A Very Large Array Search for 5 GHz Radio Transients and Variables at Low Galactic Latitudes

We present the results of a 5 GHz survey with the Very Large Array (VLA) and the expanded VLA, designed to search for short-lived (≾1 day) transients and to characterize the variability of radio sources at milli-Jansky levels. A total sky area of 2.66 deg^2, spread over 141 fields at low Galactic latitudes (b≅6-8 deg), was observed 16 times with a cadence that was chosen to sample timescales of days, months, and years. Most of the data were reduced, analyzed, and searched for transients in near real-time. Interesting candidates were followed up using visible light telescopes (typical delays of 1-2 hr) and the X-ray Telescope on board the Swift satellite. The final processing of the data revealed a single possible transient with a peak flux density of f_ν≅2.4 mJy. This implies a transient's sky surface density of κ(f_ν > 1.8 mJy) = 0.039^(+0.13 +0.18)_(–0.032,–0.038) deg^(–2) (1σ, 2σ confidence errors). This areal density is roughly consistent with the sky surface density of transients from the Bower et al. survey extrapolated to 1.8 mJy. Our observed transient areal density is consistent with a neutron star's origin for these events. Furthermore, we use the data to measure the source variability on timescales of days to years, and we present the variability structure function of 5 GHz sources. The mean structure function shows a fast increase on ≈1 day timescale, followed by a slower increase on timescales of up to 10 days. On timescales between 10 and 60 days, the structure function is roughly constant. We find that ≳30% of the unresolved sources brighter than 1.8 mJy are variables at the >4σ confidence level, presumably mainly due to refractive scintillation

A suffix tree or not a suffix tree?

In this paper we study the structure of suffix trees. Given an unlabeled tree τ on n nodes and suffix links of its internal nodes, we ask the question ”Is τ a suffix tree?”, i.e., is there a string S whose suffix tree has the same topological structure as τ? We place no restrictions on S, in particular we do not require that S ends with a unique symbol. This corresponds to considering the more general definition of implicit or extended suffix trees. Such general suffix trees have many applications and are for example needed to allow efficient updates when suffix trees are built online. Deciding if τ is a suffix tree is not an easy task, because, with no restrictions on the final symbol, we cannot guess the length of a string that realizes τ from the number of leaves. And without an upper bound on the length of such a string, it is not even clear how to solve the problem by an exhaustive search. In this paper, we prove that τ is a suffix tree if and only if it is realized by a string S of length n−1, and we give a linear-time algorithm for inferring S when the first letter on each edge is known. This generalizes the work of I et al. [Discrete Appl. Math. 163, 2014]

A nonlinear dynamic model of DNA with a sequence-dependent stacking term

No simple model exists that accurately describes the melting behavior and breathing dynamics of double-stranded DNA as a function of nucleotide sequence. This is especially true for homogenous and periodic DNA sequences, which exhibit large deviations in melting temperature from predictions made by additive thermodynamic contributions. Currently, no method exists for analysis of the DNA breathing dynamics of repeats and of highly G/C- or A/T-rich regions, even though such sequences are widespread in vertebrate genomes. Here, we extend the nonlinear Peyrard–Bishop–Dauxois (PBD) model of DNA to include a sequence-dependent stacking term, resulting in a model that can accurately describe the melting behavior of homogenous and periodic sequences. We collect melting data for several DNA oligos, and apply Monte Carlo simulations to establish force constants for the 10 dinucleotide steps (CG, CA, GC, AT, AG, AA, AC, TA, GG, TC). The experiments and numerical simulations confirm that the GG/CC dinucleotide stacking is remarkably unstable, compared with the stacking in GC/CG and CG/GC dinucleotide steps. The extended PBD model will facilitate thermodynamic and dynamic simulations of important genomic regions such as CpG islands and disease-related repeats

Long duration radio transients lacking optical counterparts are possibly Galactic Neutron Stars

(abridged) Recently, a new class of radio transients in the 5-GHz band was detected by Bower et al. We present new deep near-Infrared (IR) observations of the field containing these transients, and find no counterparts down to a limiting magnitude of K=20.4 mag. We argue that the bright (>1 Jy) radio transients recently reported by Kida et al. are consistent with being additional examples of the Bower et al. transients. We refer to these groups of events as "long-duration radio transients". The main characteristics of this population are: time scales longer than 30 minute but shorter than several days; rate, ~10^3 deg^-2 yr^-1; progenitors sky surface density of >60 deg^-2 (95% C.L.) at Galactic latitude ~40 deg; 1.4-5 GHz spectral slopes, f_\nu ~ \nu^alpha, with alpha>0; and most notably the lack of any counterparts in quiescence in any wavelength. We rule out an association with many types of objects. Galactic brown-dwarfs or some sort of exotic explosions remain plausible options. We argue that an attractive progenitor candidate for these radio transients is the class of Galactic isolated old neutron stars (NS). We confront this hypothesis with Monte-Carlo simulations of the space distribution of old NSs, and find satisfactory agreement for the large areal density. Furthermore, the lack of quiescent counterparts is explained quite naturally. In this framework we find: the mean distance to events in the Bower et al. sample is of order kpc; the typical distance to the Kida et al. transients are constrained to be between 30 pc and 900 pc (95% C.L.); these events should repeat with a time scale of order several months; and sub-mJy level bursts should exhibit Galactic latitude dependence. We discuss possible mechanisms giving rise to the observed radio emission.Comment: Submitted to ApJ, 17 pages, 10 figure

Single Molecule Statistics and the Polynucleotide Unzipping Transition

We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force value of order 10 pN, with different critical behavior for homopolymers and for random heteropolymers. We extend results on the disorder-averaged behavior of DNA's with random sequences to the more experimentally accessible problem of unzipping a single DNA molecule. As the applied force approaches the critical value, the double-stranded DNA unravels in a series of discrete, sequence-dependent steps that allow it to reach successively deeper energy minima. Plots of extension versus force thus take the striking form of a series of plateaus separated by sharp jumps. Similar qualitative features should reappear in micromanipulation experiments on proteins and on folded RNA molecules. Despite their unusual form, the extension versus force curves for single molecules still reveal remnants of the disorder-averaged critical behavior. Above the transition, the dynamics of the unzipping fork is related to that of a particle diffusing in a random force field; anomalous, disorder-dominated behavior is expected until the applied force exceeds the critical value for unzipping by roughly 5 pN.Comment: 40 pages, 18 figure

The Apache Point Observatory Galactic Evolution Experiment (APOGEE) Spectrographs

We describe the design and performance of the near-infrared (1.51--1.70 micron), fiber-fed, multi-object (300 fibers), high resolution (R = lambda/delta lambda ~ 22,500) spectrograph built for the Apache Point Observatory Galactic Evolution Experiment (APOGEE). APOGEE is a survey of ~ 10^5 red giant stars that systematically sampled all Milky Way populations (bulge, disk, and halo) to study the Galaxy's chemical and kinematical history. It was part of the Sloan Digital Sky Survey III (SDSS-III) from 2011 -- 2014 using the 2.5 m Sloan Foundation Telescope at Apache Point Observatory, New Mexico. The APOGEE-2 survey is now using the spectrograph as part of SDSS-IV, as well as a second spectrograph, a close copy of the first, operating at the 2.5 m du Pont Telescope at Las Campanas Observatory in Chile. Although several fiber-fed, multi-object, high resolution spectrographs have been built for visual wavelength spectroscopy, the APOGEE spectrograph is one of the first such instruments built for observations in the near-infrared. The instrument's successful development was enabled by several key innovations, including a "gang connector" to allow simultaneous connections of 300 fibers; hermetically sealed feedthroughs to allow fibers to pass through the cryostat wall continuously; the first cryogenically deployed mosaic volume phase holographic grating; and a large refractive camera that includes mono-crystalline silicon and fused silica elements with diameters as large as ~ 400 mm. This paper contains a comprehensive description of all aspects of the instrument including the fiber system, optics and opto-mechanics, detector arrays, mechanics and cryogenics, instrument control, calibration system, optical performance and stability, lessons learned, and design changes for the second instrument.Comment: 81 pages, 67 figures, PASP, accepte

Data and Image Transfer Using Mobile Phones to Strengthen Microscopy-Based Diagnostic Services in Low and Middle Income Country Laboratories

Background: The emerging market of mobile phone technology and its use in the health sector is rapidly expanding and connecting even the most remote areas of world. Distributing diagnostic images over the mobile network for knowledge sharing, feedback or quality control is a logical innovation. Objective: To determine the feasibility of using mobile phones for capturing microscopy images and transferring these to a central database for assessment, feedback and educational purposes. Methods: A feasibility study was carried out in Uganda. Images of microscopy samples were taken using a prototype connector that could fix a variety of mobile phones to a microscope. An Information Technology (IT) platform was set up for data transfer from a mobile phone to a website, including feedback by text messaging to the end user. Results: Clear images were captured using mobile phone cameras of 2 megapixels (MP) up to 5MP. Images were sent by mobile Internet to a website where they were visualized and feedback could be provided to the sender by means of text message. Conclusion: The process of capturing microscopy images on mobile phones, relaying them to a central review website and feeding back to the sender is feasible and of potential benefit in resource poor settings. Even though the system needs furthe

A thermodynamic approach to designing structure-free combinatorial DNA word sets

An algorithm is presented for the generation of sets of non-interacting DNA sequences, employing existing thermodynamic models for the prediction of duplex stabilities and secondary structures. A DNA ‘word’ structure is employed in which individual DNA ‘words’ of a given length (e.g. 12mer and 16mer) may be concatenated into longer sequences (e.g. four tandem words and six tandem words). This approach, where multiple word variants are used at each tandem word position, allows very large sets of non-interacting DNA strands to be assembled from combinations of the individual words. Word sets were generated and their figures of merit are compared to sets as described previously in the literature (e.g. 4, 8, 12, 15 and 16mer). The predicted hybridization behavior was experimentally verified on selected members of the sets using standard UV hyperchromism measurements of duplex melting temperatures (T(m)s). Additional experimental validation was obtained by using the sequences in formulating and solving a small example of a DNA computing problem

Computational genes: a tool for molecular diagnosis and therapy of aberrant mutational phenotype

<p>Abstract</p> <p>Background</p> <p>A finite state machine manipulating information-carrying DNA strands can be used to perform autonomous molecular-scale computations at the cellular level.</p> <p>Results</p> <p>We propose a new finite state machine able to detect and correct aberrant molecular phenotype given by mutated genetic transcripts. The aberrant mutations trigger a cascade reaction: specific molecular markers as input are released and induce a spontaneous self-assembly of a wild type protein or peptide, while the mutational disease phenotype is silenced. We experimentally demostrated in <it>in vitro </it>translation system that a viable protein can be autonomously assembled.</p> <p>Conclusion</p> <p>Our work demostrates the basic principles of computational genes and particularly, their potential to detect mutations, and as a response thereafter administer an output that suppresses the aberrant disease phenotype and/or restores the lost physiological function.</p