The Substance of a Sermon

The Substance of a Sermon, by Elijah Hedding

3'-UTR SIRF: A database for identifying clusters of short interspersed repeats in 3' untranslated regions

BACKGROUND:Short (~5 nucleotides) interspersed repeats regulate several aspects of post-transcriptional gene expression. Previously we developed an algorithm (REPFIND) that assigns P-values to all repeated motifs in a given nucleic acid sequence and reliably identifies clusters of short CAC-containing motifs required for mRNA localization in Xenopus oocytes.DESCRIPTION:In order to facilitate the identification of genes possessing clusters of repeats that regulate post-transcriptional aspects of gene expression in mammalian genes, we used REPFIND to create a database of all repeated motifs in the 3' untranslated regions (UTR) of genes from the Mammalian Gene Collection (MGC). The MGC database includes seven vertebrate species: human, cow, rat, mouse and three non-mammalian vertebrate species. A web-based application was developed to search this database of repeated motifs to generate species-specific lists of genes containing specific classes of repeats in their 3'-UTRs. This computational tool is called 3'-UTR SIRF (Short Interspersed Repeat Finder), and it reveals that hundreds of human genes contain an abundance of short CAC-rich and CAG-rich repeats in their 3'-UTRs that are similar to those found in mRNAs localized to the neurites of neurons. We tested four candidate mRNAs for localization in rat hippocampal neurons by in situ hybridization. Our results show that two candidate CAC-rich (Syntaxin 1B and Tubulin beta4) and two candidate CAG-rich (Sec61alpha and Syntaxin 1A) mRNAs are localized to distal neurites, whereas two control mRNAs lacking repeated motifs in their 3'-UTR remain primarily in the cell body.CONCLUSION:Computational data generated with 3'-UTR SIRF indicate that hundreds of mammalian genes have an abundance of short CA-containing motifs that may direct mRNA localization in neurons. In situ hybridization shows that four candidate mRNAs are localized to distal neurites of cultured hippocampal neurons. These data suggest that short CA-containing motifs may be part of a widely utilized genetic code that regulates mRNA localization in vertebrate cells. The use of 3'-UTR SIRF to search for new classes of motifs that regulate other aspects of gene expression should yield important information in future studies addressing cis-regulatory information located in 3'-UTRs.

Efficient Support for Common Relations in Lightweight Formal Reasoning Systems

In work that involves mathematical rigor, there are numerous benefits to adopting a representation of models and arguments that can be supplied to a formal reasoning or verification system: reusability, automatic evaluation of examples, and verification of consistency and correctness. However, accessibility has not been a priority in the design of formal verification tools that can provide these benefits. In earlier work [Lap09a], we attempt to address this broad problem by proposing several specific design criteria organized around the notion of a natural context: the sphere of awareness a working human user maintains of the relevant constructs, arguments, experiences, and background materials necessary to accomplish the task at hand. This work expands one aspect of the earlier work by considering more extensively an essential capability for any formal reasoning system whose design is oriented around simulating the natural context: native support for a collection of mathematical relations that deal with common constructs in arithmetic and set theory. We provide a formal definition for a context of relations that can be used to both validate and assist formal reasoning activities. We provide a proof that any algorithm that implements this formal structure faithfully will necessary converge. Finally, we consider the efficiency of an implementation of this formal structure that leverages modular implementations of well-known data structures: balanced search trees and transitive closures of hypergraphs.

Atomic layer deposition of copper – study through density functional theory

The wonder of the last century has been the rapid development in technology. One of the sectors that it has touched immensely is the electronic industry. There has been exponential development in the field and scientists are pushing new horizons. There is an increased dependence in technology for every individual from different strata in the society. Atomic Layer Deposition (ALD) is a unique technique for growing thin films. It is widely used in the semiconductor industry. Films as thin as few nanometers can be deposited using this technique. Although this process has been explored for a variety of oxides, sulphides and nitrides, a proper method for deposition of many metals is missing. Metals are often used in the semiconductor industry and hence are of significant importance. A deficiency in understanding the basic chemistry at the nanoscale for possible reactions has delayed the improvement in metal ALD. In this thesis, we study the intrinsic chemistry involved for Cu ALD. This work reports computational study using Density Functional Theory as implemented in TURBOMOLE program. Both the gas phase and surface reactions are studied in most of the cases. The merits and demerits of a promising transmetallation reaction have been evaluated at the beginning of the study. Further improvements in the structure of precursors and coreagent have been proposed. This has led to the proposal of metallocenes as co-reagents and Cu(I) carbene compounds as new set of precursors. A three step process for Cu ALD that generates ligand free Cu layer after every ALD pulse has also been studied. Although the chemistry has been studied under the umbrella of Cu ALD the basic principles hold true for ALD of other metals (e.g. Co, Ni, Fe ) and also for other branches of science like thin film deposition other than ALD, electrochemical reactions, etc.

At the Vanguard of Design Science: First Impressions and Early Findings from Ongoing Research

Published Version

STUDIES AND PERFORMANCES OF TRANSCRIPTIONS FOR CELLO FROM THE VIOLIN REPERTOIRE

The potential of the violoncello as a solo instrument was recognized and supported by cellists such as Luigi Boccherini (1743-1805), Luis Duport (1749-1819), Auguste Franchomme (1808-1884), and Alfredo Piatti (1822-1901). These pioneers composed technically demanding etudes, exercises, and caprices for the cello that were comparable to those already present in the violin literature. Even so, in the late nineteenth century and early twentieth century, considerably fewer substantial works were brought forth for the cello as compared with the violin. Consequently, many cellists such as Luigi Silva (1903-1961), Gregor Piatigorsky (1903-1976), Pierre Fournier (1906-1986), and Janos Starker (b. 1924) selected notable pieces from the violin repertoire and transcribed these for the cello. Some composers themselves actually adapted for the cello their own works originally written for the violin. Johannes Brahms with his Violin Sonata Op. 78, Igor Stravinsky with his Suite Italienne, and Béla Bartók with his First Rhapsody all belong to this category. Adaptations such as these further raised awareness among composers and performers of the possibilities of the cello as an independent and expressive instrument. Thus, many composers from the early 1900s to the present were encouraged to write increasing numbers of more soloistic and demanding works for cello. Herein, I explore the repertoire of cello transcriptions in order to analyze the differences between the original and transcribed versions and the challenges found therein. The performer may attempt to recreate the effect originally intended for the violin or, more daringly, may strive to search for alternate presentations of the music more suitable and expressive of the cello's own character. The project includes two recitals of the following transcribed works presented at the University of Maryland College Park, School of Music: Sonata in A by César Franck, transcribed by Jules Delsart, Variations on a Theme from Rossini by Nicolo Paganini, transcribed by Fournier, Suite Italienne by Igor Stravinsky, transcribed with the help of Piatigorsky, Sonatina Op. 137, No. 1 by Franz Schubert, transcribed by Starker, First Rhapsody by Béla Bartók and Sonata, Op. 108 by Johannes Brahms, transcribed by Hsiao-mei Sun.

Eco-evolutionary dynamics: intertwining ecological and evolutionary processes in contemporary time.

Evolution occurring over contemporary time scales can have important effects on populations, communities, and ecosystems. Recent studies show that the magnitude of these effects can be large and can generate feedbacks that further shape evolution.

Mechanical regulation of chondrogenesis.

Mechanical factors play a crucial role in the development of articular cartilage in vivo. In this regard, tissue engineers have sought to leverage native mechanotransduction pathways to enhance in vitro stem cell-based cartilage repair strategies. However, a thorough understanding of how individual mechanical factors influence stem cell fate is needed to predictably and effectively utilize this strategy of mechanically-induced chondrogenesis. This article summarizes some of the latest findings on mechanically stimulated chondrogenesis, highlighting several new areas of interest, such as the effects of mechanical stimulation on matrix maintenance and terminal differentiation, as well as the use of multifactorial bioreactors. Additionally, the roles of individual biophysical factors, such as hydrostatic or osmotic pressure, are examined in light of their potential to induce mesenchymal stem cell chondrogenesis. An improved understanding of biomechanically-driven tissue development and maturation of stem cell-based cartilage replacements will hopefully lead to the development of cell-based therapies for cartilage degeneration and disease.

Colonizing the heart from the epicardial side.

The clinical use of stem cells, such as bone marrow-derived and, more recently, resident cardiac stem cells, offers great promise for treatment of myocardial infarction and heart failure. The epicardium-derived cells have also attracted attention for their angiogenic paracrine actions and ability to differentiate into cardiomyocytes and vascular cells when activated during cardiac injury. In a recent study, Chong and colleagues have described a distinct population of epicardium-derived mesenchymal stem cells that reside in a perivascular niche of the heart and have a broad multilineage potential. Exploring the therapeutic capacity of these cells will be an exciting future endeavor.

Jung’s cultural writing: spiral essays and performing symbols (in literature)

Performance is a key ingredient of Jung’s writings on culture and of the function of the Jungian symbol in literature. This paper will compare and contrast Jung’s performance of cultural analysis and healing in his essays with the way his notion of the symbol works in literature to knit the individual psyche into the collective. It will explore Jung’s unique essay form of the spiral as a literary innovation, and look at the way a Jungian reading of literary reveals a significant contribution to cultural studies. [From the Author]

Loris Gréaud — french and fanciful

Review of ICA exhibition by Loris Gréaud