Implementing Arithmetic and Other Analytic Operations By Transcriptional Regulation

The transcriptional regulatory machinery of a gene can be viewed as a computational device, with transcription factor concentrations as inputs and expression level as the output. This view begs the question: what kinds of computations are possible? We show that different parameterizations of a simple chemical kinetic model of transcriptional regulation are able to approximate all four standard arithmetic operations: addition, subtraction, multiplication, and division, as well as various equality and inequality operations. This contrasts with other studies that emphasize logical or digital notions of computation in biological networks. We analyze the accuracy and precision of these approximations, showing that they depend on different sets of parameters, and are thus independently tunable. We demonstrate that networks of these “arithmetic” genes can be combined to accomplish yet more complicated computations by designing and simulating a network that detects statistically significant elevations in a time-varying signal. We also consider the much more general problem of approximating analytic functions, showing that this can be achieved by allowing multiple transcription factor binding sites on the promoter. These observations are important for the interpretation of naturally occurring networks and imply new possibilities for the design of synthetic networks

Optimal Low-Rank Matrix Completion: Semidefinite Relaxations and Eigenvector Disjunctions

Low-rank matrix completion consists of computing a matrix of minimal complexity that recovers a given set of observations as accurately as possible. Unfortunately, existing methods for matrix completion are heuristics that, while highly scalable and often identifying high-quality solutions, do not possess any optimality guarantees. We reexamine matrix completion with an optimality-oriented eye. We reformulate these low-rank problems as convex problems over the non-convex set of projection matrices and implement a disjunctive branch-and-bound scheme that solves them to certifiable optimality. Further, we derive a novel and often tight class of convex relaxations by decomposing a low-rank matrix as a sum of rank-one matrices and incentivizing that two-by-two minors in each rank-one matrix have determinant zero. In numerical experiments, our new convex relaxations decrease the optimality gap by two orders of magnitude compared to existing attempts, and our disjunctive branch-and-bound scheme solves nxn rank-r matrix completion problems to certifiable optimality in hours for n

Concert recording 2018-10-02

[Track 1]. Canson für 4 Posaunen / Samuel Scheidt -- [Track 2]. Horizon of the aten / Anthony Barfield -- [Track 3]. Crisantemi / Giocomo Puccini -- [Track 4]. Elegy / William Grant Still arranged by Mixdorf -- [Track 5]. Mambo from West side story / Leonard Bernstein arranged by Mixdorf -- [Track 6]. Suite pour Quatour de Trombones. I. Moderato maestoso II. Andantino III. Tempo di Menuetto IV. Choral - Andante maestoso V. Scherzo / Désiré Dondeyne -- [Track 7]. Rusalka\u27s Song to the moon from Rusalka / Antonín Dvořák arranged by Mixdorf -- [Track 8]. That\u27s a plenty / Lew Pollack arranged by Gale

Shallow-Water Coral Communities Support the Separation of Marine Ecoregions on the West-Central Florida Gulf Coast

Florida’s west coast is a 170,000 km2 bedrock shelf (west Florida shelf, WFS) comprised of north-south discontinuous carbonate outcroppings extending more than 200 km from the intertidal zone to a depth of 200 m. These outcrops support diverse benthic communities, which contribute to a multi-billion dollar recreational and commercial fishing industry, yet only about 5% of their extent has been studied in detail. Benthic communities shift over a 6.5° geographic range, but the locations of these shifts are not well-defined. Previous studies have suggested a break in biogeographic regions at Tampa Bay, south at Cape Romano, and north at Cedar Key. The goal of this study was to map and investigate the shallow WFS marine hardbottom north and south of Tampa Bay, FL to identify differences in benthic communities and identify ecoregion boundaries. Habitat mapping yielded 295.89 km2 of hardbottom which differed in extent between Sarasota and Pasco counties. Benthic surveys tabulated 4,079 stony coral colonies of nine species and 1,918 soft corals. Stony corals were dominated by Siderastrea radians, Oculina robusta, Solenastrea hyades, and Cladocora arbuscula less than 10 cm in diameter. Distinct differences in these communities were evident from south to north. The main community shift indicated an ecoregion boundary at, or very near, the mouth of Tampa Bay. Another shift associated with the Bahamas Fracture Zone (BFZ) occurred at the Pinellas and Pasco County border. The outputs of this work provide the first detailed benthic habitat map of the area, a detailed survey of the composition of hardbottom benthic communities in the region, identify Tampa Bay as a coastal benthic biogeographic transition, and illustrate the influence of the BFZ on coastal communities. These findings illustrate a need for additional WFS benthic research and mapping to give a more comprehensive understanding of coral community biogeography in the context of future warming conditions and the potential tropicalization. Unifying seafloor mapping data, mapping new areas with high probability of hardbottom resources, and collecting benthic community data over broader scales will refine community biogeographic zonation. This is a necessary precursor to any long-term community monitoring to detect spatial shifts in communities and population modeling

Speeding up ecological and evolutionary computations in R; essentials of high performance computing for biologists

Computation has become a critical component of research in biology. A risk has emerged that computational and programming challenges may limit research scope, depth, and quality. We review various solutions to common computational efficiency problems in ecological and evolutionary research. Our review pulls together material that is currently scattered across many sources and emphasizes those techniques that are especially effective for typical ecological and environmental problems. We demonstrate how straightforward it can be to write efficient code and implement techniques such as profiling or parallel computing. We supply a newly developed R package (aprof) that helps to identify computational bottlenecks in R code and determine whether optimization can be effective. Our review is complemented by a practical set of examples and detailed Supporting Information material (S1–S3 Texts) that demonstrate large improvements in computational speed (ranging from 10.5 times to 14,000 times faster). By improving computational efficiency, biologists can feasibly solve more complex tasks, ask more ambitious questions, and include more sophisticated analyses in their research

Laser-Based Propagation of Human iPS and ES Cells Generates Reproducible Cultures with Enhanced Differentiation Potential

Proper maintenance of stem cells is essential for successful utilization of ESCs/iPSCs as tools in developmental and drug discovery studies and in regenerative medicine. Standardization is critical for all future applications of stem cells and necessary to fully understand their potential. This study reports a novel approach for the efficient, consistent expansion of human ESCs and iPSCs using laser sectioning, instead of mechanical devices or enzymes, to divide cultures into defined size clumps for propagation. Laser-mediated propagation maintained the pluripotency, quality, and genetic stability of ESCs/iPSCs and led to enhanced differentiation potential. This approach removes the variability associated with ESC/iPSC propagation, significantly reduces the expertise, labor, and time associated with manual passaging techniques and provides the basis for scalable delivery of standardized ESC/iPSC lines. Adoption of standardized protocols would allow researchers to understand the role of genetics, environment, and/or procedural effects on stem cells and would ensure reproducible production of stem cell cultures for use in clinical/therapeutic applications

The Impact of Composition and Morphology on Ionic Conductivity of Silk/Cellulose Bio-Composites Fabricated from Ionic Liquid and Varying Percentages of Coagulation Agents.

Blended biocomposites created from the electrostatic and hydrophobic interactions between polysaccharides and structural proteins exhibit useful and unique properties. However, engineering these biopolymers into applicable forms is challenging due to the coupling of the material’s physicochemical properties to its morphology, and the undertaking that comes with controlling this. In this particular study, numerous properties of the Bombyx mori silk and microcrystalline cellulose biocomposites blended using ionic liquid and regenerated with various coagulation agents were investigated. Specifically, the relationship between the composition of polysaccharide-protein bio-electrolyte membranes and the resulting morphology and ionic conductivity is explored using numerous characterization techniques, including scanning electron microscopy (SEM), Fourier transform infrared spectroscopy (FTIR), thermal gravimetric analysis (TGA), differential scanning calorimetry (DSC), X-ray scattering, atomic force microscopy (AFM) based nanoindentation, and dielectric relaxation spectroscopy (DRS). The results revealed that when silk is the dominating component in the biocomposite, the ionic conductivity is higher, which also correlates with higher β-sheet content. However, when cellulose becomes the dominating component in the biocomposite, this relationship is not observed; instead, cellulose semicrystallinity and mechanical properties dominate the ionic conduction

The Grizzly, January 25, 2000

Bear Country Blanketed by Snow • Bigger, Better UC Beginning in the Year 2000 • Fatal Seton Hall Fire Burns in Heart of Nation • Young Boy Caught in Middle of International Custody Battle • Politician\u27s Hit-and-Run Comes Back to Haunt Him • Dickinson Librarian Imprisoned by Chinese • Collegeville Squares • The Memory of Dr. Martin Luther King Celebrated at Ursinus • Rape: What is it?? • Opinion: Russia\u27s New Year\u27s Revolution Cause for Concern?; Better Communication, Lower Prices Keys to Fixing Book-Buying Woes • Explore Careers and Gain Experience with Career Planit • Swimming Drops a Tough One to Western Maryland • Ursinus Men\u27s Basketball Atop the Centennial Conference East Division • Sports Profile: Lindsey Glah • UC Bears Defense Upsets Rosemont • Indoor Track: The Winter Warriors • Centennial Conference Coaches Attend Snell Symposium at UChttps://digitalcommons.ursinus.edu/grizzlynews/1456/thumbnail.jp