Representing Graph Families with Edge Grammars

An edge grammar is a formal mechanism for representing families of related graphs (binary trees, hypercubes, meshes, etc.). Given an edge grammar, larger graphs in the family are derived from simple basis graphs using edge rewriting rules. A drawback to many graph grammars is that they cannot represent some important, highly regular graph families such as the family of shuffie-exchange graphs. Edge grammars, however, exist for all "computable " graph families, and simple edge gramma.rs exist for most regular graph families. In this paper, we define and illuskate edge grammars and analyze them in the context of formal language theory. Our results include hierarchy and decidability properties. Since this work originally was motivated by a need to represent graph families found in parallel computation, the application of edge grammars in this context is also discussed

Evaluating the Biogeochemical Cycle of Selenium in San Francisco Bay Through Modeling

A biogeochemical model was developed to simulate salinity, total suspended material, phytoplankton biomass, dissolved selenium concentrations (selenite, selenate, and organic selenide), and particulate selenium concentrations (selenite + selenate, elemental selenium, and organic selenide) in the San Francisco Bay estuary. Model-generated estuarine profiles of total dissolved selenium reproduced observed estuarine profiles at a confidence interval of 91- 99% for 8 different years under various environmental conditions. The model accurately reproduced the observed dissolved speciation at confidence intervals of 81-98% for selenite, 72-91% for selenate, and 60-96% for organic selenide. For particulate selenium, model-simulated estuarine profiles duplicated the observed behavior of total particulate selenium (76-93%), elemental selenium (80-97%), selenite + selenate (77-82%), and organic selenide (70-83%). Discrepancies between model simulations and the observed data provided insights into the estuarine biogeochemical cycle of selenium that were largely unknown (e.g., adsorption/desorption). Forecasting simulations investigated how an increase in the discharge from the San Joaquin River and varying refinery inputs affect total dissolved and particulate selenium within the estuary. These model runs indicate that during high river flows the refinery signal is undetectable, but when river flow is low (70- day residence time) total particle-associated selenium concentrations can increase to \u3e2 µg g-1 . Increasing the San Joaquin River discharge could also increase the total particle-associated selenium concentrations to \u3e1 µg g-1 . For both forecasting simulations, particle-associated selenium was predicted to be higher than current conditions and reached levels where selenium could accumulate in the estuarine food web

Change Management in the Consumer Electronics Industry

The objective of this project was to assess the stress management techniques of an engineering department within Company A, a leader in the rapidly changing consumer electronics industry. Extensive research into stress, health effects, stress and change management, and assessment tools revealed the close relationship between the manager-employee engagement level and the resulting level of felt stress. Using a seven-factor survey with a benchmark, the work environment was compared to the benchmark during business as usual and during a technology change event. The result was that Company A was strong in five areas and weak in two categories, demands and relationships, and remained so through time of change. Based on further research, specific improvement methods were recommended

The Parthenon, January 23, 2015

The Parthenon, Marshall University’s student newspaper, is published by students Monday through Friday during the regular semester and weekly Thursday during the summer. The editorial staff is responsible for the news and the editorial content

Localization of TFIIB binding regions using serial analysis of chromatin occupancy

<p>Abstract</p> <p>Background:</p> <p>RNA Polymerase II (RNAP II) is recruited to core promoters by the pre-initiation complex (PIC) of general transcription factors. Within the PIC, transcription factor for RNA polymerase IIB (TFIIB) determines the start site of transcription. TFIIB binding has not been localized, genome-wide, in metazoans. Serial analysis of chromatin occupancy (SACO) is an unbiased methodology used to empirically identify transcription factor binding regions. In this report, we use TFIIB and SACO to localize TFIIB binding regions across the rat genome.</p> <p>Results:</p> <p>A sample of the TFIIB SACO library was sequenced and 12,968 TFIIB genomic signature tags (GSTs) were assigned to the rat genome. GSTs are 20–22 base pair fragments that are derived from TFIIB bound chromatin. TFIIB localized to both non-protein coding and protein-coding loci. For 21% of the 1783 protein-coding genes in this sample of the SACO library, TFIIB binding mapped near the characterized 5' promoter that is upstream of the transcription start site (TSS). However, internal TFIIB binding positions were identified in 57% of the 1783 protein-coding genes. Internal positions are defined as those within an inclusive region greater than 2.5 kb downstream from the 5' TSS and 2.5 kb upstream from the transcription stop. We demonstrate that both TFIIB and TFIID (an additional component of PICs) bound to internal regions using chromatin immunoprecipitation (ChIP). The 5' cap of transcripts associated with internal TFIIB binding positions were identified using a cap-trapping assay. The 5' TSSs for internal transcripts were confirmed by primer extension. Additionally, an analysis of the functional annotation of mouse 3 (FANTOM3) databases indicates that internally initiated transcripts identified by TFIIB SACO in rat are conserved in mouse.</p> <p>Conclusion:</p> <p>Our findings that TFIIB binding is not restricted to the 5' upstream region indicates that the propensity for PIC to contribute to transcript diversity is far greater than previously appreciated.</p

Quantum-noise--randomized data-encryption for WDM fiber-optic networks

We demonstrate high-rate randomized data-encryption through optical fibers using the inherent quantum-measurement noise of coherent states of light. Specifically, we demonstrate 650Mbps data encryption through a 10Gbps data-bearing, in-line amplified 200km-long line. In our protocol, legitimate users (who share a short secret-key) communicate using an M-ry signal set while an attacker (who does not share the secret key) is forced to contend with the fundamental and irreducible quantum-measurement noise of coherent states. Implementations of our protocol using both polarization-encoded signal sets as well as polarization-insensitive phase-keyed signal sets are experimentally and theoretically evaluated. Different from the performance criteria for the cryptographic objective of key generation (quantum key-generation), one possible set of performance criteria for the cryptographic objective of data encryption is established and carefully considered.Comment: Version 2: Some errors have been corrected and arguments refined. To appear in Physical Review A. Version 3: Minor corrections to version

Quantum Mutual Information Capacity for High Dimensional Entangled States

High dimensional Hilbert spaces used for quantum communication channels offer the possibility of large data transmission capabilities. We propose a method of characterizing the channel capacity of an entangled photonic state in high dimensional position and momentum bases. We use this method to measure the channel capacity of a parametric downconversion state, achieving a channel capacity over 7 bits/photon in either the position or momentum basis, by measuring in up to 576 dimensions per detector. The channel violated an entropic separability bound, suggesting the performance cannot be replicated classically.Comment: 5 pages, 2 figure

A data mining study of g-quadruplexes and their effect on DNA replication

Title from PDF of title page, viewed on May 25, 2012Thesis advisor: Deendayal DinakarpandianVitaIncludes bibliographic references (p. 42-43)Thesis (M.S.)--School of Computing and Engineering. University of Missouri--Kansas City, 2012G-quadruplexes are guanine rich sequences of DNA that can form non-Watson-Crick four stranded structures. They have been found to exist in various regions of the genome and are believed to play a biological role. We hypothesize that the presence of these structures poses a barrier to DNA replication by standard DNA polymerases and thus requires the intervention of alternative robust but error-prone polymerases for the completion of DNA replication. To test this hypothesis in silico, we assumed that the presence of error-prone replication could be inferred by studying the degree of variation at these sites. We analyzed the density of single nucleotide polymorphisms in the neighborhood of potential Gquadruplex sequences in the human genome. The analysis shows a significantly higher density of single nucleotide polymorphisms within G-quadruplexes. Further, there is evidence of a directional bias in the extent of error, seen as an asymmetry in the incidence of single nucleotide polymorphisms on either side of quadruplexes. Taken together, the evidence favors the hypothesis that G-quadruplexes have a deleterious effect on the fidelity of DNA replication. A secondary research goal of the thesis is to reduce the number of false positives in the prediction of G-quadruplexes based only on sequence information. Most current algorithms are regular expression searches based on sequences that have shown potential to form G-quadruplexes. Using the results from our investigation on sequence variation, predicted melting temperature and machine learning models, attributes derived solely from the sequences were analyzed to determine if classification can be accurately performed. We conclude that factors external to the sequence may be important in determining if and when G-quadruplexes form.Introduction -- SNP dentistry analysis -- Melting temperature analysis -- Machine learning analysis -- Conclusio

Devloping a Course in the History of Biology

Studies in course design have indicated that it is much more efficient to implement an active learning environment for students. Participation through discussions and activities results in a greater intake of knowledge by the students. This course was designed to incorporate multidisciplinary skills in the classroom. The History of Biology integrates a scientific lab section with a history class. Microscopes is a sample unit in the course and incorporates scientific concepts and historical information.The lab section introduces the students to the lesson by having them use critical thinking skills in order to grasp important concepts prior to the lecture. Other project ideas have been included to show an approach to a different historical time period with modern scientific advancements