Inconsistencies of genome annotations in apicomplexan parasites revealed by 5'-end-one-pass and full-length sequences of oligo-capped cDNAs

<p>Abstract</p> <p>Background</p> <p>Apicomplexan parasites are causative agents of various diseases including malaria and have been targets of extensive genomic sequencing. We generated 5'-EST collections for six apicomplexa parasites using our full-length oligo-capping cDNA library method. To improve upon the current genome annotations, as well as to validate the importance for physical cDNA clone resources, we generated a large-scale collection of full-length cDNAs for several apicomplexa parasites.</p> <p>Results</p> <p>In this study, we used a total of 61,056 5'-end-single-pass cDNA sequences from <it>Plasmodium falciparum</it>, <it>P. vivax</it>, <it>P. yoelii</it>, <it>P. berghei</it>, <it>Cryptosporidium parvum</it>, and <it>Toxoplasma gondii</it>. We compared these partially sequenced cDNA sequences with the currently annotated gene models and observed significant inconsistencies between the two datasets. In particular, we found that on average 14% of the exons in the current gene models were not supported by any cDNA evidence, and that 16% of the current gene models may contain at least one mis-annotation and should be re-evaluated. We also identified a large number of transcripts that had been previously unidentified. For 732 cDNAs in <it>T. gondii</it>, the entire sequences were determined in order to evaluate the annotated gene models at the complete full-length transcript level. We found that 41% of the <it>T. gondii </it>gene models contained at least one inconsistency. We also identified and confirmed by RT-PCR 140 previously unidentified transcripts found in the intergenic regions of the current gene annotations. We show that the majority of these discrepancies are due to questionable predictions of one or two extra exons in the upstream or downstream regions of the genes.</p> <p>Conclusion</p> <p>Our data indicates that the current gene models are likely to still be incomplete and have much room for improvement. Our unique full-length cDNA information is especially useful for further refinement of the annotations for the genomes of apicomplexa parasites.</p

Comparasite: a database for comparative study of transcriptomes of parasites defined by full-length cDNAs

Comparasite is a database for comparative studies of transcriptomes of parasites. In this database, each data is defined by the full-length cDNAs from various apicomplexan parasites. It integrates seven individual databases, Full-Parasites, consisting of numerous full-length cDNA clones that we have produced and sequenced: 12 484 cDNA sequences from Plasmodium falciparum, 11 262 from Plasmodium yoelii, 9633 from Plasmodium vivax, 1518 from Plasmodium berghei, 7400 from Toxoplasma gondii, 5921 from Cryptosporidium parvum and 10 966 from the tapeworm Echinococcus multilocularis. Putatively counterpart gene groups are clustered and comparative analysis of any combination of six apicomplexa species is implemented, such as interspecies comparisons regarding protein motifs (InterPro), predicted subcellular localization signals (PSORT), transmembrane regions (SOSUI) or upstream promoter elements. By specifying keywords and other search conditions, Comparasite retrieves putative counterpart gene groups containing a given feature in common or in a species-specific manner. By enabling multi-faceted comparative analyses of genes of apicomplexa protozoa, monophyletic organisms that have evolved to diversify to parasitize various hosts by adopting complex life cycles, Comparasite should help elucidate the mechanism behind parasitism. Our full-length cDNA databases and Comparasite are accessible from

Evaluating outcomes of the child and adolescent psychiatric unit: A prospective study

<p>Abstract</p> <p>Background</p> <p>The aims of this prospective study are to clarify the outcomes of child psychiatric inpatient treatment and to identify factors associated with patient improvement.</p> <p>Methods</p> <p>The attending psychiatrist used the Children's Global Assessment Scale (CGAS) to assess youths at admission to and discharge from a child and adolescent psychiatric unit in Japan(N = 126, mean age = 12.8, SD = 1.9). Hospital records gathered sociodemographic and clinical variables. In addition, youths and their primary caregivers assessed themselves using the Youth Self Report (YSR) and the Child Behavior Checklist (CBCL), respectively. Longitudinal analyses compared each scales' baseline and discharge scores. We also examined factors associated with changes in functioning (CGAS).</p> <p>Results</p> <p>Longitudinal comparisons revealed that CGAS, CBCL and YSR scores showed improvement over time (CGAS: t = -14.40, p = 0.00; CBCL: t = 3.80, p = 0.00; YSR: t = 2.40, p = 0.02). Linear regressions determined that the factors associated with improvement in CGAS included age, lower CGAS scores at admission, frequency of group therapy and psychiatric diagnosis.</p> <p>Conclusions</p> <p>This evaluation of children and adolescents in an inpatient unit demonstrated clinical improvement over time and identified factors associated with said improvement.</p

Fully non-linear equivalence of delta N and covariant formalisms

We explicitly show the fully non-linear equivalence of the $\delta$N and the covariant formalisms for the superhorizon curvature perturbations, which enables us to safely evaluate the non-Gaussian quantities of the curvature perturbation in either formalism. We also discuss isocurvature perturbations in the covariant formalism and clarify the relation between the fully non-linear evolution of the curvature covector and that of the curvature perturbation for multiple interacting fluids.Comment: 11 pages, minor changes, version accepted by PR

Multi-Region and Multi-Component Thermal Fluid Analysis of Hydrothermal Oxidative Decomposition Reactor

To elucidate the corrosion mechanism of a hydrothermal oxidation decomposition reactor for the treatment of polychlorinated biphenyls (PCBs), a coupled thermal fluid analysis of the heat transfer between two mixtures of fluids with different physical properties and the reactor body was executed using OpenFOAM. Based on the analysis results, we propose a method to evaluate the corrosion risk at the solid-liquid interface by focusing on three factors: (1) the corrosion temperature of reactor vessel, (2) the amount of fluid deposition that causes corrosion, and (3) the wall shear stress on the solid-liquid interface. Variation of corrosion risk with operating conditions of the reactor is discussed

Thermal Fluid Coupled Analysis of Hydrothermal Destruction Reactor

Multi-regionally coupled analysis of thermal fluid flow and heat conduction of solid using OpenFOAM is carried out to clarify the behavior of hydrothermal oxidative destruction reactor of polychlorinated biphenyls (PCBs). Internal fluid of the reactor assumes a single-phase hot water without chemical reactions considering temperature dependence of thermophysical properties. Compressible Navier-Stokes equation with buoyancy force and energy equation with gravity term are alternately solved for the thermal fluid analysis. In order to consider conjugate heat transfer between the internal fluid and the reactor vessel, two-regionally coupled analysis of the fluid and vessel was executed by chtMultiRegionFoam solver in the OpenFOAM. To verify coupling effect, the multi-regionally coupled analyses results were compared with thermal fluid analysis of the internal fluid or heat conduction analysis of the vessel

Cross-sectional particle measurement in the resonance domain on the substrate through scatterometry

We developed a versatile method for three-dimensional shape measurement where a specific particle can be selected on the substrate and its cross-sectional shape and size can be measured. A non-contact fast measurement is possible for the particle in the resonance domain. We applied rigorous coupled-wave analysis to the particle and calculated the diffraction patterns, comparing the patterns with the experimental results to obtain the size and shape. The shape and position of the focusing spot on the scattering particle was controlled precisely. With this method, the category of the analyzable object is extended to more shapes, such as rectangles and triangles, in addition to a conventional ellipsoid

Investigation of the Utility and Safety of Dynamic Computed Tomography with Vasodilators

Background: Dynamic computed tomography (CT) angiography is useful for evaluating of hepatic vascularity. Although vasodilators increase hepatic blood flow, the utility of dynamic CT with vasodilators is unclear. Here we investigated the utility and safety of dynamic CT with vasodilators. Methods: A prospective case-control radiographic evaluation using abdominal dynamic CT with and without vasodilator was performed at a single center between October 2015 and September 2016. We compared the CT values in Hounsfield units of the aorta; celiac artery; and common, right, and left hepatic arteries in the arterial phase and the main trunk; right and left branches of the portal vein; and right, middle, and left hepatic veins in the portal phase with and without vasodilators. The region of interest was set in each element of the liver vasculature. Four radiological technologists independently and visually compared the scores of the portal vein (P-score) and hepatic vein (V-score) on a 5-point scale with and without vasodilators. Results: The CT values of arteries and veins using vasodilators were significantly higher than those without vasodilators. With and without vasodilators, the P-scores were 3.1 ± 1.2 and 4.0 ± 1.1 (P < 0.05) and the V-scores were 3.3 ± 1.4 and 4.3 ± 1.0 (P < 0.05). Only one patient with vasodilator use had transient hypotension and recovered immediately without medication. Conclusion: Dynamic CT with vasodilators can provides better visualization of vascular structures