SCOPE: a web server for practical de novo motif discovery

SCOPE is a novel parameter-free method for the de novo identification of potential regulatory motifs in sets of coordinately regulated genes. The SCOPE algorithm combines the output of three component algorithms, each designed to identify a particular class of motifs. Using an ensemble learning approach, SCOPE identifies the best candidate motifs from its component algorithms. In tests on experimentally determined datasets, SCOPE identified motifs with a significantly higher level of accuracy than a number of other web-based motif finders run with their default parameters. Because SCOPE has no adjustable parameters, the web server has an intuitive interface, requiring only a set of gene names or FASTA sequences and a choice of species. The most significant motifs found by SCOPE are displayed graphically on the main results page with a table containing summary statistics for each motif. Detailed motif information, including the sequence logo, PWM, consensus sequence and specific matching sites can be viewed through a single click on a motif. SCOPE's efficient, parameter-free search strategy has enabled the development of a web server that is readily accessible to the practising biologist while providing results that compare favorably with those of other motif finders. The SCOPE web server is at <http://genie.dartmouth.edu/scope>

3. Launching the New Enterprise

As the academic year of 1945-46 approached, the intensity of activity in preparation for actually opening the school in the fall term became overwhelming. Incredible though it may seem, Ives and Day were able in a period of a few weeks to assemble the nucleus of a faculty, several of whom formed a continuing source of counsel and advice both during the school’s formative years and thereafter. Includes: The First Dean and the School’s Dedication; A Participant’s View of the Early Years; Ives Moves On; Several Views of Martin P. Catherwood; The Founders

Superfluid to solid crossover in a rotating Bose-Einstein condensed gas

The properties of a rotating Bose-Einstein condensate confined in a prolate cylindrically symmetric trap are explored both analytically and numerically. As the rotation frequency increases, an ever greater number of vortices are energetically favored. Though the cloud anisotropy and moment of inertia approach those of a classical fluid at high frequencies, the observed vortex density is consistently lower than the solid-body estimate. Furthermore, the vortices are found to arrange themselves in highly regular triangular arrays, with little distortion even near the condensate surface. These results are shown to be a direct consequence of the inhomogeneous confining potential.Comment: 4+e pages, 5 embedded figures, revte

Stationary solutions of the one-dimensional nonlinear Schroedinger equation: II. Case of attractive nonlinearity

All stationary solutions to the one-dimensional nonlinear Schroedinger equation under box or periodic boundary conditions are presented in analytic form for the case of attractive nonlinearity. A companion paper has treated the repulsive case. Our solutions take the form of bounded, quantized, stationary trains of bright solitons. Among them are two uniquely nonlinear classes of nodeless solutions, whose properties and physical meaning are discussed in detail. The full set of symmetry-breaking stationary states are described by the $C_{n}$ character tables from the theory of point groups. We make experimental predictions for the Bose-Einstein condensate and show that, though these are the analog of some of the simplest problems in linear quantum mechanics, nonlinearity introduces new and surprising phenomena.Comment: 11 pages, 9 figures -- revised versio

Quantum key distribution with 1.25 Gbps clock synchronization

We have demonstrated the exchange of sifted quantum cryptographic key over a 730 meter free-space link at rates of up to 1.0 Mbps, two orders of magnitude faster than previously reported results. A classical channel at 1550 nm operates in parallel with a quantum channel at 845 nm. Clock recovery techniques on the classical channel at 1.25 Gbps enable quantum transmission at up to the clock rate. System performance is currently limited by the timing resolution of our silicon avalanche photodiode detectors. With improved detector resolution, our technique will yield another order of magnitude increase in performance, with existing technology.Comment: 6 pages, 3 figures, 99 kB .pdf documen

The role of religion in the longer-range future, April 6, 7, and 8, 2006

This repository item contains a single issue of the Pardee Conference Series, a publication series that began publishing in 2006 by the Boston University Frederick S. Pardee Center for the Study of the Longer-Range Future. This conference that took place during April 6, 7, and 8, 2006. Co-organized by David Fromkin, Director, Frederick S. Pardee Center for the Study of the Longer-Range Future, and Ray L. Hart, Dean ad interim Boston University School of TheologyThe conference brought together some 40 experts from various disciplines to ponder upon the “great dilemma” of how science, religion, and the human future interact. In particular, different panels looked at trends in what is happening to religion around the world, questions about how religion is impacting the current political and economic order, and how the social dynamics unleashed by science and by religion can be reconciled.Carnegie Council on Ethics and International Affair

Stationary solutions of the one-dimensional nonlinear Schroedinger equation: I. Case of repulsive nonlinearity

All stationary solutions to the one-dimensional nonlinear Schroedinger equation under box and periodic boundary conditions are presented in analytic form. We consider the case of repulsive nonlinearity; in a companion paper we treat the attractive case. Our solutions take the form of stationary trains of dark or grey density-notch solitons. Real stationary states are in one-to-one correspondence with those of the linear Schr\"odinger equation. Complex stationary states are uniquely nonlinear, nodeless, and symmetry-breaking. Our solutions apply to many physical contexts, including the Bose-Einstein condensate and optical pulses in fibers.Comment: 11 pages, 7 figures -- revised versio

Vortex stability of interacting Bose-Einstein condensates confined in anisotropic harmonic traps

Vortex states of weakly-interacting Bose-Einstein condensates confined in three-dimensional rotating harmonic traps are investigated numerically at zero temperature. The ground state in the rotating frame is obtained by propagating the Gross-Pitaevskii equation for the condensate in imaginary time. The total energies between states with and without a vortex are compared, yielding critical rotation frequencies that depend on the anisotropy of the trap and the number of atoms. Vortices displaced from the center of nonrotating traps are found to have long lifetimes for sufficiently large numbers of atoms. The relationship between vortex stability and bound core states is explored.Comment: 5 pages, 2 embedded figures, revtex. To appear in Phys. Rev. Let

Muscle damage is linked to cytokine changes following a 160-km race

Abstract Muscle damage and perceived soreness following the 160-km Western States Endurance Run were related to changes in plasma cytokines and use of nonsteroidal anti-inXammatory drugs (NSAIDS). Subjects included 60 ultramarathoners (mean § SE, age 45.3 § 1.1 years) who Wnished the race in under 30 h (26.3 § 0.4 h). Blood samples were collected the morning prior to and immediately following the race, and subjects recorded muscle soreness during the week following the race using a 10-point Likert scale (DOMS). Seven plasma cytokines were measured including IL-6, IL-10, IL-8, IL-1ra, granulocyte colony-stimulating factor (G-CSF), monocyte chemotactic protein 1 (MCP-1), and macrophage inXammatory protein 1 (MIP-1 ). Cytokine changes were compared between NSAID users and nonusers, and correlated with creatine phosphokinase (CPK) and DOMS. SigniWcant increases were measured for all seven cytokines, with the greatest fold increases seen for IL-6 (125£), IL-10 (24£), and G-CSF (12£). CPK was correlated with changes in IL-6, G-CSF, IL-10, IL-1ra, and MCP-1 (r D .49-.68), (P &lt; .001), but not IL-8 or MIP-1 . DOMS averaged 7.1 § 0.3 the day after the race, and 5.0 § 0.3, 2.5 § 0.2, and 1.6 § 0.1 3 days, 5 days, and 7 days post-race, respectively, and each was correlated with CPK (r D .40-.63, P &lt; .001) and changes in IL-6, G-CSF, IL-10, and MCP-1 (r D .28-.77, P &lt; .05). A comparison of NSAID users (72% of athletes) and nonusers showed no diVerences in CPK or DOMS, but did reveal greater increases in Wve of seven cytokines in the NSAID users (P &lt; .05). In conclusion, muscle damage in athletes competing in a 160-km race was signiWcantly correlated with post-race DOMS and increases in Wve of seven cytokines. NSAID users did not experience a reduction in muscle damage or DOMS, but did have higher post-race plasma levels in Wve of seven cytokines