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Organic amendments are applied in organic farming systems to provide nutrients for crop uptake and to improve soil health. Compost is often favored over fresh manure for food safety reasons, while fresh manure can be a valuable source of readily available nitrogen (N). However, the potential for fresh versus composted manure to differentially affect soil microbial and N-cycling functional communities over multiple seasons remains unknown. We compared the effect of composted vs. fresh cattle manure on soil microbial communities using taxonomic and functional approaches. Soils were collected from field plots with three organic N treatments: control (no amendment), composted manure (compost, 224 kg/ha total N), and fresh manure (manure, 224 kg/ha total N) in an organic production system. Illumina amplicon sequencing was used to comprehensively assess the bacterial community (16S rRNA genes), fungal community (ITS), ureolytic community (ureC), chitinolytic community (chiA), bacterial ammonia oxidizers (AOB amoA), and nitrite oxidizers (Nitrospira nxrB). The results showed that both compost and manure treatment significantly changed the soil microbial communities. Manure had a stronger effect than compost on soil bacterial and fungal community composition, as well as on the ureolytic and chitinolytic communities, while compost treated soils had higher microbial richness than manure treated soils. Both taxonomic and functional approaches showed that the microbial community was more responsive to fresh manure than to compost. Manure treated soil also had more complex microbial interactions than compost treated soil. The abundance and community composition of N-cycling functional groups often played more limited roles than soil chemical properties (soil organic carbon, extractable organic carbon, and pH) in driving N-cycling processes. Results from our study may guide strategies for the management of organic amendments in organic farming systems and provide insights into the linkages between soil microbial communities and soil function.

The effort for combating the COVID-19 pandemic around the world has resulted in a huge amount of data, e.g., from testing, contact tracing, modelling, treatment, vaccine trials, and more. In addition to numerous challenges in epidemiology, healthcare, biosciences, and social sciences, there has been an urgent need to develop and provide visualisation and visual analytics (VIS) capacities to support emergency responses under difficult operational conditions. In this paper, we report the experience of a group of VIS volunteers who have been working in a large research and development consortium and providing VIS support to various observational, analytical, model-developmental, and disseminative tasks. In particular, we describe our approaches to the challenges that we have encountered in requirements analysis, data acquisition, visual design, software design, system development, team organisation, and resource planning. By reflecting on our experience, we propose a set of recommendations as the first step towards a methodology for developing and providing rapid VIS capacities to support emergency responses.

PurposeTo improve the spatial/temporal resolution of whole-heart coronary MR angiography by developing a variable-density (VD) 3D cones acquisition suitable for image reconstruction with parallel imaging and compressed sensing techniques.MethodsA VD 3D cones trajectory design incorporates both radial and spiral trajectory undersampling techniques to achieve higher resolution. This design is used to generate a VD 3D cones trajectory with 0.8 mm/66 ms isotropic spatial/temporal resolution, using a similar number of readouts as our previous fully sampled cones trajectory (1.2 mm/100 ms). Scans of volunteers and patients are performed to evaluate the performance of the VD trajectory, using non-Cartesian L1 -ESPIRiT for high-resolution image reconstruction.ResultsWith gridding reconstruction, the high-resolution scans experience an expected drop in signal-to-noise and contrast-to-noise ratios, but with L1 -ESPIRiT, the apparent noise is substantially reduced. Compared with 1.2 mm images, in each volunteer, the L1 -ESPIRiT 0.8 mm images exhibit higher vessel sharpness values in the right and left anterior descending arteries.ConclusionCoronary MR angiography with isotropic submillimeter spatial resolution and high temporal resolution can be performed with VD 3D cones to improve the depiction of coronary arteries.

PurposeTo implement a nonrigid autofocus motion correction technique to improve respiratory motion correction of free-breathing whole-heart coronary magnetic resonance angiography acquisitions using an image-navigated 3D cones sequence.Methods2D image navigators acquired every heartbeat are used to measure superior-inferior, anterior-posterior, and right-left translation of the heart during a free-breathing coronary magnetic resonance angiography scan using a 3D cones readout trajectory. Various tidal respiratory motion patterns are modeled by independently scaling the three measured displacement trajectories. These scaled motion trajectories are used for 3D translational compensation of the acquired data, and a bank of motion-compensated images is reconstructed. From this bank, a gradient entropy focusing metric is used to generate a nonrigid motion-corrected image on a pixel-by-pixel basis. The performance of the autofocus motion correction technique is compared with rigid-body translational correction and no correction in phantom, volunteer, and patient studies.ResultsNonrigid autofocus motion correction yields improved image quality compared to rigid-body-corrected images and uncorrected images. Quantitative vessel sharpness measurements indicate superiority of the proposed technique in 14 out of 15 coronary segments from three patient and two volunteer studies.ConclusionThe proposed technique corrects nonrigid motion artifacts in free-breathing 3D cones acquisitions, improving image quality compared to rigid-body motion correction.

BACKGROUND: Sale of organic foods is one of the fastest growing market segments within the global food industry. People often buy organic food because they believe organic farms produce more nutritious and better tasting food from healthier soils. Here we tested if there are significant differences in fruit and soil quality from 13 pairs of commercial organic and conventional strawberry agroecosystems in California. METHODOLOGY/PRINCIPAL FINDINGS: At multiple sampling times for two years, we evaluated three varieties of strawberries for mineral elements, shelf life, phytochemical composition, and organoleptic properties. We also analyzed traditional soil properties and soil DNA using microarray technology. We found that the organic farms had strawberries with longer shelf life, greater dry matter, and higher antioxidant activity and concentrations of ascorbic acid and phenolic compounds, but lower concentrations of phosphorus and potassium. In one variety, sensory panels judged organic strawberries to be sweeter and have better flavor, overall acceptance, and appearance than their conventional counterparts. We also found the organically farmed soils to have more total carbon and nitrogen, greater microbial biomass and activity, and higher concentrations of micronutrients. Organically farmed soils also exhibited greater numbers of endemic genes and greater functional gene abundance and diversity for several biogeochemical processes, such as nitrogen fixation and pesticide degradation. CONCLUSIONS/SIGNIFICANCE: Our findings show that the organic strawberry farms produced higher quality fruit and that their higher quality soils may have greater microbial functional capability and resilience to stress. These findings justify additional investigations aimed at detecting and quantifying such effects and their interactions.

Rat and human very low density lipoproteins (VLDL) were fractionated by zonal ultracentrifugation, yielding sharply defined fractions with narrow sedimentation limits. Sedimentation coefficients for the individual fractions were determined at two densities with the analytical ultracentrifuge, and the results were analyzed to yield buoyant densities and molecular weights for the particles in each fraction. For the rat lipoproteins, the weight concentrations of triglycerides, cholesterol, phospholipid, and protein were determined for each fraction, and their molar concentrations of apolipoprotein B were measured with a radioimmunoassay. For the human lipoproteins the corresponding values were taken from Patsch et al. (Patsch, W., J. R. Patsch, G. M. Kostner, S. Sailer, and H. Braunsteiner. 1978. Isolation of subfractions of human very low density lipoproteins by zonal ultracentrifugation. J. Biol. Chem. 253:4911-4915). From these data, a ratio of the number of apoB peptides to the number of lipoprotein particles was calculated for each fraction. This ratio was close to 1 for all VLDL fractions, ranging in particle diameter from about 40 to 80 mm and 30 to 50 mm, respectively, for rat and human VLDL. The majority rat VLDL contain B-48 rather than B-100 as their (single) apoB peptide. Based on these data, we proposed that only a single copy of B-48 is required for VLDL assembly in rat liver, unless nascent hepatic VLDL contain additional apoB peptides which are uniformly lost from the plasma VLDL particles when they are analyzed.