Mid-Infrared Spectra of Classical AGN Observed with the Spitzer Space Telescope

Full low resolution (65<R<130) and high resolution (R~600) spectra between 5 microns and 37 microns obtained with the Infrared Spectrograph (IRS) on the Spitzer Space Telescope are presented for eight classical active galactic nuclei (AGN) which have been extensively studied previously. Spectra of these AGN are presented as comparison standards for the many objects, including sources at high redshift, which are being observed spectroscopically in the mid-infrared for the first time using the IRS. The AGN are NGC4151, Markarian 3, I Zwicky 1, NGC 1275, Centaurus A, NGC 7469, Markarian 231, and NGC 3079. These sources are used to demonstrate the range of infrared spectra encountered in objects which have widely different classification criteria at other wavelengths but which unquestionably contain AGN. Overall spectral characteristics - including continuum shape, nebular emission lines, silicate absorption and emission features, and PAH emission features - are considered to understand how spectral classifications based on mid-infrared spectra relate to those previously derived from optical spectra. The AGN are also compared to the same parameters for starburst galaxies such as NGC 7714 and the compact, low metallicity starburst SBS 0335-052 previously observed with the IRS. Results confirm the much lower strengths of PAH emission features in AGN, but there are no spectral parameters in this sample which unambiguously distinguish AGN and starbursts based only on the slopes of the continuous spectra.Comment: Accepted by Ap

Quantum Hall effect in InAsSb quantum wells at elevated temperatures

We have characterized the electronic properties of a high-mobility two-dimensional electron system in modulation doped InAsSb quantum wells and compare them to InSb quantum wells grown in a similar fashion. Using temperature-dependent Shubnikov-de Haas experiments as well as FIR transmission we find an effective mass of $m^{\ast} \approx$ 0.022$m_{e}$, which is lower than in the investigated InSb quantum well, but due to a rather strong confinement still higher than in the corresponding bulk compound. The effective $g$-factor was determined to be $g^{\ast} \approx$ 21.9. These results are also corroborated by $k \cdot p$ band structure calculations. When spin polarizing the electrons in a tilted magnetic field, the $g$-factor is significantly enhanced by electron-electron interactions, reaching a value as large as $g^{\ast}$ = 60 at a spin polarization P = 0.75. Finally, we show that due to the low effective mass the quantum Hall effect in our particular sample can be observed up to a temperature of 60 K and we propose scenarios how to increase this temperature even further.Comment: 12 pages, 15 figure

Spitzer IRS Spectra of Optically Faint Infrared Sources with Weak Spectral Features

Spectra have been obtained with the low-resolution modules of the Infrared Spectrograph (IRS) on the Spitzer Space Telescope (Spitzer) for 58 sources having f$_{\nu}$(24 micron) > 0.75 mJy. Sources were chosen from a survey of 8.2 deg$^{2}$ within the NOAO Deep Wide-Field Survey region in Bootes (NDWFS) using the Multiband Imaging Photometer (MIPS) on the Spitzer Space Telescope. Most sources are optically very faint (I > 24mag). Redshifts have previously been determined for 34 sources, based primarily on the presence of a deep 9.7 micron silicate absorption feature, with a median z of 2.2. Spectra are presented for the remaining 24 sources for which we were previously unable to determine a confident redshift because the IRS spectra show no strong features. Optical photometry from the NDWFS and infrared photometry with MIPS and the Infrared Array Camera on the Spitzer Space Telescope (IRAC) are given, with K photometry from the Keck I telescope for some objects. The sources without strong spectral features have overall spectral energy distributions (SEDs) and distributions among optical and infrared fluxes which are similar to those for the sources with strong absorption features. Nine of the 24 sources are found to have feasible redshift determinations based on fits of a weak silicate absorption feature. Results confirm that the "1 mJy" population of 24 micron Spitzer sources which are optically faint is dominated by dusty sources with spectroscopic indicators of an obscured AGN rather than a starburst. There remain 14 of the 58 sources observed in Bootes for which no redshift could be estimated, and 5 of these sources are invisible at all optical wavelengths.Comment: Accepted by Ap

Maximum Flux Transition Paths of Conformational Change

Given two metastable states A and B of a biomolecular system, the problem is to calculate the likely paths of the transition from A to B. Such a calculation is more informative and more manageable if done for a reduced set of collective variables chosen so that paths cluster in collective variable space. The computational task becomes that of computing the "center" of such a cluster. A good way to define the center employs the concept of a committor, whose value at a point in collective variable space is the probability that a trajectory at that point will reach B before A. The committor "foliates" the transition region into a set of isocommittors. The maximum flux transition path is defined as a path that crosses each isocommittor at a point which (locally) has the highest crossing rate of distinct reactive trajectories. (This path is different from that of the MaxFlux method of Huo and Straub.) It is argued that such a path is nearer to an ideal path than others that have been proposed with the possible exception of the finite-temperature string method path. To make the calculation tractable, three approximations are introduced, yielding a path that is the solution of a nonsingular two-point boundary-value problem. For such a problem, one can construct a simple and robust algorithm. One such algorithm and its performance is discussed.Comment: 7 figure

A particle swarm optimization-based algorithm for finding gapped motifs

<p>Abstract</p> <p>Background</p> <p>Identifying approximately repeated patterns, or motifs, in DNA sequences from a set of co-regulated genes is an important step towards deciphering the complex gene regulatory networks and understanding gene functions.</p> <p>Results</p> <p>In this work, we develop a novel motif finding algorithm (PSO+) using a population-based stochastic optimization technique called Particle Swarm Optimization (PSO), which has been shown to be effective in optimizing difficult multidimensional problems in continuous domains. We propose a modification of the standard PSO algorithm to handle discrete values, such as characters in DNA sequences. The algorithm provides several features. First, we use both consensus and position-specific weight matrix representations in our algorithm, taking advantage of the efficiency of the former and the accuracy of the latter. Furthermore, many real motifs contain gaps, but the existing methods usually ignore them or assume a user know their exact locations and lengths, which is usually impractical for real applications. In comparison, our method models gaps explicitly, and provides an easy solution to find gapped motifs without any detailed knowledge of gaps. Our method allows the presence of input sequences containing zero or multiple binding sites.</p> <p>Conclusion</p> <p>Experimental results on synthetic challenge problems as well as real biological sequences show that our method is both more efficient and more accurate than several existing algorithms, especially when gaps are present in the motifs.</p

Efficacy of different types of cognitive enhancers for patients with schizophrenia. A meta-analysis

Cognitive impairment is a core feature of schizophrenia, which is predictive for functional outcomes and is, therefore, a treatment target in itself. Yet, literature on efficacy of different pharmaco-therapeutic options is inconsistent. This quantitative review provides an overview of studies that investigated potential cognitive enhancers in schizophrenia. We included pharmacological agents, which target different neurotransmitter systems and evaluated their efficacy on overall cognitive functioning and seven separate cognitive domains. In total, 93 studies with 5630 patients were included. Cognitive enhancers, when combined across all different neurotransmitter systems, which act on a large number of different mechanisms, showed a significant (yet small) positive effect size of 0.10 (k = 51, p = 0.023; 95% CI = 0.01 to 0.18) on overall cognition. Cognitive enhancers were not superior to placebo for separate cognitive domains. When analyzing each neurotransmitter system separately, agents acting predominantly on the glutamatergic system showed a small significant effect on overall cognition (k = 29, Hedges’ g = 0.19, p = 0.01), as well as on working memory (k = 20, Hedges’ g = 0.13, p = 0.04). A sub-analysis of cholinesterase inhibitors (ChEI) showed a small effect on working memory (k = 6, Hedges’ g = 0.26, p = 0.03). Other sub-analyses were positively nonsignificant, which may partly be due to the low number of studies we could include per neurotransmitter system. Overall, this meta-analysis showed few favorable effects of cognitive enhancers for patients with schizophrenia, partly due to lack of power. There is a lack of studies involving agents acting on other than glutamatergic and cholinergic systems, especially of those targeting the dopaminergic system

Timed inhibition of CDC7 increases CRISPR-Cas9 mediated templated repair.

Repair of double strand DNA breaks (DSBs) can result in gene disruption or gene modification via homology directed repair (HDR) from donor DNA. Altering cellular responses to DSBs may rebalance editing outcomes towards HDR and away from other repair outcomes. Here, we utilize a pooled CRISPR screen to define host cell involvement in HDR between a Cas9 DSB and a plasmid double stranded donor DNA (dsDonor). We find that the Fanconi Anemia (FA) pathway is required for dsDonor HDR and that other genes act to repress HDR. Small molecule inhibition of one of these repressors, CDC7, by XL413 and other inhibitors increases the efficiency of HDR by up to 3.5 fold in many contexts, including primary T cells. XL413 stimulates HDR during a reversible slowing of S-phase that is unexplored for Cas9-induced HDR. We anticipate that XL413 and other such rationally developed inhibitors will be useful tools for gene modification

Gene Expression Profiles Distinguish the Carcinogenic Effects of Aristolochic Acid in Target (Kidney) and Non-target (Liver) Tissues in Rats

BACKGROUND: Aristolochic acid (AA) is the active component of herbal drugs derived from Aristolochia species that have been used for medicinal purposes since antiquity. AA, however, induced nephropathy and urothelial cancer in people and malignant tumors in the kidney and urinary tract of rodents. Although AA is bioactivated in both kidney and liver, it only induces tumors in kidney. To evaluate whether microarray analysis can be used for distinguishing the tissue-specific carcinogenicity of AA, we examined gene expression profiles in kidney and liver of rats treated with carcinogenic doses of AA. RESULTS: Microarray analysis was performed using the Rat Genome Survey Microarray and data analysis was carried out within ArrayTrack software. Principal components analysis and hierarchical cluster analysis of the expression profiles showed that samples were grouped together according to the tissues and treatments. The gene expression profiles were significantly altered by AA treatment in both kidney and liver (p < 0.01; fold change > 1.5). Functional analysis with Ingenuity Pathways Analysis showed that there were many more significantly altered genes involved in cancer-related pathways in kidney than in liver. Also, analysis with Gene Ontology for Functional Analysis (GOFFA) software indicated that the biological processes related to defense response, apoptosis and immune response were significantly altered by AA exposure in kidney, but not in liver. CONCLUSION: Our results suggest that microarray analysis is a useful tool for detecting AA exposure; that analysis of the gene expression profiles can define the differential responses to toxicity and carcinogenicity of AA from kidney and liver; and that significant alteration of genes associated with defense response, apoptosis and immune response in kidney, but not in liver, may be responsible for the tissue-specific toxicity and carcinogenicity of AA

Angular dependence of resistivity in the superconducting state of NdFeAsO0.82_{0.82}F0.18_{0.18} single crystals

We report the results of angle dependent resistivity of NdFeAsO$_{0.82}$F$_{0.18}$ single crystals in the superconducting state. By doing the scaling of resistivity within the frame of the anisotropic Ginzburg-Landau theory, it is found that the angle dependent resistivity measured under different magnetic fields at a certain temperature can be collapsed onto one curve. As a scaling parameter, the anisotropy $\Gamma$ can be determined for different temperatures. It is found that $\Gamma(T)$ increases slowly with decreasing temperature, varying from $\Gamma \simeq$ 5.48 at T=50 K to $\Gamma \simeq$ 6.24 at T=44 K. This temperature dependence can be understood within the picture of multi-band superconductivity.Comment: 7 pages, 4 figure

Clinical disorders affecting mesopic vision

Vision in the mesopic range is affected by a number of inherited and acquired clinical disorders. We review these conditions and summarize the historical background, describing the clinical characteristics alongside the genetic basis and molecular biological mechanisms giving rise to rod and cone dysfunction relevant to twilight vision. The current diagnostic gold standards for each disease are discussed and curative and symptomatic treatment strategies are summarized