Group I aptazymes as genetic regulatory switches

BACKGROUND: Allosteric ribozymes (aptazymes) that have extraordinary activation parameters have been generated in vitro by design and selection. For example, hammerhead and ligase ribozymes that are activated by small organic effectors and protein effectors have been selected from random sequence pools appended to extant ribozymes. Many ribozymes, especially self-splicing introns, are known control gene regulation or viral replication in vivo. We attempted to generate Group I self-splicing introns that were activated by a small organic effector, theophylline, and to show that such Group I aptazymes could mediate theophylline-dependent splicing in vivo. RESULTS: By appending aptamers to the Group I self-splicing intron, we have generated a Group I aptazyme whose in vivo splicing is controlled by exogenously added small molecules. Substantial differences in gene regulation could be observed with compounds that differed by as little as a single methyl group. The effector-specificity of the Group I aptazyme could be rationally engineered for new effector molecules. CONCLUSION: Group I aptazymes may find applications as genetic regulatory switches for generating conditional knockouts at the level of mRNA or for developing economically viable gene therapies

Inertial and viscous flywheel sensing of nanoparticles

Rotational dynamics often challenge physical intuition while enabling unique realizations, from the rotor of a gyroscope that maintains its orientation regardless of the outer gimbals, to a tennis racket that rotates around its handle when tossed face-up in the air. In the context of inertial mass sensing, which can measure mass with atomic precision, rotational dynamics are normally considered a complication hindering measurement interpretation. Here, we exploit the rotational dynamics of a microfluidic device to develop a new modality in inertial resonant sensing. Combining theory with experiments, we show that this modality normally measures the volume of the particle while being insensitive to its density. Paradoxically, particle density only emerges when fluid viscosity becomes dominant over inertia. We explain this paradox via a viscosity-driven, hydrodynamic coupling between the fluid and the particle that activates the rotational inertia of the particle, converting it into a viscous flywheel. This modality now enables the simultaneous measurement of particle volume and mass in fluid, using a single, high-throughput measurement.Comment: 20 pages, 4 figures, 12 s. figures, 2 s. table

Spectral transitions in networks

We study the level spacing distribution p(s) in the spectrum of random networks. According to our numerical results, the shape of p(s) in the Erdos-Renyi (E-R) random graph is determined by the average degree , and p(s) undergoes a dramatic change when is varied around the critical point of the percolation transition, =1. When > 1, the p(s) is described by the statistics of the Gaussian Orthogonal Ensemble (GOE), one of the major statistical ensembles in Random Matrix Theory, whereas at =1 it follows the Poisson level spacing distribution. Closely above the critical point, p(s) can be described in terms of an intermediate distribution between Poisson and the GOE, the Brody-distribution. Furthermore, below the critical point p(s) can be given with the help of the regularised Gamma-function. Motivated by these results, we analyse the behaviour of p(s) in real networks such as the Internet, a word association network and a protein protein interaction network as well. When the giant component of these networks is destroyed in a node deletion process simulating the networks subjected to intentional attack, their level spacing distribution undergoes a similar transition to that of the E-R graph.Comment: 11 pages, 5 figure

Deep 1.1 mm-wavelength imaging of the GOODS-S field by AzTEC/ASTE - I. Source catalogue and number counts

[Abridged] We present the first results from a 1.1 mm confusion-limited map of the GOODS-S field taken with AzTEC on the ASTE telescope. We imaged a 270 sq. arcmin field to a 1\sigma depth of 0.48 - 0.73 mJy/beam, making this one of the deepest blank-field surveys at mm-wavelengths ever achieved. Although our GOODS-S map is extremely confused, we demonstrate that our source identification and number counts analyses are robust, and the techniques discussed in this paper are relevant for other deeply confused surveys. We find a total of 41 dusty starburst galaxies with S/N >= 3.5 within this uniformly covered region, where only two are expected to be false detections. We derive the 1.1mm number counts from this field using both a "P(d)" analysis and a semi-Bayesian technique, and find that both methods give consistent results. Our data are well-fit by a Schechter function model with (S', N(3mJy), \alpha) = (1.30+0.19 mJy, 160+27 (mJy/deg^2)^(-1), -2.0). Given the depth of this survey, we put the first tight constraints on the 1.1 mm number counts at S(1.1mm) = 0.5 mJy, and we find evidence that the faint-end of the number counts at S(850\mu m) < 2.0 mJy from various SCUBA surveys towards lensing clusters are biased high. In contrast to the 870 \mu m survey of this field with the LABOCA camera, we find no apparent under-density of sources compared to previous surveys at 1.1 mm. Additionally, we find a significant number of SMGs not identified in the LABOCA catalogue. We find that in contrast to observations at wavelengths < 500 \mu m, MIPS 24 \mu m sources do not resolve the total energy density in the cosmic infrared background at 1.1 mm, demonstrating that a population of z > 3 dust-obscured galaxies that are unaccounted for at these shorter wavelengths potentially contribute to a large fraction (~2/3) of the infrared background at 1.1 mm.Comment: 21 pages, 9 figures. Accepted to MNRAS

Submillimeter galaxies behind the Bullet Cluster (1E 0657-56)

Clusters of galaxies are effective gravitational lenses able to magnify background galaxies and making it possible to probe the fainter part of the galaxy population. Submillimeter galaxies, which are believed to be star-forming galaxies at typical redshifts of 2 to 3, are a major contaminant to the extended Sunyaev-Zeldovich (SZ) signal of galaxy clusters. For a proper quantification of the SZ signal the contribution of submillimeter galaxies needs to be quantified. The aims of this study are to identify submillimeter sources in the field of the Bullet Cluster (1E 0657-56), a massive cluster of galaxies at z~0.3, measure their flux densities at 870 micron, and search for counterparts at other wavelengths to constrain their properties. We carried out deep observations of the submillimeter continuum emission at 870 micron using the Large APEX BOlometer CAmera (LABOCA) on the Atacama Pathfinder EXperiment (APEX) telescope. Several numerical techniques were used to quantify the noise properties of the data and extract sources. In total, seventeen sources were found. Thirteen of them lie in the central 10 arcminutes of the map, which has a pixel sensitivity of 1.2 mJy per 22 arcsec beam. After correction for flux boosting and gravitational lensing, the number counts are consistent with published submm measurements. Nine of the sources have infrared counterparts in Spitzer maps. The strongest submm detection coincides with a source previously reported at other wavelengths, at an estimated redshift z~2.7. If the submm flux arises from two images of a galaxy magnified by a total factor of 75, as models have suggested, its intrinsic flux would be around 0.6 mJy, consistent with an intrinsic luminosity below 10^12 L_sun.Comment: Accepted by A&A, 15 pages, 11 figure

Substance Use Prevention Services in Juvenile Justice and Behavioral Health: Results from a National Survey

BACKGROUND: This study examined the national availability of substance use prevention (SUP) within juvenile justice (JJ) and their primary behavioral health (BH) providers, and the relationships between the availability of SUP and agency-level measures of organizational structure, staffing, and youth characteristics. A three-stage national probability sampling process was used to select participants for a national survey that included, among other facets of community supervision (CS) and BH practices, questions on agency characteristics, youth characteristics, whether the agency/provider directly provided SUP services, and whether the agency/provider directly provided substance use and/or mental health treatment. This paper focuses on SUP services along with agency/provider and youth characteristics related to providing SUP. RESULTS: The response rate for both CS agencies (n = 195) and BH providers (n = 271) was 96%. Complex samples logistic regression initially examined univariate associations of each variable and identified candidates for a final multivariate model. Overall, only one-third of CS and BH providers reported offering SUP services, with BH providers being significantly more likely than CS agencies to provide SUP services. In addition, likelihood of SUP was significantly lower among agencies where the substance use distribution of the caseload was below the median. Controlling for master\u27s level staff and the substance use distribution, CS agencies were about 67% less likely to offer SUP when compared to BH providers. CONCLUSIONS: Given the high rates of substance use among justice-involved youth and that substance use is an established risk for several negative behaviors, outcomes, and health conditions, these findings suggest that evidence-based prevention services should likely be expanded in justice settings, and perhaps included as part of CS programs, even when youth do not initially present with SU service needs

AzTEC Millimetre Survey of the COSMOS Field - II. Source Count Overdensity and Correlations with Large-Scale Structure

We report an over-density of bright sub-millimetre galaxies (SMGs) in the 0.15 sq. deg. AzTEC/COSMOS survey and a spatial correlation between the SMGs and the optical-IR galaxy density at z <~ 1.1. This portion of the COSMOS field shows a ~ 3-sigma over-density of robust SMG detections when compared to a background, or "blankfield", population model that is consistent with SMG surveys of fields with no extragalactic bias. The SMG over-density is most significant in the number of very bright detections (14 sources with measured fluxes S(1.1mm) > 6 mJy), which is entirely incompatible with sample variance within our adopted blank-field number densities and infers an over-density significance of >> 4. We find that the over-density and spatial correlation to optical-IR galaxy density are most consistent with lensing of a background SMG population by foreground mass structures along the line of sight, rather than physical association of the SMGs with the z <~ 1.1 galaxies/clusters. The SMG positions are only weakly correlated with weak-lensing maps, suggesting that the dominant sources of correlation are individual galaxies and the more tenuous structures in the region and not the massive and compact clusters. These results highlight the important roles cosmic variance and large-scale structure can play in the study of SMGs.Comment: 12 pages, 11 figures, 2 tables, accepted for publication in MNRA

Uncovering the overlapping community structure of complex networks in nature and society

Many complex systems in nature and society can be described in terms of networks capturing the intricate web of connections among the units they are made of. A key question is how to interpret the global organization of such networks as the coexistence of their structural subunits (communities) associated with more highly interconnected parts. Identifying these a priori unknown building blocks (such as functionally related proteins, industrial sectors and groups of people) is crucial to the understanding of the structural and functional properties of networks. The existing deterministic methods used for large networks find separated communities, whereas most of the actual networks are made of highly overlapping cohesive groups of nodes. Here we introduce an approach to analysing the main statistical features of the interwoven sets of overlapping communities that makes a step towards uncovering the modular structure of complex systems. After defining a set of new characteristic quantities for the statistics of communities, we apply an efficient technique for exploring overlapping communities on a large scale. We find that overlaps are significant, and the distributions we introduce reveal universal features of networks. Our studies of collaboration, word-association and protein interaction graphs show that the web of communities has non-trivial correlations and specific scaling properties.Comment: The free academic research software, CFinder, used for the publication is available at the website of the publication: http://angel.elte.hu/clusterin

Scaling and Formulary cross sections for ion-atom impact ionization

The values of ion-atom ionization cross sections are frequently needed for many applications that utilize the propagation of fast ions through matter. When experimental data and theoretical calculations are not available, approximate formulas are frequently used. This paper briefly summarizes the most important theoretical results and approaches to cross section calculations in order to place the discussion in historical perspective and offer a concise introduction to the topic. Based on experimental data and theoretical predictions, a new fit for ionization cross sections is proposed. The range of validity and accuracy of several frequently used approximations (classical trajectory, the Born approximation, and so forth) are discussed using, as examples, the ionization cross sections of hydrogen and helium atoms by various fully stripped ions.Comment: 46 pages, 8 figure

On the evolution of clustering of 24um-selected galaxies

This paper investigates the clustering properties of a complete sample of 1041 24um-selected sources brighter than F[24um]=400 uJy in the overlapping region between the SWIRE and UKIDSS UDS surveys. We have concentrated on the two (photometric) interval ranges z=[0.6-1.2] (low-z sample) and z>1.6 (high-z sample) as it is in these regions were we expect the mid-IR population to be dominated by intense dust-enshrouded activity such as star formation and black hole accretion. Investigations of the angular correlation function produce a correlation length are r0~15.9 Mpc for the high-z sample and r0~8.5 Mpc for the low-z one. Comparisons with physical models reveal that the high-z sources are exclusively associated with very massive (M>~10^{13} M_sun)haloes, comparable to those which locally host groups-to-clusters of galaxies, and are very common within such (rare) structures. Conversely, lower-z galaxies are found to reside in smaller halos (M_min~10^{12} M_sun) and to be very rare in such systems. While recent studies have determined a strong evolution of the 24um luminosity function between z~2 and z~0, they cannot provide information on the physical nature of such an evolution. Our clustering results instead indicate that this is due to the presence of different populations of objects inhabiting different structures, as active systems at z<~1.5 are found to be exclusively associated with low-mass galaxies, while very massive sources appear to have concluded their active phase before this epoch. Finally, we note that the small-scale clustering data seem to require steep profiles for the distribution of galaxies within their halos. This is suggestive of close encounters and/or mergers which could strongly favour both AGN and star-formation activity.Comment: 13 pages, 8 figures, to appear in MNRA