Currently, circRNA studies are shifting from the identification of circular transcripts to understanding their biological functions. However, such endeavors have been limited by large-scale determination of their full-length sequences and also by the inability of accurate quantification at the isoform level. Here, we propose a new feature, reverse overlap (RO), for circRNA detection, which outperforms back-splice junction (BSJ)-based methods in identifying low-abundance circRNAs. By combining RO and BSJ features, we present a novel approach for effective reconstruction of full-length circRNAs and isoform-level quantification from the transcriptome. We systematically compared the difference between the BSJ-level and isoform-level differential expression analyses using human liver tumor and normal tissues and highlight the necessity of deepening circRNA studies to the isoform-level resolution. The CIRI-full software can be accessed at https://sourceforge.net/projects/ciri.Electronic supplementary materialThe online version of this article (10.1186/s13073-019-0614-1) contains supplementary material, which is available to authorized users.

Vegetated buffer strips were evaluated for their ability to remove waterborne Cryptosporidium parvum from surface and shallow subsurface flow during simulated rainfall rates of 15 or 40 mm/h for 4 h. Log 10 reductions for spiked C. parvum oocysts ranged from 1.0 to 3.1 per m of vegetated buffer, with buffers set at 5 to 20% slope, 85 to 99% fescue cover, soil textures of either silty clay (19:47:34 sand-silt-clay), loam (45:37:18), or sandy loam (70:25:5), and bulk densities of between 0.6 to 1.7 g/cm 3 . Vegetated buffers constructed with sandy loam or higher soil bulk densities were less effective at removing waterborne C. parvum (1-to 2-log 10 reduction/m) compared to buffers constructed with silty clay or loam or at lower bulk densities (2-to 3-log 10 reduction/m). The effect of slope on filtration efficiency was conditional on soil texture and soil bulk density. Based on these results, a vegetated buffer strip comprised of similar soils at a slope of <20% and a length of >3 m should function to remove >99.9% of C. parvum oocysts from agricultural runoff generated during events involving mild to moderate precipitation.Cryptosporidium parvum has emerged as a widespread and persistent waterborne microbial pathogen, with specific genotypes able to be transmitted ambidirectionally between livestock and humans (e.g., amphixenotic) (6,42,46,54). Although we still do not know the percentage of annual cases of human cryptosporidiosis that are attributable to livestock-derived waterborne C. parvum (39), reducing the likelihood that animal agricultural operations will contaminate surface water with infective C. parvum oocysts will help safeguard both water quality and public health (51). Several strategies exist for minimizing the likelihood that an animal agricultural operation contaminates surface water with infective C. parvum oocysts. For example, one such strategy is to reduce the incidence of C. parvum infection or the intensity of fecal shedding of C. parvum oocysts by livestock populations, thereby reducing the rate of environmental loading of C. parvum per livestock unit (26,36). These herd-health efforts remain hampered by our poor understanding of the medical ecology of C. parvum within livestock populations (3,4,16,40), how to interrupt transmission between the biological reservoir and susceptible animals (3, 40), and the lack of an affordable vaccine that has been proven to be efficacious in commercial agricultural settings (23,47).A second strategy is to manage the manure produced by livestock so that the survivability and off-site transport of infective C. parvum are substantially reduced (3,20,30,53,55). One strategy being advocated for minimizing the transport potential of C. parvum oocysts from animal manure to surface water is to place vegetated buffer strips between animal agricultural operations and vulnerable surface water supplies (10,12,15,32,38,51,59,60). Optimal design criteria for on-farm vegetated buffer strips currently do not exist for waterborne microbial contaminants. Moreover, studies ...

Domestic cats are one of the most popular pets globally, but the process of their domestication is not well understood. Near Eastern wildcats are thought to have been attracted to food sources in early agricultural settlements, following a commensal pathway to domestication. Early evidence for close human-cat relationships comes from a wildcat interred near a human on Cyprus ca. 9,500 y ago, but the earliest domestic cats are known only from Egyptian art dating to 4,000 y ago. Evidence is lacking from the key period of cat domestication 9,500-4,000 y ago. We report on the presence of cats directly dated between 5560-5280 cal B.P. in the early agricultural village of Quanhucun in Shaanxi, China. These cats were outside the wild range of Near Eastern wildcats and biometrically smaller, but within the size-range of domestic cats. The δ 13 C and δ 15 N values of human and animal bone collagen revealed substantial consumption of millet-based foods by humans, rodents, and cats. Ceramic storage containers designed to exclude rodents indicated a threat to stored grain in Yangshao villages. Taken together, isotopic and archaeological data demonstrate that cats were advantageous for ancient farmers. Isotopic data also show that one cat ate less meat and consumed more millet-based foods than expected, indicating that it scavenged among or was fed by people. This study offers fresh perspectives on cat domestication, providing the earliest known evidence for commensal relationships between people and cats.zooarchaeology | felid | mutualism | stable isotopes | Quanhucun site

[1] Complex transport behavior other than advection-dispersion, simple retardation, and first-order removal has been observed in many biocolloid transport experiments in porous media. Such nonideal transport behavior is particularly evident in the late time elution of biocolloids at low concentrations. Here we present a series of saturated column experiments that were designed to measure the breakthrough and long-term elution of Cryptosporidium parvum in medium sand for a few thousand pore volumes after the initial source of oocysts was removed. For a wide range of ionic strengths, I, we consistently observe slower-than-Fickian, power law tailing. The slope of the tail is flatter for higher I. At very high ionic strength the slope decays to a rate slower than t À1 . To explain this behavior, we propose a new filtration model based on the continuous time random walk (CTRW) theory. Our theory upscales heterogeneities at both the pore-scale geometry of the flow field and the grain surface physicochemical properties that affect biocolloid attachment and detachment. Pore-scale heterogeneities in fluid flow are shown to control the breakthrough of a conservative tracer but are shown to have negligible effect on oocyst transport. In our experiments, C. parvum transport is dominated by the effects of physicochemical heterogeneities. The CTRW model provides a parsimonious theory of nonreactive and reactive transport. The CTRW filtration process is controlled by three parameters, L, b, and c, which are related to the overall breakthrough retardation (R = 1 + L), the slope of the power law tail (b), and the transition to a slower than t À1 decay (c).Citation: Cortis, A., T. Harter, L. Hou, E. R. Atwill, A. I. Packman, and P. G. Green (2006), Transport of Cryptosporidium parvum in porous media: Long-term elution experiments and continuous time random walk filtration modeling, Water Resour. Res., 42, W12S13,

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Abstract. How and where to improve water quality within an agricultural watershed requires data at a spatial scale that corresponds with individual management decision units on an agricultural operation. This is particularly true in the context of water quality regulations, such as Total Maximum Daily Loads (TMDLs), that identify agriculture as one source of non-point source pollution through larger tributary watershed scale and above and below water quality investigations. We have conducted a systems approach study of 10 coastal dairies and ranches to document fecal coliform concentration and loading to surface waters at the management decision unit scale. Water quality samples were collected on a storm event basis from loading units that included: manure management systems; gutters; storm drains; pastures; and corrals and lots. In addition, in-stream samples were collected above and below the dairy facilities and from a control watershed, managed for light grazing and without a dairy facility or human residence and corresponding septic system. Samples were analyzed for fecal coliform concentration by membrane filtration. Instantaneous discharge was measured for each collected sample. Storm runoff was also calculated using the curve number method (SCS, 1985). Results for a representative dairy as well as the entire 10 dairy data set are presented. Fecal coliform concentrations demonstrate high variability both within and between loading units. Fecal coliform concentrations for pastures range from 206 to 2,288,888 cfu/100 ml and for lots from 1,933 to 166,105,000 cfu/100 ml. Mean concentrations for pastures and lots are 121,298 (SE = 62,222) and 3,155,584 (SE = 1,902,713) cfu/100 ml, respectively. Fecal coliform load from units of concentrated animals and manure are significantly more than units such as pastures while storm flow amounts were significantly less. Compared with results from earlier tributary scale studies in the watershed, this systems approach has generated water quality data that is beneficial for management decisions because of its scale and representation of current management activities. These results are facilitating on-farm changes through the cooperative efforts of dairy managers, regulatory agency staff, and sources of technical and financial assistance.

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