BackgroundTransposable elements are major evolutionary forces which can cause new genome structure and species diversification. The role of transposable elements in the expansion of nucleotide-binding and leucine-rich-repeat proteins (NLRs), the major disease-resistance gene families, has been unexplored in plants.ResultsWe report two high-quality de novo genomes (Capsicum baccatum and C. chinense) and an improved reference genome (C. annuum) for peppers. Dynamic genome rearrangements involving translocations among chromosomes 3, 5, and 9 were detected in comparison between C. baccatum and the two other peppers. The amplification of athila LTR-retrotransposons, members of the gypsy superfamily, led to genome expansion in C. baccatum. In-depth genome-wide comparison of genes and repeats unveiled that the copy numbers of NLRs were greatly increased by LTR-retrotransposon-mediated retroduplication. Moreover, retroduplicated NLRs are abundant across the angiosperms and, in most cases, are lineage-specific.ConclusionsOur study reveals that retroduplication has played key roles for the massive emergence of NLR genes including functional disease-resistance genes in pepper plants.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-017-1341-9) contains supplementary material, which is available to authorized users.

Background Electronic personal health records (PHRs) are increasingly recognized and used as a tool to address various challenges stemming from the scattered and incompatible personal health information that exists in the contemporary US health care system. Although activity around PHR development and deployment has increased in recent years, little has been reported regarding the use and utility of PHRs among low-income and/or elderly populations.Objective The aim was to assess the use and utility of PHRs in a low-income, elderly population.Methods We deployed a Web-based, institution-neutral PHR system, the Personal Health Information Management System (PHIMS), in a federally funded housing facility for low-income and elderly residents. We assessed use and user satisfaction through system logs, questionnaire surveys, and user group meetings.Results Over the 33-month study period, 70 residents participated; this number was reduced to 44 by the end of the study. Although the PHIMS was available for free and personal assistance and computers with Internet connection were provided without any cost to residents, only 13% (44/330) of the eligible residents used the system, and system usage was limited. Almost one half of the users (47%, 33/70) used the PHIMS only on a single day. Use was also highly correlated with the availability of in-person assistance; 77% of user activities occurred while the assistance was available. Residents’ ability to use the PHR system was limited by poor computer and Internet skills, technophobia, low health literacy, and limited physical/cognitive abilities. Among the 44 PHIMS users, 14 (32%) responded to the questionnaire. In this selected subgroup of survey participants, the majority (82%, 9/11) used the PHIMS three times or more and reported that it improved the quality of overall health care they received.Conclusions Our findings suggest that those who can benefit the most from a PHR system may be the least able to use it. Disparities in access to and use of computers, the Internet, and PHRs may exacerbate health care inequality in the future.

Tracing of left-ventricular epicardial and endocardial borders on echocardiographic sequences is essential for quantification of cardiac function. The authors designed a method based on an extension of active contour models to detect both epicardial and endocardial borders on short-axis cardiac sequences spanning the entire cardiac cycle. They validated the results by comparing the computer-generated boundaries to the boundaries manually outlined by four expert observers on 44 clinical data sets. The mean boundary distance between the computer-generated boundaries and the manually outlined boundaries was 2.80 mm (sigma=1.28 mm) for the epicardium and 3.61 (sigma=1.68 mm) for the endocardium. These distances were comparable to interobserver distances, which had a mean of 3.79 mm (sigma=1.53 mm) for epicardial borders and 2.67 mm (sigma=0.88 mm) for endocardial borders. The correlation coefficient between the areas enclosed by the computer-generated boundaries and the average manually outlined boundaries was 0.95 for epicardium and 0.91 for endocardium. The algorithm is fairly insensitive to the choice of the initial curve. Thus, the authors have developed an effective and robust algorithm to extract left-ventricular boundaries from echocardiographic sequences.

It is possible to distinguish between papillary carcinomas and other lesions with the thyroid stiffness index calculated from US elastography using carotid arterial pulsation.

The resistance switching current-voltage (I-V) characteristics in polycrystalline NiO films were investigated in the temperature range of 10K<T<300K. Very clear reversible resistive switching phenomena were observed in the entire temperature range. An analysis of the temperature dependence of the resistance switching transport revealed additional features, not reported in previous studies, that weak metallic conduction and correlated barrier polaron hopping coexist in the high-resistance off state and that relative dominance depends on the temperature and defect configuration. In addition, the authors propose that metallic Ni defects, existing near polycrystalline (or granular) boundaries, play a key role in the formation of a metallic channel.

Automatic prostate segmentation in ultrasound images is a challenging task due to speckle noise, missing boundary segments, and complex prostate anatomy. One popular approach has been the use of deformable models. For such techniques, prior knowledge of the prostate shape plays an important role in automating model initialization and constraining model evolution. In this paper, we have modeled the prostate shape using deformable superellipses. This model was fitted to 594 manual prostate contours outlined by five experts. We found that the superellipse with simple parametric deformations can efficiently model the prostate shape with the Hausdorff distance error (model versus manual outline) of 1.32 +/- 0.62 mm and mean absolute distance error of 0.54 +/- 0.20 mm. The variability between the manual outlinings and their corresponding fitted deformable superellipses was significantly less than the variability between human experts with p-value being less than 0.0001. Based on this deformable superellipse model, we have developed an efficient and robust Bayesian segmentation algorithm. This algorithm was applied to 125 prostate ultrasound images collected from 16 patients. The mean error between the computer-generated boundaries and the manual outlinings was 1.36 +/- 0.58 mm, which is significantly less than the manual interobserver distances. The algorithm was also shown to be fairly insensitive to the choice of the initial curve.

A new speckle reduction method, i.e., Laplacian pyramid-based nonlinear diffusion (LPND), is proposed for medical ultrasound imaging. With this method, speckle is removed by nonlinear diffusion filtering of bandpass ultrasound images in Laplacian pyramid domain. For nonlinear diffusion in each pyramid layer, a gradient threshold is automatically determined by a variation of median absolute deviation (MAD) estimator. The performance of the proposed LPND method has been compared with that of other speckle reduction methods, including the recently proposed speckle reducing anisotropic diffusion (SRAD) and nonlinear coherent diffusion (NCD). In simulation and phantom studies, an average gain of 1.55 dB and 1.34 dB in contrast-to-noise ratio was obtained compared to SRAD and NCD, respectively. The visual comparison of despeckled in vivo ultrasound images from liver and carotid artery shows that the proposed LPND method could effectively preserve edges and detailed structures while thoroughly suppressing speckle. These preliminary results indicate that the proposed speckle reduction method could improve image quality and the visibility of small structures and fine details in medical ultrasound imaging.

Objective. The purpose of this study was to evaluate the feasibility of ultrasound thyroid elastography using carotid artery pulsation as the compression source and its potential for differential diagnosis of thyroid nodules. Methods. Baseband sonographic data were acquired for 16 thyroid nodules from 12 patients. The natural pulsation of the carotid artery was used as the compression source, and thyroid strain was estimated offline. For quantitative assessment of thyroid tissue stiffness, a new metric called the thyroid stiffness index (TSI) was computed as the ratio of strain near the carotid artery (high-strain region) to that of a stiff region (low-strain region) inside a thyroid nodule. The stiffness information from elastography was correlated with histopathologic findings. Results. The TSI for papillary carcinoma (n = 9) was higher than the TSI for a benign nodular goiter (n = 6), indicating that papillary carcinoma is stiffer than a benign nodular goiter (P < .05). In 1 patient, we were able to distinguish a papillary carcinoma nodule and a benign nodular goiter located in the same thyroid lobe based on the stiffness information obtained from elastography. This suggests that elastography could be used for guiding fine-needle aspiration biopsy to a thyroid nodule with a high probability of cancer. Conclusions.The results from this preliminary study indicate the feasibility of the pulsation-induced thyroid elastography. Ultrasound thyroid elastography using carotid artery pulsation appears to have the potential for noninvasively differentiating papillary carcinoma from benign nodular goiter. Future studies are needed to evaluate the efficacy of elastography in detecting thyroid cancer and guiding thyroid biopsies. Key words: carotid artery pulsation; elastography; thyroid; thyroid stiffness index; ultrasound.Received February 5, 2007,