Polarization rotation via a monoclinic phase in the piezoelectric 92%PbZn1/3Nb2/3O3-8%PbTiO3

The origin of ultrahigh piezoelectricity in the relaxor ferroelectric PbZn1/3Nb2/3O3-PbTiO3 was studied with an electric field applied along the [001] direction. The zero-field rhombohedral R phase starts to follow the direct polarization path to tetragonal symmetry via an intermediate monoclinic M phase, but then jumps irreversibly to an alternate path involving a different type of monoclinic distortion. Details of the structure and domain configuration of this novel phase are described. This result suggests that there is a nearby R-M phase boundary as found in the Pb(Ti,Zr)O3 system.Comment: REVTeX file. 4 pages. New version after referees' comment

Boundary-crossing identities for diffusions having the time-inversion property

We review and study a one-parameter family of functional transformations, denoted by (S (β)) β∈ℝ, which, in the case β<0, provides a path realization of bridges associated to the family of diffusion processes enjoying the time-inversion property. This family includes Brownian motions, Bessel processes with a positive dimension and their conservative h-transforms. By means of these transformations, we derive an explicit and simple expression which relates the law of the boundary-crossing times for these diffusions over a given function f to those over the image of f by the mapping S (β), for some fixed β∈ℝ. We give some new examples of boundary-crossing problems for the Brownian motion and the family of Bessel processes. We also provide, in the Brownian case, an interpretation of the results obtained by the standard method of images and establish connections between the exact asymptotics for large time of the densities corresponding to various curves of each family

Neutron Diffraction Study of Field Cooling Effects on Relaxor Ferroelectrics Pb[(Zn_{1/3} Nb_{2/3})_{0.92} Ti_{0.08}] O_{3}

High-temperature (T) and high-electric-field (E) effects on Pb[(Zn_{1/3} Nb_{2/3})_{0.92} Ti_{0.08}]O_3 (PZN-8%PT) were studied comprehensively by neutron diffraction in the ranges 300 <= T <= 550 K and 0 <= E <= 15 kV/cm. We have focused on how phase transitions depend on preceding thermal and electrical sequences. In the field cooling process (FC, E parallel [001] >= 0.5 kV/cm), a successive cubic (C) --> tetragonal (T) --> monoclinic (M_C) transition was observed. In the zero field cooling process (ZFC), however, we have found that the system does not transform to the rhombohedral (R) phase as widely believed, but to a new, unidentified phase, which we call X. X gives a Bragg peak profile similar to that expected for R, but the c-axis is always slightly shorter than the a-axis. As for field effects on the X phase, we found an irreversible X --> M_C transition via another monoclinic phase (M_A) as expected from a previous report [Noheda et al. Phys. Rev. Lett. 86, 3891 (2001)]. At a higher electric field, we confirmed a c-axis jump associated with the field-induced M_C --> T transition, which was observed by strain and x-ray diffraction measurements.Comment: 8 pages, 9 figures, revise

The Sequence Ontology: a tool for the unification of genome annotations

The Sequence Ontology ( SO) is a structured controlled vocabulary for the parts of a genomic annotation. SO provides a common set of terms and definitions that will facilitate the exchange, analysis and management of genomic data. Because SO treats part-whole relationships rigorously, data described with it can become substrates for automated reasoning, and instances of sequence features described by the SO can be subjected to a group of logical operations termed extensional mereology operators

Origin of the high piezoelectric response in PbZr(1-x)TixO3

High resolution x-ray powder diffraction measurements on poled PbZr(1-x)TixO3 (PZT) ceramic samples close to the rhombohedral-tetragonal phase boundary (the so-called morphotropic phase boundary, MPB) have shown that for both rhombohedral and tetragonal compositions, the piezoelectric elongation of the unit cell does not occur along the polar directions but along those directions associated with the monoclinic distortion. This work provides the first direct evidence for the origin of the very high piezoelectricity in PZT.Comment: 4 pages, 4 EPS figures embedded. More specific title and abstract. To appear in Phys. Rev. Let

Rank Statistics in Biological Evolution

We present a statistical analysis of biological evolution processes. Specifically, we study the stochastic replication-mutation-death model where the population of a species may grow or shrink by birth or death, respectively, and additionally, mutations lead to the creation of new species. We rank the various species by the chronological order by which they originate. The average population N_k of the kth species decays algebraically with rank, N_k ~ M^{mu} k^{-mu}, where M is the average total population. The characteristic exponent mu=(alpha-gamma)/(alpha+beta-gamma)$ depends on alpha, beta, and gamma, the replication, mutation, and death rates. Furthermore, the average population P_k of all descendants of the kth species has a universal algebraic behavior, P_k ~ M/k.Comment: 4 pages, 3 figure

Addition-Deletion Networks

We study structural properties of growing networks where both addition and deletion of nodes are possible. Our model network evolves via two independent processes. With rate r, a node is added to the system and this node links to a randomly selected existing node. With rate 1, a randomly selected node is deleted, and its parent node inherits the links of its immediate descendants. We show that the in-component size distribution decays algebraically, c_k ~ k^{-beta}, as k-->infty. The exponent beta=2+1/(r-1) varies continuously with the addition rate r. Structural properties of the network including the height distribution, the diameter of the network, the average distance between two nodes, and the fraction of dangling nodes are also obtained analytically. Interestingly, the deletion process leads to a giant hub, a single node with a macroscopic degree whereas all other nodes have a microscopic degree.Comment: 8 pages, 5 figure

Transcriptional profiling of the ductus arteriosus: Comparison of rodent microarrays and human RNA sequencing

DA closure is crucial for the transition from fetal to neonatal life. This closure is supported by changes to the DA’s signaling and structural properties that distinguish it from neighboring vessels. Examining transcriptional differences between these vessels is key to identifying genes or pathways responsible for DA closure. Several microarray studies have explored the DA transcriptome in animal models but varied experimental designs have led to conflicting results. Thorough transcriptomic analysis of the human DA has yet to be performed. A clear picture of the DA transcriptome is key to guiding future research endeavors, both to allow more targeted treatments in the clinical setting, and to understand the basic biology of DA function. In this review, we use a cross-species cross-platform analysis to consider all available published rodent microarray data and novel human RNAseq data in order to provide high priority candidate genes for consideration in future DA studies

HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

The resolution of genome-wide association studies (GWAS) is limited by the linkage disequilibrium (LD) structure of the population being studied. Selecting the most likely causal variants within an LD block is relatively straightforward within coding sequence, but is more difficult when all variants are intergenic. Predicting functional non-coding sequence has been recently facilitated by the availability of conservation and epigenomic information. We present HaploReg, a tool for exploring annotations of the non-coding genome among the results of published GWAS or novel sets of variants. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state in nine cell types, conservation across mammals and their effect on regulatory motifs. Sets of SNPs, such as those resulting from GWAS, are analyzed for an enrichment of cell type-specific enhancers. HaploReg will be useful to researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation. The HaploReg database is available at http://compbio.mit.edu/HaploReg.National Institutes of Health (U.S.) (R01-HG004037)National Institutes of Health (U.S.) (RC1-HG005334)National Science Foundation (U.S.) (HG005334

Error, reproducibility and sensitivity : a pipeline for data processing of Agilent oligonucleotide expression arrays

Background Expression microarrays are increasingly used to obtain large scale transcriptomic information on a wide range of biological samples. Nevertheless, there is still much debate on the best ways to process data, to design experiments and analyse the output. Furthermore, many of the more sophisticated mathematical approaches to data analysis in the literature remain inaccessible to much of the biological research community. In this study we examine ways of extracting and analysing a large data set obtained using the Agilent long oligonucleotide transcriptomics platform, applied to a set of human macrophage and dendritic cell samples. Results We describe and validate a series of data extraction, transformation and normalisation steps which are implemented via a new R function. Analysis of replicate normalised reference data demonstrate that intrarray variability is small (only around 2% of the mean log signal), while interarray variability from replicate array measurements has a standard deviation (SD) of around 0.5 log2 units ( 6% of mean). The common practise of working with ratios of Cy5/Cy3 signal offers little further improvement in terms of reducing error. Comparison to expression data obtained using Arabidopsis samples demonstrates that the large number of genes in each sample showing a low level of transcription reflect the real complexity of the cellular transcriptome. Multidimensional scaling is used to show that the processed data identifies an underlying structure which reflect some of the key biological variables which define the data set. This structure is robust, allowing reliable comparison of samples collected over a number of years and collected by a variety of operators. Conclusions This study outlines a robust and easily implemented pipeline for extracting, transforming normalising and visualising transcriptomic array data from Agilent expression platform. The analysis is used to obtain quantitative estimates of the SD arising from experimental (non biological) intra- and interarray variability, and for a lower threshold for determining whether an individual gene is expressed. The study provides a reliable basis for further more extensive studies of the systems biology of eukaryotic cells