Analysis of the generation of photon pairs in periodically poled lithium niobate

The process of spontaneous parametric down-conversion (SPDC) in nonlinear crystals makes it fairly easy to generate entangled photon states. It has been known for some time that the conversion efficiency can be improved by employing quasi-phase-matching in periodically poled crystals. Using two single-photon detectors, we have analyzed the photon pairs generated by SPDC in a periodically poled lithium niobate crystal pumped by a femtosecond laser. Several parameters could be varied in our setup, allowing us to obtain data in close agreement with both thermal and Poissonian photon-pair distributions.Comment: 4 pages, 4 figures, uses ws-procs10x7.cls; v2: Sign in equation (5) correcte

A New Test for the Absorption Mechanism of GPS Radio Sources Using Polarization Properties

We consider the use of polarization properties as a means to discriminate between Synchrotron Self-Absorption (SSA) and Free--Free Absorption (FFA) in GHz-Peaked Spectrum (GPS) sources. The polarization position angle (PA) of synchrotron radiation at high frequencies for the optically thin regime is perpendicular to the magnetic field, whereas it is parallel to the magnetic field at low frequencies for the optically thick regime. Therefore, SSA produces a change in PA of $90^{\circ}$ across the spectral peak, while FFA does not result in such a change. We analyzed polarization data from VLA observations for six GPS sources to see if such a change in PA was present. Our results indicate that there is no significant evidence for $90^{\circ}$ change in PA across the spectral peak, suggesting that FFA is more likely than SSA for low-frequency cutoffs in these sources

VLBI observations of the most radio-loud, narrow-line quasar SDSS J094857.3+002225

We observed the narrow-line quasar SDSS J094857.3+002225, which has the highest known radio loudness for a narrow-line Seyfert~1 galaxy (NLS1), at 1.7--15.4 GHz with the Very Long Baseline Array (VLBA). This is the first very-long-baseline interferometry (VLBI) investigation for a radio-loud NLS1. We independently found very high brightness temperatures from (1) its compactness in a VLBA image and (2) flux variation among the VLBA observation, our other observations with the VLBA, and the Very Large Array (VLA). A Doppler factor larger than 2.7--5.5 was required to meet an intrinsic limit of brightness temperature in the rest frame. This is evidence for highly relativistic nonthermal jets in an NLS1. We suggest that the Doppler factor is one of the most crucial parameters determining the radio loudness of NLS1s. The accretion disk of SDSS J094857.3+002225 is probably in the very high state, rather than the high/soft state, by analogy with X-ray binaries with strong radio outbursts and superluminal jets such as GRS 1915+105.Comment: 6 pages, 2 figures, accepted for publication in PAS

Very Long Baseline Array Imaging of Parsec-scale Radio Emissions in Nearby Radio-quiet Narrow-line Seyfert 1 Galaxies

We conducted Very Long Baseline Array (VLBA) observations of seven nearby narrow-line Seyfert 1 (NLS1) galaxies at 1.7 GHz (18cm) with milli-arcsecond resolution. This is the first systematic very long baseline interferometry (VLBI) study focusing on the central parsec-scale regions of radio-quiet NLS1s. Five of the seven were detected at a brightness temperature of >~5x10^6 K and contain radio cores with high brightness temperatures of >6x10^7 K, indicating a nonthermal process driven by jet-producing central engines as is observed in radio-loud NLS1s and other active galactic nucleus (AGN) classes. VLBA images of MRK 1239, MRK 705, and MRK 766 exhibit parsec-scale jets with clear linear structures. A large portion of the radio power comes from diffuse emission components that are distributed within the nuclear regions (<~300 pc), which is a common characteristic throughout the observed NLS1s. Jet kinetic powers limited by the Eddington limit may be insufficient to allow the jets escape to kiloparsec scales for these radio-quiet NLS1s with low-mass black holes of <~10^7 M_sun.Comment: 12 pages, 3 figures, 3 tables, accepted for publication in Ap

Time Variation of Rotation Measure Gradient in 3C 273 Jet

The existence of a gradient in the Faraday rotation measure (RM) of the quasar 3C 273 jet is confirmed by follow-up observations. A gradient transverse to the jet axis is seen for more than 20 mas in projected distance. Taking account of the viewing angle, we estimate it to be more than 100 pc. Comparing to the distribution of the RM in 1995, we detect a time variation of it at the same distance from the core over 7 yr. We discuss the origin of the Faraday rotation based on this rapid time variation. We rule out foreground media such as a narrow-line region, and suggest a helical magnetic field in the sheath region as the origin of this gradient of the RM.Comment: 12 pages, 4 figures, published in Ap

Time-resolved detection of light-induced conformational changes of heliorhodopsin

Heliorhodopsins (HeRs) are a new category of rhodopsins. They exist as a dimer and exhibit a characteristic inverted topology. HeRs bind all-trans-retinal as a chromophore in the dark, and its isomerization to the 13-cis form by light illumination leads to a photocyclic reaction involving several photo-intermediates: K, L, M, and O. In this study, the kinetics of conformational changes of HeR from Thermoplasmatales archaeon SG8-52-1 (TaHeR) were studied by the transient grating (TG) and circular dichroism (CD) methods. The TG method reveals that the diffusion coefficient (D) does not change until the O formation suggesting no significant conformation change at the surface of the protein during the early steps of the reaction. Subsequently, D decreases upon the O formation. Although two time constants (202 mu s and 2.6 ms) are observed for the conversion from the M to O by the absorption detection, D decreases only at the first step (202 mu s). Light-induced unfolding of helical structure is detected by the CD method. To examine the contribution of a characteristic helix in the intracellular loop 1 (ICL1 helix), Tyr93 on the ICL1 helix was replaced by Gly (Y93G), and the reaction of this mutant was also investigated. It was found that this replacement partially suppresses the D-change, although the CD-change is almost the same as that of the wild type. These results are interpreted in terms of different sensitivities of TG and CD methods, that is, D is sensitive to the structure of the solvent-exposed surface and selectively observes the conformational change in the ICL1 region. It is suggested that the structure of hydrophilic residues in the ICL1 helix is changed during this process

Statistical and Machine Learning Approaches to Predict Gene Regulatory Networks From Transcriptome Datasets

Statistical and machine learning (ML)-based methods have recently advanced in construction of gene regulatory network (GRNs) based on high-throughput biological datasets. GRNs underlie almost all cellular phenomena; hence, comprehensive GRN maps are essential tools to elucidate gene function, thereby facilitating the identification and prioritization of candidate genes for functional analysis. High-throughput gene expression datasets have yielded various statistical and ML-based algorithms to infer causal relationship between genes and decipher GRNs. This review summarizes the recent advancements in the computational inference of GRNs, based on large-scale transcriptome sequencing datasets of model plants and crops. We highlight strategies to select contextual genes for GRN inference, and statistical and ML-based methods for inferring GRNs based on transcriptome datasets from plants. Furthermore, we discuss the challenges and opportunities for the elucidation of GRNs based on large-scale datasets obtained from emerging transcriptomic applications, such as from population-scale, single-cell level, and life-course transcriptome analyses

Effect of Obstructive Jaundice and Nitric Oxide on the Profiles of Intestinal Bacterial Flora in Wild and iNOS−/− Mice

We previously reported that the plasma level of endotoxin and colonic expression of IgA in the mouse increased with obstructive jaundice induced by bile duct ligation (BDL). To elucidate the mechanism of the BDL-induced increase, we analyzed the effect of BDL on intestinal flora in wild type and inducible nitric oxide synthase (iNOS)-deficient mice (iNOS−/−) using the terminal restriction fragment length polymorphism analysis (T-RFLP) and 16S rDNA clone libraries. The amounts of bacterial DNA detected in fecal samples from both animal groups pretreated with antibiotics were extremely low as compared with untreated groups. We found that the profiles of enteric bacteria changed markedly after BDL. The bacterial composition is significantly different between not only wild type and iNOS−/− mice but also those before and after BDL, respectively. Among enteric bacteria examined, Lactobacillus murinus was found to increase markedly after BDL in rectum of both animal groups. However, Escherichia coli markedly increased after BDL in the iNOS−/− mice. These findings suggest that profiles of enteric flora change markedly in animals during obstructive jaundice by some mechanism that is affected by bile constituents and iNOS-derived NO