Locating regions in a sequence under density constraints

Several biological problems require the identification of regions in a sequence where some feature occurs within a target density range: examples including the location of GC-rich regions, identification of CpG islands, and sequence matching. Mathematically, this corresponds to searching a string of 0s and 1s for a substring whose relative proportion of 1s lies between given lower and upper bounds. We consider the algorithmic problem of locating the longest such substring, as well as other related problems (such as finding the shortest substring or a maximal set of disjoint substrings). For locating the longest such substring, we develop an algorithm that runs in O(n) time, improving upon the previous best-known O(n log n) result. For the related problems we develop O(n log log n) algorithms, again improving upon the best-known O(n log n) results. Practical testing verifies that our new algorithms enjoy significantly smaller time and memory footprints, and can process sequences that are orders of magnitude longer as a result.Comment: 17 pages, 8 figures; v2: minor revisions, additional explanations; to appear in SIAM Journal on Computin

Planet Formation in the Outer Solar System

This paper reviews coagulation models for planet formation in the Kuiper Belt, emphasizing links to recent observations of our and other solar systems. At heliocentric distances of 35-50 AU, single annulus and multiannulus planetesimal accretion calculations produce several 1000 km or larger planets and many 50-500 km objects on timescales of 10-30 Myr in a Minimum Mass Solar Nebula. Planets form more rapidly in more massive nebulae. All models yield two power law cumulative size distributions, N_C propto r^{-q} with q = 3.0-3.5 for radii larger than 10 km and N_C propto r^{-2.5} for radii less than 1 km. These size distributions are consistent with observations of Kuiper Belt objects acquired during the past decade. Once large objects form at 35-50 AU, gravitational stirring leads to a collisional cascade where 0.1-10 km objects are ground to dust. The collisional cascade removes 80% to 90% of the initial mass in the nebula in roughly 1 Gyr. This dust production rate is comparable to rates inferred for alpha Lyr, beta Pic, and other extrasolar debris disk systems.Comment: invited review for PASP, March 2002. 33 pages of text and 12 figure

Anharmonicity-induced isostructural phase transition of Zirconium under pressure

We have performed a detailed x-ray diffraction structural study of Zr under pressure and unambiguously identify the existence of a first-order isostructural bcc-to-bcc phase transition near 58 GPa. First-principles quantum molecular dynamics lattice dynamics calculations support the existence of this phase transition, in excellent agreement with experimental results, triggered by anharmonic effects. Our results highlight the potential ubiquity of anharmonically driven isostructural transitions within the periodic table under pressure and calls for follow-up experimental and theoretical studies

Searching a bitstream in linear time for the longest substring of any given density

Given an arbitrary bitstream, we consider the problem of finding the longest substring whose ratio of ones to zeroes equals a given value. The central result of this paper is an algorithm that solves this problem in linear time. The method involves (i) reformulating the problem as a constrained walk through a sparse matrix, and then (ii) developing a data structure for this sparse matrix that allows us to perform each step of the walk in amortised constant time. We also give a linear time algorithm to find the longest substring whose ratio of ones to zeroes is bounded below by a given value. Both problems have practical relevance to cryptography and bioinformatics.Comment: 22 pages, 19 figures; v2: minor edits and enhancement

Planetary Migration and Extrasolar Planets in the 2/1 Mean-Motion Resonance

We analyze the possible relationship between the current orbital elements fits of known exoplanets in the 2/1 mean-motion resonance and the expected orbital configuration due to migration. It is found that, as long as the orbital decay was sufficiently slow to be approximated by an adiabatic process, all captured planets should be in apsidal corotations. In other words, they should show a simultaneous libration of both the resonant angle and the difference in longitudes of pericenter. We present a complete set of corotational solutions for the 2/1 commensurability, including previously known solutions and new results. Comparisons with observed exoplanets show that current orbital fits of three known planetary systems in this resonance are either consistent with apsidal corotations (GJ876 and HD82943) or correspond to bodies with uncertain orbits (HD160691). Finally, we discuss the applicability of these results as a test for the planetary migration hypothesis itself. If all future systems in this commensurability are found to be consistent with corotational solutions, then resonance capture of these bodies through planetary migration is a working hypothesis. Conversely, If any planetary pair is found in a different configuration, then either migration did not occur for those bodies, or it took a different form than currently believed.Comment: Submitted to MNRA

Cancer-Associated Fibroblasts Neutralize the Anti-tumor Effect of CSF1 Receptor Blockade by Inducing PMN-MDSC Infiltration of Tumors.

Tumor-associated macrophages (TAM) contribute to all aspects of tumor progression. Use of CSF1R inhibitors to target TAM is therapeutically appealing, but has had very limited anti-tumor effects. Here, we have identified the mechanism that limited the effect of CSF1R targeted therapy. We demonstrated that carcinoma-associated fibroblasts (CAF) are major sources of chemokines that recruit granulocytes to tumors. CSF1 produced by tumor cells caused HDAC2-mediated downregulation of granulocyte-specific chemokine expression in CAF, which limited migration of these cells to tumors. Treatment with CSF1R inhibitors disrupted this crosstalk and triggered a profound increase in granulocyte recruitment to tumors. Combining CSF1R inhibitor with a CXCR2 antagonist blocked granulocyte infiltration of tumors and showed strong anti-tumor effects

Role of Esrrg in the Fibrate-Mediated Regulation of Lipid Metabolism Genes in Human ApoA-I Transgenic Mice

We have used a new ApoA-I transgenic mouse model to identify by global gene expression profiling, candidate genes that affect lipid and lipoprotein metabolism in response to fenofibrate treatment. Multilevel bioinformatical analysis and stringent selection criteria (2-fold change, 0% false discovery rate) identified 267 significantly changed genes involved in several molecular pathways. The fenofibrate-treated group did not have significantly altered levels of hepatic human APOA-I mRNA and plasma ApoA-I compared with the control group. However, the treatment increased cholesterol levels to 1.95-fold mainly due to the increase in high-density lipoprotein (HDL) cholesterol. The observed changes in HDL are associated with the upregulation of genes involved in phospholipid biosynthesis and lipid hydrolysis, as well as phospholipid transfer protein. Significant upregulation was observed in genes involved in fatty acid transport and β-oxidation, but not in those of fatty acid and cholesterol biosynthesis, Krebs cycle and gluconeogenesis. Fenofibrate changed significantly the expression of seven transcription factors. The estrogen receptor-related gamma gene was upregulated 2.36-fold and had a significant positive correlation with genes of lipid and lipoprotein metabolism and mitochondrial functions, indicating an important role of this orphan receptor in mediating the fenofibrate-induced activation of a specific subset of its target genes.National Institutes of Health (HL48739 and HL68216); European Union (LSHM-CT-2006-0376331, LSHG-CT-2006-037277); the Biomedical Research Foundation of the Academy of Athens; the Hellenic Cardiological Society; the John F Kostopoulos Foundatio

On the growth and orbital evolution of giant planets in layered protoplanetary disks

We present the results of hydrodynamic simulations of the growth and orbital evolution of giant planets embedded in a protoplanetary disk with a dead-zone. The aim is to examine to what extent the presence of a dead-zone affects the rates of mass accretion and migration for giant planets. We performed 3D numerical simulations using a grid-based hydrodynamics code. In these simulations of non-magnetised disks, the dead-zone is treated as a region where the vertical profile of the viscosity depends on the distance from the equatorial plane. We consider dead-zones with vertical sizes, H_dz, ranging from 0 to H_dz=2.3H, where H is the disk scale-height. For all models, the vertically integrated viscous stress, and the related mass flux through the disk, have the same value, such that the simulations test the dependence of planetary mass accretion and migration on the vertical distribution of the viscous stress. For each model, an embedded 30 earth-masses planet on a fixed circular orbit is allowed to accrete gas from the disk. Once the planet mass becomes equal to that of Saturn or Jupiter, we allow the planet orbit to evolve due to gravitational interaction with the disk. We find that the time scale over which a protoplanet grows to become a giant planet is essentially independent of the dead-zone size, and depends only on the total rate at which the disk viscously supplies material to the planet. For Saturn-mass planets, the migration rate depends only weakly on the size of the dead-zone for H_dz< 1.5H, but becomes slower when H_dz=2.3H. This effect is due to the desaturation of corotation torques which originate from residual material in the partial-gap region. For Jupiter-mass planets, there is a clear tendency for the migration to proceed more slowly as the size of the dead-zone increases.Comment: Accepted for publication in A&A. 10 pages, 12 figure

Statistics of Q-Oscillators, Quons and Relation to Fractional Satistics

The statistics of $q$-oscillators, quons and to some extent, of anyons are studied and the basic differences among these objects are pointed out. In particular, the statistical distributions for different bosonic and fermionic $q$-oscillators are found for their corresponding Fock space representations in the case when the hamiltonian is identified with the number operator. In this case and for nonrelativistic particles, the single-particle temperature Green function is defined with $q$-deformed periodicity conditions. The equations of state for nonrelativistic and ultrarelativistic bosonic $q$-gases in an arbitrary space dimension are found near Bose statistics, as well as the one for an anyonic gas near Bose and Fermi statistics. The first corrections to the second virial coefficients are also evaluated. The phenomenon of Bose-Einstein condensation in the $q$-deformed gases is also discussed.Comment: 21 pages, Latex, HU-TFT-93-2

Scattering Theory and PT\mathcal{P}\mathcal{T}-Symmetry

We outline a global approach to scattering theory in one dimension that allows for the description of a large class of scattering systems and their $\mathcal{P}$-, $\mathcal{T}$-, and $\mathcal{P}\mathcal{T}$-symmetries. In particular, we review various relevant concepts such as Jost solutions, transfer and scattering matrices, reciprocity principle, unidirectional reflection and invisibility, and spectral singularities. We discuss in some detail the mathematical conditions that imply or forbid reciprocal transmission, reciprocal reflection, and the presence of spectral singularities and their time-reversal. We also derive generalized unitarity relations for time-reversal-invariant and $\mathcal{P}\mathcal{T}$-symmetric scattering systems, and explore the consequences of breaking them. The results reported here apply to the scattering systems defined by a real or complex local potential as well as those determined by energy-dependent potentials, nonlocal potentials, and general point interactions.Comment: Slightly expanded revised version, 38 page