DNA sequences classification and computation scheme based on the symmetry principle

The DNA sequences containing multifarious novel symmetrical structure frequently play crucial role in how genomes work. Here we present a new scheme for understanding the structural features and potential mathematical rules of symmetrical DNA sequences using a method containing stepwise classification and recursive computation. By defining the symmetry of DNA sequences, we classify all sequences and conclude a series of recursive equations for computing the quantity of all classes of sequences existing theoretically; moreover, the symmetries of the typical sequences at different levels are analyzed. The classification and quantitative relation demonstrate that DNA sequences have recursive and nested properties. The scheme may help us better discuss the formation and the growth mechanism of DNA sequences because it has a capability of educing the information about structure and quantity of longer sequences according to that of shorter sequences by some recursive rules. Our scheme may provide a new stepping stone to the theoretical characterization, as well as structural analysis, of DNA sequences

Implementing and reasoning about hash-consed data structures in Coq

We report on four different approaches to implementing hash-consing in Coq programs. The use cases include execution inside Coq, or execution of the extracted OCaml code. We explore the different trade-offs between faithful use of pristine extracted code, and code that is fine-tuned to make use of OCaml programming constructs not available in Coq. We discuss the possible consequences in terms of performances and guarantees. We use the running example of binary decision diagrams and then demonstrate the generality of our solutions by applying them to other examples of hash-consed data structures

Chemical concrete machine

The chemical concrete machine is a graph rewriting system which uses only local moves (rewrites), seen as chemical reactions involving molecules which are graphs made up by 4 trivalent nodes. It is Turing complete, therefore it might be used as a model of computation in algorithmic chemistry

Refactoring pattern matching

Defining functions by pattern matching over the arguments is advantageous for understanding and reasoning, but it tends to expose the implementation of a datatype. Significant effort has been invested in tackling this loss of modularity; however, decoupling patterns from concrete representations while maintaining soundness of reasoning has been a challenge. Inspired by the development of invertible programming, we propose an approach to program refactoring based on a right-invertible language rinv—every function has a right (or pre-) inverse. We show how this new design is able to permit a smooth incremental transition from programs with algebraic datatypes and pattern matching, to ones with proper encapsulation, while maintaining simple and sound reasoning

The SDSS-III Baryon Oscillation Spectroscopic Survey: Quasar Target Selection for Data Release Nine

The SDSS-III Baryon Oscillation Spectroscopic Survey (BOSS), a five-year spectroscopic survey of 10,000 deg^2, achieved first light in late 2009. One of the key goals of BOSS is to measure the signature of baryon acoustic oscillations in the distribution of Ly-alpha absorption from the spectra of a sample of ~150,000 z>2.2 quasars. Along with measuring the angular diameter distance at z\approx2.5, BOSS will provide the first direct measurement of the expansion rate of the Universe at z > 2. One of the biggest challenges in achieving this goal is an efficient target selection algorithm for quasars over 2.2 < z < 3.5, where their colors overlap those of stars. During the first year of the BOSS survey, quasar target selection methods were developed and tested to meet the requirement of delivering at least 15 quasars deg^-2 in this redshift range, out of 40 targets deg^-2. To achieve these surface densities, the magnitude limit of the quasar targets was set at g <= 22.0 or r<=21.85. While detection of the BAO signature in the Ly-alpha absorption in quasar spectra does not require a uniform target selection, many other astrophysical studies do. We therefore defined a uniformly-selected subsample of 20 targets deg^-2, for which the selection efficiency is just over 50%. This "CORE" subsample will be fixed for Years Two through Five of the survey. In this paper we describe the evolution and implementation of the BOSS quasar target selection algorithms during the first two years of BOSS operations. We analyze the spectra obtained during the first year. 11,263 new z>2.2 quasars were spectroscopically confirmed by BOSS. Our current algorithms select an average of 15 z > 2.2 quasars deg^-2 from 40 targets deg^-2 using single-epoch SDSS imaging. Multi-epoch optical data and data at other wavelengths can further improve the efficiency and completeness of BOSS quasar target selection. [Abridged]Comment: 33 pages, 26 figures, 12 tables and a whole bunch of quasars. Submitted to Ap

Who Are User Entrepreneurs? Findings on Innovation, Founder Characteristics, and Firm Characteristics

Documents the prevalence of innovators who create products or services for their own use then start firms, by industry and type. Examines founder and firm characteristics, revenue growth, job creation, R&D investment, and intellectual property creation