Sketching and sampling approaches for fast and accurate long read classification

In modern sequencing experiments, identifying the sources of the reads is a crucial need. In metagenomics, where each read comes from one of potentially many members of a community, it can be important to identify the exact species the read is from. In other settings, it is important to distinguish which reads are from the targeted sample and which are from potential contaminants. In both cases, identification of the correct source of a read enables further investigation of relevant reads, while minimizing wasted work. This task is particularly challenging for long reads, which can have a substantial error rate that obscures the origins of each read. Existing tools for the read classification problem are often alignment or index-based, but such methods can have large time and/or space overheads. In this work, we investigate the effectiveness of several sampling and sketching-based approaches for read classification. In these approaches, a chosen sampling or sketching algorithm is used to generate a reduced representation (a "screen") of potential source genomes for a query readset before reads are streamed in and compared against this screen. Using a query read's similarity to the elements of the screen, the methods predict the source of the read. Such an approach requires limited pre-processing, stores and works with only a subset of the input data, and is able to perform classification with a high degree of accuracy. The sampling and sketching approaches investigated include uniform sampling, methods based on MinHash and its weighted and order variants, a minimizer-based technique, and a novel clustering-based sketching approach. We demonstrate the effectiveness of these techniques both in identifying the source microbial genomes for reads from a metagenomic long read sequencing experiment, and in distinguishing between long reads from organisms of interest and potential contaminant reads. We then compare these approaches to existing alignment, index and sketching-based tools for read classification, and demonstrate how such a method is a viable alternative for determining the source of query reads. Finally, we present a reference implementation of these approaches at https://github.com/arun96/sketching.

Effects of Road De-Icing Salts on Two Amphibian Species, Rana Sylvatica and Rana Pipiens, and Their Trematode Parasites

With ongoing amphibian declines, it is essential to determine possible contributors such as diseases and environmental contaminants that may increase susceptibility. A potential contaminant is road salt (mainly NaCl), which leaches into aquatic environments. I examined whether road salts make larval amphibians (tadpoles) more susceptible to trematode parasite infection, and also how these affect free-living trematode infectious stages (cercariae). I exposed Rana sylvatica (wood frogs) and R. pipiens (northern leopard frogs) to control, medium (400 mg/L), and high salt (800 mg/L) treatments, and then to trematodes. High salt tended to reduce wood frog anti-parasite behaviour and resistance to infection but the opposite was seen for R. pipiens, although these tadpoles had elevated lymphocyte counts in high salinity. Trematodes were differentially affected by increased salinities. The results suggest that host-parasite-environment interactions are complex, with species differentially affected by contaminants, which may lead to community shifts in predominant hosts and parasite species.

Effects of Road De-Icing Salts on Two Amphibian Species, Rana Sylvatica and Rana Pipiens, and Their Trematode Parasites

With ongoing amphibian declines, it is essential to determine possible contributors such as diseases and environmental contaminants that may increase susceptibility. A potential contaminant is road salt (mainly NaCl), which leaches into aquatic environments. I examined whether road salts make larval amphibians (tadpoles) more susceptible to trematode parasite infection, and also how these affect free-living trematode infectious stages (cercariae). I exposed Rana sylvatica (wood frogs) and R. pipiens (northern leopard frogs) to control, medium (400 mg/L), and high salt (800 mg/L) treatments, and then to trematodes. High salt tended to reduce wood frog anti-parasite behaviour and resistance to infection but the opposite was seen for R. pipiens, although these tadpoles had elevated lymphocyte counts in high salinity. Trematodes were differentially affected by increased salinities. The results suggest that host-parasite-environment interactions are complex, with species differentially affected by contaminants, which may lead to community shifts in predominant hosts and parasite species.

Fallopia japonica (Japanese knotweed).

F. japonica is an extremely invasive weed despite its lack of extensive sexual reproduction in most of its introduced range. It is included on various lists of invasive weeds and is one of the 100 worst invasive species as identified by the IUCN. It is a potential contaminant of soil, and its ability to tolerate a remarkable range of soil types and climates means that it has the potential to spread much further than it has to date. It has gained a fearsome reputation for breaking through hard structures in the built environment and being almost impossible to eradicate once it has taken hold and is often recognized as one of the most pernicious weeds in any recipient country.

Comparison of Microporous Minerals for Potential Contaminant Uptake

<p>Microporous minerals have many industrial applications, from filtration to contaminant immobilization. Natural and synthetic minerals, including zeolites, clays, and silica aerogel, represent a few examples of microporous minerals with distinctive structures, surface charges, and porosity. Analysis and comparison of their crystal structures are necessary to determine how each mineral may be suited for contaminant uptake. Here we assessed the structure of microporous minerals, specifically rowleyite, clinoptilolite, vermiculite, and silica aerogel.  Raman spectroscopy, X-ray fluorescence, and X-ray powder diffraction were used to create and model atomic mineral structures to visualize atomic and macroscope features. Taking into account pore size and surface charge each mineral was reviewed to find the best fit with regards to heavy metal uptake, mainly Pb (lead). Overall, we provide a comparative framework to assess microporous minerals that will inform future flow-through experiments for heavy metal uptake.</p>

A complete search for redshift z ≳ 6.5 quasars in the VIKING survey

ABSTRACT We present the results of a new, deeper, and complete search for high-redshift 6.5 < z < 9.3 quasars over 977 deg2 of the VISTA Kilo-Degree Infrared Galaxy (VIKING) survey. This exploits a new list-driven data set providing photometry in all bands Z, Y, J, H, Ks, for all sources detected by VIKING in J. We use the Bayesian model comparison (BMC) selection method of Mortlock et al., producing a ranked list of just 21 candidates. The sources ranked 1, 2, 3, and 5 are the four known z > 6.5 quasars in this field. Additional observations of the other 17 candidates, primarily DESI Legacy Survey photometry and ESO FORS2 spectroscopy, confirm that none is a quasar. This is the first complete sample from the VIKING survey, and we provide the computed selection function. We include a detailed comparison of the BMC method against two other selection methods: colour cuts and minimum-χ2 SED fitting. We find that: (i) BMC produces eight times fewer false positives than colour cuts, while also reaching 0.3 mag deeper, (ii) the minimum-χ2 SED-fitting method is extremely efficient but reaches 0.7 mag less deep than the BMC method, and selects only one of the four known quasars. We show that BMC candidates, rejected because their photometric SEDs have high χ2 values, include bright examples of galaxies with very strong [O iii] λλ4959,5007 emission in the Y band, identified in fainter surveys by Matsuoka et al. This is a potential contaminant population in Euclid searches for faint z > 7 quasars, not previously accounted for, and that requires better characterization.

Identifying Contaminant Intrusion in Water Distribution Networks under Water Flow and Sensor Report Time Uncertainties

Contamination events in water distribution networks (WDNs) could have severe health and economic consequences. Contaminants can be deliberately or accidentally introduced into the WDN. Quick identification of the injection location and time is important in devising a mitigation plan to prevent further spread of the contaminant in the network. A method of identifying the possible intrusion point in a given network and reporting data is to use an inverse calculation by backtracking the potential path of the contaminant in the network. However, there is an element of uncertainty in the data used for calculation, particularly in water flow and sensor report time. Given the uncertainties, a method was developed in this study for fast and accurate contaminant source identification. This paper proposes a comparison filter of results by first identifying potential contaminant locations through backtracking, followed by a forward calculation to determine the injection time range, thereby reducing the potential suspects and providing likeliness comparison among the suspects. The effectiveness of the proposed method was examined by applying it to a benchmark WDN. By simulating uncertainties and filtering through the results, several possible contaminant intrusion locations and times were identified.

Fallopia japonica (Japanese knotweed).

F. japonica is an extremely invasive weed despite its lack of extensive sexual reproduction in most of its introduced range. It is included on various lists of invasive weeds and is one of the 100 worst invasive species as identified by the IUCN. It is a potential contaminant of soil, and its ability to tolerate a remarkable range of soil types and climates means that it has the potential to spread much further than it has to date. It has gained a fearsome reputation for breaking through hard structures in the built environment and being almost impossible to eradicate once it has taken hold and is often recognized as one of the most pernicious weeds in any recipient country.