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Enterovirus 71 (EV71) is a common cause of hand, foot, and mouth disease and sometimes causes severe neurologic complications, mainly in children. We report a case of adult-onset encephalitis caused [...]

Abstract Background High-density oligonucleotide arrays are effective tools for genotyping numerous loci simultaneously. In small genome species (genome size: < ~300 Mb), whole-genome DNA hybridization to expression arrays has been used for various applications. In large genome species, transcript hybridization to expression arrays has been used for genotyping. Although rice is a fully sequenced model plant of medium genome size (~400 Mb), there are a few examples of the use of rice oligonucleotide array as a genotyping tool. Results We compared the single feature polymorphism (SFP) detection performance of whole-genome and transcript hybridizations using the Affymetrix GeneChip® Rice Genome Array, using the rice cultivars with full genome sequence, japonica cultivar Nipponbare and indica cultivar 93-11. Both genomes were surveyed for all probe target sequences. Only completely matched 25-mer single copy probes of the Nipponbare genome were extracted, and SFPs between them and 93-11 sequences were predicted. We investigated optimum conditions for SFP detection in both whole genome and transcript hybridization using differences between perfect match and mismatch probe intensities of non-polymorphic targets, assuming that these differences are representative of those between mismatch and perfect targets. Several statistical methods of SFP detection by whole-genome hybridization were compared under the optimized conditions. Causes of false positives and negatives in SFP detection in both types of hybridization were investigated. Conclusions The optimizations allowed a more than 20% increase in true SFP detection in whole-genome hybridization and a large improvement of SFP detection performance in transcript hybridization. Significance analysis of the microarray for log-transformed raw intensities of PM probes gave the best performance in whole genome hybridization, and 22,936 true SFPs were detected with 23.58% false positives by whole genome hybridization. For transcript hybridization, stable SFP detection was achieved for highly expressed genes, and about 3,500 SFPs were detected at a high sensitivity (> 50%) in both shoot and young panicle transcripts. High SFP detection performances of both genome and transcript hybridizations indicated that microarrays of a complex genome (e.g., of Oryza sativa) can be effectively utilized for whole genome genotyping to conduct mutant mapping and analysis of quantitative traits such as gene expression levels.

Abstract Background High-density short oligonucleotide microarrays are useful tools for studying biodiversity, because they can be used to investigate both nucleotide and expression polymorphisms. However, when different strains (or species) produce different signal intensities after mRNA hybridization, it is not easy to determine whether the signal intensities were affected by nucleotide or expression polymorphisms. To overcome this difficulty, nucleotide and expression polymorphisms are currently examined separately. Results We have developed SNEP, a new method that allows simultaneous detection of both nucleotide and expression polymorphisms. SNEP involves a robust statistical procedure based on the idea that a nucleotide polymorphism observed at the probe level can be regarded as an outlier, because the nucleotide polymorphism can reduce the hybridization signal intensity. To investigate the performance of SNEP, we used three species: barley, rice and mice. In addition to the publicly available barley data, we obtained new rice and mouse data from the strains with available genome sequences. The sensitivity and false positive rate of nucleotide polymorphism detection were estimated based on the sequence information. The robustness of expression polymorphism detection against nucleotide polymorphisms was also investigated. Conclusion SNEP performed well regardless of the genome size and showed a better performance for nucleotide polymorphism detection, when compared with other previously proposed methods. The R-software 'SNEP' is available at http://www.ism.ac.jp/~fujisawa/SNEP/.

Abstract Background Proteomic data obtained from mass spectrometry have attracted great interest for the detection of early-stage cancer. However, as mass spectrometry data are high-dimensional, identification of biomarkers is a key problem. Results This paper proposes the use of "common" peaks in data as biomarkers. Analysis is conducted as follows: data preprocessing, identification of biomarkers, and application of AdaBoost to construct a classification function. Informative "common" peaks are selected by AdaBoost. AsymBoost is also examined to balance false negatives and false positives. The effectiveness of the approach is demonstrated using an ovarian cancer dataset. Conclusion Continuous covariates and discrete covariates can be used in the present approach. The difference between the result for the continuous covariates and that for the discrete covariates was investigated in detail. In the example considered here, both covariates provide a good prediction, but it seems that they provide different kinds of information. We can obtain more information on the structure of the data by integrating both results.

This study experimentally investigated the atomic structure of a single-crystalline Mn-doped BiFeO3 (BFO) thin film using X-ray fluorescence holography with synchrotron radiation. Bi atoms can be reconstructed from both Fe Kβ and Mn Kα fluorescence X-ray holograms, indicating Mn doping at B sites in ABO3-type perovskite structure. The fluorescence intensity of the 1st to 4th nearest Bi atoms around target Fe atoms was lower than those around Mn atoms, confirming the selective formation of Bi vacancies around Fe atoms. In contrast, the 5th to 8th nearest Bi atoms around Fe atoms showed higher intensities than those around Mn atoms, indicating that the Mn-doped BFO thin film had a double-perovskite-like structure. These results provide important information that helps elucidate the mechanism by which Mn doping modifies the conductivity of BFO. [ABSTRACT FROM AUTHOR]

Bismuth-layer-structured multiferroic Bi5Ti3FeO15 (BTFO15) (number of pseudoperovskite blocks, m=4) and natural-superlattice-structured Bi4Ti3O12-Bi5Ti3FeO15 (BIT-BTFO15) (m=3 or 4) thin films were prepared on (001)-oriented and (110)-oriented La-doped (3.73 wt %) SrTiO3 (La-STO) single-crystal substrates using pulsed laser deposition. X-ray diffraction patterns of these thin films on (001) La-STO single crystals indicated that the obtained thin films were single-phase (00l)-oriented layered perovskite, and that the BIT-BTFO15 (m=3 or 4) natural-superlattice structure was also obtained. On (110) La-STO single crystal, layered perovskite (11l)-oriented thin films were also obtained. Moreover, cross-sectional transmission electron microscope images of these thin films revealed four pseudoperovskite blocks (m=4) in the BTFO15 thin films, and an intergrowth structure of three and four pseudoperovskite blocks (m=3 or 4) in BIT-BTFO15 sandwiched by two (Bi2O2)2+ layers. In ferroelectric D-E hysteresis loop measurements, BTFO15 (m=4) and BIT-BTFO15 (m=3 or 4) thin films on (110) La-doped STO single crystals produced clear ferroelectric hysteresis loops with double remanent polarizations (2Pr) of 49 μC/cm2 and 44 μC/cm2, respectively. However, BTFO15 and BIT-BTFO15 thin films on (001) La-doped STO single crystals had paraelectric characteristics. These results demonstrate that the spontaneous polarization vectors of the BTFO15 and BIT-BTFO15 thin films were parallel to the a axis of their unit cells. [ABSTRACT FROM AUTHOR]

The stress influence of the structural and ferroelectric properties of polycrystalline BiFeO3 (BFO) thin films has been investigated using a membrane substrate for relaxing stress. Reciprocal space mapping (RSM) measurement has been performed to confirm the stress dependence of the crystal structure of polycrystalline BFO thin films on the Pt (200 nm)/TiO2 (50 nm)/SiO2 (600 nm)/Si (625 μm) substrate (stress-constrained BFO film) and the Pt (200 nm)/TiO2 (50 nm)/SiO2 (600 nm)/Si (15 μm) membrane substrate (stress-relaxed BFO film). The BFO thin films prepared by pulsed laser deposition were polycrystalline and mainly exhibit a texture with (001) and (110) plane orientations. From the RSM results, the crystal structure of the (001)-oriented domain changes from Pm monoclinic to Cm monoclinic or to R3c rhombohedral due to stress relaxation. Moreover, at room temperature as well as at 150 K, remanent polarization (Pr) increases and double coercive field (2Ec) decreases (in the latter case from 88 to 94 μC/cm2 and from 532 to 457 kV/cm, respectively) due to relaxing stress. The enhancement of ferroelectricity is attributed to the crystal structural deformation and/or transition and angle change between the polarization direction and film plane. [ABSTRACT FROM AUTHOR]

The epitaxial growth, structural properties, and ferroelectric properties of bismuth lanthanum nickel titanate (Bi1-xLax) (Ni0.5Ti0.5)O3 (BLNT) thin films deposited on Pt(100)/MgO(100) substrates by rf magnetron sputtering have been investigated using x-ray diffraction, transmission electron microscope, and polarization–electric field hysteresis loop measurements. The ferroelectric BLNT(00ℓ) phase with c-axis orientation and a single-phase tetragonal perovskite structure appeared at x>=0.3. The tetragonality (c/a) increased significantly from 1.004 to 1.028 with increasing La content. The fabricated BLNT films of x>=0.3 indicated the apparent fourfold rotational symmetry observed for a MgO(202) substrate, a bottom Pt(202) electrode, and a BLNT(101) ferroelectric film, based on [lowercase_phi_synonym] scan measurements. These results imply that the present La-substituted BLNT films are grown heteroepitaxially at x>=0.3. It was confirmed that Bi in the BLNT films is in a trivalent state at A sites in the perovskite crystal, based on x-ray anomalous diffraction measurements and x-ray absorption near edge structure spectra. The sputtering technique using compacted powder targets designed by taking the bond dissociation energy of metal oxides into account provided epitaxial perovskite-structured BLNT thin films on Pt(100)/MgO(100) substrates. It is shown that the c-axis oriented epitaxial BLNT film exhibits a hysteresis loop shape with a Pr value of 12 μC/cm2 that is comparable to typical high-performance Bi3.25La0.75Ti3O12 (BLT) film. [ABSTRACT FROM AUTHOR]

Bismuth-layer-structured multiferroic [Bi.sub.5][Ti.sub.3]Fe[O.sub.15] (BTFO15) and natural-superlattice-structured [Bi.sub.4][Ti.sub.3][O.sub.12]-[Bi.sub.5][Ti.sub.3]Fe[O.sub.15] (BIT-BTFO15) thin films are prepared on (001)-oriented and (110)-oriented La-doped SrTi[O.sub.3] (La-STO) single-crystal substrates by using pulsed laser deposition. The results have shown that the spontaneous polarization vectors of the BTFO15 and BIT-BTFO15 thin films are parallel to the a axis of their unit cells.

The stress influence of the structural and ferroelectric properties of polycrystalline BiFe[O.sub.3] (BFO) thin films is examined by using a membrane substrate for relaxing stress. The increase in the ferroelectricity is attributed to the crystal structural deformation and transition and angle change between the polarization direction and film plane.

A 64‐year‐old man presented with back pain and dysesthesia in the arms. Neurological examination results were unremarkable. T2‐weighted MRI revealed an abnormal intensity mimicking myelitis with longitudinally extensive spinal cord lesions. Contrast‐enhanced T1‐weighted MRI revealed an enhanced intramedullary mass at the Th7 level. CSF showed slight pleocytosis and elevated protein levels. CT and PET of the whole body showed no significant findings. The lesion was removed surgically and was compatible with capillary hemangioma histologically. Postoperatively, his symptoms and the long cord lesion were resolved. This case indicates that marked edema mimicking myelitis can be caused by intramedullary capillary hemangioma. [ABSTRACT FROM AUTHOR]