Changes in sexual signals are greater than changes in ecological traits in a dichromatic group of fishes

Understanding the mechanisms by which phenotypic divergence occurs is central to speciation research. These mechanisms can be revealed by measuring differences in traits that are subject to different selection pressures; greater influence of different types of selection can be inferred from greater divergence in associated traits. Here, we address the potential roles of natural and sexual selection in promoting phenotypic divergence between species of snubnose darters by comparing differences in body shape, an ecologically relevant trait, and male color, a sexual signal. Body shape was measured using geometric morphometrics, and male color was measured using digital photography and visual system‐dependent color values. Differences in male color are larger than differences in body shape across eight allopatric, phylogenetically independent species pairs. While this does not exclude the action of divergent natural selection, our results suggest a relatively more important role for sexual selection in promoting recent divergence in darters. Variation in the relative differences between male color and body shape across species pairs reflects the continuous nature of speciation mechanisms, ranging from ecological speciation to speciation by sexual selection alone.     

Plaque hemorrhage in carotid artery disease: Pathogenesis,clinical and biomechanical considerations

Stroke remains the most prevalent disabling illness today, with internal carotid artery luminal stenosis due to atheroma formation responsible for the majority of ischemic cerebrovascular events. Severity of luminal stenosis continues to dictate both patient risk stratification and the likelihood of surgical intervention. But there is growing evidence to suggest that plaque morphology may help improve pre-existing risk stratification criteria. Plaque components such a fibrous tissue, lipid rich necrotic core and calcium have been well investigated but plaque hemorrhage (PH) has been somewhat overlooked. In this review we discuss the pathogenesis of PH, its role in dictating plaque vulnerability, PH imaging techniques, marterial properties of atherosclerotic tissues, in particular, those obtained based on in vivo measurements and effect of PH in modulating local biomechanics.     

Conventional digital cameras as a tool for assessing leaf area index and biomass for cereal breeding

Affordable and easy-to-use methods for assessing biomass and leaf area index （LAI） would be of interest in most breeding programs. Here, we describe the evaluation of a protocol for photographic sampling and image analysis aimed at providing low-labor yet robust indicators of biomass and LAI. In this trial, two genotypes of triticale, two of bread wheat, and four of tritordeum were studied. At six dates during the growing cycle, biomass and LAI were measured destructively, and digital photography was taken on the same dates. Several vegetation indices were calculated from each image. The results showed that repeatable and consistent values of the indices were obtained in consecutive photographic samplings on the same plots. The photographic indices were highly correlated with the destructive measure-ments, though the magnitude of the correlation was lower after anthesis. This work shows that photographic assess-ment of biomass and LAI can be fast, affordable, have good repeatability, and can be used under bright and overcast skies. A practical vegetation index derived from pictures is the fraction of green pixels over the total pixels of the image, and as it shows good correlations with all biomass variables, is the most robust to lighting conditions and has easy interpretation.     

Content-based histopathology image retrieval using CometCloud

Background

The development of digital imaging technology is creating extraordinary levels of accuracy that provide support for improved reliability in different aspects of the image analysis, such as content-based image retrieval, image segmentation, and classification. This has dramatically increased the volume and rate at which data are generated. Together these facts make querying and sharing non-trivial and render centralized solutions unfeasible. Moreover, in many cases this data is often distributed and must be shared across multiple institutions requiring decentralized solutions. In this context, a new generation of data/information driven applications must be developed to take advantage of the national advanced cyber-infrastructure (ACI) which enable investigators to seamlessly and securely interact with information/data which is distributed across geographically disparate resources. This paper presents the development and evaluation of a novel content-based image retrieval (CBIR) framework. The methods were tested extensively using both peripheral blood smears and renal glomeruli specimens. The datasets and performance were evaluated by two pathologists to determine the concordance.

Results

The CBIR algorithms that were developed can reliably retrieve the candidate image patches exhibiting intensity and morphological characteristics that are most similar to a given query image. The methods described in this paper are able to reliably discriminate among subtle staining differences and spatial pattern distributions. By integrating a newly developed dual-similarity relevance feedback module into the CBIR framework, the CBIR results were improved substantially. By aggregating the computational power of high performance computing (HPC) and cloud resources, we demonstrated that the method can be successfully executed in minutes on the Cloud compared to weeks using standard computers.

Conclusions

In this paper, we present a set of newly developed CBIR algorithms and validate them using two different pathology applications, which are regularly evaluated in the practice of pathology. Comparative experimental results demonstrate excellent performance throughout the course of a set of systematic studies. Additionally, we present and evaluate a framework to enable the execution of these algorithms across distributed resources. We show how parallel searching of content-wise similar images in the dataset significantly reduces the overall computational time to ensure the practical utility of the proposed CBIR algorithms.     

Impact of variance components on reliability of absolute quantification using digital PCR

Background

Digital polymerase chain reaction (dPCR) is an increasingly popular technology for detecting and quantifying target nucleic acids. Its advertised strength is high precision absolute quantification without needing reference curves. The standard data analytic approach follows a seemingly straightforward theoretical framework but ignores sources of variation in the data generating process. These stem from both technical and biological factors, where we distinguish features that are 1) hard-wired in the equipment, 2) user-dependent and 3) provided by manufacturers but may be adapted by the user. The impact of the corresponding variance components on the accuracy and precision of target concentration estimators presented in the literature is studied through simulation.

Results

We reveal how system-specific technical factors influence accuracy as well as precision of concentration estimates. We find that a well-chosen sample dilution level and modifiable settings such as the fluorescence cut-off for target copy detection have a substantial impact on reliability and can be adapted to the sample analysed in ways that matter. User-dependent technical variation, including pipette inaccuracy and specific sources of sample heterogeneity, leads to a steep increase in uncertainty of estimated concentrations. Users can discover this through replicate experiments and derived variance estimation. Finally, the detection performance can be improved by optimizing the fluorescence intensity cut point as suboptimal thresholds reduce the accuracy of concentration estimates considerably.

Conclusions

Like any other technology, dPCR is subject to variation induced by natural perturbations, systematic settings as well as user-dependent protocols. Corresponding uncertainty may be controlled with an adapted experimental design. Our findings point to modifiable key sources of uncertainty that form an important starting point for the development of guidelines on dPCR design and data analysis with correct precision bounds. Besides clever choices of sample dilution levels, experiment-specific tuning of machine settings can greatly improve results. Well-chosen data-driven fluorescence intensity thresholds in particular result in major improvements in target presence detection. We call on manufacturers to provide sufficiently detailed output data that allows users to maximize the potential of the method in their setting and obtain high precision and accuracy for their experiments.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2105-15-283) contains supplementary material, which is available to authorized users.     

Quantification of epigenetic biomarkers: an evaluation of established and emerging methods for DNA methylation analysis

Background

DNA methylation is an important epigenetic mechanism in several human diseases, most notably cancer. The quantitative analysis of DNA methylation patterns has the potential to serve as diagnostic and prognostic biomarkers, however, there is currently a lack of consensus regarding the optimal methodologies to quantify methylation status. To address this issue we compared five analytical methods: (i) MethyLight qPCR, (ii) MethyLight digital PCR (dPCR), methylation-sensitive and -dependent restriction enzyme (MSRE/MDRE) digestion followed by (iii) qPCR or (iv) dPCR, and (v) bisulfite amplicon next generation sequencing (NGS). The techniques were evaluated for linearity, accuracy and precision.

Results

MethyLight qPCR displayed the best linearity across the range of tested samples. Observed methylation measured by MethyLight- and MSRE/MDRE-qPCR and -dPCR were not significantly different to expected values whilst bisulfite amplicon NGS analysis over-estimated methylation content. Bisulfite amplicon NGS showed good precision, whilst the lower precision of qPCR and dPCR analysis precluded discrimination of differences of < 25% in methylation status. A novel dPCR MethyLight assay is also described as a potential method for absolute quantification that simultaneously measures both sense and antisense DNA strands following bisulfite treatment.

Conclusions

Our findings comprise a comprehensive benchmark for the quantitative accuracy of key methods for methylation analysis and demonstrate their applicability to the quantification of circulating tumour DNA biomarkers by using sample concentrations that are representative of typical clinical isolates.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1174) contains supplementary material, which is available to authorized users.     

兔VX2肝癌模型制作改良及影像学评价

目的 对兔VX2 肝癌模型制作进行改良,以用于介入治疗学研究,同时探讨瘤灶的CT 表现及CT 在检测瘤灶中的作用.方法 将VX2瘤细胞接种于兔皮下使其成瘤并传代;新西兰兔24只,以改良嵌插法建立移植性肝癌模型,于建模后7、14、21 d分别行超声、CT及血管造影检查,用于检测兔肝VX2 瘤灶,评估瘤灶生长变化;随后处死动物,进行尸解,评估影像检查结果.结果 24只（100%） 动物以改良嵌插法建立移植性肝癌模型全部成功.瘤灶以种植后2周CT显示最清楚和典型,直径1 cm～2 cm 左右,平扫呈低密度或等密度,动脉早期明显强化,门脉期呈低密度,与周围肝组织分界较清楚.肝动脉造影显示肿瘤富血供.而种植后超过3 周的肿瘤大部分发生坏死.结论 嵌插改良法是一种值得推广的建立移植性肝癌模型的方法;在对瘤灶进行影像学评价上应尽量选择CT检查,接种后1 周左右的瘤灶较小而难以观察;2 周左右呈肝动脉源性血供丰富的约1 cm～2 cm的实体瘤,造影征像为肿瘤血管与肿瘤染色;3 周以上瘤灶大多出现明显示坏死;因此对1～2cm大小的兔VX2 肝癌瘤体,最适合行血管造影检查.     

Computational and mathematical modeling of the effects of tailbeat frequency and flexural stiffness in swimming fish

In this paper we describe how we combine computational and mathematical models to form virtual fish to explore different hypotheses about the impact of centra. We show how we create simulation models using a combination of a mathematical model of a fish-like robot using caudal fin propulsion, a propulsion model, and an optimizer, to explore the impact of centra under various scenarios. The optimizer uses the mathematical model to construct valid configurations of the digital robot and uses the utility function and propulsion model to evaluate the performance of each configuration. The evaluations are used to explore the adaptive landscape and find high-performing configurations. Our results show that the high-performing configurations have both increased (flexural) stiffness of the tail and higher tailbeat frequencies.     

Detecting Abnormalities in Choroidal Vasculature in a Mouse Model of Age-related Macular Degeneration by Time-course Indocyanine Green Angiography

Indocyanine Green Angiography (or ICGA) is a technique performed by ophthalmologists to diagnose abnormalities of the choroidal and retinal vasculature of various eye diseases such as age-related macular degeneration (AMD). ICGA is especially useful to image the posterior choroidal vasculature of the eye due to its capability of penetrating through the pigmented layer with its infrared spectrum. ICGA time course can be divided into early, middle, and late phases. The three phases provide valuable information on the pathology of eye problems. Although time-course ICGA by intravenous (IV) injection is widely used in the clinic for the diagnosis and management of choroid problems, ICGA by intraperitoneal injection (IP) is commonly used in animal research. Here we demonstrated the technique to obtain high-resolution ICGA time-course images in mice by tail-vein injection and confocal scanning laser ophthalmoscopy. We used this technique to image the choroidal lesions in a mouse model of age-related macular degeneration. Although it is much easier to introduce ICG to the mouse vasculature by IP, our data indicate that it is difficult to obtain reproducible ICGA time course images by IP-ICGA. In contrast, ICGA via tail vein injection provides high quality ICGA time-course images comparable to human studies. In addition, we showed that ICGA performed on albino mice gives clearer pictures of choroidal vessels than that performed on pigmented mice. We suggest that time-course IV-ICGA should become a standard practice in AMD research based on animal models.