LASR-Guided Stellar Photometric Variability Subtraction: The Linear Algorithm For Significance Reduction

We develop a technique for removing stellar variability in the light curves of $\delta$-Scuti and similar stars. Our technique, which we name the Linear Algorithm for Significance Reduction (LASR), subtracts oscillations from a time series by minimizing their statistical significance in frequency space. We demonstrate that LASR can subtract variable signals of near-arbitrary complexity and can robustly handle close frequency pairs and overtone frequencies. We demonstrate that our algorithm performs an equivalent fit as prewhitening to the straightforward variable signal of KIC 9700322. We also show that LASR provides a better fit to seismic activity than prewhitening in the case of the complex $\delta$-Scuti KOI-976.Comment: 9 pages, 5 figures, accepted for publication in Astronomy & Astrophysics. Pseudocode and github link to code included in manuscrip

A robust and efficient method for estimating enzyme complex abundance and metabolic flux from expression data

A major theme in constraint-based modeling is unifying experimental data, such as biochemical information about the reactions that can occur in a system or the composition and localization of enzyme complexes, with highthroughput data including expression data, metabolomics, or DNA sequencing. The desired result is to increase predictive capability resulting in improved understanding of metabolism. The approach typically employed when only gene (or protein) intensities are available is the creation of tissue-specific models, which reduces the available reactions in an organism model, and does not provide an objective function for the estimation of fluxes, which is an important limitation in many modeling applications. We develop a method, flux assignment with LAD (least absolute deviation) convex objectives and normalization (FALCON), that employs metabolic network reconstructions along with expression data to estimate fluxes. In order to use such a method, accurate measures of enzyme complex abundance are needed, so we first present a new algorithm that addresses quantification of complex abundance. Our extensions to prior techniques include the capability to work with large models and significantly improved run-time performance even for smaller models, an improved analysis of enzyme complex formation logic, the ability to handle very large enzyme complex rules that may incorporate multiple isoforms, and depending on the model constraints, either maintained or significantly improved correlation with experimentally measured fluxes. FALCON has been implemented in MATLAB and ATS, and can be downloaded from: https://github.com/bbarker/FALCON. ATS is not required to compile the software, as intermediate C source code is available, and binaries are provided for Linux x86-64 systems. FALCON requires use of the COBRA Toolbox, also implemented in MATLAB.Comment: 30 pages, 12 figures, 4 table

Uncertainty as a Key Influence in the Decision To Admit Patients with Transient Ischemic Attack

Background Patients with transient ischemic attacks (TIA) are at high risk of subsequent vascular events. Hospitalization improves quality of care, yet admission rates for TIA patients vary considerably. Objectives We sought to identify factors associated with the decision to admit patents with TIA. Design We conducted a secondary analysis of a prior study’s data including semi-structured interviews, administrative data, and chart review. Participants We interviewed multidisciplinary clinical staff involved with TIA care. Administrative data included information for TIA patients in emergency departments or inpatient settings at VA medical centers (VAMCs) for fiscal years (FY) 2011 and 2014. Chart reviews were conducted on a subset of patients from 12 VAMCs in FY 2011. Approach For the qualitative data, we focused on interviewees’ responses to the prompt: “Tell me what influences you in the decision to or not to admit TIA patients.” We used administrative data to identify admission rates and chart review data to identify ABCD2 scores (a tool to classify stroke risk after TIA). Key Results Providers’ decisions to admit TIA patients were related to uncertainty in several domains: lack of a facility TIA-specific policy, inconsistent use of ABCD2 score, and concerns about facilities’ ability to complete a timely workup. There was a disconnect between staff perceptions about TIA admission and facility admission rates. According to chart review data, staff at facilities with higher admission rates in FY 2011 reported consistent reliance on ABCD2 scores and related guidelines in admission decision-making. Conclusions Many factors contributed to decisions regarding admitting a patient with TIA; however, clinicians’ uncertainty appeared to be a key driver. Further quality improvement interventions for TIA care should focus on facility adoption of TIA protocols to address uncertainty in TIA admission decision-making and to standardize timely evaluation of TIA patients and delivery of secondary prevention strategies

Coordinated induction of cell survival signaling in the inflamed microenvironment of the prostate

PURPOSE: Both prostate cancer and benign prostatic hyperplasia are associated with inflammatory microenvironments. Inflammation is damaging to tissues, but it is unclear how the inflammatory microenvironment protects specialized epithelial cells that function to proliferate and repair the tissue. The objective of this study is to characterize the cell death and cell survival response of the prostatic epithelium in response to inflammation. METHODS: We assessed induction of cell death (TNF, TRAIL, TWEAK, FasL) and cell survival factors (IGFs, hedgehogs, IL-6, FGFs, and TGFs) in inflamed and control mouse prostates by ELISA. Cell death mechanisms were determined by immunoblotting and immunofluorescence for cleavage of caspases and TUNEL. Survival pathway activation was assessed by immunoblotting and immunofluorescence for Mcl-1, Bcl-2, Bcl-XL, and survivin. Autophagy was determined by immunoblotting and immunofluorescence for free and membrane associated light chain 3 (LC-3). RESULTS: Cleavage of all four caspases was significantly increased during the first 2 days of inflammation, and survival protein expression was substantially increased subsequently, maximizing at 3 days. By 5 days of inflammation, 50% of prostatic epithelial cells expressed survivin. Autophagy was also evident during the recovery phase (3 days). Finally, immunofluorescent staining of human specimens indicates strong activation of survival proteins juxtaposed to inflammation in inflamed prostate specimens. CONCLUSIONS: The prostate responds to deleterious inflammation with induction of cell survival mechanisms, most notably survivin and autophagy, demonstrating a coordinated induction of survival factors that protects and expands a specialized set of prostatic epithelial cells as part of the repair and recovery process during inflammation

Characterization of Fusobacterium isolates from the respiratory tract of white-tailed deer (Odocoileus virginianus)

A total of 23 clinical isolates of Fusobacterium spp. were recovered at necropsy over a 2-year period from the respiratory tract of white-tailed deer (Odocoileus virginianus). Isolates were identified as Fusobacterium varium (18/23), Fusobacterium necrophorum subsp. funduliforme (3/23), and Fusobacterium necrophorum subsp. necrophorum (2/23). Using polymerase chain reaction–based detection of virulence genes, all F. necrophorum isolates were positive for the promoter region of the leukotoxin operon and the hemagglutinin-related protein gene, while all F. varium isolates were negative. The presence of the leukotoxin gene in F. necrophorum isolates and the absence of this gene in F. varium isolates were confirmed by Southern hybridization using 2 separate probes. Toxicity to bovine polymorphonuclear leukocytes was observed with all F. necrophorum isolates, but was not observed in any F. varium isolates. Susceptibility to antimicrobials was markedly different for F. varium as compared to F. necrophorum. In summary, no evidence of leukotoxin production was detected in any of the 23 F. varium isolates used in the current study. The data suggests that F. varium, the most common species isolated, may be a significant pathogen in deer with a different virulence mechanism than F. necrophorum

siRNA screen of the human signaling proteome identifies the PtdIns(3,4,5)P3-mTOR signaling pathway as a primary regulator of transferrin uptake

A survey of 1,804 human dicer-generated signaling siRNAs using automated quantitative imaging identified the phosphatidylinositol-3,4,5-trisphosphate-mTOR signaling pathway as a primary regulator of iron-transferrin uptake

Developing Government Renewable Energy Projects

The US Army Corps of Engineers has retained Idaho National Laboratory (INL) to conduct a study of past INL experiences and complete a report that identifies the processes that are needed for the development of renewable energy projects on government properties. The INL has always maintained expertise in power systems and applied engineering and INL’s renewable energy experiences date back to the 1980’s when our engineers began performing US Air Force wind energy feasibility studies and development projects. Over the last 20+ years of working with Department of Defense and other government agencies to study, design, and build government renewable projects, INL has experienced the do’s and don’ts for being successful with a project. These compiled guidelines for government renewable energy projects could include wind, hydro, geothermal, solar, biomass, or a variety of hybrid systems; however, for the purpose of narrowing the focus of this report, wind projects are the main topic discussed throughout this report. It is our thought that a lot of what is discussed could be applied, possibly with some modifications, to other areas of renewable energy. It is also important to note that individual projects (regardless the type) vary to some degree depending on location, size, and need but in general these concepts and directions can be carried over to the majority of government renewable energy projects. This report focuses on the initial development that needs to occur for any project to be a successful government renewable energy project

A Comparison of Real Time Thermal Rating Systems in the U.S. and the UK

Real-Time Thermal Rating is a smart grid technology that allows the rating of electrical conductors to be increased based on local weather conditions. Overhead lines are conventionally given a conservative, constant seasonal rating based on seasonal and regional worst case scenarios rather than actual, say, local hourly weather predictions. This paper provides a report of two pioneering schemes—one in the United States of America and one in the United Kingdom—in which Real-Time Thermal Ratings have been applied. Thereby, we demonstrate that observing the local weather conditions in real time leads to additional capacity and safer operation. Secondly, we critically compare both approaches and discuss their limitations. In doing so, we arrive at novel insights which will inform and improve future Real-Time Thermal Rating projects