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

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

The Rumsfeld Paradigm: Knowns and Unknowns in Characterizing Habitats Used by the Endangered Sharp-tailed Snake, Contia tenuis, in Southwestern British Columbia

The Sharp-tailed Snake, Contia tenuis, has a small and highly fragmented range in British Columbia, where it is considered endangered. Known sites are few in number and generally small in spatial extent; numbers of snakes apparently are correspondingly low. Furthermore, most known sites for the species are on private lands in areas that are fairly heavily developed or being developed. Thus, the species is under serious threat of habitat alteration or loss. Although land stewardship has been a valuable conservation tool in this case, we also need to identify the key habitat requirements of Sharp-tailed Snakes to identify potential new sites, modify former or potential ones, or even create new ones. In this study, we compared sites known to harbour Sharp-tailed Snakes with those that seemed subjectively similar and therefore potentially suitable. We also compared these known and potential sites with randomly chosen nearby locations. Variability of most measured features was high, both within and among site/location categories. Nonetheless, we found significant differences between known and potential sites and between those locations and random ones. Overall, locations known to be used by snakes had a more southerly aspect, more rock cover, shallower soil and litter, and less shrub cover than other sites. This study was constrained by the small number of known sites for Sharp-tailed Snakes in southwestern British Columbia, making our conclusions suggestive rather than definitive. Future work should incorporate additional variables. It also might be useful to undertake comparative habitat studies elsewhere in the range of the Sharp-tailed Snake where it is more common

Blind ending vessels on diagnostic laparoscopy for nonpalpable testis: Is a nubbin present?

IntroductionThe traditional management paradigm for nonpalpable testis (NPT) has been that inguinal or scrotal exploration for a nubbin may be omitted when blind ending vessels are observed during diagnostic laparoscopy. Our aim was to examine whether blind ending vessels excluded the presence of a nubbin in a series of boys who underwent exploration in this setting.Materials and methodsUsing a surgical database and chart review, pre-pubertal boys (≤12 years) with the diagnosis of undescended or atrophic testis who underwent a diagnostic laparoscopy for unilateral NPT between 2000 and 2015 were retrospectively identified. Physical exam, procedural and pathologic findings were confirmed by chart review.Results595 boys underwent diagnostic laparoscopy for NPT by 11 surgeons. Of these, 318 had an intra-abdominal testis and 18 underwent diagnostic laparoscopy alone. Of the remaining 259, 32 had an open internal ring and inguinal or scrotal exploration was performed. The remaining 227 with a closed ring comprised the cohort for our analysis, of whom 188 had vessels entering the ring, 36 had blind ending vessels, and in three the vessel status was unavailable. In the 188 boys with vessels entering the ring, 164 (87%) had a nubbin excised during inguinal or scrotal exploration, of which 93% were grossly identified as an atrophic testis. Pathology confirmed the presence of hemosiderin in 44% and calcifications in 54%. In the 36 boys with blind ending vessels, 26 (72%) had a nubbin excised during inguinal or scrotal exploration, of which 96% were grossly identified as an atrophic testis. Pathology confirmed hemosiderin in 54% and calcifications in 58%. All seven cases with both blind ending vas and vessels had an atrophic testis grossly identified. Of all 207 excised remnants in this series, nubbins with viable testicular elements (seminiferous tubules in 11, germ cells in two) were only excised during cases that reported a non-atretic vas or any vessels entering the internal ring.ConclusionIn this large multi-institutional series, blind ending vessels were associated with a nubbin noted during inguinal or scrotal exploration in the majority of cases. Based on this series if the surgeon's goal is to remove all nubbins, exploration is necessary regardless of vessel appearance. However, viable testicular elements were rarely identified and only when either a non-atretic vas or any vessels were observed to enter the ring