The urban ecology of Iron Age Tel Megiddo: using microvertebrate remains as ancient bio-indicators

Peer reviewedPreprin

Subtree power analysis finds optimal species for comparative genomics

Sequence comparison across multiple organisms aids in the detection of regions under selection. However, resource limitations require a prioritization of genomes to be sequenced. This prioritization should be grounded in two considerations: the lineal scope encompassing the biological phenomena of interest, and the optimal species within that scope for detecting functional elements. We introduce a statistical framework for optimal species subset selection, based on maximizing power to detect conserved sites. In a study of vertebrate species, we show that the optimal species subset is not in general the most evolutionarily diverged subset. Our results suggest that marsupials are prime sequencing candidates.Comment: 16 pages, 3 figures, 3 table

Energy in one dimensional linear waves in a string

We consider the energy density and energy transfer in small amplitude, one-dimensional waves on a string, and find that the common expressions used in textbooks for the introductory physics with calculus course give wrong results for some cases, including standing waves. We discuss the origin of the problem, and how it can be corrected in a way appropriate for the introductory calculus based physics course.Comment: 5 page

Determination of the resistivity anisotropy of SrRuO3_{3} by measuring the planar Hall effect

We have measured the planar Hall effect in epitaxial thin films of the itinerant ferromagnet SrRuO3 patterned with their current paths at different angles relative to the crystallographic axes. Based on the results, we have determined that SrRuO3 exhibits small resistivity anisotropy in the entire temperature range of our measurements (between 2 to 300 K); namely, both above and below its Curie temperature (~150 K). It means that in addition to anisotropy related to magnetism, the resistivity anisotropy of SrRuO3 has an intrinsic, nonmagnetic source. We have found that the two sources of anisotropy have competing effects

Identification and correction of systematic error in high-throughput sequence data

A feature common to all DNA sequencing technologies is the presence of base-call errors in the sequenced reads. The implications of such errors are application specific, ranging from minor informatics nuisances to major problems affecting biological inferences. Recently developed “next-gen” sequencing technologies have greatly reduced the cost of sequencing, but have been shown to be more error prone than previous technologies. Both position specific (depending on the location in the read) and sequence specific (depending on the sequence in the read) errors have been identified in Illumina and Life Technology sequencing platforms. We describe a new type of _systematic_ error that manifests as statistically unlikely accumulations of errors at specific genome (or transcriptome) locations. We characterize and describe systematic errors using overlapping paired reads form high-coverage data. We show that such errors occur in approximately 1 in 1000 base pairs, and that quality scores at systematic error sites do not account for the extent of errors. We identify motifs that are frequent at systematic error sites, and describe a classifier that distinguishes heterozygous sites from systematic error. Our classifier is designed to accommodate data from experiments in which the allele frequencies at heterozygous sites are not necessarily 0.5 (such as in the case of RNA-Seq). Systematic errors can easily be mistaken for heterozygous sites in individuals, or for SNPs in population analyses. Systematic errors are particularly problematic in low coverage experiments, or in estimates of allele-specific expression from RNA-Seq data. Our characterization of systematic error has allowed us to develop a program, called SysCall, for identifying and correcting such errors. We conclude that correction of systematic errors is important to consider in the design and interpretation of high-throughput sequencing experiments

From non-Brownian Functionals to a Fractional Schr\"odinger Equation

We derive backward and forward fractional Schr\"odinger type of equations for the distribution of functionals of the path of a particle undergoing anomalous diffusion. Fractional substantial derivatives introduced by Friedrich and co-workers [PRL {\bf 96}, 230601 (2006)] provide the correct fractional framework for the problem at hand. In the limit of normal diffusion we recover the Feynman-Kac treatment of Brownian functionals. For applications, we calculate the distribution of occupation times in half space and show how statistics of anomalous functionals is related to weak ergodicity breaking.Comment: 5 page

A nonpolynomial Schroedinger equation for resonantly absorbing gratings

We derive a nonlinear Schroedinger equation with a radical term, in the form of the square root of (1-|V|^2), as an asymptotic model of the optical medium built as a periodic set of thin layers of two-level atoms, resonantly interacting with the electromagnetic field and inducing the Bragg reflection. A family of bright solitons is found, which splits into stable and unstable parts, exactly obeying the Vakhitov-Kolokolov criterion. The soliton with the largest amplitude, which is |V| = 1, is found in an explicit analytical form. It is a "quasi-peakon", with a discontinuity of the third derivative at the center. Families of exact cnoidal waves, built as periodic chains of quasi-peakons, are found too. The ultimate solution belonging to the family of dark solitons, with the background level |V| = 1, is a dark compacton, also obtained in an explicit analytical form. Those bright solitons which are unstable destroy themselves (if perturbed) attaining the critical amplitude, |V| = 1. The dynamics of the wave field around this critical point is studied analytically, revealing a switch of the system into an unstable phase. Collisions between bright solitons are investigated too. The collisions between fast solitons are quasi-elastic, while slowly moving ones merge into breathers, which may persist or perish (in the latter case, also by attaining |V| = 1).Comment: Physical Review A, in pres

Mass loss by a scalar charge in an expanding universe

We study the phenomenon of mass loss by a scalar charge -- a point particle that acts a source for a noninteracting scalar field -- in an expanding universe. The charge is placed on comoving world lines of two cosmological spacetimes: a de Sitter universe, and a spatially-flat, matter-dominated universe. In both cases, we find that the particle's rest mass is not a constant, but that it changes in response to the emission of monopole scalar radiation by the particle. In de Sitter spacetime, the particle radiates all of its mass within a finite proper time. In the matter-dominated cosmology, this happens only if the charge of the particle is sufficiently large; for smaller charges the particle first loses some of its mass, but then regains it all eventually.Comment: 11 pages, RevTeX4, Accepted for Phys. Rev.

Self force on particle in orbit around a black hole

We study the self force acting on a scalar charge in uniform circular motion around a Schwarzschild black hole. The analysis is based on a direct calculation of the self force via mode decomposition, and on a regularization procedure based on Ori's mode-sum regularization prescription. We find the four self-force at arbitrary radii and angular velocities (both geodesic and non-geodesic), in particular near the black hole, where general-relativistic effects are strongest, and for fast motion. We find the radial component of the self force to be repulsive or attractive, depending on the orbit.Comment: RevTeX, 4 pages, 4 Encapsulated PostScript figures. Submitted to Phys. Rev. Let

Improving SIEM for critical SCADA water infrastructures using machine learning

Network Control Systems (NAC) have been used in many industrial processes. They aim to reduce the human factor burden and efficiently handle the complex process and communication of those systems. Supervisory control and data acquisition (SCADA) systems are used in industrial, infrastructure and facility processes (e.g. manufacturing, fabrication, oil and water pipelines, building ventilation, etc.) Like other Internet of Things (IoT) implementations, SCADA systems are vulnerable to cyber-attacks, therefore, a robust anomaly detection is a major requirement. However, having an accurate anomaly detection system is not an easy task, due to the difficulty to differentiate between cyber-attacks and system internal failures (e.g. hardware failures). In this paper, we present a model that detects anomaly events in a water system controlled by SCADA. Six Machine Learning techniques have been used in building and evaluating the model. The model classifies different anomaly events including hardware failures (e.g. sensor failures), sabotage and cyber-attacks (e.g. DoS and Spoofing). Unlike other detection systems, our proposed work helps in accelerating the mitigation process by notifying the operator with additional information when an anomaly occurs. This additional information includes the probability and confidence level of event(s) occurring. The model is trained and tested using a real-world dataset