Identification of Outlying Observations with Quantile Regression for Censored Data

Outlying observations, which significantly deviate from other measurements, may distort the conclusions of data analysis. Therefore, identifying outliers is one of the important problems that should be solved to obtain reliable results. While there are many statistical outlier detection algorithms and software programs for uncensored data, few are available for censored data. In this article, we propose three outlier detection algorithms based on censored quantile regression, two of which are modified versions of existing algorithms for uncensored or censored data, while the third is a newly developed algorithm to overcome the demerits of previous approaches. The performance of the three algorithms was investigated in simulation studies. In addition, real data from SEER database, which contains a variety of data sets related to various cancers, is illustrated to show the usefulness of our methodology. The algorithms are implemented into an R package OutlierDC which can be conveniently employed in the \proglang{R} environment and freely obtained from CRAN

Aid for skills development

노트 : Background paper prepared for the Education for All Global Monitoring Report 2012Youth and skills: Putting education to wor

Coordination between Bradyrhizobium and Pseudomonas alleviates salt stress in soybean through altering root system architecture

It is a well accepted strategy to improve plant salt tolerance through inoculation with beneficial microorganisms. However, its underlying mechanisms still remain unclear. In the present study, hydroponic experiments were conducted to evaluate the effects of Bradyrhizobium japonicum USDA 110 with salt-tolerant Pseudomonas putida TSAU1 on growth, protein content, nitrogen, and phosphorus uptake as well as root system architecture of soybean (Glycine max L.) under salt stress. The results indicated that the combined inoculation with USDA 110 and TSAU1 significantly improved plant growth, nitrogen and phosphorus contents, and contents of soluble leaf proteins under salt stress compared to the inoculation with the symbiont alone or compared to un-inoculated ones. The root architectural traits, like root length, surface area, project area, and root volume; as well as nodulation traits were also significantly increased by co-inoculation with USDA 110 and TSAU1. The plant-growth promoting rhizobacteria (PGPR) P. putida strain TSAU1 could improve the symbiotic interaction between the salt-stressed soybean and B. japonicum USDA 110. In conclusion, inoculation with B. japonicum and salt-tolerant P. putida synergistically improved soybean salt tolerance through altering root system architecture facilitating nitrogen and phosphorus acquisition, and nodule formation.Peer reviewe

Comparison of Clinico-Radiological Features between Congenital Cystic Neuroblastoma and Neonatal Adrenal Hemorrhagic Pseudocyst

OBJECTIVE: To evaluate the radiological and clinical findings of congenital cystic neuroblastomas as compared with those of the cystic presentation of neonatal adrenal hemorrhage. MATERIALS AND METHODS: We analyzed the US (n = 52), CT (n = 24), and MR (n = 4) images as well as the medical records of 28 patients harboring congenital cystic neuroblastomas (n = 16) and neonatal adrenal hemorrhagic pseudocysts (n = 14). The history of prenatal detection, location, size, presence of outer wall enhancement, internal septations, solid portion, calcification, turbidity, vascular flow on a Doppler examination, and evolution patterns were compared in two groups of cystic lesions, by Fischer's exact test. RESULTS: All (100%) neuroblastomas and three (21%) of the 14 hemorrhagic pseudocysts were detected prenatally. Both groups of cystic lesions occurred more frequently on the right side; 11 of 16 (69%) for neuroblastomas and 11 of 14 (79%) for hemorrhagic pseudocysts. The size, presence of solid portion, septum, enhancement, and turbidity did not differ significantly (p > 0.05) between the two groups of cystic lesions. However, tiny calcifications (n = 3) and vascular flow on color Doppler US (n = 3) were noted in only neuroblastomas. The cystic neuroblastomas became complex solid and cystic masses, and did not disappear for up to 90 days in the three following cases, whereas 11 of the 14 (79%) hemorrhagic pseudocysts disappeared completely and the three remaining (27%) evolved to calcifications only. CONCLUSION: Although the imaging findings of two groups of cystic lesions were similar, prenatal detection, the presence of calcification on initial images, vascularity on color Doppler US, and evolution to a more complex mass may all favor neuroblastomasope

Serial CT Findings of Paragonimus Infested Dogs and the Micro-CT Findings of the Worm Cysts

OBJECTIVE: To investigate the serial CT findings of Paragonimus westermani infected dogs and the microscopic structures of the worm cysts using Micro-CT. MATERIALS AND METHODS: This study was approved by the committee on animal research at our institution. Fifteen dogs infected with P. westermani underwent serial contrast-enhanced CT scans at pre-infection, after 10 days of infection, and monthly thereafter until six months for determining the radiologic-pathologic correlation. Three dogs (one dog each time) were sacrificed at 1, 3 and 6 months, respectively. After fixation of the lungs, both multi-detector CT and Micro-CT were performed for examining the worm cysts. RESULTS: The initial findings were pleural effusion and/or subpleural ground-glass opacities or linear opacities at day 10. At day 30, subpleural and peribronchial nodules appeared with hydropneumothorax and abdominal or chest wall air bubbles. Cavitary change and bronchial dilatation began to be seen on CT scan at day 30 and this was mostly seen together with mediastinal lymphadenopathy at day 60. Thereafter, subpleural ground-glass opacities and nodules with or without cavitary changes were persistently observed until day 180. After cavitary change of the nodules, the migratory features of the subpleural or peribronchial nodules were seen on all the serial CT scans. Micro-CT showed that the cyst wall contained dilated interconnected tubular structures, which had communications with the cavity and the adjacent distal bronchus. CONCLUSION: The CT findings of paragonimiasis depend on the migratory stage of the worms. The worm cyst can have numerous interconnected tubular channels within its own wall and these channels have connections with the cavity and the adjacent distal bronchus

Robust estimation of microbial diversity in theory and in practice

Quantifying diversity is of central importance for the study of structure, function and evolution of microbial communities. The estimation of microbial diversity has received renewed attention with the advent of large-scale metagenomic studies. Here, we consider what the diversity observed in a sample tells us about the diversity of the community being sampled. First, we argue that one cannot reliably estimate the absolute and relative number of microbial species present in a community without making unsupported assumptions about species abundance distributions. The reason for this is that sample data do not contain information about the number of rare species in the tail of species abundance distributions. We illustrate the difficulty in comparing species richness estimates by applying Chao's estimator of species richness to a set of in silico communities: they are ranked incorrectly in the presence of large numbers of rare species. Next, we extend our analysis to a general family of diversity metrics ("Hill diversities"), and construct lower and upper estimates of diversity values consistent with the sample data. The theory generalizes Chao's estimator, which we retrieve as the lower estimate of species richness. We show that Shannon and Simpson diversity can be robustly estimated for the in silico communities. We analyze nine metagenomic data sets from a wide range of environments, and show that our findings are relevant for empirically-sampled communities. Hence, we recommend the use of Shannon and Simpson diversity rather than species richness in efforts to quantify and compare microbial diversity.Comment: To be published in The ISME Journal. Main text: 16 pages, 5 figures. Supplement: 16 pages, 4 figure

Hepatic Radiofrequency Ablation Using Multiple Probes: Ex Vivo and In Vivo Comparative Studies of Monopolar versus Multipolar Modes

OBJECTIVE: We wanted to compare the efficiency of multipolar radiofrequency ablation (RFA) using three perfused-cooled electrodes with multiple overlapping and simultaneous monopolar techniques for creating an ablation zone in ex vivo bovine livers and in in vivo porcine livers. MATERIALS AND METHODS: In the ex vivo experiments, we used a 200 W generator (Valleylab, CC-3 model) and three perfused-cooled electrodes or internally cooled electrodes to create 30 coagulation zones by performing consecutive monopolar RFA (group A, n = 10), simultaneous monopolar RFA (group B, n = 10) or multipolar RFA (group C, n = 10) in explanted bovine livers. In the consecutive mode, three ablation spheres were created by sequentially applying 150 watts radiofrequency (RF) energy to the internally cooled electrodes for 12 minutes each for a total of 36 minutes. In the simultaneous monopolar and multipolar modes, RF energy was concurrently applied to the three perfused-cooled electrodes for 20 minutes at 150 watt with instillation of 6% hypertonic saline at 2 mL/min. During RFA, we measured the temperatures of the treated area at its center. The changes in impedance, the current and liver temperature during RFA, as well as the dimensions of the thermal ablation zones, were compared among the three groups. In the in vivo experiments, three coagulations were created by performing multipolar RFA in a pig via laparotomy with using same parameter as the ex vivo study. RESULTS: In the ex vivo experiments, the impedance was gradually decreased during the RFA in groups B and C, but in group A, the impedance was increased during RFA and this induced activation by the pulsed RF technique. In groups A, B and C, the mean final-temperature values were 80+/-10 degrees C, 69+/-18 degrees C and 79+/-12 degrees C, respectively (p < 0.05). The multipolar mode created a larger volume of ablation than did the other modes: 37.6+/-4.0 cm3 (group A); 44.9+/-12.7 cm3 (group B); and 78.9+/-6.9 cm3 (group C) (p < 0.05). In the in vivo experiment, the pig well tolerated the RFA procedure and no major complications occurred during the 4 days of the follow-up period. The mean volume of coagulations produced by multipolar RFA in the pig liver was 60.5+/-17.9 cm3. CONCLUSION: For the multiple probe RFA, the multipolar mode with hypertonic saline instillation was more efficient in generating larger areas of thermal ablation than either the consecutive or simultaneous monopolar modes.ope

Genome-wide analysis of DNA methylation patterns in horse

Background: DNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. Although the horse reference genome and whole transcriptome data are publically available the global DNA methylation data are yet to be known. Results: We report the first genome-wide DNA methylation characteristics data from skeletal muscle, heart, lung, and cerebrum tissues of thoroughbred (TH) and Jeju (JH) horses, an indigenous Korea breed, respectively by methyl-DNA immunoprecipitation sequencing. The analysis of the DNA methylation patterns indicated that the average methylation density was the lowest in the promoter region, while the density in the coding DNA sequence region was the highest. Among repeat elements, a relatively high density of methylation was observed in long interspersed nuclear elements compared to short interspersed nuclear elements or long terminal repeat elements. We also successfully identified differential methylated regions through a comparative analysis of corresponding tissues from TH and JH, indicating that the gene body regions showed a high methylation density. Conclusions: We provide report the first DNA methylation landscape and differentially methylated genomic regions (DMRs) of thoroughbred and Jeju horses, providing comprehensive DMRs maps of the DNA methylome. These data are invaluable resource to better understanding of epigenetics in the horse providing information for the further biological function analyses.open1