Three dimensional quantification of soil hydraulic properties using X-ray Computed Tomography and image based modelling

We demonstrate the application of a high-resolution X-ray Computed Tomography (CT) method to quantify water distribution in soil pores under successive reductive drying. We focus on the wet end of the water release characteristic (WRC) (0 to -75 kPa) to investigate changes in soil water distribution in contrasting soil textures (sand and clay) and structures (sieved and field structured), to determine the impact of soil structure on hydraulic behaviour. The 3D structure of each soil was obtained from the CT images (at a 10 µm resolution). Stokes equations for flow were solved computationally for each measured structure to estimate hydraulic conductivity. The simulated values obtained compared extremely well with the measured saturated hydraulic conductivity values. By considering different sample sizes we were able to identify that the smallest possible representative sample size which is required to determine a globally valid hydraulic conductivity

Phacelia (Phacelia tanacetifolia Benth.) affects soil structure differently depending on soil texture

Aims: We studied the effects of Phacelia tanacetifolia, increasingly used as a cover-crop species in arable agricultural systems, upon soil structural properties in the context of two contrasting soil textures. We hypothesised there would be differential effects of the plants upon soil structure contingent on the texture. Methods: A sandy-loam and a clay soil were destructured by passing through 2 mm sieves, and planted with Phacelia in a replicated pot experiment, with associated unplanted controls. X-ray Computed Tomography was used to visualise and quantify the soil pore networks in 3D. Results: For the sandy-loam soil, there was no impact of plants upon aggregate size distribution porosity, pore connectivity, and pore surface density decreased in the presence of plants, whereas for the clay, there was a significant increase of aggregates <1000 μm, the porosity was constant, the pore-connectivity decreased, and surface density increased in the presence of plants. Conclusions: Plants can impact the structural genesis of soil depending on its inherent textural characteristics, leading to a differential development of pore architecture in different contexts. These results have implications both from an ecological perspective and in terms of the prescription of plants to remediate or condition soil structure in managed systems

Thirteen Questions about Using Machine Learning in Causal Research (You Won't Believe the Answer to Number 10!)

Machine learning is gaining prominence in the health sciences, where much of its use has focused on datadriven prediction. However, machine learning can also be embedded within causal analyses, potentially reducing biases arising from model misspecification. Using a question-and-answer format, we provide an introduction and orientation for epidemiologists interested in using machine learning but concerned about potential bias or loss of rigor due to use of "black box"models. We conclude with sample software code that may lower the barrier to entry to using these techniques

3D analysis of the soil porous architecture under long term contrasting management systems by X-ray Computed Tomography

The development of adequate soil structure is important for achieving good physical status, which influences the sustainability of agricultural areas. Different management systems lead to the development of a wide range of soil pore network characteristics. The objective of this research was to analyze the effect of three contrasting tillage systems (zero-tillage, ZT; reduced tillage, RT; conventional tillage, CT) in the soil porous system of an Oxisol. Samples were collected from the surface layer (0-10 cm). An area under secondary forest (F) was also assessed to provide an undisturbed reference. X-ray Computed Tomography (μCT) scanning of undisturbed soil samples and image analysis were employed for analysis of the pore network. The soil under ZT had the smallest porosity in comparison to the other 23 management systems. The conventionally tilled soil had the largest porosity and the most connected pores. One large connected pore was responsible for around 90% of the porosity of the resolvable pores (>35 μm) studied for all the management systems. Pores of elongated shapes, which enhance water movement through the soil, were the most frequent pores in terms of shape

2D vs. 3D pain visualization: User preferences in a spinal cord injury cohort

This is the post-print version of the Article. The official published version can be accessed from the link below - Copyright @ 2011 Springer VerlagResearch on pain experienced after Spinal Cord Injury (SCI) has revealed that not only are there several types of pain present in the same individual with this kind of trauma, but also that people who suffer such an injury can describe the characteristics of the same type of pain in different ways. Making it possible, therefore, to more precisely describe pain experience could prove to be vital for an increased quality of life. Accordingly, fifteen individuals with pain after SCI were asked to describe their pain experience using a 3 Dimensional (3D) model of the human body that could be used as an aid in communicating their pain. The results of this study suggest that the consensus of the participants approved the ability of the 3D model to more accurately describe their pain, an encouraging outcome towards the use of 3D technology in support of post SCI pain rehabilitation

Life at the extreme:Plant-driven hotspots of soil nutrient cycling in the hyper-arid core of the Atacama Desert

The hyperarid core of the Atacama Desert represents one of the most intense environments on Earth, often being used as an analog for Mars regolith. The area is characterized by extremes in climate (e.g., temperature, humidity, UV irradiation) and edaphic factors (e.g., hyper-salinity, high pH, compaction, high perchlorates, and low moisture, phosphorus and organic matter). However, the halophytic C4 plant Distichlis spicata appears to be one of the few species on the planet that can thrive in this environment. Within this habitat it captures windblown sand leading to the formation of unique structures and the generation of above-ground phyllosphere soil. Using a combination of approaches (e.g., X-ray Computed Tomography, TXRF, δ13C/δ15N isotope profiling, microbial PLFAs, 14C turnover, phosphate sorption isotherms) we examined the factors regulating the biogeochemical cycling of nitrogen (N), phosphorus (P) and carbon (C) in both vegetated and unvegetated areas. Our results showed that D. spicata rhizomes with large aerenchyma were able to break through the highly cemented topsoil layer leading to root proliferation in the underlying soil. The presence of roots increased soil water content, P availability and induced a change in microbial community structure and promoted microbial growth and activity. In contrast, soil in the phyllosphere exhibited almost no biological activity. Organic C stocks and recent C4 plant derived input increased as follows: phyllosphere (1941 g C m−2; 85% recent) &gt; soils under plants (575–748 g C m−2; 55–60%) &gt; bare soils (491–642 g C m−2; 9–17%). Due to the high levels of nitrate in soil (&gt;2 t ha−1) and high rates of P sorption/precipitation, our data suggest that the microbial activity is both C and P, but not N limited. Root-mediated salt uptake combined with foliar excretion and dispersal of NaCl into the surrounding area indicated that D. spicata was responsible for actively removing ca. 55% of the salt from the rhizosphere. We also demonstrate that NH3 emissions may represent a major N loss pathway from these soil ecosystems during the processing of organic N. We attribute this to NH3 volatilization to the high pH of the soil and slow rates of nitrification. In conclusion, we demonstrate that the extremophile D. spicata physically, chemically and biologically reengineers the soil to create a highly bioactive hotspot within the climate-extreme of the Atacama Desert.</p

Network models of soil porous structure

Soils sustain life on Earth. In times of increasing anthropogenic demands on soils [1] there is growing need to seek for novel approaches to understand the relationships between the soil porous structure and specific soil functions. Recently [2-4], soil pore structure was described as a complex network of pores using spatially embedded varying fitness network model [2] or heterogeneous preferential attachment scheme [3-4], both approaches revealing the apparent scale-free topology of soils. Here, we show, using a large set of soil images of structures obtained by X-ray computed tomography that both methods predict topological similar networks of soil pore structures. Furthermore, by analyzing the node-node link correlation properties of the obtained networks we suggest an approach to quantify the complexity of soil pore structur

Street Audits to Measure Neighborhood Disorder: Virtual or In-Person?

Neighborhood conditions may influence a broad range of health indicators, including obesity, injury, and psychopathology. In particular, neighborhood physical disorder - a measure of urban deterioration - is thought to encourage crime and high-risk behaviors, leading to poor mental and physical health. In studies to assess neighborhood physical disorder, investigators typically rely on time-consuming and expensive in-person systematic neighborhood audits. We compared 2 audit-based measures of neighborhood physical disorder in the city of Detroit, Michigan: One used Google Street View imagery from 2009 and the other used an in-person survey conducted in 2008. Each measure used spatial interpolation to estimate disorder at unobserved locations. In total, the virtual audit required approximately 3% of the time required by the in-person audit. However, the final physical disorder measures were significantly positively correlated at census block centroids (r = 0.52), identified the same regions as highly disordered, and displayed comparable leave-one-out cross-validation accuracy. The measures resulted in very similar convergent validity characteristics (correlation coefficients within 0.03 of each other). The virtual audit-based physical disorder measure could substitute for the in-person one with little to no loss of precision. Virtual audits appear to be a viable and much less expensive alternative to in-person audits for assessing neighborhood conditions

Mooney et al. Respond to "observing Neighborhood Physical Disorder"

[No abstract available