Open-Source Computerized Patient-Reported Outcomes: Case Studies Illustrating Fifteen Years of Evolution

Thesis (Master's)--University of Washington, 2016-06Over a fifteen year period, Patient Reported Outcomes ("PRO") applications to support over forty clinical and research projects have driven the evolution of an open-source computerized PRO system ("cPRO", http://cprohealth.org). The projects varied widely in PRO content, clinical domain, and workflows. Detailed case studies of six major implementations of the cPRO system offer a framework to understand the socio-technical challenges and opportunities in collecting computerized PROs and incorporating PROs into clinical care, patient-centered tools, and research

Fungal-induced protein hyperacetylation in maize identified by acetylome profiling.

Lysine acetylation is a key posttranslational modification that regulates diverse proteins involved in a range of biological processes. The role of histone acetylation in plant defense is well established, and it is known that pathogen effector proteins encoding acetyltransferases can directly acetylate host proteins to alter immunity. However, it is unclear whether endogenous plant enzymes can modulate protein acetylation during an immune response. Here, we investigate how the effector molecule HC-toxin (HCT), a histone deacetylase inhibitor produced by the fungal pathogen Cochliobolus carbonum race 1, promotes virulence in maize through altering protein acetylation. Using mass spectrometry, we globally quantified the abundance of 3,636 proteins and the levels of acetylation at 2,791 sites in maize plants treated with HCT as well as HCT-deficient or HCT-producing strains of C. carbonum Analyses of these data demonstrate that acetylation is a widespread posttranslational modification impacting proteins encoded by many intensively studied maize genes. Furthermore, the application of exogenous HCT enabled us to show that the activity of plant-encoded enzymes (histone deacetylases) can be modulated to alter acetylation of nonhistone proteins during an immune response. Collectively, these results provide a resource for further mechanistic studies examining the regulation of protein function by reversible acetylation and offer insight into the complex immune response triggered by virulent C. carbonum

Whole-lake food web model indicates alewife invasion fueled lake trout restoration and altered patterns of trophic flow Lake Champlain

International audienceFood web responses to invasion can be context-dependent and therefore difficult to predict based only on invasion histories. Alewives (Alosa pseudoharengus) had generally negative impacts on the native fish communities of the Laurentian Great Lakes after they invaded in the 19th century and were thus expected to negatively impact the Lake Champlain food web after entering the lake in 2003. We evaluated the impact of alewives on the Lake Champlain food web by compiling 25 years of biomass, abundance, and diet data and constructing an Ecopath with Ecosim model of the coldwater food web. Model projections indicated that, contrary to the Great Lakes experience, biomass of native predators increased, mortality rates decreased, and overall trophic level of the pelagic fish community decreased after alewife entered the system. Consequently, the amount of primary production supporting predator biomass increased in response to the addition of prey fish production. The model suggests that alewife invasion in Lake Champlain could have altered food web structure by transferring more energy to tertiary consumers via pelagic pathways at the expense of other energy pathways and "jump started" wild lake trout recruitment by expanding the forage base. In contrast to the Great Lakes response to alewife invasion, Lake Champlain may represent an alternate trajectory for alewife invasion and demonstrates that alewife impacts are context-dependent

Technical Description of the Distribute Project: A Community-based Syndromic Surveillance System Implementation

This paper describes the design of a syndromic surveillance system implemented for community-based monitoring of influenza-like illness. The system began as a collaboration between colleagues from state and large metropolitan area health jurisdictions, academic institutions, and the non-profit, International Society for Disease Surveillance. Over the six influenza seasons from 2006 to 2012, the system was automated and enhanced, with new features and infrastructure, and the resulting, reliable, enterprise grade system supported peer comparisons between 44 state and local public health jurisdictions who voluntarily contributed summarized data on influenza-like illness and gastrointestinal syndromes. The system was unusual in that it addressed the needs of a widely distributed, voluntary, community engaged in real-time data integration to support operational public health.Keywords: syndromic surveillance, secondary use of health data, Internet, public health standards, surveillance practic

Temporal and spatial auxin responsive networks in maize primary roots

Auxin is a key regulator of root morphogenesis across angiosperms. To better understand auxin regulated networks underlying maize root development we have characterized auxin responsive transcription across two time points (30 and 120 minutes) and four regions of the primary root: the meristematic zone, elongation zone, cortex, and stele. Hundreds of auxin-regulated genes involved in diverse biological processes were quantified in these different root regions. In general, most auxin regulated genes are region unique and are predominantly observed in differentiated tissues compared to the root meristem. Auxin gene regulatory networks (GRNs) were reconstructed with these data to identify key transcription factors that may underlie auxin responses in maize roots. Additionally, Auxin Response Factor (ARF) subnetworks were generated to identify target genes which exhibit tissue or temporal specificity in response to auxin. These networks describe novel molecular connections underlying maize root development and provide a foundation for functional genomic studies in a key crop.This is a preprint made available through bioRxiv at doi:10.1101/2022.02.01.478706. It is made available under a CC-BY-NC-ND 4.0 International license