Bilateral edge filter: photometrically weighted, discontinuity based edge detection

Edge-detection algorithms have the potential to play an increasingly important role both in single particle analysis (for the detection of randomly oriented particles), and in tomography (for the segmentation of 3D volumes). However, the majority of traditional linear filters are significantly affected by noise as well as artefacts, and offer limited selectivity. The Bilateral edge filter presented here is an adaptation of the Bilateral filter [Jiang, W., Baker, M.L., Wu, Q., Bajaj, C., Chiu, W., 2003. Applications of a bilateral denoising filter in biological electron microscopy. J. Struct. Biol. 144, 114-122] designed for enhanced edge detection. It uses photometric weighting to identify significant discontinuities (representing edges), minimizing artefacts and noise. Compared with common edge-detectors (LoG, Marr-Hildreth) the Bilateral edge filter yielded significantly better results. Indeed data was of a similar quality to that of the Canny edge-detector, which is considered as a leading standard in edge detection [Basu, M., 2002. Gaussian-based edge-detection methods-a survey. IEEE Trans. Syst. Man Cybern. C Appl. Rev. 32, 252-260]. Compared to the Canny edge-detector the Bilateral edge-detector has the advantages that it only requires the adjustment of a single parameter, is theoretically faster for reasonably sized images, and can be used in selective contrast enhancement of images. The simplicity and speed of the filter for single particle and tomographic analysis are discussed.     

Major histocompatibility polymorphism associated with resistance towards amoebic gill disease in Atlantic salmon (Salmo salar L.)

The association between major histocompatibility (MH) polymorphism and the severity of infection by amoebic gill disease (AGD) was investigated across 30 full sibling families of Atlantic salmon. Individuals were challenged with AGD for 19days and then their severity of infection scored by histopathological examination of the gills. Fish were then genotyped for the MH class I (Sasa-UBA) and MH class II alpha (Sasa-DAA) genes using polymorphic repeats embedded within the 3' untranslated regions of the Sasa-UBA and Sasa-DAA genes. High variation in the severity of infection was observed across the sample material, ranging from 0% to 85% gill filaments infected. In total, seven Sasa-DAA-3UTR and ten Sasa-UBA-3UTR marker alleles were identified across the 30 families. A significant association between the marker allele Sasa-DAA-3UTR 239 and a reduction in AGD severity was detected. There was also a significant association found between AGD severity and the presence of two Sasa-DAA-3UTR genotypes. While the associations between MH allele/genotypes and AGD severity reported herein may be statistically significant, the small sample sizes observed for some alleles and genotypes means these associations should be considered as suggestive and future research is required to verify their biological significance.     

A molecular phylogeny of the nightjars (Aves: Caprimulgidae) suggests extensive conservation of primitive morphological traits across multiple lineages

We report a molecular re-assessment of the classification of the nightjars which draws conclusions that are strongly at odds with the traditional, morphology-based classifications. We used maximum likelihood and Bayesian methods to compare the cytochrome b gene for 14 species from seven of the 15 genera of the Caprimulgidae and partial cytochrome b sequence data was available for a further seven species including three further genera. We found that within the Caprimulgidae there were four geographically isolated clades with bootstrap support greater than 70%. One of these clades contained just Chordeiles species, the remaining three clades each contained a mixture of genera including Caprimulgus sp. A clade of exclusively South American nightjars included the genera Caprimulgus, Uropsalis, Eleopthreptus and Hydropsalis. A clade of African and Eurasian birds included Caprimulgus and Macrodipteryx. Phalaenoptilus nuttallii and Caprimulgus vociferous formed a clade of North American birds. Two ecological factors appear to make morphological classification potentially misleading: first, the apparent retention of primitive anti-predator and foraging-related traits across genetically divergent groups; second, rapid divergence in other traits, especially those related to mating, which generate high levels of morphological divergence between species that are genetically very similar. The cytochrome b data suggests that the genus Caprimulgus is not monophyletic and is restricted to Africa and Eurasia and that Caprimulgus species from outside this area have been misclassified as a consequence of retention of primitive adaptations for crepuscular/nocturnal living. Some other genera also appear to have little support from the cytochrome b data.     

Effect of nutritionally enriched coffee consumption on aerobic and anaerobic exercise performance

The purpose of this study was to compare nutritionally enriched JavaFit coffee (JF) to commercially available decaffeinated coffee (P) with regard to impact on endurance and anaerobic power performance in a physically active, college-aged population. Ten subjects (8 men, 2 women) performed two 30-second Wingate anaerobic power tests and 2 cycle ergometer tests (75% VO2 max) to exhaustion. Mean VO2 was measured during each endurance exercise protocol. Excess postexercise oxygen consumption (EPOC) and respiratory exchange ratio (RER) were recorded for 30 minutes following all exercise sessions. Area under the curve analysis was used to compare EPOC between JF and P for all exercise sessions. No differences were seen between JF and P in any of the power performance measures. However, time to exhaustion was significantly (p = 0.05) higher in JF (35.3 +/- 15.2 minutes) compared with P (27.3 +/- 10.7 minutes). No difference between JF and P were seen in EPOC in either the aerobic or anaerobic exercise sessions. A significant (p < 0.05) difference in average 30-minute postanaerobic power exercise RER was seen between JF (0.87 +/- 0.04) and P (0.83 +/- 0.03), but not following endurance exercise. A nutritionally-enriched coffee beverage appears to enhance time to exhaustion during aerobic exercise, but does not provide an ergogenic benefit during anaerobic exercise.     

A simple centrifugal dehydration force method to characterize water compartments in fresh and post-mortem fish muscle

A centrifugal dehydration force (CDF) method to quantify changes in tissue hydration in fresh and in post-mortem muscular fish tail tissue is presented. The data obtained were used to assess fluid flow rate from tissues and the size of hydration compartments expressed in g water/g dry mass (DM). Curve fit analysis demonstrated that muscle tissue has three detectable water compartments. Application of the method to the fresh fish indicated the presence of a large non-bulk water compartment (3.14 g water/g DM) with a much smaller (0.11 g water/g DM) inner non-bulk water sub-compartment in addition to a comparatively small bulk water compartment (0.99 g water/g DM). At 10 min and at 4h post-mortem, no significant change in size or flow rate of the water compartments was observed. At 24h post-mortem the muscular fish tissue, stored in water, swelled with statistically significant increase in total water and in the bulk water compartment but no significant change in the size of the non-bulk water compartments. The water flow rate from the non-bulk water compartment was, however, increased significantly in the 24h dead tissue. This simple CDF method has application for quantization of bulk and non-bulk water compartments in other biological and non-biological systems.     

A low-cost instrumented spatial linkage accurately determines ASIS position during cycle ergometry

The purpose of this study was to develop and evaluate an alternative method for determining the position of the anterior superior iliac spine (ASIS) during cycling. The approach used in this study employed an instrumented spatial linkage (ISL) system to determine the position of the ASIS in the parasagittal plane. A two-segment ISL constructed using aluminum segments, bearings, and digital encoders was tested statically against a calibration plate and dynamically against a video-based motion capture system. Four well-trained cyclists provided data at three pedaling rates. Statically, the ISL had a mean horizontal error of 0.03 +/- 0.21 mm and a mean vertical error of -0.13 +/- 0.59 mm. Compared with the video-based motion capture system, the agreement of the location of the ASIS had a mean error of 0.30 +/- 0.55 mm for the horizontal dimension and -0.27 +/- 0.60 mm for the vertical dimension. The ISL system is a cost-effective, accurate, and valid measure for two-dimensional kinematic data within a range of motion typical for cycling.     

Genetic quality of individuals impacts population dynamics

Ample evidence exists that an increase in the inbreeding level of a population reduces the value of fitness components such as fecundity and survival. It does not follow, however, that these decreases in the components of fitness impact population dynamics in a way that increases extinction risk, because virtually all species produce far more offspring than can actually survive. We analyzed the effects of the genetic quality (mean fitness) of individuals on the population growth rate of seven natural populations in each of two species of wolf spider in the genus Rabidosa , statistically controlling for environmental factors. We show that populations of different sizes, and different inbreeding levels, differ in population dynamics for both species. Differences in population growth rates are especially pronounced during stressful environmental conditions (low food availability) and the stressful environment affects smaller populations (<500 individuals) disproportionately. Thus, even in an invertebrate with an extremely high potential growth rate and strong density-dependent mortality rates, genetic factors contribute directly to population dynamics and, therefore, to extinction risk. This is only the second study to demonstrate an impact of the genetic quality of individual genotypes on population dynamics in a wild population and the first to document strong inbreeding–environment interactions for fitness among populations. Endangered species typically exist at sizes of a few hundred individuals and human activities degrade habitats making them innately more stressful (e.g. global climate change). Therefore, the interaction between genetic factors and environmental stress has important implications for efforts aimed at conserving the Earth's biodiversity.     

Electronically subtracting expression patterns from a mixed cell population

MOTIVATION: Biological samples frequently contain multiple cell-types that each can play a crucial role in the development and/or regulation of adjacent cells or tissues. The search for biomarkers, or expression patterns of, one cell-type in those samples can be a complex and time-consuming process. Ordinarily, extensive laboratory bench work must be performed to separate the mixed cell population into its subcomponents, such that each can be accurately characterized. RESULTS: We have developed a methodology to electronically subtract gene expression in one or more components of a mixed cell population from a mixture, to reveal the expression patterns of other minor or difficult to isolate components. Examination of simulated data indicates that this procedure can reliably determine the expression patterns in cell-types that contribute as little as 5% of the total expression in a mixed cell population. We re-analyzed microarray expression data from the viral infection of macrophages and from the T-cells of wild type and Foxp3 deletion mice. Using our subtraction methodology, we were able to substantially improve the identification of genes involved in processes of subcomponent portions of these samples.     

Interstitial norepinephrine concentrations in skeletal muscle of ischemic heart failure

During exercise, sympathetic nerve responses are accentuated in heart failure (HF), and this enhances norepinephrine (NE) release and evokes vasoconstriction. Two key pathophysiological responses could contribute to the greater NE release: 1) increased sympathetic nerve discharge and 2) increased NE in the neurovascular junction for a given level of sympathetic discharge. In this report, we focus on the second of these two general issues and test the following hypotheses: 1) in HF for a given level of sympathetic nerve stimulation, NE concentration in the interstitium (an index of neurovascular NE) would be greater, and 2) the greater interstitial NE concentration would be linked to reduced NE uptake. Studies were performed in rats 8-10 wk after induction of myocardial infarction (MI). Interstitial NE samples were collected from microdialysis probes inserted into the hindlimb muscle. Dialysate concentration of NE was determined by the HPLC method. First, interstitial NE concentration increased during electrical stimulation of the lumbar sympathetic nerves in eight control rats. An increase in interstitial NE concentration was significantly greater in 10 rats with severe MI. Additionally, an NE uptake-1 inhibitor (desipramine, 1 microM) was injected into the arterial blood supply of the muscle in six control and eight MI rats. Desipramine increased interstitial NE concentration by 24% in control and by only 3% (P < 0.05 vs. control) in MI rats. In conclusion, given levels of electrical stimulation of the lumbar sympathetic nerve lead to higher interstitial NE concentration in HF. This effect is due, in part, to reduced NE uptake-1 in HF.