Digital Commons Network^™

Inhibition Of Enterobacter Cloacae And Klebsiella Oxytoca By Garlic (Allium Sativum L.) And Garlic Pills, Lucinda Choules, Dennis A. Gravatt, Stephen M. Kosovich, Wei Yuan, Ping Wang, Ron Havner

Faculty Publications

Multidrug resistant infections and superinfections are increasing globally. Intrinsic and acquired resistance to multiple antibiotics by bacteria from the Enterobacteriaceae family exasperate treatment efforts by clinicians. Carbapenem antibiotics were once relied upon to treat multidrug resistant infections. However, Carbapenem Resistant Enterobacteriaceae (CRE) infections are becoming more common, requiring that an alternative treatment be found. This study trialed an ancient cure, Fresh Garlic Extract (FGE) created from garlic (Allium sativum L.) and commercially prepared garlic pills against two opportunistic Enterobacteriaceae in vitro utilizing: disc diffusion, well diffusion (introducing DIFF-bolts), and HPLC. FGE and four brands of garlic pills inhibited the growth …

Expansion Of The Manage Database With Forest And Drainage Studies, Daren R. Harmel, Laura E. Christianson, Matthew W. Mcbroom, Douglas R. Smith, Kori D. Higgs

Faculty Publications

The “Measured Annual Nutrient loads from AGricultural Environments” (MANAGE) database was published in 2006 to expand an early 1980s compilation of nutrient export (load) data from cultivated and pasture/range land at the field or farm scale. Then in 2008, MANAGE was updated with 15 additional studies, and nitrogen (N) and phosphorus (P) concentrations in runoff were added. Since then, MANAGE has undergone significant expansion adding N and P water quality along with relevant management and site characteristic data from: (1) 30 runoff studies from forested land uses, (2) 91 drainage water quality studies from drained land, and (3) 12 additional …

Quality And Yield Of Seven Forages Grown Under Partial Shading Of A Simulated Silvopastoral System In East Texas, J. Hill, K. Farrish, B. Oswald, L. Young, A. Shadow

Faculty Publications

The goal of this project is to evaluate the growth and nutritional characteristics of seven forages, including various warm season native grasses, grown under simulated partial shading (50 percent typical of a loblolly pine silvopastoral system in east Texas. The results are from year two of a three year study. In order to meet the overall objective, individual, slatted shade structures were constructed that simulate the quantity, quality, and overall light regime found beneath loblolly pine stands arranged for silvopasture. The forages selected for the study include ‘Tifton 9’ bahiagrass (Paspalum notatum), ‘Tifton 85’ bermudagrass (Cynodon dactylon), ‘Alamo’ switchgrass (Panicum …

Road-Edge Effects On Herpetofauna In A Lowland Amazonian Rainforest, Ross J. Maynard, Nathalie C. Aall, Daniel Saenz, Paul S. Hamilton, Matthew Kwiatkowski

Faculty Publications

The impact of roads on the flora and fauna of Neotropical rainforest is perhaps the single biggest driver of habitat modification and population declines in these ecosystems. We investigated the road-edge effect of a low-use dirt road on amphibian and reptile abundance, diversity, and composition within adjacent lowland Amazonian rainforest at San José de Payamino, Ecuador. The road has been closed to vehicle traffic since its construction in 2010. Thus, effects from vehicle mortality, vehicle-related pollution, and road noise were not confounding factors. Herpetofauna were surveyed using both visual encounter surveys and drift fences with pitfall and funnel traps at …

Bioarchaeological Investigations Of Nineteenth-Century African American Burials At The Pioneer Cemetery (41bo202) In Brazoria, Texas, Aaron R. Norment, Jeremy W. Pye, Cory J. Broehm, Douglas K. Boyd

Index of Texas Archaeology: Open Access Gray Literature from the Lone Star State

A search for unmarked graves in the state-owned right of way and underneath the pavement of State Highway 332 resulted in the discovery and archeological excavation of 11 unmarked graves associated with Pioneer Cemetery, an African American burial ground in Brazoria, Texas. Prewitt and Associates, Inc., conducted the fieldwork for the Texas Department of Transportation’s Archeological Studies Program. Between 2008 and 2012, the 11 unmarked graves were discovered, exhumed, analyzed, and then reinterred in Pioneer Cemetery in September 2012. This report describes the bioarcheological investigations of those burials along with 3 other unmarked burials that were previously exhumed and reburied …

Systematic Intensive Pedestrian Survey Of The Helotes Hike-Bike Trail Helotes, Bexar County, Texas, David M. Yelacic

Index of Texas Archaeology: Open Access Gray Literature from the Lone Star State

As a result of a City of Helotes undertaking funded by TxDOT, an intensive pedestrian survey was carried across approximately seven total acres of trail and park space, as well as a pedestrian bridge, improvements to the parking and sidewalk space (i.e., benches and trashcans) along Riggs Road, and pedestrian crossing at Scenic Loop Road and Highway 16. Work was carried out in coordination with TxDOT and the THC under Antiquities Permit Number 7512, issued to David Yelacic, RPA, and fieldwork was conducted in late December 2015 by Yelacic with assistance from Tanner Jason, field scientist. Overall, systematic pedestrian survey …

Cultural Resources Survey Conducted During February 2016 South Eagle Ford Zone Atascosa, La Salle, And Mcmullen Counties, Phil Schoch, Reign Clark, Ron Ralph

Index of Texas Archaeology: Open Access Gray Literature from the Lone Star State

During the month of February 2016, Goshawk Environmental Consulting, Inc. (Goshawk) conducted one cultural resources survey within the Eagle Ford Play, South Eagle Ford Zone, at the request of EOG Resources, Inc. (EOG). The project subjected to cultural resources investigation was the Cuellar Unit #11H Flowline. The Area of Potential Effect (APE) was a 75-foot (23-meter [m]) wide right-of-way (ROW), consisting of a 50-foot (15-m) wide permanent easement and a 25-foot (8-m) wide temporary construction easement. The investigation was conducted by Goshawk archeologist Phil Schoch with Mitch Juenke. Phil Schoch served as primary author and Reign Clark and Ron Ralph …

Cultural Resources Surveys Conducted During February 2016 Central Eagle Ford Zone De Witt, Gonzales, Karnes, Lavaca, And Wilson Counties, Phil Schoch, Reign Clark, Ron Ralph

Index of Texas Archaeology: Open Access Gray Literature from the Lone Star State

During February 2016, Goshawk Environmental Consulting, Inc. (Goshawk) conducted one cultural resources survey within the Eagle Ford Play, Central Eagle Ford Zone at the request of EOG Resources, Inc. (EOG). The project subjected to cultural resources investigation was the proposed Denali Unit #101H Access Road right-of-way (ROW). The Area of Potential Effect (APE) for the project was a 75-foot (23-meter [m]) wide ROW, consisting of a 50-foot (15-m) wide permanent easement and a 25-foot (8-m) wide temporary construction easement. The investigation was conducted by Goshawk archeologist Phil Schoch with Bear Aspra. Phil Schoch served as primary author and Reign Clark …

Eliminating Antibiotic Use In Animal Production: Responding To Scientific Evidence Of An Impending Global Health Crisis, Sabrina R. Rearick

Duquesne Law Review

No abstract provided.

Recent Morphodynamic Evolution Of The Largest Uninhibited Island In The Yangtze (Changjiang) Estuary During 1998-2014: Influence Of The Anthropogenic Interference, Wen Wei, Xuefei Mei, Zhijun Dai, Zhenghong Tang

Community and Regional Planning Program: Faculty Scholarly and Creative Activity

Estuarine geomorphology worldwide has greatly changed in the Anthropocene due to intensive human inferences in river basin and within estuary, which has received increasing global concerns. Here, recent morphodynamic evolution of Jiuduan Shoal (JDS), the largest uninhabited island in the Yangtze (Changjiang) Estuary, and associated controlling factors were analyzed based on unique high-resolution seasonal-surveyed bathymetric data during 1998–2014. It can be indicated that JDS presents novel 12 and 48 months fluctuations though significant accretion was detected on high flats above −2 m. Meanwhile, morphodynamic evolution of JDS during 1998–2014 was divided into three stages: significant siltation on land-ward half of …

Western North Pacific Integrated Physical-Biogeochemical Ocean Observation Experiment (Inbox): Part 1.Specifications And Chronology Of The S1-Inbox Floats, Ryuichiro Inoue, Toshio Suga, Shinya Kouketsu, Toshiyuki Kita, Shigeki Hosoda, Taiyo Kobayashi, Kanako Sato, Hiroyuki Nakajima, Takeshi Kawano

Journal of Marine Research

An interdisciplinary project called the Western North Pacific Integrated Physical-Biogeochemical Ocean Observation Experiment (INBOX) has been conducted since 2011. In the oligotrophic subtropics south of the Kuroshio Extension near biogeochemical mooring S1 (30° N, 145° E), 18 floats, each with a dissolved oxygen sensor, have been deployed in a 150 × 150 km square area. With the horizontal (30 km) and temporal (2 days) resolution of the data, we observed an upper ocean structure associated with mesoscale eddies and ocean responses to atmospheric forcing. The data set obtained from the S1-INBOX study was used to elucidate the impacts of physical …

Western North Pacific Integrated Physical-Biogeochemical Ocean Observation Experiment (Inbox): Part 3. Mesoscale Variability Of Dissolved Oxygen Concentrations Observed By Multiple Floats During S1-Inbox, Shinya Kouketsu, Ryuichiro Inoue, Toshio Suga

Journal of Marine Research

As part of the interdisciplinary project S1-INBOX (Western North Pacific Integrated Physical-Biogeochemical Ocean Observation Experiment conducted around the S1 biogeochemical mooring site), we used data from more than 18 floats and a biogeochemical mooring S1 (near 30° N, 145° E) to investigate temporal and spatial changes in the shallow oxygen maximum (SOM) associated with a mesoscale cyclonic eddy. On the northern edge of the cyclonic eddy, patches (linear dimensions of 20–40 km) with relatively high oxygen concentrations were observed around the SOM. The patterns of the oxygen concentrations reflected the fact that changes of the depths of the isopycnal surfaces …

Simultaneous Determination Of 3-Mercaptopyruvate And Cobinamide In Plasma By Liquid Chromatography–Tandem Mass Spectrometry, Michael W. Stutelberg, Joseph K. Dzisam, Alexandre R. Monteil, Ilona Petrikovics, Gerry R. Boss, Steven E. Patterson, Gary A. Rockwood, Brian A. Logue

Chemistry and Biochemistry Faculty Publications

The current suite of Food and Drug Administration (FDA) approved antidotes (i.e., sodium nitrite, sodium thiosulfate, and hydroxocobalamin) are effective for treating cyanide poisoning, but individually, each antidote has major limitations (e.g., large effective dosage or delayed onset of action). To mitigate these limitations, next-generation cyanide antidotes are being investigated, including 3-mercaptopyruvate (3-MP) and cobinamide (Cbi). Analytical methods capable of detecting these therapeutics individually and simultaneously (for combination therapy) are essential for the development of 3-MP and Cbi as potential cyanide antidotes. Therefore, a liquid chromatography–tandem mass-spectrometry method for the simultaneous analysis of 3-MP and Cbi was developed. Sample preparation …

Meta-Analysis: Risk Of Tics With Psychostimulant Use In Randomized, Placebo-Controlled Trials, Stephanie Celeste Cohen

Yale Medicine Thesis Digital Library

Clinical practice currently restricts the use of psychostimulant medications in children with tics or a family history of tics for fear that tics will develop or worsen as a side effect of treatment. Our goal was to conduct a meta-analysis to examine the risk of new onset or worsening of tics as an adverse event of psychostimulants in randomized, placebo-controlled trials.

We conducted a PubMed search to identify all double-blind, randomized, placebo-controlled trials examining the efficacy of psychostimulant medications in the treatment of children with attention-deficit/hyperactivity disorder (ADHD). We used a fixed effects meta-analysis with risk ratio of new onset …

Baroclinic Instability Over Topography: Unstable At Any Wave Number, Joseph Pedlosky

Journal of Marine Research

The instability of an inviscid, baroclinic vertically sheared current of uniform potential vorticity, flowing along a uniform topographic slope, becomes linearly unstable at all wave numbers if the flow is in the direction of propagation of topographic waves. The parameter region of instability in the plane of scaled topographic slope versus wave number then extends to arbitrarily large wave numbers at large slopes. The weakly nonlinear treatment of the problem reveals the existence of a nonlinear enhancement of the instability close to one of the two boundaries of this parametrically narrow unstable region. Because the domain of instability becomes exponentially …

Carbon Cycling In Santa Barbara Basin Sediments: A Modeling Study, David J. Burdige, Tomoko Komada, Cédric Magen, Jeffrey P. Chanton

Journal of Marine Research

The primary input of organic matter to almost all marine sediments comes from deposition at the sediment surface. However, in many continental margin settings, reduced carbon can also be added to sediments from below—for example, from “deep” geologic hydrocarbon reservoirs derived from ancient source rocks or from the decomposition of deeply buried gas hydrate deposits. To examine the impact of these two differing reduced carbon inputs on sediment biogeochemistry, a modified reaction-transport model for anoxic marine sediments is described here and applied to data from sediment cores in Santa Barbara Basin to a depth of 4.6 m. Excellent model fits …

Mechanisms Controlling Vertical Variability Of Subsurface Chlorophyll Maxima In A Mode-Water Eddy, Qian P. Li, Dennis A. Hansell

Journal of Marine Research

An intense subsurface chlorophyll enhancement was found repeatedly within the core of a mode-water eddy during a 2-month period. Two controls on chlorophyll concentrations in this deep chlorophyll maximum (DCM) layer are noted: chlorophyll concentration is controlled by nutrients at low nutrient concentrations and by light when nutrients are saturating. To synthesize these results, a simple one-dimensional nutrient-phytoplankton model is developed by including the effects of phytoplankton self-shading for light attenuation, depth-dependent phytoplankton specific loss, and density-associated nutrient fluctuation in the deep layer. The model is parameterized using eddy data including not only vertical diffusivity, sinking velocity, and chlorophyll-to-carbon ratios, …

Convective Mixing By Internal Waves In The Puerto Rico Trench, Hans Van Haren, Louis Gostiaux

Journal of Marine Research

A 2.4 km long deep-sea mooring was deployed for 14 months in the Puerto Rico Trench, the deepest part of the Atlantic Ocean. Below its top buoyancy package, the mooring line held a 200 m long string of high-resolution temperature sensors and a current meter. Over the instrumented range between 6,004 and 6,204 m, waters are very weakly stratified, with local buoyancy frequency equaling about 1.9 times the semidiurnal tidal frequency. Besides quiescent waters, the detailed observations show regular vertical turbulent overturning associated with periodic warming and driven by internal tidal and inertial waves. During such episodes, the 4-day and …

Methane Dynamics In Santa Barbara Basin (Usa) Sediments As Examined With A Reaction-Transport Model, David J. Burdige, Tomoko Komada, Cédric Magen, Jeffrey P. Chanton

Journal of Marine Research

Here we describe a new reaction-transport model that quantitatively examines δ¹³C profiles of pore-water methane and dissolved inorganic carbon (DIC) (δ¹³C_CH4 and δ¹³C_DIC) in the anoxic sediments of the Santa Barbara Basin (California Borderland region). Best-fit solutions of the model to these data suggest that CO₂ reduction is the predominant form of methanogenesis in these sediments. These solutions also accurately reproduce the isotope depth profiles, including a broad minimum in the δ¹³C_DIC profile and a much sharper (angular) minimum in the δ¹³C_CH4 profile, both …

Western North Pacific Integrated Physical-Biogeochemical Ocean Observation Experiment (Inbox): Part 2. Biogeochemical Responses To Eddies And Typhoons Revealed From The S1 Mooring And Shipboard Measurements, Ryuichiro Inoue, Makio C. Honda, Tetsuichi Fujiki, Kazuhiko Matsumoto, Shinya Kouketsu, Toshio Suga, Toshiro Saino

Journal of Marine Research

An interdisciplinary project called S1-INBOX (Western North Pacific Integrated PhysicalBiogeochemical Ocean Observation Experiment conducted around the S1 biogeochemical mooring site) was carried out during the summer of 2011 in the oligotrophic, subtropical North Pacific Ocean near biogeochemical mooring S1 (30° N, 145° E). Results from the S1 mooring during S1-INBOX revealed a large export flux at a depth of 200 m, a high chlorophyll a concentration in the deep chlorophyll maximum layer, and a high potential photochemical efficiency of photosystem II. These phenomena were associated with vertical uplift of isopycnal surfaces at the edge of a cyclonic eddy and a …

Residual Water Transport In The Marsdiep Tidal Inlet Inferred From Observations And A Numerical Model, Maximiliano G. Sassi, Theo Gerkema, Matias Duran-Matute, Janine J. Nauw

Journal of Marine Research

At tidal inlets, large amounts of water are exchanged with the adjacent sea during the tidal cycle. The residual flows, the net effect of ebb and flood, are generally small compared with the gross flux; they vary in magnitude and sign from one tidal period to the other; and their long-term mean varies from year to year. Here, we focus on the temporal variability of the residual flows in the Marsdiep tidal inlet, which is the western-most inlet of the Wadden Sea, a tidal lagoon along the coasts of the Netherlands, Germany, and Denmark. We compare the transport from a …

Facts And Figures 2016-2017, Office Of Communications And Marketing

Facts and Figures

No abstract provided.

Variable Selection For Case-Cohort Studies With Failure Time Outcome, Andy Ni, Jianwen Cai, Donglin Zeng

Memorial Sloan-Kettering Cancer Center, Dept. of Epidemiology & Biostatistics Working Paper Series

Case-cohort designs are widely used in large cohort studies to reduce the cost associated with covariate measurement. In many such studies the number of covariates is very large, so an efficient variable selection method is necessary. In this paper, we study the properties of variable selection using the smoothly clipped absolute deviation penalty in a case-cohort design with a diverging number of parameters. We establish the consistency and asymptotic normality of the maximum penalized pseudo-partial likelihood estimator, and show that the proposed variable selection procedure is consistent and has an asymptotic oracle property. Simulation studies compare the finite sample performance …

Virginia Peregrine Falcon Monitoring And Management Program: Year 2016 Report, B. D. Watts, M U. Watts

CCB Technical Reports

The peregrine falcon (Falco peregrinus) was believed to be extirpated as a breeding species in Virginia by the early 1960s. An aggressive restoration program was initiated in 1978 that included the release of 115 captive-reared birds on the Coastal Plain (1978-1985) and 127 birds in the mountains (1985-1993). This program resulted in the first breeding of the modern era in 1982. Since this time, the population has proceeded through a rapid establishment phase followed by a consolidation phase. However, more than 95% of all breeding activity over the past 30 years has occurred on the Coastal Plain with very limited …

Status And Distribution Of The Eastern Black Rail Along The Atlantic And Gulf Coasts Of North America, B. D. Watts

CCB Technical Reports

No abstract provided.

Assessment Of Potential Impacts To Avian Species From A Proposed 750 Foot Guyed Tower At Nasa’S Goddard Space Flight Center’S Wallops Flight Facility On Wallops Island, Virginia, B. J. Paxton, M D. Wilson

CCB Technical Reports

• NASA has proposed A 750 foot guyed instrumentation tower to be constructed on Wallops Island, VA at one of two locations. • Wallops Island is embedded within a critical location along the Atlantic Flyway that supports millions of avian species annually, many of which are of conservation concern. Since this tower has the potential to act as a collision hazard for birds, NASA has requested a synthesis of existing information on the species exposure and relative vulnerability to the proposed construction. • The proposed tower site and its alternative are relatively identical with respect to location from shoreline or …

Using Validation Data To Adjust The Inverse Probability Weighting Estimator For Misclassified Treatment, Danielle Braun, Corwin Zigler, Francesca Dominici, Malka Gorfine

Harvard University Biostatistics Working Paper Series

The inverse probability weighting (IPW) estimator is widely used to estimate the treatment effect in observational studies in which patient characteristics might not be balanced by treatment group. The estimator assumes that treatment assignment, is error-free, but in reality treatment assignment can be measured with error. This arises in the context of comparative effectiveness research, using administrative data sources in which accurate procedural or billing codes are not always available. We show the bias introduced to the estimator when using error-prone treatment assignment, and propose an adjusted estimator using a validation study to eliminate this bias. In simulations, we explore …

Estimation And Inference For The Mediation Proportion, Daniel Nevo, Xiaomei Liao, Donna Spiegelman

Harvard University Biostatistics Working Paper Series

In epidemiology, public health and social science, mediation analysis is often undertaken to investigate the extent to which the effect of a risk factor on an outcome of interest is mediated by other covariates. A pivotal quantity of interest in such an analysis is the mediation proportion. A common method for estimating it, termed the "difference method'', compares estimates from models with and without the hypothesized mediator. However, rigorous methodology for estimation and statistical inference for this quantity has not previously been available. We formulated the problem for the Cox model and generalized linear models, and utilize a data duplication …

Moving Beyond The Conventional Stratified Analysis To Estimate An Overall Treatment Efficacy With The Data From A Comparative Randomized Clinical Study, Lu Tian, Fei Jiang, Takahiro Hasegawa, Hajime Uno, Marc Alan Pfeffer, L.J. Wei

Harvard University Biostatistics Working Paper Series

No abstract provided.

Annual Report, 2015-2016, Connecticut College

Annual Reports

No abstract provided.