Earthquake Size Distribution: Power-Law with Exponent Beta = 1/2?

We propose that the widely observed and universal Gutenberg-Richter relation is a mathematical consequence of the critical branching nature of earthquake process in a brittle fracture environment. These arguments, though preliminary, are confirmed by recent investigations of the seismic moment distribution in global earthquake catalogs and by the results on the distribution in crystals of dislocation avalanche sizes. We consider possible systematic and random errors in determining earthquake size, especially its seismic moment. These effects increase the estimate of the parameter beta of the power-law distribution of earthquake sizes. In particular, we find that estimated beta-values may be inflated by 1-3% because relative moment uncertainties decrease with increasing earthquake size. Moreover, earthquake clustering greatly influences the beta-parameter. If clusters (aftershock sequences) are taken as the entity to be studied, then the exponent value for their size distribution would decrease by 5-10%. The complexity of any earthquake source also inflates the estimated beta-value by at least 3-7%. The centroid depth distribution also should influence the beta-value, an approximate calculation suggests that the exponent value may be increased by 2-6%. Taking all these effects into account, we propose that the recently obtained beta-value of 0.63 could be reduced to about 0.52--0.56: near the universal constant value (1/2) predicted by theoretical arguments. We also consider possible consequences of the universal beta-value and its relevance for theoretical and practical understanding of earthquake occurrence in various tectonic and Earth structure environments. Using comparative crystal deformation results may help us understand the generation of seismic tremors and slow earthquakes and illuminate the transition from brittle fracture to plastic flow.Comment: 46 pages, 2 tables, 11 figures 53 pages, 2 tables, 12 figure

Strangeness in Compact Stars

We discuss the impact of strange hadrons, in particular hyperons, on the gross features of compact stars and on core-collapse supernovae. Hyperons are likely to be the first exotic species which appears around twice normal nuclear matter density in the core of neutron stars. Their presence largely influences the mass-radius relation of compact stars, the maximum mass, the cooling of neutron stars, the stability with regard to the emission of gravitational waves from rotation-powered neutron stars and the possible early onset of the QCD phase transition in core-collapse supernovae. We outline also the constraints from subthreshold kaon production in heavy-ion collisions for the maximum possible mass of neutron stars.Comment: 8 pages, invited talk given at the 10th International Conference on Hypernuclear and Strange Particle Physics (HYP-X) September 14-18, 2009, Tokai, Ibaraki, Japan, ref. and acknowledgment adde

Expanding the MicroRNA Targeting Code: Functional Sites with Centered Pairing

Most metazoan microRNA (miRNA) target sites have perfect pairing to the seed region, located near the miRNA 5′ end. Although pairing to the 3′ region sometimes supplements seed matches or compensates for mismatches, pairing to the central region has been known to function only at rare sites that impart Argonaute-catalyzed mRNA cleavage. Here, we present “centered sites,” a class of miRNA target sites that lack both perfect seed pairing and 3′-compensatory pairing and instead have 11–12 contiguous Watson-Crick pairs to the center of the miRNA. Although centered sites can impart mRNA cleavage in vitro (in elevated Mg[superscript 2+]), in cells they repress protein output without consequential Argonaute-catalyzed cleavage. Our study also identified extensively paired sites that are cleavage substrates in cultured cells and human brain. This expanded repertoire of cleavage targets and the identification of the centered site type help explain why central regions of many miRNAs are evolutionarily conserved.National Institutes of Health (U.S.)Damon Runyon Cancer Research Foundation. Fellowship Awar

Chemical speciation and mobilization of copper and zinc in naturally contaminated mine soils with citric and tartaric acids

A one-step extraction procedure and a leaching column experiment were performed to assess the effects of citric and tartaric acids on Cu and Zn mobilization in naturally contaminated mine soils to facilitate assisted phytoextraction. A speciation modeling of the soil solution and the metal fractionation of soils were performed to elucidate the chemical processes that affected metal desorption by organic acids. Different extracting solutions were prepared, all of which contained 0.01 M KNO3 and different concentrations of organic acids: control without organic acids, 0.5 mM citric, 0.5 mM tartaric, 10 mM citric, 10 mM tartaric, and 5 mM citric +5 mM tartaric. The results of the extraction procedure showed that higher concentrations of organic acids increased metal desorption, and citric acid was more effective at facilitating metal desorption than tartaric acid. Metal desorption was mainly influenced by the decreasing pH and the dissolution of Fe and Mn oxides, not by the formation of soluble metal–organic complexes as was predicted by the speciation modeling. The results of the column study reported that low concentrations of organic acids did not significantly increase metal mobilization and that higher doses were also not able to mobilize Zn. However, 5–10 mM citric acid significantly promoted Cu mobilization (from 1 mg kg−1 in the control to 42 mg kg−1 with 10 mM citric acid) and reduced the exchangeable (from 21 to 3 mg kg−1) and the Fe and Mn oxides (from 443 to 277 mg kg−1) fractions. Citric acid could efficiently facilitate assisted phytoextraction techniques

Quantitative principles of cis-translational control by general mRNA sequence features in eukaryotes.

BackgroundGeneral translational cis-elements are present in the mRNAs of all genes and affect the recruitment, assembly, and progress of preinitiation complexes and the ribosome under many physiological states. These elements include mRNA folding, upstream open reading frames, specific nucleotides flanking the initiating AUG codon, protein coding sequence length, and codon usage. The quantitative contributions of these sequence features and how and why they coordinate to control translation rates are not well understood.ResultsHere, we show that these sequence features specify 42-81% of the variance in translation rates in Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, Mus musculus, and Homo sapiens. We establish that control by RNA secondary structure is chiefly mediated by highly folded 25-60 nucleotide segments within mRNA 5' regions, that changes in tri-nucleotide frequencies between highly and poorly translated 5' regions are correlated between all species, and that control by distinct biochemical processes is extensively correlated as is regulation by a single process acting in different parts of the same mRNA.ConclusionsOur work shows that general features control a much larger fraction of the variance in translation rates than previously realized. We provide a more detailed and accurate understanding of the aspects of RNA structure that directs translation in diverse eukaryotes. In addition, we note that the strongly correlated regulation between and within cis-control features will cause more even densities of translational complexes along each mRNA and therefore more efficient use of the translation machinery by the cell

Unique and conserved MicroRNAs in wheat chromosome 5D revealed by next-generation sequencing

MicroRNAs are a class of short, non-coding, single-stranded RNAs that act as post-transcriptional regulators in gene expression. miRNA analysis of Triticum aestivum chromosome 5D was performed on 454 GS FLX Titanium sequences of flow sorted chromosome 5D with a total of 3,208,630 good quality reads representing 1.34x and 1.61x coverage of the short (5DS) and long (5DL) arms of the chromosome respectively. In silico and structural analyses revealed a total of 55 miRNAs; 48 and 42 miRNAs were found to be present on 5DL and 5DS respectively, of which 35 were common to both chromosome arms, while 13 miRNAs were specific to 5DL and 7 miRNAs were specific to 5DS. In total, 14 of the predicted miRNAs were identified in wheat for the first time. Representation (the copy number of each miRNA) was also found to be higher in 5DL (1,949) compared to 5DS (1,191). Targets were predicted for each miRNA, while expression analysis gave evidence of expression for 6 out of 55 miRNAs. Occurrences of the same miRNAs were also found in Brachypodium distachyon and Oryza sativa genome sequences to identify syntenic miRNA coding sequences. Based on this analysis, two other miRNAs: miR1133 and miR167 were detected in B. distachyon syntenic region of wheat 5DS. Five of the predicted miRNA coding regions (miR6220, miR5070, miR169, miR5085, miR2118) were experimentally verified to be located to the 5D chromosome and three of them : miR2118, miR169 and miR5085, were shown to be 5D specific. Furthermore miR2118 was shown to be expressed in Chinese Spring adult leaves. miRNA genes identified in this study will expand our understanding of gene regulation in bread wheat

Genome-Wide Expression Profiling of the <i>Arabidopsis</i> Female Gametophyte Identifies Families of Small, Secreted Proteins

The female gametophyte of flowering plants, the embryo sac, develops within the diploid (sporophytic) tissue of the ovule. While embryo sac–expressed genes are known to be required at multiple stages of the fertilization process, the set of embryo sac–expressed genes has remained poorly defined. In particular, the set of genes responsible for mediating intracellular communication between the embryo sac and the male gametophyte, the pollen grain, is unknown. We used high-throughput cDNA sequencing and whole-genome tiling arrays to compare gene expression in wild-type ovules to that in dif1 ovules, which entirely lack embryo sacs, and myb98 ovules, which are impaired in pollen tube attraction. We identified nearly 400 genes that are downregulated in dif1 ovules. Seventy-eight percent of these embryo sac–dependent genes were predicted to encode for secreted proteins, and 60% belonged to multigenic families. Our results define a large number of candidate extracellular signaling molecules that may act during embryo sac development or fertilization; less than half of these are represented on the widely used ATH1 expression array. In particular, we found that 37 out of 40 genes encoding Domain of Unknown Function 784 (DUF784) domains require the synergid-specific transcription factor MYB98 for expression. Several DUF784 genes were transcribed in synergid cells of the embryo sac, implicating the DUF784 gene family in mediating late stages of embryo sac development or interactions with pollen tubes. The coexpression of highly similar proteins suggests a high degree of functional redundancy among embryo sac genes.</p

The depression impairment scale for parents (DISP): a new scale for the measurement of impairment in depressed parents

Children of depressed parents are at increased risk of developing mood disorders but mechanisms of intrafamilial transmission are currently unclear. One rarely investigated area is the impact of depression on a parent's everyday functioning. Currently there are no validated assessments of depression-specific parental impairment. The creation of such a measure would complement depression symptom counts, providing a more comprehensive account of the parent's depression. We therefore aimed to develop a valid and reliable measure of impairment specifically associated with parental depression. In a longitudinal study of parents with recurrent unipolar depression and their offspring, we collected data from 337 parents. These participants completed the Depression Impairment Scale for Parents (DISP), a questionnaire assessing depression-associated impairment in multiple domains of functioning. Factor analysis revealed that this measure consisted of two factors - impairment in routine tasks/activities and impairment in family functioning - that together accounted for 51.04% of variance. The scale evidenced good internal consistency (Cronbach's alpha=0.82). The DISP also displayed good construct and criterion validity as evidenced by significant associations with established measures of depression severity and global impairment. These results demonstrate that the DISP is a valid and reliable measure of depression-associated impairment in parents. © 2013 Elsevier Ireland Ltd

Supermassive Black Holes in Galactic Nuclei: Past, Present and Future Research

This review discusses the current status of supermassive black hole research, as seen from a purely observational standpoint. Since the early '90s, rapid technological advances, most notably the launch of the Hubble Space Telescope, the commissioning of the VLBA and improvements in near-infrared speckle imaging techniques, have not only given us incontrovertible proof of the existence of supermassive black holes, but have unveiled fundamental connections between the mass of the central singularity and the global properties of the host galaxy. It is thanks to these observations that we are now, for the first time, in a position to understand the origin, evolution and cosmic relevance of these fascinating objects.Comment: Invited Review, 114 pages. Because of space requirements, this version contains low resolution figures. The full resolution version can be downloaded from http://www.physics.rutgers.edu/~lff/publications.htm