Smectic Liquid-Crystalline Structure of Skyrmions in Chiral Magnet Co_{8.5}Zn_{7.5}Mn_{4}(110) Thin Film.

The organizing of magnetic skyrmions shows several forms similar to atomic arrays of solid states. Using Lorentz transmission electron microscopy, we report the first direct observation of a stable liquid-crystalline structure of skyrmions in chiral magnet Co_{8.5}Zn_{7.5}Mn_{4}(110) thin film, caused by magnetic anisotropy and chiral surface twist. Elongated skyrmions are oriented and periodically arranged only in the ⟨110⟩ directions, whereas they exhibit short-range order along the ⟨001⟩ directions, indicating a smectic skyrmion state. In addition, skyrmions possess anisotropic interaction with an opposite sign depending on the crystal orientation, in contrast to existing isotropic interaction.

Microscopic gain analysis of modulation-doped GeSn/SiGeSn quantum wells: epitaxial design toward high-temperature lasing.

Threshold carrier densities of GeSn quantum well (QW) lasers and the physical reason of low-temperature lasing of current GeSn laser are investigated through the comparison of threshold carrier densities of conventional III-V QW lasers. Electrons distributed over L-band is the main cause of decreased gain for GeSn QWs. To increase the gain (and improve the laser characteristics), a modulation-doped GeSn QW is proposed and the material gain is analyzed based on many-body theory for both qualitative and quantitative simulation. Significant gain increase can be expected for n-type modulation doping QWs. The doping condition for elevated temperature lasing is discussed and it was found that material gain curve similar to III-V QW is obtained for GeSn QW with n-type modulation doping of 6 × 1018 cm-3. It was also found that unlike III-V QW lasers, n-type modulation doping is more effective for high-speed operation in terms of differential gain than p-type modulation doping.

Si-based Mach-Zehnder wavelength/mode multi/demultiplexer for a WDM/MDM transmission system.

We propose and experimentally demonstrate a low-loss and low-crosstalk Mach-Zehnder mode/wavelength multi/demultiplexer for WDM/MDM transmission based on a Si-photonics platform. A broadband 3-dB mode divider, which is also newly devised here, makes it possible to compose a Mach-Zehnder filter for "mode" and "wavelength" simultaneously. Transmission characteristics of fabricated 3-dB mode dividers are in excellent agreement with theoretical results. Mach-Zehnder filters using the 3-dB mode divider with a free spectral range (FSR) of 20 and 1 nm are also fabricated and the modal crosstalk is less than -24 dB in the 40-nm wavelength range for the MZ filter with an FSR of 20 nm. The tuning of the peak wavelength position by the TiN heater is also demonstrated.

Location, size and age at onset of metamorphosis in the Japanese eel Anguilla japonica.

This study clarifies the location, size and age at the onset of metamorphosis in Japanese eels Anguilla japonica through oceanic surveys, rearing experiments and analyses of the morphology and otoliths of leptocephali and glass eels. Twenty-eight metamorphosing leptocephali were collected in the mesoscale eddy region to the east of Taiwan during research expeditions in 2004. Rearing experiments showed that the total length (LT ) of leptocephali decreased by an average of 12·5% during metamorphosis and 13·9% during the 2-12 h after death. Thus, the mean back-calculated LT at the onset of metamorphosis for 630 glass eels from Taiwan and Japan was estimated at 67·8 ± 2·7 mm (mean ± S.D.). The estimated mean ante-mortem size of the fully grown pre-metamorphic leptocephali collected in 2004 was 64·6 ± 3·4 mm, which was consistent with the LT estimate for glass eels. Otolith analysis showed that the mean age at the onset of metamorphosis was 137 ± 15 days and indicated that Japanese eels may have a recruitment route through the mesoscale eddies to the east of Taiwan in addition to the direct transfer route from the North Equatorial Current to the Kuroshio Current.

Risk of haemolytic uraemic syndrome caused by shiga-toxin-producing Escherichia coli infection in adult women in Japan.

Shiga-toxin-producing Escherichia coli (STEC) infections usually cause haemolytic uraemic syndrome (HUS) equally in male and female children. This study investigated the localization of globotriaosylceramide (Gb3) in human brain and kidney tissues removed from forensic autopsy cases in Japan. A fatal case was used as a positive control in an outbreak of diarrhoeal disease caused by STEC O157:H7 in a kindergarten in Urawa in 1990. Positive immunodetection of Gb3 was significantly more frequent in female than in male distal and collecting renal tubules. To correlate this finding with a clinical outcome, a retrospective analysis of the predictors of renal failure in the 162 patients of two outbreaks in Japan was performed: one in Tochigi in 2002 and the other in Kagawa Prefecture in 2005. This study concludes renal failure, including HUS, was significantly associated with female sex, and the odds ratio was 4·06 compared to male patients in the two outbreaks. From 2006 to 2009 in Japan, the risk factor of HUS associated with STEC infection was analysed. The number of males and females and the proportion of females who developed HUS were calculated by age and year from 2006 to 2009. In 2006, 2007 and 2009 in adults aged >20 years, adult women were significantly more at risk of developing HUS in Japan.

Key factors for the dynamic ETEM observation of single atoms.

We present further modifications to aberration-corrected environmental transmission electron microscopy (AC-ETEM) for the dynamic HRTEM observation of single atoms. Additional pumping levels that include three additional turbomolecular pumps (TMPs) enable a base pressure of 3.5 × 10(-5) Pa in the sample chamber. The effect of these additional TMPs on image resolution was measured in reciprocal space using information limit (Young's fringes) on a standard cross grating sample and also with platinum (Pt) single atoms on an amorphous carbon film (Pt/a-carbon). The Pt/a-carbon was used for measuring the effect of gas pressure on single-atom imaging in addition to the evaluation of vibrations of TMPs, samples, magnetic lenses and a microscope column of the AC-ETEM. TMPs did not affect the ETEM imaging performance when an anti-vibration table was used, and 0.10-nm resolution was achieved. Dynamic ETEM observation of Pt single atoms was achieved in 4.0 × 10(-2) Pa of air, using a modified AC-ETEM system and a high-speed CCD camera with a time resolution of 0.05 s.

Changes of human menisci in osteoarthritic knee joints.

OBJECTIVE: To investigate the changes of knee menisci in osteoarthritis (OA) in human. METHODS: OA and control menisci were obtained from 42 end-stage OA knees with medial involvement and 28 non-arthritic knees of age-matched donors, respectively. The change of menisci in OA was evaluated by histology, and gene expression of major matrix components and anabolic factors was analyzed in the anterior horn segments by quantitative PCR (qPCR). In those regions of menisci, the rate of collagen neo-synthesis was evaluated by [(3)H]proline incorporation, and the change of matrix was investigated by ultrastructural observation and biomechanical measurement. RESULTS: In OA menisci, the change in histology was rather moderate in the anterior horn segments. However, despite the modest change in histology, the expression of type I, II, III procollagens was dramatically increased in those regions. The expression of insulin-like growth factor 1 (IGF-1) was markedly enhanced in OA menisci, which was considered to be responsible, at least partly, for the increase in procollagen gene expression. Interestingly, in spite of marked increase in procollagen gene expression, incorporation of [(3)H]proline increased only modestly in OA menisci, and impaired collagen synthesis was suggested. This finding was consistent with the results of ultrastructural observation and biomechanical measurement, which indicated that the change of meniscal matrix was modest in the macroscopically preserved areas of OA menisci. CONCLUSION: Although the expression of major matrix components was markedly enhanced, matrix synthesis was enhanced only modestly, and the changes of matrix in human OA menisci were rather modest in the non-degenerated areas.

Single nucleotide polymorphisms in chum salmon (Oncorhynchus keta) mitochondrial DNA derived from restriction site haplotype information.

Single nucleotide polymorphisms (SNPs) are useful genetic markers for the management and conservation of commercially important species such as salmon. Informative markers can be derived from data obtained for other purposes. We used restriction endonuclease data from earlier work to identify potentially useful restriction sites in chum salmon (Oncorhynchus keta). With the aid of a newly generated complete mitochondrial DNA sequence (accession number AP010773), we identified the SNP responsible for each restriction site variant, designed rapid genotyping assays, and surveyed the SNPs in more than 400 individuals. The restriction site analysis and the SNP genotyping assays were almost perfectly concordant. Some reasons for the non-concordance were identified and discussed.

Application of single nucleotide polymorphisms to non-model species: a technical review.

Single nucleotide polymorphisms (SNPs) have gained wide use in humans and model species and are becoming the marker of choice for applications in other species. Technology that was developed for work in model species may provide useful tools for SNP discovery and genotyping in non-model organisms. However, SNP discovery can be expensive, labour intensive, and introduce ascertainment bias. In addition, the most efficient approaches to SNP discovery will depend on the research questions that the markers are to resolve as well as the focal species. We discuss advantages and disadvantages of several past and recent technologies for SNP discovery and genotyping and summarize a variety of SNP discovery and genotyping studies in ecology and evolution.

Photonic bandgap fibers with resonant structures for tailoring the dispersion.

Numerical simulations on different kinds of realistic photonic bandgap fibers exhibiting reversed dispersion slope for the propagating fundamental mode are reported. We show that reversed or flat dispersion functions in a wide wavelength range using hollow-core, air-silica photonic bandgap fibers and solid core Bragg fibers with step-index profile can be obtained by introducing resonant structures in the fiber cladding. We evaluate the dispersion and confinement loss profiles of these fibers from the Helmholtz eigenvalue equation and the calculated fiber properties are used to investigate the propagation of chirped femtosecond pulses through serially connected hollow core fiber compressors.

Reversed dispersion slope photonic bandgap fibers for broadband dispersion control in femtosecond fiber lasers.

Higher-order-mode solid and hollow core photonic bandgap fibers exhibiting reversed or zero dispersion slope over tens or hundreds of nanometer bandwidths within the bandgap are presented. This attractive feature makes them well suited for broadband dispersion control in femtosecond pulse fiber lasers, amplifiers and optical parametric oscillators. The canonical form of the dispersion profile in photonic bandgap fibers is modified by a partial reflector layer/interface placed around the core forming a 2D cylindrical Gires-Tournois type interferometer. This small perturbation in the index profile induces a frequency dependent electric field distribution of the preferred propagating higher-order-mode resulting in a zero or reversed dispersion slope.

Design and simulation of 1310 nm and 1480 nm single-mode photonic crystal fiber Raman lasers.

We have numerically investigated the Raman lasing characteristics of a highly nonlinear photonic crystal fiber (HNPCF). HNPCF Raman lasers are designed to deliver outputs at 1.3 microm and 1.48 microm wavelengths through three and six cascades of Raman Stokes cavities when the pumps of 1117 nm and 1064 nm are injected into HNPCF module, respectively. A quantum efficiency of approximately 47% was achieved in a short length of HNPCF for 1.3 microm lasing wavelength. The HNPCF design is modified further to operate in single-mode fashion keeping intact its Raman lasing characteristics. The modified HNPCF design consists of two air-hole rings where the higher-order modes in the central core are suppressed by enhancing their leakage losses drastically, thus ceasing their propagation in the short length of HNPCF. On the other hand, the fundamental mode is well confined to the central core region, unaffecting its lasing performances. Further, the lasing characteristics of HNPCF at 1480 nm are compared with conventional highly nonlinear fiber Raman laser operating at 1480 nm. It is found that one can reduce the fiber length by five times in case of HNPCF with nearly similar conversion efficiency.

Bend-insensitive lasing characteristics of single-mode, large-mode-area ytterbium-doped photonic crystal fiber.

The bend-insensitive lasing characteristics of a newly designed ytterbium-doped photonic crystal fiber (YPCF) are evaluated numerically. The designed YPCF remains single-mode and possesses large-mode-area of 1400 microm(2) at 1064 nm wavelength with the beam quality factor (M(2)) of 1.15, suggesting a diffraction-limited and continuous-wave lasing operation. The doped-region size is optimized for maximum conversion efficiency and it is found through numerical simulations that the doped radius should be more than 21 microm. The "mode expansion", which is the self-expansion of the fundamental mode within the doped region with wavelength increments on bending the fiber, is the basic physical mechanism to give the bend-insensitive lasing performances of YPCF. It leads to an unusual variation of overlap factor when the wavelength is increased. A 41 cm long piece of YPCF demonstrates more than 83% of slope efficiency with 75% of conversion efficiency when pumped with a 975 nm laser source delivering an input power of 1 W.

Strategies for realizing photonic crystal fiber bandpass filters.

Numerical design strategies are presented to achieve efficient broad or narrow band-pass filters based on index-guiding, solid-core, and single-mode photonic crystal fibers (PCFs). The filtering characteristics have been verified through BPM solver. By scaling the pitch constant, the bandpass window can be shifted accordingly. The fiber design constitutes a fluorine-doped central core, enlarged air-holes surrounding the down-doped core, and small air-holes in the cladding. The proposed bandpass filter is based on controlling the leakage losses, so one can tune filter characteristics simply by changing its length. From numerical simulations we show that for large values of air-hole diameter in the first ring, the bandpass window is narrow, while for low doping concentration and small sized air-holes in the first ring, bandpass window is very broad. We also simulate how the hole-size and number of rings in the PCF cladding affects the device characteristics. We find that a 5-cm long PCF with down-doped core and eleven rings of air-holes can result in approximately 440 nm 3-dB bandwidth with more than 90% of transmission. The longer device has reduced transmission and smaller 3-dB bandwidth. Tolerance analysis has also been performed to check the impact of fiber tolerances on the performance of the PCF bandpass filter. It has been observed that the decrement in cladding hole-diameter by 1% reduces the transmission to 21% from its peak value of 93%, however +/-1% tolerance in the inner hole-diameter degrades the transmission to 75% from its peak.

Measurement of chromatic dispersion and Raman gain efficiency of a hole-assisted fiber: Influence of bend.

We have experimentally measured the Raman gain efficiency (RGE) and chromatic dispersion (CD) of a hole-assisted fiber (HAF). The RGE of a HAF was characterized using standard pump on/off technique while the CD of the fiber was measured using optical network analyzer. Theoretical simulations of the modal characteristics and the RGE of HAF were carried out using an accurate full-vectorial finite element method. Further, the bending effects on the CD and the RGE of a HAF with a smallest feasible bending radius are demonstrated. It was found that the CD increases while the RGE is decreased by bending HAF in a smallest bending radius of 5 mm. Numerical predictions from the theory are shown to be in good agreement with the experimental results.

Mitogenomic evolution and interrelationships of the Cypriniformes (Actinopterygii: Ostariophysi): the first evidence toward resolution of higher-level relationships of the world's largest freshwater fish clade based on 59 whole mitogenome sequences.

Fishes of the order Cypriniformes are almost completely restricted to freshwater bodies and number > 3400 species placed in 5 families, each with poorly defined subfamilies and/or tribes. The present study represents the first attempt toward resolution of the higher-level relationships of the world's largest freshwater-fish clade based on whole mitochondrial (mt) genome sequences from 53 cypriniforms (including 46 newly determined sequences) plus 6 outgroups. Unambiguously aligned, concatenated mt genome sequences (14,563 bp) were divided into 5 partitions (first, second, and third codon positions of the protein-coding genes, rRNA genes, and tRNA genes), and partitioned Bayesian analyses were conducted, with protein-coding genes being treated in 3 different manners (all positions included; third codon positions converted into purine [R] and pyrimidine [Y] [RY-coding]; third codon positions excluded). The resultant phylogenies strongly supported monophyly of the Cypriniformes as well as that of the families Cyprinidae, Catostomidae, and a clade comprising Balitoridae + Cobitidae, with the 2 latter loach families being reciprocally paraphyletic. Although all of the data sets yielded nearly identical tree topologies with regard to the shallower relationships, deeper relationships among the 4 major clades (the above 3 major clades plus Gyrinocheilidae, represented by a single species Gyrinocheilus aymonieri in this study), were incongruent depending on the data sets. Treatment of the rapidly saturated third codon-position transitions appeared to be a source of such incongruities, and we advocate that RY-coding, which takes only transversions into account, effectively removes this likely "noise" from the data set and avoids the apparent lack of signal by retaining all available positions in the data set.