in Kandahar. A causal linkage, however, was not established with the ventilator. This study suggests that infection control efforts and further research should be focused on the military field hospital environment to prevent further multi-drug resistant <it>A. baumannii </it>infections in injured soldiers.</p

The Rise of Adaptive Platform Trials in Critical Care

As durable learning research systems, adaptive platform trials represent a transformative new approach to accelerating clinical evaluation and discovery in critical care. This Perspective provides a brief introduction to the concept of adaptive platform trials, describes several established and emerging platforms in critical care, and surveys some opportunities and challenges for their implementation and impact.<br/

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

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

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