Predicting cover crop biomass by lightweight UAS-based RGB and NIR photography: an applied photogrammetric approach

Easy-to-capture and robust plant status indicators are important factors when implementing precision agriculture techniques on fields. In this study, aerial red, green and blue color space (RGB) photography and near-infrared (NIR) photography was performed on an experimental field site with nine different cover crops. A lightweight unmanned aerial system (UAS) served as platform, consumer cameras as sensors. Photos were photogrammetrically processed to orthophotos and digital surface models (DSMs). In a first validation step, the spatial precision of RGB orthophotos (x and y, ± 0.1 m) and DSMs (z, ± 0.1 m) was determined. Then, canopy cover (CC), plant height (PH), normalized differenced vegetation index (NDVI), red edge inflection point (REIP), and green red vegetation index (GRVI) were extracted. In a second validation step, the PHs derived from the DSMs were compared with ground truth ruler measurements. A strong linear relationship was observed (R ² = 0.80?0.84). Finally, destructive biomass samples were taken and compared with the remotely-sensed characteristics. Biomass correlated best with plant height (PH), and good approximations with linear regressions were found (R ² = 0.74 for four selected species, R ² = 0.58 for all nine species). CC and the vegetation indices (VIs) showed less significant and less strong overall correlations, but performed well for certain species. It is therefore evident that the use of DSM-based PHs provides a feasible approach to a species-independent non-destructive biomass determination, where the performance of VIs is more species-dependent.     

Mobile low-cost 3D camera maize crop height measurements under field conditions

To tackle global challenges such as food supply and renewable energy provision, the improvement of efficiency and productivity in agriculture is of high importance. Site-specific information about crop height plays an important role in reaching these goals. Crop height can be derived with a variety of approaches including the analysis of three-dimensional (3D) geodata. Crop height values derived from 3D geodata of maize (1.88 and 2.35 m average height) captured with a low-cost 3D camera were examined. Data were collected with a unique measurement setup including the mobile mounting of the 3D camera, and data acquisition under field conditions including wind and sunlight. Furthermore, the data were located in a global co-ordinate system with a straightforward approach, which can strongly reduce computational efforts and which can subsequently support near real-time data processing in the field. Based upon a comparison between crop height values derived from 3D geodata captured with the low-cost approach, and high-end terrestrial laser scanning reference data, minimum RMS and standard deviation values of 0.13 m (6.91% of average crop height), and maximum R² values of 0.79 were achieved. It can be concluded that the crop height measurements derived from data captured with the introduced setup can provide valuable input for tasks such as biomass estimation. Overall, the setup is considered to be a valuable extension for agricultural machines which will provide complementary crop height measurements for various agricultural applications.     

Spatial scaling of soil salinity indices along a temporal coastal reclamation area transect in China using wavelet analysis

High spatial variability of soil salinity in coastal reclamation regions makes it difficult to obtain accurate scale-dependent information. The objectives of this study were to describe the spatial patterns of saline-sodic soil properties (using soil pH, electrical conductivity (EC_1:5) and sodium ion content (SIC) as indicators) and to gain knowledge of the scaling relationships between those variables. The soil pH, EC_1:5 and SIC data were measured at intervals of 285 m along a 13,965-m temporal transect in a coastal region of China. The spatial variability of soil pH was weak but it was strong for soil EC_1:5 and SIC at the measurement scale. There was a significant positive correlation between soil EC_1:5 and SIC, while correlations between soil pH and either EC_1:5 or SIC were weak and negative. For each saline-sodic soil parameter, the variability changed with the decomposition scales. The high-variance area at the larger scales (≥570 m) occupied less than 10% of the total area in the local wavelet spectrum, which meant that the spatial variations of the salinity indicators were insignificant at these scales. For local wavelet coherency, at a scale of 1500–2800 m and a sampling distance of 0–4500 m, the covariance was statistically significant between any two of the saline-sodic soil parameters.     

Chlorogenic acid,a metabolite identified by untargeted metabolome analysis in resistant tomatoes,inhibits the colonization by Alternaria alternata by inhibiting alternariol biosynthesis

Tomato fruits can be contaminated by saprophytic strains of Alternaria alternata which is the reason for the frequent occurrence of Alternaria toxins like alternariol, alternariol monomethylether or tenuazonic acid in these types of products. It was shown earlier that alternariol is a colonization factor for tomatoes. In the current analysis two different tomato genotypes were analysed by untargeted comprehensive two-dimensional gas chromatography mass spectrometry (GC×GC-MS). This analysis revealed clear differences in the metabolic profiles which were paralleled by differences in resistance towards Alternaria colonization. One of the genotypes was more resistant against A. alternata infection and contained high amounts of chlorogenic acid in contrast to the other genotype which was sensitive against infection. In in vitro analysis, chlorogenic acid reduced alternariol biosynthesis during the first days of growth of A. alternata. Expression analysis of the alternariol polyketide synthase gene, a key gene in the biosynthesis of alternariol, also revealed a temporal reduction in its expression in the first phases of growth. However by chromatographic analysis it could be demonstrated that chlorogenic acid was degraded over time. This degradation leads to a relief of inhibition resulting in an only temporal inhibition of alternariol biosynthesis. In vivo colonization experiments revealed that chlorogenic acid reduces colonization of tomatoes by A. alternata in a concentration dependent manner, which however is partly counteracted by the addition of alterariol.     

Estimating nocturnal ecosystem respiration from the vertical turbulent flux and change in storage of CO2

Micrometeorological measurements of nighttime ecosystem respiration can be systematically biased when stable atmospheric conditions lead to drainage flows associated with decoupling of air flow above and within plant canopies. The associated horizontal and vertical advective fluxes cannot be measured using instrumentation on the single towers typically used at micrometeorological sites. A common approach to minimize bias is to use a threshold in friction velocity, u_*, to exclude periods when advection is assumed to be important, but this is problematic in situations when in-canopy flows are decoupled from the flow above. Using data from 25 flux stations in a wide variety of forest ecosystems globally, we examine the generality of a novel approach to estimating nocturnal respiration developed by van Gorsel et al. (van Gorsel, E., Leuning, R., Cleugh, H.A., Keith, H., Suni, T., 2007. Nocturnal carbon efflux: reconciliation of eddy covariance and chamber measurements using an alternative to the u_*-threshold filtering technique. Tellus 59B, 397–403, Tellus, 59B, 307-403). The approach is based on the assumption that advection is small relative to the vertical turbulent flux (F_C) and change in storage (F_S) of CO₂ in the few hours after sundown. The sum of F_C and F_S reach a maximum during this period which is used to derive a temperature response function for ecosystem respiration. Measured hourly soil temperatures are then used with this function to estimate respiration R_Rmax. The new approach yielded excellent agreement with (1) independent measurements using respiration chambers, (2) with estimates using ecosystem light-response curves of F_c + F_s extrapolated to zero light, R_LRC, and (3) with a detailed process-based forest ecosystem model, R_cast. At most sites respiration rates estimated using the u_*-filter, R_ust, were smaller than R_Rmax and R_LRC. Agreement of our approach with independent measurements indicates that R_Rmax provides an excellent estimate of nighttime ecosystem respiration.     

Clinical presentation, treatment, and outcome of dacryocystitis in rabbits: a retrospective study of 28 cases (2003–2007)

Objective  To document the clinical presentation, diagnostics, treatment, and clinical outcome of rabbits with dacryocystitis.
Materials and methods  This retrospective study included 28 rabbits diagnosed with dacryocystitis. Available records of clinical and ophthalmological examinations, bacteriological samplings, diagnostic imaging, and treatment were reviewed. A telephone survey of the owners was conducted to evaluate recovery and recurrences.
Results  The mean age of the 28 rabbits presenting with ocular discharge from the nasolacrimal duct was 4.4 years. In 25 rabbits (89%), dacryocystitis was a unilateral finding. No underlying cause could be determined in 10 animals (35%). Dental malocclusion was observed in 14 rabbits (50%) and rhinitis in two animals (7%), with one animal showing both symptoms (4%). One rabbit (4%) presented with panophthalmitis. Most animals (96%) received topical antibiotic treatment. If necessary, additional topical (acetylcysteine, vitamin A ointment, nonsteroidals) or systemic treatment (antibiotics, nonsteroidals, paramunity inducer, and glucocorticoids) was provided. The mean duration of therapy was 5.8 weeks. The nasolacrimal duct was flushed in 27 of 31 affected eyes (87%). Dentistry was performed in 80% of the animals suffering from malocclusion. Regarding the clinical outcome, 12 animals (43%) showed complete recovery, eight rabbits (28%) were euthanized, three (11%) died due to unrelated causes, and three (11%) were lost to follow-up. Two rabbits (7%) continue to display signs of dacryocystitis and are being treated symptomatically by the owners.
Conclusions  This study reports the clinical presentation, treatment, and outcome of dacryocystitis in rabbits and outlines the importance of examination of the oral cavity, diagnostic imaging, and bacteriologic sampling.     

Control charts applied to simulated sow herd datasets

Statistical control charts were used to detect process change in pig production. Two charts were tested to detect small deviations in production processes: the cumulative sum (CUSUM) control chart and the exponentially weighted moving average (EWMA) control chart. A Monte-Carlo simulation was used for developing an optimal design of the EWMA and the CUSUM charts. The traits piglets born in total and the return to oestrus rate were considered. Over a given time period, small shifts were purposely implemented to test the performance of the charts. The average time to signal (ATS) and false positive rate (FPR) were taken as classification parameters to evaluate the performance of the charts. All shifts in the number of piglets born in total were detected with CUSUM and EWMA control charts. The trait piglets born in total showed an ATS ranging from 1.3 (FPR = 33.5%) to 6.8 weeks (FPR = 1.2%) using the CUSUM chart. The EWMA chart presented an ATS which ranged between 2.0 (FPR = 14.9%) and 6.3 (FPR = 1.9%) weeks. The application of the CUSUM to the return to oestrus rate resulted in an ATS of 2.6 (FPR =  38.3%) to 15.6 weeks (FPR = 3.0%) and the EWMA chart produced a signal between 4.1 (FPR = 14.5%) and 16.4 weeks (FPR = 1.4%). Both charts appear to be useful tools for tracking commercial swine farm processes and detecting emerging change in process performance.     

Detection of fluoroquinolone resistance level in clinical canine and feline Escherichia coli pathogens using rapid real-time PCR assay

Fluoroquinolones are used to treat infections caused by Escherichia coli in canine and feline veterinary patients, particularly those infecting the urinary tract. The gyrA gene is a primary target causing fluoroquinolone resistance in Gram negative coliforms, with mutations in codons 83 and 87 generally associated with high-level of resistance E. coli clinical isolates. We have developed a fluorescence resonance energy transfer (FRET) quantitative PCR to identify enrofloxacin-resistance in clinical E. coli isolates that carry mutations in codons 83 and 87 of gyrA. This real-time quantitative PCR assay is rapid, economical, and sensitive compared with cultured antimicrobial susceptibility testing. The assay identified as few as four genome copies per reaction from culture and 19 genome copies in urine. For the 70 isolates tested, the sensitivity was 87.5% (95% CI = 75–95.3%) (n = 42/48), specificity was 100% (95% CI = 87.3–100%) (n = 22/22), whereas accuracy was 91.4% (95% CI = 82.3–97%) (n = 64/70). Furthermore, we were able to accurately differentiate between the wild type and mutants E. coli directly from infected canine urine samples (n = 5) within 2 h. These results were confirmed by sequence alignments of the PCR products and comparison with the susceptibility testing. The FRET-PCR assay appears to have promising clinical application as an early diagnostic tool for rapid and sensitive detection and differentiation of the level of fluoroquinolone resistance among clinical E. coli isolates that may facilitate design of the dosing regimen.     

Clinical evaluation of pimecrolimus eye drops for treatment of canine keratoconjunctivitis sicca: a comparison with cyclosporine A

The aim of this study was to evaluate the efficacy of pimecrolimus oil-based eye drops in alleviating the clinical signs of keratoconjunctivitis sicca (KCS) in dogs and to compare the efficacy with that of cyclosporine A (CsA) ointment. An open-label, multicenter study enrolling 44 dogs previously untreated with CsA was conducted. Dogs were randomly assigned to a treatment group and medicated twice daily for 8 weeks. After that time the mean increase (+/-SEM) in the Schirmer tear test was 9.2+/-1.6 mm/min in the pimecrolimus group and 5.8+/-1.1 mm/min in the CsA group (P=0.085). The improvement in clinical signs of inflammation in eyes treated with pimecrolimus was significantly greater than in eyes treated with CsA (P=0.02). The results show that 1% pimecrolimus oily eye drops are as safe as and more effective than CsA ointment in controlling KCS in dogs.