Theory of stripes in quasi two dimensional rare-earth tritellurides

Even though the rare-earth tritellurides are tetragonal materials with a quasi two dimensional (2D) band structure, they have a "hidden" 1D character. The resultant near-perfect nesting of the Fermi surface leads to the formation of a charge density wave (CDW) state. We show that for this band structure, there are two possible ordered phases: A bidirectional "checkerboard" state would occur if the CDW transition temperature were sufficiently low, whereas a unidirectional "striped" state, consistent with what is observed in experiment, is favored when the transition temperature is higher. This result may also give some insight into why, in more strongly correlated systems, such as the cuprates and nickelates, the observed charge ordered states are generally stripes as opposed to checkerboards.Comment: Added contents and references, changed title and figures. Accepted to PR

Role of the Srs2-Rad51 Interaction Domain in Crossover Control in Saccharomyces cerevisiae.

Saccharomyces cerevisiae Srs2, in addition to its well-documented antirecombination activity, has been proposed to play a role in promoting synthesis-dependent strand annealing (SDSA). Here we report the identification and characterization of an SRS2 mutant with a single amino acid substitution (srs2-F891A) that specifically affects the Srs2 pro-SDSA function. This residue is located within the Srs2-Rad51 interaction domain and embedded within a protein sequence resembling a BRC repeat motif. The srs2-F891A mutation leads to a complete loss of interaction with Rad51 as measured through yeast two-hybrid analysis and a partial loss of interaction as determined through protein pull-down assays with purified Srs2, Srs2-F891A, and Rad51 proteins. Even though previous work has shown that internal deletions of the Srs2-Rad51 interaction domain block Srs2 antirecombination activity in vitro, the Srs2-F891A mutant protein, despite its weakened interaction with Rad51, exhibits no measurable defect in antirecombination activity in vitro or in vivo Surprisingly, srs2-F891A shows a robust shift from noncrossover to crossover repair products in a plasmid-based gap repair assay, but not in an ectopic physical recombination assay. Our findings suggest that the Srs2 C-terminal Rad51 interaction domain is more complex than previously thought, containing multiple interaction sites with unique effects on Srs2 activity

Tamm states and nonlinear surface modes in photonic crystals

We predict the existence of surface gap modes, known as Tamm states for electronic systems, in truncated photonic crystals formed by two types of dielectric rods. We investigate the energy threshold, dispersion, and modal symmetries of the surface modes, and also demonstrate the existence and tunability of nonlinear Tamm states in binary photonic crystals with nonlinear response.Comment: 11 pages, 3 figures, submitted to Optics Communication

Immittance Matching for Multi-dimensional Open-system Photonic Crystals

An electromagnetic (EM) Bloch wave propagating in a photonic crystal (PC) is characterized by the immittance (impedance and admittance) of the wave. The immittance is used to investigate transmission and reflection at a surface or an interface of the PC. In particular, the general properties of immittance are useful for clarifying the wave propagation characteristics. We give a general proof that the immittance of EM Bloch waves on a plane in infinite one- and two-dimensional (2D) PCs is real when the plane is a reflection plane of the PC and the Bloch wavevector is perpendicular to the plane. We also show that the pure-real feature of immittance on a reflection plane for an infinite three-dimensional PC is good approximation based on the numerical calculations. The analytical proof indicates that the method used for immittance matching is extremely simplified since only the real part of the immittance function is needed for analysis without numerical verification. As an application of the proof, we describe a method based on immittance matching for qualitatively evaluating the reflection at the surface of a semi-infinite 2D PC, at the interface between a semi-infinite slab waveguide (WG) and a semi-infinite 2D PC line-defect WG, and at the interface between a semi-infinite channel WG and a semi-infinite 2D PC slab line-defect WG.Comment: 8 pages, 6 figure

New Constraints on Cosmic Reionization from the 2012 Hubble Ultra Deep Field Campaign

Understanding cosmic reionization requires the identification and characterization of early sources of hydrogen-ionizing photons. The 2012 Hubble Ultra Deep Field (UDF12) campaign has acquired the deepest infrared images with the Wide Field Camera 3 aboard Hubble Space Telescope and, for the first time, systematically explored the galaxy population deep into the era when cosmic microwave background (CMB) data indicates reionization was underway. The UDF12 campaign thus provides the best constraints to date on the abundance, luminosity distribution, and spectral properties of early star-forming galaxies. We synthesize the new UDF12 results with the most recent constraints from CMB observations to infer redshift-dependent ultraviolet (UV) luminosity densities, reionization histories, and electron scattering optical depth evolution consistent with the available data. Under reasonable assumptions about the escape fraction of hydrogen ionizing photons and the intergalactic medium clumping factor, we find that to fully reionize the universe by redshift z~6 the population of star-forming galaxies at redshifts z~7-9 likely must extend in luminosity below the UDF12 limits to absolute UV magnitudes of M_UV\sim -13 or fainter. Moreover, low levels of star formation extending to redshifts z~15-25, as suggested by the normal UV colors of z\simeq7-8 galaxies and the smooth decline in abundance with redshift observed by UDF12 to z\simeq10, are additionally likely required to reproduce the optical depth to electron scattering inferred from CMB observations.Comment: Version accepted by ApJ (originally submitted Jan 5, 2013). The UDF12 website can be found at http://udf12.arizona.ed

Shape-based peak identification for ChIP-Seq

We present a new algorithm for the identification of bound regions from ChIP-seq experiments. Our method for identifying statistically significant peaks from read coverage is inspired by the notion of persistence in topological data analysis and provides a non-parametric approach that is robust to noise in experiments. Specifically, our method reduces the peak calling problem to the study of tree-based statistics derived from the data. We demonstrate the accuracy of our method on existing datasets, and we show that it can discover previously missed regions and can more clearly discriminate between multiple binding events. The software T-PIC (Tree shape Peak Identification for ChIP-Seq) is available at http://math.berkeley.edu/~vhower/tpic.htmlComment: 12 pages, 6 figure

FindPeaks 3.1: a tool for identifying areas of enrichment from massively parallel short-read sequencing technology

Summary: Next-generation sequencing can provide insight into protein–DNA association events on a genome-wide scale, and is being applied in an increasing number of applications in genomics and meta-genomics research. However, few software applications are available for interpreting these experiments. We present here an efficient application for use with chromatin-immunoprecipitation (ChIP-Seq) experimental data that includes novel functionality for identifying areas of gene enrichment and transcription factor binding site locations, as well as for estimating DNA fragment size distributions in enriched areas. The FindPeaks application can generate UCSC compatible custom ‘WIG’ track files from aligned-read files for short-read sequencing technology. The software application can be executed on any platform capable of running a Java Runtime Environment. Memory requirements are proportional to the number of sequencing reads analyzed; typically 4 GB permits processing of up to 40 million reads

Trigger Point Injections for Headache Disorders: Expert Consensus Methodology and Narrative Review

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/109332/1/head12442.pd

Motor Learning Induces Plasticity in the Resting Brain—Drumming Up a Connection

Neuroimaging methods have recently been used to investigate plasticity-induced changes in brain structure. However, little is known about the dynamic interactions between different brain regions after extensive coordinated motor learning such as drumming. In this article, we have compared the resting-state functional connectivity (rs-FC) in 15 novice healthy participants before and after a course of drumming (30-min drumming sessions, 3 days a week for 8 weeks) and 16 age-matched novice comparison participants. To identify brain regions showing significant FC differences before and after drumming, without a priori regions of interest, a multivariate pattern analysis was performed. Drum training was associated with an increased FC between the posterior part of bilateral superior temporal gyri (pSTG) and the rest of the brain (i.e., all other voxels). These regions were then used to perform seed-to-voxel analysis. The pSTG presented an increased FC with the premotor and motor regions, the right parietal lobe and a decreased FC with the cerebellum. Perspectives and the potential for rehabilitation treatments with exercise-based intervention to overcome impairments due to brain diseases are also discussed