Segmentation of 3D images of plant tissues at multiple scales using the level set method

Background

Developmental biology has made great strides in recent years towards the quantification of cellular properties during development. This requires tissues to be imaged and segmented to generate computerised versions that can be easily analysed. In this context, one of the principal technical challenges remains the faithful detection of cellular contours, principally due to variations in image intensity throughout the tissue. Watershed segmentation methods are especially vulnerable to these variations, generating multiple errors due notably to the incorrect detection of the outer surface of the tissue.

Results

We use the level set method (LSM) to improve the accuracy of the watershed segmentation in different ways. First, we detect the outer surface of the tissue, reducing the impact of low and variable contrast at the surface during imaging. Second, we demonstrate a new edge function for a level set, based on second order derivatives of the image, to segment individual cells. Finally, we also show that the LSM can be used to segment nuclei within the tissue.

Conclusion

The watershed segmentation of the outer cell layer is demonstrably improved when coupled with the LSM-based surface detection step. The tool can also be used to improve watershed segmentation at cell-scale, as well as to segment nuclei within a tissue. The improved segmentation increases the quality of analysis, and the surface detected by our algorithm may be used to calculate local curvature or adapted for other uses, such as mathematical simulations.

     

Composition of vitamin supplements in Spanish poultry diets

1. The composition of 106 vitamin supplements used in about 85% of the Spanish poultry production diets were studied. Vitamin supplements were grouped by production classes and, for broilers and pullets, also by feeding periods. 2. Four vitamins (niacin, alpha-tocopherol, pantothenic acid, and riboflavin) comprised over 87% of the vitamin supplements by weight (choline excluded), whereas alpha-tocopherol and retinol represented from 51% to 60% of the total vitamin cost. 3. The highest and lowest vitamin supplementation rates were for broilers in the starter and withdrawal periods (106 and 44 mg/kg, respectively) and the mean values for breeders, pullets and layers were 104, 58, and 48 mg/kg, respectively. 4. Supplements with higher vitamin contents showed less variability in their composition. Retinol, cholecalciferol, riboflavin and pantothenic acid showed the lowest variability within supplements (6% to 36% CV), whereas alpha-tocopherol, menadione, thiamin and biotin showed the highest (40% to 224% CV). 5. Vitamin supplementation rates were compared with requirements, taking into account the dietary contribution. In general, vitamin fortification exceeded the NRC recommendations, using a high safety margin for some vitamins such as vitamin A (from 2.6 to 7.8) and for some poultry classes such as breeders (3.2).     

EFFECTS OF FLUID AND COMPUTED TOMOGRAPHIC TECHNICAL FACTORS ON CONSPICUITY OF CANINE AND FELINE NASAL TURBINATES

Turbinate destruction is an important diagnostic criterion in canine and feline nasal computed tomography (CT). However decreased turbinate visibility may also be caused by technical CT settings and nasal fluid. The purpose of this experimental, crossover study was to determine whether fluid reduces conspicuity of canine and feline nasal turbinates in CT and if so, whether CT settings can maximize conspicuity. Three canine and three feline cadaver heads were used. Nasal slabs were CT‐scanned before and after submerging them in a water bath; using sequential, helical, and ultrahigh resolution modes; with images in low, medium, and high frequency image reconstruction kernels; and with application of additional posterior fossa optimization and high contrast enhancing filters. Visible turbinate length was measured by a single observer using manual tracing. Nasal density heterogeneity was measured using the standard deviation (SD) of mean nasal density from a region of interest in each nasal cavity. Linear mixed‐effect models using the R package ‘nlme’, multivariable models and standard post hoc Tukey pair‐wise comparisons were performed to investigate the effect of several variables (nasal content, scanning mode, image reconstruction kernel, application of post reconstruction filters) on measured visible total turbinate length and SD of mean nasal density. All canine and feline water‐filled nasal slabs showed significantly decreased visibility of nasal turbinates (P < 0.001). High frequency kernels provided the best turbinate visibility and highest SD of aerated nasal slabs, whereas medium frequency kernels were optimal for water‐filled nasal slabs. Scanning mode and filter application had no effect on turbinate visibility.     

Diterpenes from Salvia broussonetii transformed roots and their insecticidal activity

The new diterpenes brussonol (1) and iguestol (6alpha,11-dihydroxy-12-methoxy-abieta-8,11,13-triene) (2) with an icetexane and a dehydroabietane skeleton, respectively, have been isolated from hairy root cultures of Salvia broussonetii. Other previously known diterpenes, 7-oxodehydroabietane, 11-hydroxy-12-methoxyabietatriene, taxodione, inuroyleanol, ferruginol, deoxocarnosol 12-methyl ether, cryptojaponol, pisiferal, sugiol, isomanool, 14-deoxycoleon U, 6alpha-hydroxydemethylcryptojaponol, demethylsalvicanol, and demethylcryptojaponol, were also obtained from these roots. The insect antifeedant and toxic effects of several of these compounds were investigated against the insect pests Spodoptera littoralis and Leptinotarsa decemlineata. Additionally, their comparative cytotoxic effects were tested on insect Sf9 and mammalian CHO cells. Demethylsalvicanol (4) was a moderate antifeedant to L. decemlineata, whereas brussonol (1) was inactive. 14-Deoxycoleon U (15) was the strongest antifeedant, whereas demethylcryptojaponol (11) was toxic to this insect. None of these compounds had antifeedant or negative effects on S. littoralis ingestion or weight gains after oral administration. Demethylcryptojaponol (11) was cytotoxic to mammalian CHO and insect Sf9 cell lines, followed by the icetexane derivative brussonol (1), with moderate cytotoxicity in both cases. The remainder of the test compounds showed a strong selective cytotoxicty to insect Sf9 cells, with demethylsalvicanol (4) being the most active.     

Congestive Heart Failure Due to Endocardiosis of the Mitral Valves in an African Pygmy Hedgehog

A 2.5-year-old male African pygmy hedgehog (Atelerix albiventris) was presented with a 2-week history of lethargy, reduced appetite, and general weakness. Based on the clinical signs and heart valve abnormalities observed during an echocardiography examination, a provisional diagnosis of endocardiosis or endocarditis was made. Immediate therapeutic intervention consisted of furosemide, pimobendan, and amoxicillin/clavulanate. Despite medical treatment, 2 weeks following presentation, the hedgehog’s physical condition deteriorated to the point that euthanasia was recommended for the patient and agreed to by its owner. A postmortem examination was performed and tissue samples submitted for histopathology revealed a final diagnosis of valvular endocardiosis and wobbly hedgehog syndrome.     

Effect of diet on composition of cecal contents and on excretion and composition of soft and hard feces of rabbits

A total of 260 New Zealand White growing rabbits were used to study the effect of diet on chemical composition of cecal contents and on production and composition of soft and hard feces. Eight diets varying in their acid detergent fiber (9.8% to 32.7%) and starch (13% to 30%) levels were evaluated. The diet affected (P less than .01) all the variables studied, except dry matter (DM) and molar proportions of volatile fatty acids on cecal contents. An increase of dietary crude fiber increased crude fiber level in cecal contents (from 11.58% to 26.53%). However, a relatively lower proportion of fibrous material was found in the cecal contents when rabbits were fed the more fibrous diets. This suggests that dietary fiber has a direct influence on the efficiency of particle separation in the digestive tract. Crude protein and volatile fatty acid concentrations of cecal contents decreased (from 30.14% to 19.65% and from 47.8 to 36.7 mmol/liter, respectively) when dietary crude fiber increased. This could be related to availability of energy to cecal microorganisms. Ammonia concentration of cecal contents was not affected by dietary crude fiber. Daily production of soft feces varied from 14.98 to 29.59 g DM/d, and the contribution of soft feces to total DM and to crude protein intake ranged from 10.6% to 15.0% and from 12.8% to 20.5%, respectively; these values were the smallest and the largest for the least and the most fibrous diets, respectively. From this study we conclude that dietary fiber has a major effect on the digestive processes in the rabbit and that dietary starch level has no influence on any of the variables studied.     

Effect of yeast products supplementation during transition period on metabolic profile and milk production in dairy cows

Tropical Animal Health and Production - The aim of the current study was to assess the effect that supplementation with yeast culture plus enzymatically hydrolyzed yeast (YC-EHY) during the...     

Reinvigoration of Pinus radiata is associated with partial recovery of juvenile-like polyamine concentrations

Polyamine concentrations in consecutive radiata pine (Pinus radiata D. Don) grafts of 30-year-old trees on 1-year-old seedling rootstocks were analyzed by high performance liquid chromatography coupled with fluorescence detection to determine whether reinvigoration is associated with the recovery of polyamine concentrations typical of those in juvenile tissues. Reinvigoration of radiata pine was correlated with the attainment of some, but not all, polyamines characteristic of juvenile trees. In response to reinvigoration, free putrescine, the ratio of free polyamines to low molecular weight polyamine conjugates, and the relative content of putrescine versus spermidine plus spermine increased to values approaching those characteristic of juvenile tissue. In contrast, there was no noticeable change in the concentrations of low molecular weight polyamine conjugates during reinvigoration even though these conjugates increased greatly during tree maturation. We conclude that certain polyamines defined as reinvigoration markers can be used in forestry upgrading programs to assess the morphogenic ability of reinvigorated trees.     

Qualitative and quantitative polymerase chain reaction (PCR) for detection of Leishmania in spleen samples from naturally infected dogs

Because infected dogs are widely considered to be the main domestic reservoir for Leishmania infantum (syn Leishmania chagasi) parasites in Brazil, the diagnosis of canine visceral leishmaniasis (CVL) must be made both accurately and promptly. The present study attempted to standardize a conventional polymerase chain reaction (cPCR) protocol for the detection of L. infantum DNA in canine spleen samples. Quantitative PCR (qPCR) technique was used to confirm the presence of Leishmania DNA in the canine spleen fragments. A comparison was made between the efficacies of these molecular diagnostic techniques and conventional parasitological and serological methods. cPCR protocols for spleen samples were standardized using primers that amplify a 145 bp fragment, located at the parasite kinetoplast minicircle. The genus specificity of the cPCR protocol was assessed by its inability to amplify the DNA of other common canine pathogens, such as Ehrlichia canis, Babesia canis, Toxoplasma gondii and Trypanosoma cruzi. cPCR protocol sensitivity was tested by assessing the reaction detection limit, determined to be 10 fg of L. infantum reference strain DNA, which corresponds to a range of 0.03-0.1 parasites per fragment. Standardized cPCR protocol was used to detect the presence of Leishmania in 45 dog spleen samples. Our results showed that 40% of the spleen fragment cultures were positive for Leishmania parasites, 58% of the dog serum samples tested positive using ELISA, and parasite DNA was detected in 44% using qPCR, while 47% of the spleen samples using cPCR. Diagnostic methods performance was assessed and revealed a better degree of ascertainment for cPCR when compared to other diagnostic methods. The sensitivity of ELISA was 83.3%, qPCR was 83.3%, and cPCR was 88.9%; PPV for ELISA was 57.7%, qPCR was 75% and cPCR was 76.2%; the Kappa coefficients were found to be 0.40 (fair) for ELISA, 0.64 (substantial) for qPCR and 0.68 (substantial) for cPCR. In both oligosymptomatic and polysymptomatic dogs, cPCR revealed the better performance analysis when compared to other diagnostic methods. The findings presented herein establish cPCR as the most indicated test to detect Leishmania when compared to the other two diagnostic methods evaluated. Despite the fact that the qPCR protocol provides a highly accurate quantification of parasites when targeting the SSU rRNA gene, this technique does not significantly improve the diagnosis of CVL when compared with the performance of the cPCR protocol, which focused on the kinetoplast minicircle.     

Effect of type of fiber on the rate of passage and on the contribution of soft feces to nutrient intake of finishing rabbits.

One hundred thirty New Zealand White x California rabbits were used to study the influence of the source of dietary fiber on several digestive criteria. Five diets were formulated to provide 10% crude fiber (CF) on a DM basis. Sixty percent of this dietary fiber was supplied by alfalfa hay, citrus pulp, beet pulp, grape marc, or rice hulls in the diets. Weights of cecal contents, cecal ammonia concentration, and molar proportion of acetic acid in diets including pulps were higher and cecal levels of DM, CP, and molar proportion of butyric acid were lower than those of the alfalfa diet. Cecal ammonia, VFA, and CF concentrations of the grape marc diet were the lowest of all the diets studied; cecal CF level and molar proportion of acetic acid were significantly higher and CP level and molar proportion of butyric acid were lower in rice hull than in alfalfa diets. Diet had no influence on daily soft feces excretion (10 g DM/d), but N contribution of soft feces to N intake was higher in the diet with citrus pulp (18.7%) than in the other diets (12%). Mean retention time (R) was measured using fuchsin-stained feed and was found to be higher (21.3 h) in the rice hull diet and lower (9.3 h) in the grape marc diet than in the other diets. When coprophagy was prevented, R decreased by 0 to 7 h. In conclusion, the use of byproducts to substitute for traditional sources of fiber in rabbit diets influenced the retention time of the digesta in some segments of the gut and thus altered several digestive criteria.(ABSTRACT TRUNCATED AT 250 WORDS)