New Hardware and Software Innovations (for Volumetric Modeling)

19 pages (includes illustrations and maps)

Geochemical assessment of aquifer recharge effects in the southwest Denver basin

August 29, 1989.Bibliography: pages 39-41.Grant no. 14-08-0001-G1006 and G1214, Project no. 03

A whole-genome screen identifies Salmonella enterica serovar Typhi genes involved in fluoroquinolone susceptibility.

OBJECTIVES: A whole-genome screen at sub-gene resolution was performed to identify candidate loci that contribute to enhanced or diminished ciprofloxacin susceptibility in Salmonella enterica serovar Typhi. METHODS: A pool of over 1 million transposon insertion mutants of an S. Typhi Ty2 derivative were grown in a sub-MIC concentration of ciprofloxacin, or without ciprofloxacin. Transposon-directed insertion site sequencing (TraDIS) identified relative differences between the mutants that grew following the ciprofloxacin treatment compared with the untreated mutant pool, thereby indicating which mutations contribute to gain or loss of ciprofloxacin susceptibility. RESULTS: Approximately 88% of the S. Typhi strain's 4895 annotated genes were assayed, and at least 116 were identified as contributing to gain or loss of ciprofloxacin susceptibility. Many of the identified genes are known to influence susceptibility to ciprofloxacin, thereby providing method validation. Genes were identified that were not known previously to be involved in susceptibility, and some of these had no previously known phenotype. Susceptibility to ciprofloxacin was enhanced by insertion mutations in genes coding for efflux, other surface-associated functions, DNA repair and expression regulation, including phoP, barA and marA. Insertion mutations that diminished susceptibility were predominantly in genes coding for surface polysaccharide biosynthesis and regulatory genes, including slyA, emrR, envZ and cpxR. CONCLUSIONS: A genomics approach has identified novel contributors to gain or loss of ciprofloxacin susceptibility in S. Typhi, expanding our understanding of the impact of fluoroquinolones on bacteria and of mechanisms that may contribute to resistance. The data also demonstrate the power of the TraDIS technology for antibacterial research

Airborne Precision Spacing for Dependent Parallel Operations Interface Study

This paper describes a usability study of proposed cockpit interfaces to support Airborne Precision Spacing (APS) operations for aircraft performing dependent parallel approaches (DPA). NASA has proposed an airborne system called Pair Dependent Speed (PDS) which uses their Airborne Spacing for Terminal Arrival Routes (ASTAR) algorithm to manage spacing intervals. Interface elements were designed to facilitate the input of APS-DPA spacing parameters to ASTAR, and to convey PDS system information to the crew deemed necessary and/or helpful to conduct the operation, including: target speed, guidance mode, target aircraft depiction, and spacing trend indication. In the study, subject pilots observed recorded simulations using the proposed interface elements in which the ownship managed assigned spacing intervals from two other arriving aircraft. Simulations were recorded using the Aircraft Simulation for Traffic Operations Research (ASTOR) platform, a medium-fidelity simulator based on a modern Boeing commercial glass cockpit. Various combinations of the interface elements were presented to subject pilots, and feedback was collected via structured questionnaires. The results of subject pilot evaluations show that the proposed design elements were acceptable, and that preferable combinations exist within this set of elements. The results also point to potential improvements to be considered for implementation in future experiments

Expression of Cellulosome Components and Type IV Pili within the Extracellular Proteome of Ruminococcus flavefaciens 007

Funding: The Rowett Institute receives funding from SG-RESAS (Scottish Government Rural and Environmental Science and Analysis Service). Visit of M.V. was supported by research grants from FEMS and Slovene human resources development and scholarship funds. Parts of this work were funded by grants from the United States-Israel Binational Science Foundation (BSF), Jerusalem, Israel – BSF Energy Research grant to E.A.B. and B.A.W. and Regular BSF Research grants to R.L. and B.A.W. – and by the Israel Science Foundation (grant nos 966/09 and 159/07 291/08). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

AlbaTraDIS:Comparative analysis of large datasets from parallel transposon mutagenesis experiments

Bacteria need to survive in a wide range of environments. Currently, there is an incomplete understanding of the genetic basis for mechanisms underpinning survival in stressful conditions, such as the presence of anti-microbials. Transposon directed insertion-site sequencing (TraDIS) is a powerful tool to identify genes and networks which are involved in survival and fitness under a given condition by simultaneously assaying the fitness of millions of mutants, thereby relating genotype to phenotype and contributing to an understanding of bacterial cell biology. A recent refinement of this approach allows the roles of essential genes in conditional stress survival to be inferred by altering their expression. These advancements combined with the rapidly falling costs of sequencing now allows comparisons between multiple experiments to identify commonalities in stress responses to different conditions. This capacity however poses a new challenge for analysis of multiple data sets in conjunction. To address this analysis need, we have developed 'AlbaTraDIS'; a software application for rapid large-scale comparative analysis of TraDIS experiments that predicts the impact of transposon insertions on nearby genes. AlbaTraDIS can identify genes which are up or down regulated, or inactivated, between multiple conditions, producing a filtered list of genes for further experimental validation as well as several accompanying data visualisations. We demonstrate the utility of our new approach by applying it to identify genes used by Escherichia coli to survive in a wide range of different concentrations of the biocide Triclosan. AlbaTraDIS identified all well characterised Triclosan resistance genes, including the primary target, fabI. A number of new loci were also implicated in Triclosan resistance and the predicted phenotypes for a selection of these were validated experimentally with results being consistent with predictions. AlbaTraDIS provides a simple and rapid method to analyse multiple transposon mutagenesis data sets allowing this technology to be used at large scale. To our knowledge this is the only tool currently available that can perform these tasks. AlbaTraDIS is written in Python 3 and is available under the open source licence GNU GPL 3 from https://github.com/quadram-institute-bioscience/albatradis

Fragmentation and dewatering transform Great Plains stream fish communities

Citation: Perkin, J. S., Gido, K. B., Cooper, A. R., Turner, T. F., Osborne, M. J., Johnson, E. R., & Mayes, K. B. (2015). Fragmentation and dewatering transform Great Plains stream fish communities. Ecological Monographs, 85(1), 73-92. doi:10.1890/14-0121.1Biodiversity in stream networks is threatened globally by interactions between habitat fragmentation and altered hydrologic regimes. In the Great Plains of North America, stream networks are fragmented by >19000 anthropogenic barriers, and flow regimes are altered by surface water retention and groundwater extraction. We documented the distribution of anthropogenic barriers and dry stream segments in five basins covering the central Great Plains to assess effects of broad-scale environmental change on stream fish community structure and distribution of reproductive guilds. We used an information-theoretic approach to rank competing models in which fragmentation, discharge magnitude, and percentage of time streams had zero flow (a measure of desiccation) were included to predict effects of environmental alterations on the distribution of fishes belonging to different reproductive guilds. Fragmentation caused by anthropogenic barriers was most common in the eastern Great Plains, but stream desiccation became more common to the west, where rivers are underlain by the depleted (i.e., extraction > recharge) High Plains Aquifer. Longitudinal gradients in fragmentation and desiccation contributed to spatial shifts in community structure from taxonomically and functionally diverse communities dominated by pelagic reproductive guilds where fragmentation and desiccation were least, to homogenized communities dominated by benthic guilds where fragmentation and desiccation were common. Modeling results revealed these shifts were primarily associated with decline of pelagic reproductive guilds, notably small-bodied pelagophilic and lithopelagophilic fishes that declined in association with decreased fragment length and increased number of days with zero flow. Graph theory combined with a barrier prioritization approach revealed specific fragments that could be reconnected to allow fishes within these guilds to colonize currently unoccupied fragments with the mitigation or removal of small dams (<10 m height). These findings are useful for natural resource managers charged with halting or reversing the prevailing pattern of declining fish diversity in the Great Plains. Our study represents one of the most comprehensive assessments of fish diversity responses to broad-scale environmental change in the Great Plains and provides a conservation strategy for addressing the simultaneous contributions of fragmentation and flow alteration to the global freshwater biodiversity crisis

Novel methods to deal with publication biases: secondary analysis of antidepressant trials in the FDA trial registry database and related journal publications

Objective To assess the performance of novel contour enhanced funnel plots and a regression based adjustment method to detect and adjust for publication biases

Patients' continuing use of an online health record:a quantitative evaluation of 14,000 patient years of access data

BACKGROUND: Online access to all or part of their health records is widely demanded by patients and, where provided in form of patient portals, has been substantially used by at least subgroups of patients, particularly those with chronic disease. However, little is reported regarding the longer-term patient use of patient-accessible electronic health record services, which is important in allocating resources. Renal PatientView (RPV) is an established system that gives patients with chronic kidney disease access to live test results and information about their condition and treatment. It is available in most UK renal units with up to 75% of particular patient groups registered in some centers. We have analyzed patient use out to 4 years and investigated factors associated with more persistent use. OBJECTIVE: Our aim was to investigate RPV use by patients over time from initial registration in order to understand which patients choose to access RPV and the endurance of its appeal for different patient groups. METHODS: We analyzed an anonymized extract of the database underlying RPV containing information on patient registration and events including patient access and the arrival of new blood test results or letters that patients might wish to view. RESULTS: At the time of the extract, there were 11,352 patients registered on RPV for 0-42 months (median 17). More than half of registrants became persistent users, logging in a median of 2.0 times each month over post-registration intervals of up to 42 months (median 18.9). Provision of assistance with first logon was strongly associated with becoming a persistent user, even at 3 years. Logons by persistent users occurred around the time of consultations/tests, strongly suggestive of patient engagement. While indices indicative of greater deprivation were the strongest determinants of non-participation, they had negligible influence on drop-out rates among established users. CONCLUSIONS: In this mature patient portal system, a large proportion of patients made regular use of their online health records over protracted periods. The patterns and timing of use indicate strong patient interest in detailed information such as recent test results and clinic letters. Supporting patients through the first steps of establishing access to their online records is associated with much higher rates of long-term use of RPV and likely would increase use of other electronic health records provided for patients with chronic disease