Digital Commons Network^™

Cluster J Mycobacteriophages: Intron Splicing In Capsid And Tail Genes, Welkin H. Pope, Deborah Jacobs-Sera, Aaron A. Best, Gregory W. Broussard, Pamela L. Connerly, Rebekah M. Dedrick, Timothy A. Kremer, Susan Offner, Amenawon H. Ogiefo, Marie C. Pizzorno, Kate Rochenbach, Daniel A. Russell, Emily L. Stowe, Joseph Stukey, Sarah A. Thibault, James F. Conway, Roger W. Hendrix, Graham F. Hatfull

Faculty Publications

Bacteriophages isolated on Mycobacterium smegmatis mc2155 represent many distinct genomes sharing little or no DNA sequence similarity. The genomes are architecturally mosaic and are replete with genes of unknown function. A new group of genomes sharing substantial nucleotide sequences constitute Cluster J. The six mycobacteriophages forming Cluster J are morphologically members of the Siphoviridae, but have unusually long genomes ranging from 106.3 to 117 kbp. Reconstruction of the capsid by cryo-electron microscopy of mycobacteriophage BAKA reveals an icosahedral structure with a triangulation number of 13. All six phages are temperate and homoimmune, and prophage establishment involves integration into a tRNA-Leu …

Cognitively Normal Individuals With Ad Parents May Be At Risk For Developing Aging-Related Cortical Thinning Patterns Characteristic Of Ad, Derin J. Cobia, Katherine Reiter, Kathryn I. Alpert, Mary J. Kwasny, John C. Morris, John G. Csernansky, Lei Wang

Faculty Publications

Children of Alzheimer's Disease (AD) patients are at heightened risk of developing AD due to genetic influences, including the apolipoprotein E4 (ApoE4) allele. In this study, we assessed the earliest cortical changes associated with AD in 71 cognitively healthy, adult children of AD patients (AD offspring) as compared with 69 with no family history of AD (non-AD offspring). Cortical thickness measures were obtained using FreeSurfer from 1.5T magnetic resonance (MR) scans. ApoE genotyping was obtained. Primary analyses examined family history and ApoeE4 effects on cortical thickness. Secondary analyses examined age effects within groups. All comparisons were adjusted using False Discovery …

Improving Patient-Centered Care: Personal Models Of Depression Among Older Male Veterans, Erin Woodhead, Sarah Brunskill, J. Lisa Tenover, Joung Huh

Faculty Publications

A quality improvement project was undertaken at the Geriatric Research Education and Clinical Center at the VA Palo Alto Health Care System to better understand how older veterans think about depression diagnosis and treatment so that patient education efforts and communication between older veterans and their health care providers could be improved.

Decades-Long Social Memory In Bottlenose Dolphins, Jason N. Bruck

Faculty Publications

Long-term social memory is important, because it is an ecologically relevant test of cognitive capacity, it helps us understand which social relationships are remembered and it relates two seemingly disparate disciplines: cognition and sociality. For dolphins, long-term memory for conspecifics could help assess social threats as well as potential social or hunting alliances in a very fluid and complex fission-fusion social system, yet we have no idea how long dolphins can remember each other. Through a playback study conducted within a multi-institution dolphin breeding consortium (where animals are moved between different facilities), recognition of unfamiliar versus familiar signature whistles of …

Inhibition Of Soluble Epoxide Hydrolase By Fulvestrant And Sulfoxides, Christophe Morisseau, Svitlana Pakhomova, Sung Hee Hwang, Marcia E. Newcomer, Bruce D. Hammock

Faculty Publications

The soluble epoxide hydrolase (sEH) is a key enzyme in the metabolism of epoxy-fatty acids, signaling molecules involved in numerous biologies. Toward finding novel inhibitors of sEH, a library of known drugs was tested for inhibition of sEH. We found that fulvestrant, an anticancer agent, is a potent (KI = 26 nM) competitive inhibitor of sEH. From this observation, we found that alkyl-sulfoxides represent a new kind of pharmacophore for the inhibition of sEH. © 2013 Elsevier Ltd. All rights reserved.

Mobile Element Scanning (Me-Scan) Identifies Thousands Of Novel Alu Insertions In Diverse Human Populations, David J. Witherspoon, Yuhua Zhang, Jinchuan Xing, W. Scott Watkins, Hongseok Ha, Mark A. Batzer, Lynn B. Jorde

Faculty Publications

Alu retrotransposons are the most numerous and active mobile elements in humans, causing genetic disease and creating genomic diversity. Mobile element scanning (ME-Scan) enables comprehensive and affordable identification of mobile element insertions (MEI) using targeted high-throughput sequencing of multiplexed MEI junction libraries. In a single experiment, ME-Scan identifies nearly all AluYb8 and AluYb9 elements, with high sensitivity for both rare and common insertions, in 169 individuals of diverse ancestry. ME-Scan detects heterozygous insertions in single individuals with 91% sensitivity. Insertion presence or absence states determined by ME-Scan are 95% concordant with those determined by locus-specific PCR assays. By sampling diverse …

Holocene Evolution In Weathering And Erosion Patterns In The Pearl River Delta, Dengke Hu, Peter D. Clift, Philipp Böning, Robyn Hannigan, Stephen Hillier, Jerzy Blusztajn, Shiming Wan, Dorian Q. Fuller

Faculty Publications

Sediments in the Pearl River delta have the potential to record the weathering response of this river basin to climate change since 9.5 ka, most notably weakening of the Asian monsoon since the Early Holocene (∼8 ka). Cores from the Pearl River delta show a clear temporal evolution of weathering intensity, as measured by K/Al, K/Rb, and clay mineralogy, that shows deposition of less weathered sediment at a time of weakening monsoon rainfall in the Early-Mid Holocene (6.0-2.5 ka). This may reflect an immediate response to a less humid climate, or more likely reduced reworking of older deposits from river …

Lake Ice Ablation Rates From Permanently Ice-Covered Antarctic Lakes, H. A. Dugan, M. K. Obryk, P. T. Doran

Faculty Publications

In the McMurdo Dry Valleys of Antarctica, three large, permanently ice-covered, closedbasin lakes exist along the floor of Taylor Valley. Lake ice ablation (loss of ice mass) is calculated as the sum of sublimation and surface melt, and is the driver of ice-cover turnover in these systems. In Taylor Valley, both manual and automated lake ice ablation rates have been calculated from 2001 to 2011. Results indicate relatively consistent winter ablation of 0.07-0.21m (0.2-0.7mmw.e. d-1). Summer ablation of lake ice is more variable and ranges from 0.25 to 1.62m (5-31mmw.e. d-1) over an average 51 day period. Previous to this …

Initial Epidemic Area Is Strongly Associated With The Yearly Extent Of Soybean Rust Spread In North America, Christopher C. Mundt, La Rae D. Wallace, Tom W. Allen, Clayton A. Hollier, Robert C. Kemerait, Edward J. Sikora

Faculty Publications

Hosts of soybean rust (Phakopsora pachyrhizi) are sensitive to low temperatures, limiting this obligate parasite in the United States to overwintering sites in a restricted area along the Gulf Coast. This temperature sensitivity of soybean rust hosts allowed us to study spatial spread of epidemic invasions over similar territory for seven sequential years, 2005-2011. The epidemic front expanded slowly from early April through July, with the majority of expansion occurring from August through November. There was a 7.4-fold range of final epidemic extent (0.4-3.0 million km2) from the year of smallest final disease extent (2011) to that of the largest …

Threshold-Based Spraying Decision Programmes For The Red Spider Mite Tetranychus Marianae On Eggplant, G. V.P. Reddy, R. Kikuchi, J. R. Bautista

Faculty Publications

The red spider mite, Tetranychus marianae McGregor (Acari: Tetranychidae), has been an important pest of eggplant Solanum melongena L. (Solanaceae) and other vegetables in the Mariana Islands. The damage due to T. marianae has been severe and caused huge economic losses. Because no threshold levels are available for T. marianae, many growers are applying up to 12 chemical applications per eggplant cropping period. This is not only expensive, but also results in lower yields because of extensive foliar damage and development of resistance in mites to chemicals. To diminish the calendar-based chemical applications and to preclude damage to foliage and …

25-Hydroxyvitamin D Levels In African American And Nigerian Women, Ramon A. Durazo-Arvizu, John F. Aloia, Lara R. Dugas, Bamidele O. Tayo, David A. Shoham, Anne Marie Bertino, James K. Yeh, Richard S. Cooper, Amy Luke

Faculty Publications

Objectives: African Americans (AA) have substantially lower levels of circulating 25-hydroxyvitamin D (25(OH)D) than whites. We compared population-based samples of 25(OH)D in women of African descent from Nigeria and metropolitan Chicago. Methods: One hundred women of Yoruba ethnicity from southwest Nigeria and 94 African American women from metropolitan Chicago were recruited and compared using a standardized survey protocol and the same laboratory assay for 25(OH)D. Results: Mean 25(OH)D levels were 64 nmol/l among the Nigerians and 29 nmol/l among the AA. Only 10% of the values were shared in common between the groups, and 76% of the Nigerians were above …

Evidence Of Formosan Subterranean Termite Group Size And Associated Bacteria In The Suppression Of Entomopathogenic Bacteria, Bacillus Thuringiensis Subspecies Israelensis And Thuringiensis, Cai Wang, Gregg Henderson

Faculty Publications

The Formosan subterranean termite, Coptotermes formosanus Shiraki, was studied for its ability to suppress two entomopathogenic bacteria, Bacillus thuringiensis subspecies israelensis (Bti) and thuringiensis (Btt). Different group sizes (50, 25, 10, and no termites [control]) of C. formosanus were placed on well-grown Bti or Btt agar plates. On day 1, the diameters of Bti and Btt colonies in the three treatments containing termites were significantly smaller than in the controls. The diameters of Bti and Btt colonies in the 50-termite treatment were significantly smaller than in the 10-termite treatment. However, neither was significantly different from the 25-termite treatment. This group …

Why A 15 Minute Biological Detection System?, Doug Lewis

Faculty Publications

The biological defense community needs to take a hard look at the requirements and assumptions we use to develop our biological sensors. Today the point sensors currently deployed or in development can offer at best “near real time” detection. This translates into approximately 10-20 minutes from the time an agent passes over the device until an alarm is issued. Why are we working to develop detection hardware which in reality contributes little to no advantage to an operational environment? Should the DOD resist fielding (in the near term) “near real time” detection systems, and instead field slower (but much more …

Inviscid Analysis Of Extended Formation Flight, James Kless, Michael Aftosmis, Andrew Ning, Marian Nemec

Faculty Publications

Flying airplanes in extended formations, with separation distances of tens of wingspans, significantly improves safety while maintaining most of the fuel savings achieved in close formations. The present study investigates the impact of roll trim and compressibility at a fixed lift coefficient on the benefits of extended formation flight. An Euler solver with adjoint-based mesh refinement combined with a wake propagation model is used to analyze a two-body echelon formation at a separation distance of 30 spans. Two geometries are examined: a simple wing and a wing-body geometry. Energy savings, quantified by both formation drag fraction and span efficiency factor, …

Adopted Couple V. Baby Girl: Erasing The Last Vestigates Of Human Property, James G. Dwyer

Faculty Publications

No abstract provided.

Should Women Be Ordained As Pastors? Old Testament Considerations, Richard M. Davidson

Faculty Publications

No abstract provided.

James White Library: The First Seventh-Day Adventist Library For Advanced Education, Merlin D. Burt

Faculty Publications

No abstract provided.

Verifying Performance For Autonomous Robot Missions With Uncertainty, Damian M. Lyons, Ronald Arkin, Tsung-Ming Liu, Shu Jiang, Paramesh Nirmal

Faculty Publications

Establishing performance guarantees for robot missions is especially important for C-WMD applications. Software verification techniques, such as model checking (Clark 1999, Jhala & Majumdar 2009), can be applied to robotic applications but characteristics of this application area, including addition of a robot environment model and handling continuous spatial location well, exacerbate state explosion, a key weakness of these methods. We have proposed an approach to verifying robot missions that shifts the focus from state-based analysis onto the solution of a set of flow equations (Lyons et al. 2012). The key novelty introduced in this paper is a probabilistic spatial representation …

Effects Of Flow Rates And Composition Of The Filter, And Decay/Ingrowth Correction Factors Involved With The Determination Of In Situ Particulate 210po And 210pb In Seawater, Mark Baskaran, Thomas Church, Gi Hong, Anupam Kumar, Ma Qiang, Hiu Choi, Sylvain Rigaud, Kanchan Maiti

Faculty Publications

Accurate measurements of particulate ²¹⁰Po (²¹⁰Pop) and ²¹⁰Pb (²¹⁰Pbpp) are required in the investigation of (i) partitioning of Po and Pb between particulate and dissolved phases and (ii) export estimates of carbon and other key trace metals from the euphotic zone via sinking particulate matter. Based on the intercomparison of different composition of the filter material (QMA, Supor, Millipore, and Pall GN6) and flow rates (2 to 8 L min), we show how these factors affect the measured concentrations of ²¹⁰Pop and ²¹⁰Pbpp and their activity ratios (AR). As such, we recommend …

Non-Additive Effects On Decomposition From Mixing Litter Of The Invasive Mikania Micrantha H.B.K. With Native Plants, Bao Ming Chen, Shao Lin Peng, Carla M. D'Antonio, Dai Jiang Li, Wen Tao Ren

Faculty Publications

A common hypothesis to explain the effect of litter mixing is based on the difference in litter N content between mixed species. Although many studies have shown that litter of invasive non-native plants typically has higher N content than that of native plants in the communities they invade, there has been surprisingly little study of mixing effects during plant invasions. We address this question in south China where Mikania micrantha H.B.K., a non-native vine, with high litter N content, has invaded many forested ecosystems. We were specifically interested in whether this invader accelerated decomposition and how the strength of the …

Spatial And Seasonal Variability Of Dissolved Organic Matter In The Cariaco Basin, Laura Lorenzoni, Gordon T. Taylor, Claudia R. Benitez-Nelson, Dennis A. Hansell, Enrique Montes, Robert Masserini, Kent Fanning, Ramón Varela, Yrene Astor, Laurencia Guzmán, Frank E. Muller-Karger

Faculty Publications

[1] Dissolved organic carbon (DOC), nitrogen (DON), and phosphorus (DOP) were measured monthly at the CARIACO Time Series station (10°30′N, 64°40′W) in the southeastern Caribbean Sea between 2005 and 2012. Marked seasonal variability in DOC concentrations was observed, with lower values (~66 µM) in the upper water column (<75 >m) during the upwelling season (December–April) due to the injection of cool, DOC‐impoverished Subtropical Underwater from the Caribbean Sea. During the rainy season (May–November) waters were stratified and upper layer DOC concentrations increased to ~71 µM. Interannual variability in surface (1 m) concentrations of DOC was also observed in response to …

Lesions Of The Intergeniculate Leaflet Lead To A Reorganization In Circadian Regulation And A Reversal In Masking Responses To Photic Stimuli In The Nile Grass Rat, Andrew J. Gall, Laura Smale, Lily Yan, Antonio A. Nunez

Faculty Publications

Light influences the daily patterning of behavior by entraining circadian rhythms and through its acute effects on activity levels (masking). Mechanisms of entrainment are quite similar across species, but masking can be very different. Specifically, in diurnal species, light generally increases locomotor activity (positive masking), and in nocturnal ones, it generally suppresses it (negative masking). The intergeniculate leaflet (IGL), a subdivision of the lateral geniculate complex, receives direct retinal input and is reciprocally connected with the primary circadian clock, the suprachiasmatic nucleus (SCN). Here, we evaluated the influence of the IGL on masking and the circadian system in a diurnal …

The Effect Of Prenatal And Postnatal Care On Childhood Obesity, Michael M. O. Seipel, Kevin Shafer

Faculty Publications

Childhood obesity continues to be a major public health problem in the United States. If this problem is unresolved, some children will be at risk for disorders such as type 2 diabetes, high blood pressure, and cancer and will become a high economic and social burden for society. Using the National Longitudinal Survey of Youth, Child and Young Adult sample (N = 6,643), this study examined the relationship between the effect of pre- and postnatal characteristics and obesity. The findings of this study show that the probability of childhood obesity can be lessened if pregnant women do not smoke and …

First Spectroscopic Identification Of Pyrocarbonate For High Co2 Flux Membranes Containing Highly Interconnected Three Dimensional Ionic Channels, Lingling Zhang, Xinyu Huang, Changyong Qin, Kyle Brinkman, Yunhui Gong, Siwei Wang, Kevin Huang

Faculty Publications

Identification of the existence of pyrocarbonate ion C₂O₅²⁻ in molten carbonates exposed to a CO₂ atmosphere provides key support for a newly established bi-ionic transport model that explains the mechanisms of high CO₂ permeation flux observed in mixed oxide-ion andcarbonate-ion conducting (MOCC) membranes containing highly interconnected three dimensional ionic channels. Here we report the first Raman spectroscopic evidence of C₂O₅²⁻ as an active species involved in the CO₂-transport process of MOCC membranes exposed to a CO₂atmosphere. The two new broad peaks centered at 1317 cm^{−1 …}

Association Between Adverse Childhood Experiences And Diagnosis Of Cancer, Monique J. Brown, Leroy R. Thacker, Steven A. Cohen

Faculty Publications

Objective: Adverse childhood experiences (ACEs) are linked to multiple adverse health outcomes. This study examined the association between ACEs and cancer diagnosis.

Methods: Data from the 2010 Behavioral Risk Factor Surveillance System (BRFSS) survey were used. The BRFSS is the largest ongoing telephone health survey, conducted in all US states, the District of Columbia, Puerto Rico, Guam and the U.S. Virgin Islands, and provides data on a variety of health issues among the non-institutionalized adult population. Principal component analysis (PCA) was used to derive components for ACEs. Multivariable logistic regression models were used to provide adjusted odds ratios (OR) and …

Quantum Beats And Coherence Decay In Degenerate States Split By Solvation, Lev Chuntonov, Daniel G. Kuroda, Ayanjeet Ghosh, Jianqiang Ma, Robin M. Hochstrasser

Faculty Publications

Coherent dynamics of degenerate quantum states symmetry-broken on the femtosecond time scale is found to exhibit the phenomenon of quantum beats. Frequency-resolved and polarization-selective heterodyned transient grating spectroscopy enabled us to retrieve the oscillation pattern characteristic of the beating in systems undergoing ultrafast dynamical processes. This methodology applies to the general phenomena of coherence dynamics, which is important in any ultrafast multidimensional spectroscopy. A particular application to the vibrational spectroscopy of coherence in the degenerate normal modes of the tricyanomethanide anion solvated in water is explored in this study. The relaxation of the cross-polarization transient grating anisotropy is shown to …

Spatially Selective Surface Platforms For Binding Fibrinogen Prepared By Particle Lithography With Organosilanes, Lauren E. Englade-Franklin, Cha Marra K. Saner, Jayne C. Garno

Faculty Publications

We introduce an approach based on particle lithography to prepare spatially selective surface platforms of organosilanes that are suitable for nanoscale studies of protein binding. Particle lithography was applied for patterning fibrinogen, a plasma protein that has a major role in the clotting cascade for blood coagulation and wound healing. Surface nanopatterns of mercaptosilanes were designed as sites for the attachment of fibrinogen within a protein-resistant matrix of 2-[methoxy(polyethyleneoxy)propyl] trichlorosilane (PEG-silane). Preparing site-selective surfaces was problematic in our studies, because of the self-reactive properties of PEG-organosilanes. Certain organosilanes presenting hydroxyl head groups will cross react to form mixed surface multi-layers. …

Lipid Nature And Their Influence On Opening Of Redox-Active Liposomes, Martin Loew, Jerimiah C. Forsythe, Robin L. Mccarley

Faculty Publications

The pathway for content release from reduction-sensitive liposomes based on a quinone-dioleoylphosphatidylethanolamine lipid conjugate (Q-DOPE) is outlined using results from fluorescent dye content release assays as well as single- and multiple-angle light scattering. Experimental observations are consistent with a shape/size change of the reduced liposomes prior to their aggregation, with subsequent near-quantitative content release achieved only when the lipid membrane experiences conditions favorable to a lamellar to an inverted hexagonal phase transition. Addition of poly(ethyleneglycol)-modified DOPE (PEG-DOPE) to the Q-DOPE liposomal formulation results in stabilization of the lipid bilayer, whereas incorporation of DOPE yields faster content release. At high DOPE …

Halogen Photoelimination From Dirhodium Phosphazane Complexes Via Chloride-Bridged Intermediates, David C. Powers, Matthew B. Chambers, Thomas S. Teets, Noémie Elgrishi, Bryce L. Anderson, Daniel G. Nocera

Faculty Publications

Halogen photoelimination is a critical step in HX-splitting photocatalysis. Herein, we report the photoreduction of a pair of valence-isomeric dirhodium phosphazane complexes, and suggest that a common intermediate is accessed in the photochemistry of both mixed-valent and valence-symmetric complexes. The results of these investigations suggest that halogen photoelimination proceeds by two sequential photochemical reactions: ligand dissociation followed by subsequent halogen elimination. © 2013 Royal Society of Chemistry.

A Comparison Of 100 Human Genes Using An Alu Element-Based Instability Model, George W. Cook, Miriam K. Konkel, Jerilyn A. Walker, Matthew G. Bourgeois, Mitchell L. Fullerton, John T. Fussell, Heath D. Herbold, Mark A. Batzer

Faculty Publications

The human retrotransposon with the highest copy number is the Alu element. The human genome contains over one million Alu elements that collectively account for over ten percent of our DNA. Full-length Alu elements are randomly distributed throughout the genome in both forward and reverse orientations. However, full-length widely spaced Alu pairs having two Alus in the same (direct) orientation are statistically more prevalent than Alu pairs having two Alus in the opposite (inverted) orientation. The cause of this phenomenon is unknown. It has been hypothesized that this imbalance is the consequence of anomalous inverted Alu pair interactions. One proposed …