Determining cellular CTCF and cohesin abundances to constrain 3D genome models.

Achieving a quantitative and predictive understanding of 3D genome architecture remains a major challenge, as it requires quantitative measurements of the key proteins involved. Here, we report the quantification of CTCF and cohesin, two causal regulators of topologically associating domains (TADs) in mammalian cells. Extending our previous imaging studies (Hansen et al., 2017), we estimate bounds on the density of putatively DNA loop-extruding cohesin complexes and CTCF binding site occupancy. Furthermore, co-immunoprecipitation studies of an endogenously tagged subunit (Rad21) suggest the presence of cohesin dimers and/or oligomers. Finally, based on our cell lines with accurately measured protein abundances, we report a method to conveniently determine the number of molecules of any Halo-tagged protein in the cell. We anticipate that our results and the established tool for measuring cellular protein abundances will advance a more quantitative understanding of 3D genome organization, and facilitate protein quantification, key to comprehend diverse biological processes

On vertex coloring without monochromatic triangles

We study a certain relaxation of the classic vertex coloring problem, namely, a coloring of vertices of undirected, simple graphs, such that there are no monochromatic triangles. We give the first classification of the problem in terms of classic and parametrized algorithms. Several computational complexity results are also presented, which improve on the previous results found in the literature. We propose the new structural parameter for undirected, simple graphs -- the triangle-free chromatic number $\chi_3$. We bound $\chi_3$ by other known structural parameters. We also present two classes of graphs with interesting coloring properties, that play pivotal role in proving useful observation about our problem. We give/ask several conjectures/questions throughout this paper to encourage new research in the area of graph coloring.Comment: Extended abstrac

Preliminary Results from NEOWISE: An Enhancement to the Wide-field Infrared Survey Explorer for Solar System Science

The Wide-field Infrared Survey Explorer (WISE) has surveyed the entire sky at four infrared wavelengths with greatly improved sensitivity and spatial resolution compared to its predecessors, the Infrared Astronomical Satellite and the Cosmic Background Explorer. NASA's Planetary Science Division has funded an enhancement to the WISE data processing system called "NEOWISE" that allows detection and archiving of moving objects found in the WISE data. NEOWISE has mined the WISE images for a wide array of small bodies in our solar system, including near-Earth objects (NEOs), Main Belt asteroids, comets, Trojans, and Centaurs. By the end of survey operations in 2011 February, NEOWISE identified over 157,000 asteroids, including more than 500 NEOs and ~120 comets. The NEOWISE data set will enable a panoply of new scientific investigations

On Coloring Resilient Graphs

We introduce a new notion of resilience for constraint satisfaction problems, with the goal of more precisely determining the boundary between NP-hardness and the existence of efficient algorithms for resilient instances. In particular, we study $r$-resiliently $k$-colorable graphs, which are those $k$-colorable graphs that remain $k$-colorable even after the addition of any $r$ new edges. We prove lower bounds on the NP-hardness of coloring resiliently colorable graphs, and provide an algorithm that colors sufficiently resilient graphs. We also analyze the corresponding notion of resilience for $k$-SAT. This notion of resilience suggests an array of open questions for graph coloring and other combinatorial problems.Comment: Appearing in MFCS 201

Antarctic Surface Reflectivity Measurements from the ANITA-3 and HiCal-1 Experiments

The primary science goal of the NASA-sponsored ANITA project is measurement of ultra-high energy neutrinos and cosmic rays, observed via radio-frequency signals resulting from a neutrino- or cosmic ray- interaction with terrestrial matter (atmospheric or ice molecules, e.g.). Accurate inference of the energies of these cosmic rays requires understanding the transmission/reflection of radio wave signals across the ice-air boundary. Satellite-based measurements of Antarctic surface reflectivity, using a co-located transmitter and receiver, have been performed more-or-less continuously for the last few decades. Satellite-based reflectivity surveys, at frequencies ranging from 2--45 GHz and at near-normal incidence, yield generally consistent reflectivity maps across Antarctica. Using the Sun as an RF source, and the ANITA-3 balloon borne radio-frequency antenna array as the RF receiver, we have also measured the surface reflectivity over the interval 200-1000 MHz, at elevation angles of 12-30 degrees, finding agreement with the Fresnel equations within systematic errors. To probe low incidence angles, inaccessible to the Antarctic Solar technique and not probed by previous satellite surveys, a novel experimental approach ("HiCal-1") was devised. Unlike previous measurements, HiCal-ANITA constitute a bi-static transmitter-receiver pair separated by hundreds of kilometers. Data taken with HiCal, between 200--600 MHz shows a significant departure from the Fresnel equations, constant with frequency over that band, with the deficit increasing with obliquity of incidence, which we attribute to the combined effects of possible surface roughness, surface grain effects, radar clutter and/or shadowing of the reflection zone due to Earth curvature effects.Comment: updated to match publication versio

WISE/NEOWISE Observations of Comet 103P/Hartley 2

We report results based on mid-infrared photometry of comet 103P/Hartley 2 taken during 2010 May 4-13 (when the comet was at a heliocentric distance of 2.3 AU, and an observer distance of 2.0 AU) by the Wide-field Infrared Survey Explorer. Photometry of the coma at 22 μm and data from the University of Hawaii 2.2 m telescope obtained on 2010 May 22 provide constraints on the dust particle size distribution, d log n/d log m, yielding power-law slope values of alpha = –0.97 ± 0.10, steeper than that found for the inbound particle fluence during the Stardust encounter of comet 81P/Wild 2. The extracted nucleus signal at 12 μm is consistent with a body of average spherical radius of 0.6 ± 0.2 km (one standard deviation), assuming a beaming parameter of 1.2. The 4.6 μm band signal in excess of dust and nucleus reflected and thermal contributions may be attributed to carbon monoxide or carbon dioxide emission lines and provides limits and estimates of species production. Derived carbon dioxide coma production rates are 3.5(± 0.9) × 10^(24) molecules per second. Analyses of the trail signal present in the stacked image with an effective exposure time of 158.4 s yields optical-depth values near 9 × 10^(–10) at a delta mean anomaly of 0.2 deg trailing the comet nucleus, in both 12 and 22 μm bands. A minimum chi-squared analysis of the dust trail position yields a beta-parameter value of 1.0 × 10^(–4), consistent with a derived mean trail-grain diameter of 1.1/ρ cm for grains of ρ g cm^(–3) density. This leads to a total detected trail mass of at least 4 × 10^(10) ρ kg