The InDeVal insertion/deletion evaluation tool: a program for finding target regions in DNA sequences and for aiding in sequence comparison

BACKGROUND: The program InDeVal was originally developed to help researchers find known regions of insertion/deletion activity (with the exception of isolated single-base indels) in newly determined Poaceae trnL-F sequences and compare them with 533 previously determined sequences. It is supplied with input files designed for this purpose. More broadly, the program is applicable for finding specific target regions (referred to as "variable regions") in DNA sequence. A variable region is any specific sequence fragment of interest, such as an indel region, a codon or codons, or sequence coding for a particular RNA secondary structure. RESULTS: InDeVal input is DNA sequence and a template file (sequence flanking each variable region). Additional files contain the variable regions and user-defined messages about the sequence found within them (e.g., taxa sharing each of the different indel patterns). Variable regions are found by determining the position of flanking sequence (referred to as "conserved regions") using the LPAM (Length-Preserving Alignment Method) algorithm. This algorithm was designed for InDeVal and is described here for the first time. InDeVal output is an interactive display of the analyzed sequence, broken into user-defined units. Once the user is satisfied with the organization of the display, the information can be exported to an annotated text file. CONCLUSIONS: InDeVal can find multiple variable regions simultaneously (28 indel regions in the Poaceae trnL-F files) and display user-selected messages specific to the sequence variants found. InDeVal output is designed to facilitate comparison between the analyzed sequence and previously evaluated sequence. The program's sensitivity to different levels of nucleotide and/or length variation in conserved regions can be adjusted. InDeVal is currently available for Windows in Additional file 1 or from

The aging of tungsten filaments and its effect on wire surface kinetics in hot-wire chemical vapor deposition

Wire-desorbed radicals present during hot-wire chemical vapor deposition growth have been measured by quadrupole mass spectrometry. New wires produce Si as the predominant radical for temperatures above 1500 K, with a minor contribution from SiH3, consistent with previous measurements; the activation energy for the SiH3 signal suggests its formation is catalyzed. Aged wires also produce Si as the predominant radical (above 2100 K), but show profoundly different radical desorption kinetics. In particular, the Si signal exhibits a high temperature activation energy consistent with evaporation from liquid silicon. The relative abundance of the other SiHx species suggests that heterogeneous pyrolysis of SiH4 on the wire may be occurring to some extent. Chemical analysis of aged wires by Auger electron spectroscopy suggests that the aging process is related to the formation of a silicide at the surface, with silicon surface concentrations as high as 15 at. %. A limited amount (2 at. %) of silicon is observed in the interior as well, suggesting that diffusion into the wire occurs. Calculation of the relative rates for the various wire kinetic processes, coupled with experimental observations, reveals that silicon diffusion through the silicide is the slowest process, followed by Si evaporation, with SiH4 decomposition being the fastest

Investigation of a Recharge Basin to Improve Drought Resiliency and Aquifer Sustainability Rock Valley Rural Water

https://ir.uiowa.edu/igs_wrir/1017/thumbnail.jp

Aquifer Sustainability at the Osceola County Rural Water System H-Series Wellfield

https://ir.uiowa.edu/igs_wrir/1019/thumbnail.jp

Toward A Zero Energy Home: Applying Swiss Building Practices/Attitudes to U.S. Residential Construction

This project evaluated typical U.S. and Swiss homes to identify construction practices that are most energy efficient and have economic payback. A net zero energy home (ZEH) produces as much energy as is consumed in it over time. Students in a College o f Technology in a Midwest Indiana State University and a technical University in Switzerland resulted in developing models of homes that combined U.S. and Swiss standards. The project was completed in two phases: during the first phase o f this project, construction costs, energy use, and economic payback was calculated for six homes that were designed using both Swiss and U.S. standards. During the second phase of the project, cultural norms that influence energy use were explored. A survey was used to compare U.S. and Swiss college students’ lifestyles and energy habits. All homes had the same basic size and layout, but some used construction practices typical for the United States and others were designed according to Swiss guidelines for residential construction. The results of the study showed that a Swiss-style low-energy home is not cost effective for the Midwestern United States if energy costs remain low, but it could become attractive if energy rates escalate significantly. It was also recognized that technology by itself will not minimize energy consumption, a result o f the second part o f the project that explored cultural norms that influence energy use. From the survey of both U.S. and Swiss college students’ lifestyles and energy habits, it was revealed with a high level of confidence that Swiss students are more energy conscious than their U.S. counterparts

Modelling Large-Scale CO2 Leakages in the North Sea

A three dimensional hydrodynamic model with a coupled carbonate speciation sub-model is used to simulate large additions of CO2 into the North Sea, representing leakages at potential carbon sequestration sites. A range of leakage scenarios are conducted at two distinct release sites, allowing an analysis of the seasonal, inter-annual and spatial variability of impacts to the marine ecosystem. Seasonally stratified regions are shown to be more vulnerable to CO2 release during the summer as the added CO2 remains trapped beneath the thermocline, preventing outgasing to the atmosphere. On average, CO2 injected into the northern North Sea is shown to reside within the water column twice as long as an equivalent addition in the southern North Sea before reaching the atmosphere. Short-term leakages of 5000 tonnes CO2 over a single day result in substantial acidification at the release sites (up to -1.92 pH units), with significant perturbations (greater than 0.1 pH units) generally confined to a 10 km radius. Long-term CO2 leakages sustained for a year may result in extensive plumes of acidified seawater, carried by major advective pathways. Whilst such scenarios could be harmful to marine biota over confined spatial scales, continued unmitigated CO2 emissions from fossil fuels are predicted to result in greater and more long-lived perturbations to the carbonate system over the next few decades

BioTorrents: A File Sharing Service for Scientific Data

The transfer of scientific data has emerged as a significant challenge, as datasets continue to grow in size and demand for open access sharing increases. Current methods for file transfer do not scale well for large files and can cause long transfer times. In this study we present BioTorrents, a website that allows open access sharing of scientific data and uses the popular BitTorrent peer-to-peer file sharing technology. BioTorrents allows files to be transferred rapidly due to the sharing of bandwidth across multiple institutions and provides more reliable file transfers due to the built-in error checking of the file sharing technology. BioTorrents contains multiple features, including keyword searching, category browsing, RSS feeds, torrent comments, and a discussion forum. BioTorrents is available at http://www.biotorrents.net

Co-circulation of Multidrug-resistant Shigella Among Men Who Have Sex With Men in Australia.

BACKGROUND: In urban Australia, the burden of shigellosis is either in returning travelers from shigellosis-endemic regions or in men who have sex with men (MSM). Here, we combine genomic data with comprehensive epidemiological data on sexual exposure and travel to describe the spread of multidrug-resistant Shigella lineages. METHODS: A population-level study of all cultured Shigella isolates in the state of Victoria, Australia, was undertaken from 1 January 2016 through 31 March 2018. Antimicrobial susceptibility testing, whole-genome sequencing, and bioinformatic analyses of 545 Shigella isolates were performed at the Microbiological Diagnostic Unit Public Health Laboratory. Risk factor data on travel and sexual exposure were collected through enhanced surveillance forms or by interviews. RESULTS: Rates of antimicrobial resistance were high, with 17.6% (95/541) and 50.6% (274/541) resistance to ciprofloxacin and azithromycin, respectively. There were strong associations between antimicrobial resistance, phylogeny, and epidemiology. Specifically, 2 major MSM-associated lineages were identified: a Shigellasonnei lineage (n = 159) and a Shigella flexneri 2a lineage (n = 105). Of concern, 147/159 (92.4%) of isolates within the S. sonnei MSM-associated lineage harbored mutations associated with reduced susceptibility to recommended oral antimicrobials: namely, azithromycin, trimethoprim-sulfamethoxazole, and ciprofloxacin. Long-read sequencing demonstrated global dissemination of multidrug-resistant plasmids across Shigella species and lineages, but predominantly associated with MSM isolates. CONCLUSIONS: Our contemporary data highlight the ongoing public health threat posed by resistant Shigella, both in Australia and globally. Urgent multidisciplinary public health measures are required to interrupt transmission and prevent infection