A Tale of Two Narrow-Line Regions: Ionization, Kinematics, and Spectral Energy Distributions for a Local Pair of Merging Obscured Active Galaxies

We explore the gas ionization and kinematics, as well as the optical--IR spectral energy distributions for UGC 11185, a nearby pair of merging galaxies hosting obscured active galactic nuclei (AGNs), also known as SDSS J181611.72+423941.6 and J181609.37+423923.0 (J1816NE and J1816SW, $z \approx 0.04$). Due to the wide separation between these interacting galaxies ($\sim 23$ kpc), observations of these objects provide a rare glimpse of the concurrent growth of supermassive black holes at an early merger stage. We use BPT line diagnostics to show that the full extent of the narrow line emission in both galaxies is photoionized by an AGN and confirm the existence of a 10-kpc-scale ionization cone in J1816NE, while in J1816SW the AGN narrow-line region is much more compact (1--2 kpc) and relatively undisturbed. Our observations also reveal the presence of ionized gas that nearly spans the entire distance between the galaxies which is likely in a merger-induced tidal stream. In addition, we carry out a spectral analysis of the X-ray emission using data from {\em XMM-Newton}. These galaxies represent a useful pair to explore how the [\ion{O}{3}] luminosity of an AGN is dependent on the size of the region used to explore the extended emission. Given the growing evidence for AGN "flickering" over short timescales, we speculate that the appearances and impact of these AGNs may change multiple times over the course of the galaxy merger, which is especially important given that these objects are likely the progenitors of the types of systems commonly classified as "dual AGNs."Comment: 15 pages, 10 figures, accepted by the Astrophysical Journa

Investigation of the chemocatalytic and biocatalytic valorization of a range of different lignin preparations: The importance of β-O-4 content

A set of seven different lignin preparations was generated from a range of organosolv (acidic, alkaline, ammonia-treated, and dioxane-based), ionic liquid, autohydrolysis, and Kraft pretreatments of lignocelluloses. Each lignin was characterized by 2D HSQC NMR spectroscopy, showing significant variability in the β-O-4 content of the different lignin samples. Each lignin was then valorised using three biocatalytic methods (microbial biotransformation with Rhodococcus jostii RHA045, treatment with Pseudomonas fluorescens Dyp1B or Sphingobacterium sp. T2 manganese superoxide dismutase) and two chemocatalytic methods (catalytic hydrogenation using Pt/alumina catalyst, DDQ benzylic oxidation/Zn reduction). Highest product yields for DDQ/Zn valorization were observed from poplar ammonia percolation-organosolv lignin, which had the highest β-O-4 content of the investigated lignins and also gave the highest yield of syringaldehyde (243 mg L -1 ) when using R. jostii RHA045 and the most enzymatic products using P. fluorescens Dyp1B. The highest product yield from the Pt/alumina hydrogenation was observed using oak dioxasolv lignin, which also had a high β-O-4 content. In general, highest product yields for both chemocatalytic and biocatalytic valorization methods were obtained from preparations that showed highest β-O-4 content, while variable yields were obtained with preparations containing intermediate β-O-4 content, and little or no product was obtained with preparations containing low β-O-4 content

A Tale of Two Narrow-Line Regions: Ionization, Kinematics, and Spectral Energy Distributions for a Local Pair of Merging Obscured Active Galaxies

We explore the gas ionization and kinematics, as well as the optical-IR spectral energy distributions for UGC 11185, a nearby pair of merging galaxies hosting obscured active galactic nuclei (AGNs), also known as SDSS J181611.72+423941.6 and J181609.37+423923.0 (J1816NE and J1816SW, z ≈ 0.04). Due to the wide separation between these interacting galaxies (~23 kpc), observations of these objects provide a rare glimpse of the concurrent growth of supermassive black holes at an early merger stage. We use BPT line diagnostics to show that the full extent of the narrow-line emission in both galaxies is photoionized by an AGN, and confirm the existence of a 10 kpc-scale ionization cone in J1816NE, while in J1816SW the AGN narrow-line region is much more compact (1–2 kpc) and relatively undisturbed. Our observations also reveal the presence of ionized gas that nearly spans the entire distance between the galaxies, which is likely in a merger-induced tidal stream. In addition, we carry out a spectral analysis of the X-ray emission using data from XMM-Newton. These galaxies represent a useful pair to explore how the [O iii] luminosity of an AGN is dependent on the size of the region used to explore the extended emission. Given the growing evidence for AGN flickering over short timescales, we speculate that the appearances and impacts of these AGNs may change multiple times over the course of the galaxy merger, which is especially important given that these objects are likely the progenitors of the types of systems commonly classified as dual AGNs

Helical Single-Lamellar Crystals Thermotropically Formed in a Synthetic Nonracemic Chiral Main-Chain Polyester

Phase structures and transformation mechanisms of nonracemic chiral biological and synthetic polymers are fundamentally important topics in understanding their macroscopic responses in different environments. It has been known for many years that helical structures and morphologies can exist in low-ordered chiral liquid crystalline (LC) phases. However, when the chiral liquid crystals form highly ordered smectic liquid crystal phases, the helical morphology is suppressed due to the crystallization process. A double-twisted morphology has been observed in many liquid crystalline biopolymers such as dinoflaggellate chromosomes (in Prorocentrum micans) in an in vivo arrangement. Helical crystals grown from solution have been reported in the case of Bombyx mori silk fibroin crystals having the beta modification. This study describes a synthetic nonracemic chiral main-chain LC polyester that is able to thermotropically form helical single lamellar crystals. Flat single lamellar crystals can also be observed under the same crystallization condition. Moreover, flat and helical lamellae can coexist in one single lamellar crystal, within which one form can smoothly transform to the other. Both of these crystals possess the same structure, although translational symmetry is broken in the helical crystals. The polymer chain folding direction in both flat and helical lamellar crystals is determined to be identical, and it is always along the long axis of the lamellae. This finding provides an opportunity to study the chirality effect on phase structure, morphology, and transformation in condensed states of chiral materials. [S0163-1829(99)01042-5]

Soft Tissue Tumors Characterized by a Wide Spectrum of Kinase Fusions Share a Lipofibromatosis-like Neural Tumor Pattern

Gene fusions resulting in oncogenic activation of various receptor tyrosine kinases, including NTRK1-3, ALK, and RET, have been increasingly recognized in soft tissue tumors (STTs), displaying a wide morphologic spectrum and therefore diagnostically challenging. A subset of STT with NTRK1 rearrangements were recently defined as lipofibromatosis-like neural tumors (LPFNTs), being characterized by mildly atypical spindle cells with a highly infiltrative growth in the subcutis and expression of S100 and CD34 immunostains. Other emerging morphologic phenotypes associated with kinase fusions include infantile/adult fibrosarcoma and malignant peripheral nerve sheath tumor-like patterns. In this study, a large cohort of 73 STT positive for various kinase fusions, including 44 previously published cases, was investigated for the presence of an LPFNT phenotype, to better define the incidence of this distinctive morphologic pattern and its relationship with various gene fusions. Surprisingly, half (36/73) of STT with kinase fusions showed at least a focal LPFNT component defined as >10%. Most of the tumors occurred in the subcutaneous tissues of the extremities (n = 25) and trunk (n = 9) of children or young adults (<30 years old) of both genders. Two-thirds (24/36) of these cases showed hybrid morphologies with alternating LPFNT and solid areas of monomorphic spindle to ovoid tumor cells with fascicular or haphazard arrangement, while one-third (12/36) had pure LPFNT morphology. Other common histologic findings included lymphocytic infiltrates, staghorn-like vessels, and perivascular or stromal hyalinization, especially in hybrid cases. Mitotic activity was generally low (<4/10 high power fields in 81% cases), being increased only in a minority of cases. Immunoreactivity for CD34 (92% in hybrid cases, 89% in pure cases) and S100 (89% in hybrid cases, 64% in pure cases) were commonly present. The gene rearrangements most commonly involved NTRK1 (75%), followed by RET (8%) and less commonly NTRK2, NTRK3, ROS1, ALK, and MET

Bar Evolution Over the Last Eight Billion Years: A Constant Fraction of Strong Bars in GEMS

One third of present-day spirals host optically visible strong bars that drive their dynamical evolution. However, the fundamental question of how bars evolve over cosmological times has yet to be addressed, and even the frequency of bars at intermediate redshifts remains controversial. We investigate the frequency of bars out to z~1.0 drawing on a sample of 1590 galaxies from the GEMS survey, which provides morphologies from HST ACS two-color images, and highly accurate redshifts from the COMBO-17 survey. We identify spiral galaxies using the Sersic index, concentration parameter, and rest-frame color. We characterize bars and disks by fitting ellipses to F606W and F850LP images, taking advantage of the two bands to minimize bandpass shifting. We exclude highly inclined (i>60 deg) galaxies to ensure reliable morphological classifications, and apply completeness cuts of M_v <= -19.3 and -20.6. More than 40% of the bars that we detect have semi major axes a<0.5" and would be easily missed in earlier surveys without the small PSF of ACS. The bars that we can reliably detect are fairly strong (with ellipticities e>=0.4) and have a in the range ~1.2-13 kpc. We find that the optical fraction of such strong bars remains at ~(30% +- 6%) from the present-day out to look-back times of 2-6 Gyr (z~0.2-0.7) and 6-8 Gyr (z~0.7-1.0); it certainly shows no sign of a drastic decline at z>0.7. Our findings of a large and similar bar fraction at these three epochs favor scenarios in which cold gravitationally unstable disks are already in place by z~1, and where on average bars have a long lifetime (well above 2 Gyr). The distributions of structural bar properties in the two slices are, however, not statistically identical and therefore allow for the possibility that the bar strengths and sizes may evolve over time.Comment: Accepted by ApJ Letters, to appear in Nov 2004 issue. Minor revisions,updated reference

L-Edge Spectroscopy of Dilute, Radiation-Sensitive Systems Using a Transition-Edge-Sensor Array

We present X-ray absorption spectroscopy and resonant inelastic X-ray scattering (RIXS) measurements on the iron L-edge of 0.5 mM aqueous ferricyanide. These measurements demonstrate the ability of high-throughput transition-edge-sensor (TES) spectrometers to access the rich soft X-ray (100-2000eV) spectroscopy regime for dilute and radiation-sensitive samples. Our low-concentration data are in agreement with high-concentration measurements recorded by conventional grating-based spectrometers. These results show that soft X-ray RIXS spectroscopy acquired by high-throughput TES spectrometers can be used to study the local electronic structure of dilute metal-centered complexes relevant to biology, chemistry and catalysis. In particular, TES spectrometers have a unique ability to characterize frozen solutions of radiation- and temperature-sensitive samples.Comment: 19 pages, 4 figure

Double Twist in Helical Polymer Soft Crystals

In natural and synthetic materials having non-racemic chiral centers, chirality and structural ordering each play a distinct role in the formation of ordered states. Configurational chirality can be extended to morphological chirality when the phase, structures possess low liquid crystalline order. In the crystalline states the crystallization process suppresses the chiral helical morphology due to strong ordering interactions, In this Letter, we report the first observation of helical single lamellar crystals of synthetic non-racemic chiral polymers. Experimental evidence shows that the molecular chains twist along both the long and short axes of the helical lamellar crystals, which is the first time a double-twist molecular orientation in a helical crystal has been observed

Undifferentiated round cell sarcoma with BCOR internal tandem duplications (ITD) or YWHAE fusions:a clinicopathologic and molecular study

Until recently, undifferentiated round cell sarcomas (URCS) in infants have been considered a wastebasket diagnosis, composed of various pathologic entities and lacking consistent genetic alterations. The recent identification of recurrent BCOR internal tandem duplications (ITD) and less common alternative YWHAE\u2013NUTM2B/E fusions in half of infantile URCS and the majority of so-called primitive myxoid mesenchymal tumors of infancy (PMMTI) suggests a common pathogenesis with clear cell sarcoma of the kidney which also harbors the same genetic alterations. These tumors also share a similar morphology and immunoprofile, including positivity for BCOR, cyclin D1, and SATB2. In this study, we investigate the largest cohort to date of genetically confirmed URCS and PMMTI with BCOR ITD or YWHAE fusions to better define their morphologic spectrum and clinical behavior. Twenty-eight cases harbored BCOR ITD and five YWHAE fusions, occurring in 29 infants and 4 children, 19 males and 14 females. Microscopically, 20 were classified as URCS and 13 as PMMTI. Follow-up was available in 25 patients, with 14 (56%) succumbing to their diseases at a mean duration of 18-months follow-up (range: 2\u201362). Six patients remained with no evidence of disease at a mean follow-up of 63 months (range: 4\u2013192), four patients were still alive with disease (mean follow-up: 46 months, range: 4\u2013120), and one died of other causes. Local recurrence and distant metastasis were each observed in 11/25 (44%) of the patients. The overall survival was 42% at 3 years and 34% at 5 years (median survival: 26 months). There was no statistically significant survival difference between cases diagnosed as URCS and PMMTI and between those with BCOR ITD and YWHAE fusions

SOX17 Enhancer Variants Disrupt Transcription Factor Binding And Enhancer Inactivity Drives Pulmonary Hypertension

BACKGROUND: Pulmonary arterial hypertension (PAH) is a rare disease characterized by remodeling of the pulmonary arteries, increased vascular resistance, and right-sided heart failure. Genome-wide association studies of idiopathic/heritable PAH established novel genetic risk variants, including conserved enhancers upstream of transcription factor (TF) SOX17 containing 2 independent signals. SOX17 is an important TF in embryonic development and in the homeostasis of pulmonary artery endothelial cells (hPAEC) in the adult. Rare pathogenic mutations in SOX17 cause heritable PAH. We hypothesized that PAH risk alleles in an enhancer region impair TF-binding upstream of SOX17, which in turn reduces SOX17 expression and contributes to disturbed endothelial cell function and PAH development. METHODS: CRISPR manipulation and siRNA were used to modulate SOX17 expression. Electromobility shift assays were used to confirm in silico–predicted TF differential binding to the SOX17 variants. Functional assays in hPAECs were used to establish the biological consequences of SOX17 loss. In silico analysis with the connectivity map was used to predict compounds that rescue disturbed SOX17 signaling. Mice with deletion of the SOX17 signal 1 enhancer region (SOX17-4593/enhKO) were phenotyped in response to chronic hypoxia and SU5416/hypoxia. RESULTS: CRISPR inhibition of SOX17-signal 2 and deletion of SOX17signal 1 specifically decreased SOX17 expression. Electromobility shift assays demonstrated differential binding of hPAEC nuclear proteins to the risk and nonrisk alleles from both SOX17 signals. Candidate TFs HOXA5 and ROR-α were identified through in silico analysis and antibody electromobility shift assays. Analysis of the hPAEC transcriptomes revealed alteration of PAH-relevant pathways on SOX17 silencing, including extracellular matrix regulation. SOX17 silencing in hPAECs resulted in increased apoptosis, proliferation, and disturbance of barrier function. With the use of the connectivity map, compounds were identified that reversed the SOX17-dysfunction transcriptomic signatures in hPAECs. SOX17 enhancer knockout in mice reduced lung SOX17 expression, resulting in more severe pulmonary vascular leak and hypoxia or SU5416/hypoxia-induced pulmonary hypertension. CONCLUSIONS: Common PAH risk variants upstream of the SOX17 promoter reduce endothelial SOX17 expression, at least in part, through differential binding of HOXA5 and ROR-α. Reduced SOX17 expression results in disturbed hPAEC function and PAH. Existing drug compounds can reverse the disturbed SOX17 pulmonary endothelial transcriptomic signature