Impulsive Thermal X-ray Emission from a Low-lying Coronal Loop

Understanding the relationship among different emission components plays an essential role in the study of particle acceleration and energy conversion in solar flares. In flares where gradual and impulsive emission components can be readily identified the impulsive emission has been attributed to non-thermal particles. We carry out detailed analysis of H\alpha\ and X-ray observations of a GOES class B microflare loop on the solar disk. The impulsive hard X-ray emission, however, is found to be consistent with a hot, quasi-thermal origin, and there is little evidence of emission from chromospheric footpoints, which challenges conventional models of flares and reveals a class of microflares associated with dense loops. H\alpha\ observations indicate that the loop lies very low in the solar corona or even in the chromosphere and both emission and absorption materials evolve during the flare. The enhanced H\alpha\ emission may very well originate from the photosphere when the low-lying flare loop heats up the underlying chromosphere and reduces the corresponding H\alpha\ opacity. These observations may be compared with detailed modeling of flare loops with the internal kink instability, where the mode remains confined in space without apparent change in the global field shape, to uncover the underlying physical processes and to probe the structure of solar atmosphere.Comment: 10 figures, to appear on Ap

Nucleosome Structure Incorporated Histone Acetylation Site Prediction in \u3ci\u3eArabidopsis thaliana\u3c/i\u3e

BackgroundAcetylation is a crucial post-translational modification for histones, and plays a key role in gene expression regulation. Due to limited data and lack of a clear acetylation consensus sequence, a few researches have focused on prediction of lysine acetylation sites. Several systematic prediction studies have been conducted for human and yeast, but less for Arabidopsis thaliana. ResultsConcerning the insufficient observation on acetylation site, we analyzed contributions of the peptide-alignment-based distance definition and 3D structure factors in acetylation prediction. We found that traditional structure contributes little to acetylation site prediction. Identified acetylation sites of histones in Arabidopsis thaliana are conserved and cross predictable with that of human by peptide based methods. However, the predicted specificity is overestimated, because of the existence of non-observed acetylable site. Here, by performing a complete exploration on the factors that affect the acetylability of lysines in histones, we focused on the relative position of lysine at nucleosome level, and defined a new structure feature to promote the performance in predicting the acetylability of all the histone lysines in A. thaliana. ConclusionWe found a new spacial correlated acetylation factor, and defined a ε-N spacial location based feature, which contains five core spacial ellipsoid wired areas. By incorporating the new feature, the performance of predicting the acetylability of all the histone lysines in A. Thaliana was promoted, in which the previous mispredicted acetylable lysines were corrected by comparing to the peptide-based prediction

Morphological and Physiological Responses of Cornus Alba to Salt and Drought Stresses Under Greenhouse Conditions

Tatarian dogwood (Cornus alba) is an ornamental shrub with white fruits, creamy-white flowers, and red stems in fall through late winter and is widely used in residential landscape, public parks, and botanical gardens. Two greenhouse experiments were conducted to characterize the survival, morphological, aesthetic, and physiological responses of tatarian dogwood seedlings to salinity and drought stresses. In Expt. 1, tatarian dogwood seedlings grown in three soilless growing substrates (Metro-Mix 360, 560, and 902) were irrigated with a nutrient solution at an electrical conductivity (EC) of 1.2 dS·m−1 (control) or saline solution (by adding calculated amount of sodium chloride and calcium chloride) at an EC of 5.0 or 10.0 dS·m−1 once per week for 8 weeks. Results showed that substrate did not influence the growth of tatarian dogwood seedling. All plants irrigated with saline solutions at an EC of 10.0 dS·m−1 died, whereas those irrigated with saline solutions at an EC of 5.0 dS·m−1 exhibited severe foliar salt damage with an average visual score of 1.0 (on a scale of 0 to 5, with 0 = dead and 5 = excellent without foliar salt damage). Compared with the control, saline solutions at an EC of 5.0 dS·m−1 reduced plant height and shoot dry weight (DW) by 50.8% and 55.2%, respectively. Relative chlorophyll content [soil plant analysis development (SPAD) reading], chlorophyll fluorescence (Fv/Fm), and net photosynthesis rate (Pn) also decreased when plants were irrigated with saline solutions at an EC of 5.0 and 10.0 dS·m−1. Leaf sodium (Na+) concentration of tatarian dogwood seedlings irrigated with saline solutions at an EC of 5.0 and 10.0 dS·m−1 increased 11 and 40 times, respectively, compared with the control, whereas chloride (Cl-) concentration increased 25 and 33 times, respectively. In Expt. 2, tatarian dogwood seedlings were irrigated at a substrate volumetric water contents (volume of water/volume of substrate, VWC) of 15%, 20%, 25%, 30%, 35%, 40%, or 45% using a sensor-based automated irrigation system for 60 days. Results showed that drought stress decreased plant growth of tatarian dogwood seedlings with a reduction of 71%, 85%, and 87% in plant height, leaf area, and shoot DW, respectively, when VWC decreased from 45% to 15%, but all plants survived at all VWC treatments. Significant reductions of photosynthesis (Pn), stomatal conductance (gS), transpiration rate (E), and water potential were also found in plants at a VWC of 15%, compared with other VWCs. However, SPAD readings and Fv/Fm of tatarian dogwood seedlings were similar among the VWCs. In conclusion, tatarian dogwood seedlings were sensitive to the salinity levels tested in this study but could survive at all tested substrate volumetric water contents and exhibited resistance to drought conditions

Result Publication of Chinese Trials in World Health Organization Primary Registries

Result publication is the key step to improve the transparency of clinical trials.To investigate the result publication rate of Chinese trials registered in World Health Organization (WHO) primary registries.We searched 11 WHO primary registries for Chinese trials records. The progress of each trial was analyzed. We searched for the full texts of result publications cited in the registration records. For completed trials without citations, we searched PubMed, Embase, Chinese Biomedical Literature Database (Chinese), China Knowledge Resource Integrated Database, and Chinese Science and Technology Periodicals Database for result publications. The search was conducted on July 14, 2009. We also called the investigators of completed trials to ask about results publication.We identified 1294 Chinese trials records (428 in ChiCTR,743 in clinicaltrials.gov,55 in ISRCTN, 21 in ACTRN). A total of 443 trials had been completed. The publication rate of the Chinese trials in WHO primary registries is 35.2%(156/443).The publication rate of Chinese trials in clinicaltrials.gov, ChiCTR, ISRCTN, and ACRTN was 36.5% (53/145), 36.3% (89/245), 26.0%(9/44), and 55.6%(5/9), respectively. The publication rate of trials sponsored by industry(23.8%) was lower than that of sponsored by central and local government(31.7%), hospital(35.1%), and universities (40.7%). The publication rate for randomized trials was higher than that of cohort study and case-control study (33.2% versus 16.7%, 22.2%). The publication rate for interventional studies and observational studies was similar(33.4% versus 33.3%).The publication rate of the registered Chinese trials was low, with no significant difference between ChiCTR and clinicaltrials.gov. An effective mechanism is needed to promote publication of results for registered trials in China

Mass segmentation using a combined method for cancer detection

<p>Abstract</p> <p>Background</p> <p>Breast cancer is one of the leading causes of cancer death for women all over the world and mammography is thought of as one of the main tools for early detection of breast cancer. In order to detect the breast cancer, computer aided technology has been introduced. In computer aided cancer detection, the detection and segmentation of mass are very important. The shape of mass can be used as one of the factors to determine whether the mass is malignant or benign. However, many of the current methods are semi-automatic. In this paper, we investigate fully automatic segmentation method.</p> <p>Results</p> <p>In this paper, a new mass segmentation algorithm is proposed. In the proposed algorithm, a fully automatic marker-controlled watershed transform is proposed to segment the mass region roughly, and then a level set is used to refine the segmentation. For over-segmentation caused by watershed, we also investigated different noise reduction technologies. Images from DDSM were used in the experiments and the results show that the new algorithm can improve the accuracy of mass segmentation.</p> <p>Conclusions</p> <p>The new algorithm combines the advantages of both methods. The combination of the watershed based segmentation and level set method can improve the efficiency of the segmentation. Besides, the introduction of noise reduction technologies can reduce over-segmentation.</p

A robust detail preserving anisotropic diffusion for speckle reduction in ultrasound images

<p>Abstract</p> <p>Background</p> <p>Speckles in ultrasound imaging affect image quality and can make the post-processing difficult. Speckle reduction technologies have been employed for removing speckles for some time. One of the effective speckle reduction technologies is anisotropic diffusion. Anisotropic diffusion technology can remove the speckles effectively while preserving the edges of the image and thus has drawn great attention from image processing scientists. However, the proposed methods in the past have different disadvantages, such as being sensitive to the number of iterations or low capability of preserving the details of the ultrasound images. Thus a detail preserved anisotropic diffusion speckle reduction with less sensitive to the number of iterations is needed. This paper aims to develop this kind of technologies.</p> <p>Results</p> <p>In this paper, we propose a robust detail preserving anisotropic diffusion filter (RDPAD) for speckle reduction. In order to get robust diffusion, the proposed method integrates Tukey error norm function into the detail preserving anisotropic diffusion filter (DPAD) developed recently. The proposed method could prohibit over-diffusion and thus is less sensitive to the number of iterations</p> <p>Conclusions</p> <p>The proposed anisotropic diffusion can preserve the important structure information of the original image while reducing speckles. It is also less sensitive to the number of iterations. Experimental results on real ultrasound images show the effectiveness of the proposed anisotropic diffusion filter.</p

Nucleosome Structure Incorporated Histone Acetylation Site Prediction in \u3ci\u3eArabidopsis thaliana\u3c/i\u3e

Background Acetylation is a crucial post-translational modification for histones, and plays a key role in gene expression regulation. Due to limited data and lack of a clear acetylation consensus sequence, a few researches have focused on prediction of lysine acetylation sites. Several systematic prediction studies have been conducted for human and yeast, but less for Arabidopsis thaliana. Results Concerning the insufficient observation on acetylation site, we analyzed contributions of the peptide-alignment-based distance definition and 3D structure factors in acetylation prediction. We found that traditional structure contributes little to acetylation site prediction. Identified acetylation sites of histones in Arabidopsis thaliana are conserved and cross predictable with that of human by peptide based methods. However, the predicted specificity is overestimated, because of the existence of non-observed acetylable site. Here, by performing a complete exploration on the factors that affect the acetylability of lysines in histones, we focused on the relative position of lysine at nucleosome level, and defined a new structure feature to promote the performance in predicting the acetylability of all the histone lysines in A. thaliana. Conclusion We found a new spacial correlated acetylation factor, and defined a ε-N spacial location based feature, which contains five core spacial ellipsoid wired areas. By incorporating the new feature, the performance of predicting the acetylability of all the histone lysines in A. Thaliana was promoted, in which the previous mispredicted acetylable lysines were corrected by comparing to the peptide-based prediction

Feature Selection and Classification of MAQC-II Breast Cancer and Multiple Myeloma Microarray Gene Expression Data

Microarray data has a high dimension of variables but available datasets usually have only a small number of samples, thereby making the study of such datasets interesting and challenging. In the task of analyzing microarray data for the purpose of, e.g., predicting gene-disease association, feature selection is very important because it provides a way to handle the high dimensionality by exploiting information redundancy induced by associations among genetic markers. Judicious feature selection in microarray data analysis can result in significant reduction of cost while maintaining or improving the classification or prediction accuracy of learning machines that are employed to sort out the datasets. In this paper, we propose a gene selection method called Recursive Feature Addition (RFA), which combines supervised learning and statistical similarity measures. We compare our method with the following gene selection methods

Safety and immunogenicity of an MF59™-adjuvanted subunit influenza vaccine in elderly Chinese subjects

BACKGROUND: The safety and immunogenicity of an MF59™-adjuvanted subunit influenza vaccine (Sub/MF59™; FLUAD(®), Novartis Vaccines) was evaluated among elderly Chinese subjects (≥ 60 years of age). After a preliminary Phase I, open-label study (n = 25) to assess safety 1–14 days post-vaccination, a comparative observer-blind, randomised, controlled clinical trial (n = 600) was performed to assess safety and immunogenicity versus a non-adjuvanted subunit influenza vaccine (Subunit; Agrippal(®), Novartis Vaccines). Subjects were randomised (2:1) to receive Sub/MF59™ or Subunit. RESULTS: Both vaccines were well tolerated, with no vaccine-related serious adverse events reported during the Phase I trial. During the observer-blind study, local and systemic reactions were generally similar for both vaccines 1–22 days post-vaccination; however, injection-site induration was more frequent among the Subunit group (P < 0.05), and mild pain at the injection site and fever were more frequent among Sub/MF59™ recipients (P ≤ 0.005). Both vaccines induced a significant (P < 0.001) increase in geometric mean titres (GMTs) for the three strains tested, versus baseline; GMTs against A/H1N1, A/H3N2 and B were significantly higher in the Sub/MF59™ group (P = 0.034, P < 0.001 and P = 0.005, respectively). GMT ratios against A/H1N1, A/H3N2 and B were also significantly higher in the Sub/MF59™ group (P = 0.038, P < 0.001 and P = 0.006, respectively). Similarly, the percentage of subjects achieving seroprotection or seroconversion on Day 22 was greater for Sub/MF59™ recipients, reaching significance for A/H3N2 (P < 0.001). CONCLUSION: MF59™-adjuvanted subunit influenza vaccine is well tolerated by elderly Chinese subjects and induces a higher level of immunogenicity than a non-adjuvanted subunit influenza vaccine in this population that is at high risk of influenza-related complications. CLINICAL TRIAL REGISTRY: , NCT0031064

A distribution-free convolution model for background correction of oligonucleotide microarray data

IntroductionAffymetrix GeneChip® high-density oligonucleotide arrays are widely used in biological and medical research because of production reproducibility, which facilitates the comparison of results between experiment runs. In order to obtain high-level classification and cluster analysis that can be trusted, it is important to perform various pre-processing steps on the probe-level data to control for variability in sample processing and array hybridization. Many proposed preprocessing methods are parametric, in that they assume that the background noise generated by microarray data is a random sample from a statistical distribution, typically a normal distribution. The quality of the final results depends on the validity of such assumptions. ResultsWe propose a Distribution Free Convolution Model (DFCM) to circumvent observed deficiencies in meeting and validating distribution assumptions of parametric methods. Knowledge of array structure and the biological function of the probes indicate that the intensities of mismatched (MM) probes that correspond to the smallest perfect match (PM) intensities can be used to estimate the background noise. Specifically, we obtain the smallest q2 percent of the MM intensities that are associated with the lowest q1 percent PM intensities, and use these intensities to estimate background. ConclusionUsing the Affymetrix Latin Square spike-in experiments, we show that the background noise generated by microarray experiments typically is not well modeled by a single overall normal distribution. We further show that the signal is not exponentially distributed, as is also commonly assumed. Therefore, DFCM has better sensitivity and specificity, as measured by ROC curves and area under the curve (AUC) than MAS 5.0, RMA, RMA with no background correction (RMA-noBG), GCRMA, PLIER, and dChip (MBEI) for preprocessing of Affymetrix microarray data. These results hold for two spike-in data sets and one real data set that were analyzed. Comparisons with other methods on two spike-in data sets and one real data set show that our nonparametric methods are a superior alternative for background correction of Affymetrix data