Detecting spikes of wheat plants using neural networks with Laws texture energy

Background: The spike of a cereal plant is the grain-bearing organ whose physical characteristics are proxy measures of grain yield. The ability to detect and characterise spikes from 2D images of cereal plants, such as wheat, therefore provides vital information on tiller number and yield potential. Results: We have developed a novel spike detection method for wheat plants involving, firstly, an improved colour index method for plant segmentation and, secondly, a neural network-based method using Laws texture energy for spike detection. The spike detection step was further improved by removing noise using an area and height threshold. The evaluation results showed an accuracy of over 80% in identification of spikes. In the proposed method we also measure the area of individual spikes as well as all spikes of individual plants under different experimental conditions. The correlation between the final average grain yield and spike area is also discussed in this paper. Conclusions: Our highly accurate yield trait phenotyping method for spike number counting and spike area estimation, is useful and reliable not only for grain yield estimation but also for detecting and quantifying subtle phenotypic variations arising from genetic or environmental differences.Li Qiongyan, Jinhai Cai, Bettina Berger, Mamoru Okamoto and Stanley J. Miklavci

Brewing of filter coffee

We report progress on mathematical modelling of coffee grounds in a drip filter coffee machine. The report focuses on the evolution of the shape of the bed of coffee grounds during extraction with some work also carried out on the chemistry of extraction. This work was sponsored by Philips who are interested in understanding an observed correlation between the final shape of the coffee grounds and the quality of the coffee. We used experimental data gathered by Philips and ourselves to identify regimes in the coffee brewing process and relevant regions of parameter space. Our work makes it clear that a number of separate processes define the shape of the coffee bed depending on the values of the parameters involved e.g. the size of the grains and the speed of fluid flow during extraction. We began work on constructing mathematical models of the redistribution of the coffee grounds specialised to each region and on a model of extraction. A variety of analytic and numerical tools were used. Furthermore our research has progressed far enough to allow us to begin to exploit connections between this problem and other areas of science, in particular the areas of sedimentology and geomorphology, where the processes we have observed in coffee brewing have been studied

Quantitative Estimation of Wheat Phenotyping Traits Using Ground and Aerial Imagery

This study evaluates an aerial and ground imaging platform for assessment of canopy development in a wheat field. The dependence of two canopy traits, height and vigour, on fertilizer treatment was observed in a field trial comprised of ten varieties of spring wheat. A custom-built mobile ground platform (MGP) and an unmanned aerial vehicle (UAV) were deployed at the experimental site for standard red, green and blue (RGB) image collection on five occasions. Meanwhile, reference field measurements of canopy height and vigour were manually recorded during the growing season. Canopy level estimates of height and vigour for each variety and treatment were computed by image analysis. The agreement between estimates from each platform and reference measurements was statistically analysed. Estimates of canopy height derived from MGP imagery were more accurate (RMSE = 3.95 cm, R2 = 0.94) than estimates derived from UAV imagery (RMSE = 6.64 cm, R2 = 0.85). In contrast, vigour was better estimated using the UAV imagery (RMSE = 0.057, R2 = 0.57), compared to MGP imagery (RMSE = 0.063, R2 = 0.42), albeit with a significant fixed and proportional bias. The ability of the platforms to capture differential development of traits as a function of fertilizer treatment was also investigated. Both imaging methodologies observed a higher median canopy height of treated plots compared with untreated plots throughout the season, and a greater median vigour of treated plots compared with untreated plots exhibited in the early growth stages. While the UAV imaging provides a high-throughput method for canopy-level trait determination, the MGP imaging captures subtle canopy structures, potentially useful for fine-grained analyses of plants

The influence of skeletal muscle anisotropy on electroporation: in vivo study and numerical modeling

The aim of this study was to theoretically and experimentally investigate electroporation of mouse tibialis cranialis and to determine the reversible electroporation threshold values needed for parallel and perpendicular orientation of the applied electric field with respect to the muscle fibers. Our study was based on local electric field calculated with three-dimensional realistic numerical models, that we built, and in vivo visualization of electroporated muscle tissue. We established that electroporation of muscle cells in tissue depends on the orientation of the applied electric field; the local electric field threshold values were determined (pulse parameters: 8 × 100 μs, 1 Hz) to be 80 V/cm and 200 V/cm for parallel and perpendicular orientation, respectively. Our results could be useful electric field parameters in the control of skeletal muscle electroporation, which can be used in treatment planning of electroporation based therapies such as gene therapy, genetic vaccination, and electrochemotherapy

Vascular disrupting action of electroporation and electrochemotherapy with bleomycin in murine sarcoma

Electrochemotherapy has a direct cytotoxic effect on tumour cells, and presumably, a vascular disrupting effect. In this study, on the basis of the prediction of the mathematical model, histological evaluation and physiological measurements of the tumours were carried out to confirm that electroporation and electrochemotherapy of tumours have a vascular disrupting action. In the study, SA-1 solid subcutaneous sarcoma tumours in A/J mice were treated by bleomycin (BLM) given intravenously (1 mg kg−1), application of electric pulses (8 pulses, 1040 V, 100 μs, 1 Hz) or a combination of both – electrochemotherapy. The vascular effect was determined by laser Doppler flowmetry, power Doppler ultrasonographic imaging and Patent blue staining. The extent of tumour hypoxia was determined immunohistochemically by hypoxia marker pimonidazole and partial pressure of oxygen (pO2) in tumours by electron paramagnetic resonance oximetry. Electrochemotherapy with BLM induced good antitumour effect with 22 days, tumour growth delay and 38% tumour cures. The application of electric pulses to the tumours induced instant but transient tumour blood flow reduction (for 70%) that was recovered in 24 h. During this tumour blood flow reduction, we determined an increase in hypoxic tumour area for up to 30%, which was also reflected in reduced tumour oxygenation (for 70%). According to the described mathematical model, endothelial cells lining in tumour blood vessels are exposed to a ∼40% higher electric field than the surrounding tumour cells, and therefore easily electroporated, allowing access of high BLM concentration to the cytosol. Consequently, electrochemotherapy has, besides the immediate vascular disrupting action, also a delayed one (after 24 h), as a consequence of endothelial cell swelling and apoptosis demonstrated by extensive tumour necrosis, tumour hypoxia, prolonged reduction of tumour blood flow and significant tumour growth delay, and tumour cures. Our results demonstrate that in addition to the well-established direct cytotoxic effect on tumour cells, electrochemotherapy also has an indirect vascular disrupting action resulting altogether in extensive tumour cell necrosis leading to complete regression of tumours

Calcium electroporation and electrochemotherapy for cancer treatment:Importance of cell membrane composition investigated by lipidomics, calorimetry and in vitro efficacy

Abstract Calcium electroporation is a novel anti-cancer treatment investigated in clinical trials. We explored cell sensitivity to calcium electroporation and electroporation with bleomycin, using viability assays at different time and temperature points, as well as heat calorimetry, lipidomics, and flow cytometry. Three cell lines: HT29 (colon cancer), MDA-MB231 (breast cancer), and HDF-n (normal fibroblasts) were investigated for; (a) cell survival dependent on time of addition of drug relative to electroporation (1.2 kV/cm, 8 pulses, 99 µs, 1 Hz), at different temperatures (37 °C, 27 °C, 17 °C); (b) heat capacity profiles obtained by differential scanning calorimetry without added calcium; (c) lipid composition by mass spectrometry; (d) phosphatidylserine in the plasma membrane outer leaflet using flow cytometry. Temperature as well as time of drug administration affected treatment efficacy in HT29 and HDF-n cells, but not MDA-MB231 cells. Interestingly the HT29 cell line displayed a higher phase transition temperature (approximately 20 °C) versus 14 °C (HDF-n) and 15 °C (MDA-MB231). Furthermore the HT29 cell membranes had a higher ratio of ethers to esters, and a higher expression of phosphatidylserine in the outer leaflet. In conclusion, lipid composition and heat capacity of the membrane might influence permeabilisation of cells and thereby the effect of calcium electroporation and electrochemotherapy

The effect of electroporation pulses on functioning of the heart

Electrochemotherapy is an effective antitumor treatment currently applied to cutaneous and subcutaneous tumors. Electrochemotherapy of tumors located close to the heart could lead to adverse effects, especially if electroporation pulses were delivered within the vulnerable period of the heart or if they coincided with arrhythmias of some types. We examined the influence of electroporation pulses on functioning of the heart of human patients by analyzing the electrocardiogram. We found no pathological morphological changes in the electrocardiogram; however, we demonstrated a transient RR interval decrease after application of electroporation pulses. Although no adverse effects due to electroporation have been reported so far, the probability for complications could increase in treatment of internal tumors, in tumor ablation by irreversible electroporation, and when using pulses of longer durations. We evaluated the performance of our algorithm for synchronization of electroporation pulse delivery with electrocardiogram. The application of this algorithm in clinical electroporation would increase the level of safety for the patient and suitability of electroporation for use in anatomical locations presently not accessible to existing electroporation devices and electrodes