NIPTmer : rapid k-mer-based software package for detection of fetal aneuploidies

Non-invasive prenatal testing (NIPT) is a recent and rapidly evolving method for detecting genetic lesions, such as aneuploidies, of a fetus. However, there is a need for faster and cheaper laboratory and analysis methods to make NIPT more widely accessible. We have developed a novel software package for detection of fetal aneuploidies from next-generation low-coverage whole genome sequencing data. Our tool - NIPTmer - is based on counting pre-defined per-chromosome sets of unique k-mers from raw sequencing data, and applying linear regression model on the counts. Additionally, the filtering process used for k-mer list creation allows one to take into account the genetic variance in a specific sample, thus reducing the source of uncertainty. The processing time of one sample is less than 10 CPU-minutes on a high-end workstation. NIPTmer was validated on a cohort of 583 NIPT samples and it correctly predicted 37 non-mosaic fetal aneuploidies. NIPTmer has the potential to reduce significantly the time and complexity of NIPT post-sequencing analysis compared to mapping-based methods. For non-commercial users the software package is freely available at http://bioinfo.ut.ee/NIPTMer/.Peer reviewe

Sustained Domestic Vector Exposure Is Associated With Increased Chagas Cardiomyopathy Risk but Decreased Parasitemia and Congenital Transmission Risk Among Young Women in Bolivia

Vector exposure showed a direct association with Chagas cardiomyopathy, but an inverse relationship with maternal parasitemia and congenital transmission. We hypothesize that repeated antigen exposure maintains an inflammatory response, increasing cardiomyopathy, but this upregulation improves control of parasitemia during pregnanc

Gully monitoring at two locations in the Grand Canyon National Park

For more information on the USGS-the Federal source for science about the Earth, its natural and living resources, natural hazards, and the environment-visit http://www.usgs.gov or call 1-888-ASK-USGS For an overview of USGS information products, including maps, imagery, and publications, visit http://www.usgs.gov/pubprod To order this and other USGS information products, visit http://store.usgs.gov Suggested citation: Schott, N.D., Hazel, J.E., Jr., Fairley, H.C., Kaplinski, M., and Parnell, R.A., 2014, Gully monitoring at two locations in the Grand Canyon National Park, Arizona, 1996Arizona, -2010, with emphasis on documenting effects of the March 2008 highflow experiment: U.S. Geological Survey Open-File Report 2014-1211. ISSN 2331ISSN -1258 Any use of trade, product, or firm names is for descriptive purposes only and does not imply endorsement by the U.S. Government. Although this report is in the public domain, permission must be secured from the individual copyright owners to reproduce any copyrighted material contained within this report. Datums Vertical and horizontal coordinate information is referenced to the 2007 realization of the National Spatial Reference System, North American Datum of 1983, NAD83 (NSRS2007), in meters. Elevation, as used in this report, refers to GPS derived ellipsoid height above the GRS80 ellipse, in meters, and not NAVD88 orthometric height. Abstract Many archeological sites in the Grand Canyon are being impacted by gully incision. In March 2008, a high-flow experiment (2008 HFE) was conducted with the intention of redistributing fine sediment (sand, silt, and clay) from the bed of the Colorado River to higher elevations along the channel margin. Deposition of fine sediment in gully mouths has been hypothesized to slow gully erosion rates and lessen impacts to archeological sites. The effects of the 2008 HFE on gullies were evaluated by comparing the topographic changes of three gullies at two study sites before and after the 2008 HFE. Comparison results indicated that sediment was deposited in gully mouths during the 2008 HFE, and that the inundated areas nearest to the river can be extensively altered by mainstream flow during high-flow events. Additionally, the history of gully evolution at the two study sites was examined between 1996 and 2010 and indicated that gullies have been subjected to thalweg incision and gully widening processes over a decadal timescale. Although the small sample size precludes extrapolating the results to other gullies, the findings contribute to the understanding of gully erosion in archeologically significant areas and have implications for future monitoring of gully erosion and evaluating the effectiveness of check dams intended to mitigate that erosion at archaeological sites in the Grand Canyon National Park

Using Electre III to aid the choice of housing construction process within structural engineering

The Electre III model may be considered as a decision-aid technique suited to the appraisal of complex civil/structural engineering projects. This conclusion is based on an assessment that the model permits a general ordering of alternatives, even when individual pairs of options remain uncompared where there is insufficient information to distinguish between them. Also, the technique is capable of dealing with the mix of both quantitative and qualitative information obtained within an engineering project appraisal. Electre III is applied to the evaluation of 11 alternative multi-family housing systems on the basis of 7 criteria covering labour, material and energy demand. Using this case study, the benefits of Electre III over other decision models in the selection process concerned are emphasized.Structural Engineering Electre Iii Multi-CRITERIA Decision Analysis Mcda,