Life Sciences Commons^™

Effect Of Time Duration Of Digestion/Decontamination Technique On Yield Of Mycobacteria And Contamination Rates From Sterile Body Fluids (Pleural And Ascitic Fluid) And Pus Specimens, Samreen Shafiq, Faryal Saleem, Kauser Jabeen, Joveria Farooqi, Warda Alam, Sadia Hanif, Shazia Ali, Sadia Shakoor, Rumina Hasan

Department of Pathology and Laboratory Medicine

Background:
Duration of digestion/decontamination has a considerable impact on yield of mycobacteria especially from sterile body fluids and pus specimens. Additionally, duration of digestion/decontamination affects the contamination rates. This study evaluates the effect of digestion/decontamination protocol for 15 and 20min versus inoculation of media directly from the sample on contamination rates as well as the yield of mycobacteria from pus and sterile fluids other than cerebrospinal fluids.
Methods:
Pleural fluid (n=60), pus (n=48) and ascitic fluid (n=12) specimens were cultured for mycobacteria and evaluated for contamination and mycobacterial yield using three different processing methodologies: without digestion/decontamination with 5% NaOH-NALC (D/D), …

Effects Of Road And Land Use On Frog Distributions Across Spatial Scales And Regions In The Eastern And Central United States, David M. Marsh, Bradley J. Cosentino, Kara S. Jones, Joseph J. Apodaca, Karen H. Beard, Jane Margaret Bell, Christine Bozarth, Derrick Carper, Julie F. Charbonnier, Andreia Dantas, Elizabeth A. Forys, Miran Foster, Jaquelyn General, Kristen S. Genet, Macie Hanneken, Kyle R. Hess, Shane A. Hill, Faisal Iqbal, Nancy E. Karraker, Eran S. Kilpatrick, Tom A. Langen, James Langford, Kathryn Lauer, Alison J. Mccarthy, Joseph Neale, Saumya Patel, Austin Patton, Cherie Southwick, Nathaniel Stearrett, Nicholas Steijn, Mohammed Tasleem, Jospeh M. Taylor, James R. Vonesh

Wildland Resources Faculty Publications

Understanding the scales over which land use affects animal populations is critical for conservation planning, and it can provide information about the mechanisms that underlie correlations between species distributions and land use. We used a citizen science database of anuran surveys to examine the relationship between road density, land use and the distribution of frogs and toads across spatial scales and regions of the United States.

Exploratory Study Into The Awareness Of Heart Diseases Among Emirati Women (Uae) And Their Health Seeking Behaviour- A Qualitative Study, Sarah Khan, Ayesha Khoory, Dhabia Al Zaffin, Meera Al Suwaidi

All Works

© 2016 The Author(s). Background: Cardiovascular diseases were the leading cause of death in women in the United Arab Emirates (UAE) in 2010. The UAE is expected to experience a tripling of heart diseases in the next two decades as risk factors for heart diseases increase. Research shows that first year survival rates of younger women suffering from a heart attack are lower than in men. Women present with a wider range of symptoms for heart diseases than men; non-recognition of atypical symptoms may explain the delay in seeking treatment and poor prognosis following heart diseases in women. No known …

Koalas (Phascolarctos Cinereus) From Queensland Are Genetically Distinct From 2 Populations In Victoria, Christina T. Ruiz-Rodriguez, Yasuko Ishida, Neil D. Murray, Stephen J. O'Brien, Jennifer A.M. Graves, Alex D. Greenwood, Alfred L. Roca

Biology Faculty Articles

The koala (Phascolarctos cinereus) suffered population declines and local extirpation due to hunting in the early 20th century, especially in southern Australia. Koalas were subsequently reintroduced to the Brisbane Ranges (BR) and Stony Rises (SR) by translocating individuals from a population on French Island descended from a small number of founders. To examine genetic diversity and north-south differentiation, we genotyped 13 microsatellite markers in 46 wild koalas from the BR and SR, and 27 Queensland koalas kept at the US zoos. The Queensland koalas displayed much higher heterozygosity (H O = 0.73) than the 2 southern Australian koala populations examined: …

Comparison Of Carnivore, Omnivore, And Herbivore Mammalian Genomes With A New Leopard Assembly, Soonok Kim, Yun Sung Cho, Hak Min Kim, Oksung Chung, Hyunho Kim, Sungwoong Jho, Hong Seomun, Jeongho Kim, Woo Young Bang, Changmu Kim, Junghwa An, Chang Hwan Bae, Youngjune Bhak, Sungwon Jeon, Hyejun Yoon, Yumi Kim, Je Hoon Jun, Hye Jin Lee, Suan Cho, Olga Uphyrkina, Aleksey Kostyria, John Goodrich, Dale Miquelle, Melody Roelke, John Lewis, Andrey Yurchenko, Anton Bankevich, Juok Cho, Semin Lee

Biology Faculty Articles

Background: There are three main dietary groups in mammals: carnivores, omnivores, and herbivores. Currently, there is limited comparative genomics insight into the evolution of dietary specializations in mammals. Due to recent advances in sequencing technologies, we were able to perform in-depth whole genome analyses of representatives of these three dietary groups. Results: We investigated the evolution of carnivory by comparing 18 representative genomes from across Mammalia with carnivorous, omnivorous, and herbivorous dietary specializations, focusing on Felidae (domestic cat, tiger, lion, cheetah, and leopard), Hominidae, and Bovidae genomes. We generated a new high-quality leopard genome assembly, as well as two wild …

A Study Of Defensive Mechanisms Employed By Two Species Of Nudibranchs Using Toxicity And Unpalatability Analyses, Sean Youn

Independent Study Project (ISP) Collection

Nudibranchs are marine invertebrates that have developed an intriguing defense mechanism, including warning coloration and the use of chemicals accumulated through their sponge diet. The goal of this study was to determine whether the strength of chemical defenses differs between dietary and accumulated secondary metabolites for two species: Glossodoris vespa and Ceratosoma brevicaudatum. First, NMR spectroscopy was used to not only identify specific compounds in the mantle (outer covering) and the viscera (gut) but also to analyze the possibility of nudibranch species transporting more toxic compounds for defensive purposes. Next, toxicity (brine shrimp) and palatability (Palaemon shrimp) assays were used …

Pangolin Genomes And The Evolution Of Mammalian Scales And Immunity, Siew Who Choo, Mike Rayko, Tze King Tan, Ranjeev Hari, Aleksey Komissarov, Wei Yee Wee, Andrey A. Yurchenko, Sergey Kliver, Gaik Tamazian, Agostinho Antunes, Richard K. Wilson, Wesley C. Warren, Klaus Peter Koepfli, Patrick Minx, Ksenia Krasheninnikova, Antoinette Kotze, Desire L. Dalton, Elaine Vermaak, Ian C. Paterson, Pavel Dobrynin, Frankie Thomas Sitam, Jeffrine J. Rovie-Ryan, Warren E. Johnson, Aini Mohamed Yusoff, Shu Jin Luo, Kayal Vizi Karuppannan, Gang Fang, Deyou Zheng, Mark B. Gerstein

Biology Faculty Articles

Pangolins, unique mammals with scales over most of their body, no teeth, poor vision, and an acute olfactory system, comprise the only placental order (Pholidota) without a whole-genome map. To investigate pangolin biology and evolution, we developed genome assemblies of the Malayan (Manis javanica) and Chinese (M. pentadactyla) pangolins. Strikingly, we found that interferon epsilon (IFNE), exclusively expressed in epithelial cells and important in skin and mucosal immunity, is pseudogenized in all African and Asian pangolin species that we examined, perhaps impacting resistance to infection. We propose that scale development was an innovation that provided protection against injuries or stress …

Shrub Consumption And Immediate Changes In Shrub Community And Spatial Patterns By Reintroduced Fire In Yosemite National Park, California, Usa; Supplemental Information, J. A. Lutz, T. J. Furniss, S. J. Germain, K. M. L. Becker, E. M. Blomdahl, S. A. Jeronimo, C. A. Cansler, J. A. Freund, M. E. Swanson, A. J. Larson

Browse all Datasets

Fire behavior in the Yosemite Forest Dynamics Plot during the Rim Fire as captured by the USFS Fire Behavior Assessment Team and reported in Ewell, C., D.F. Smith, M. Hilden, S. Greene, D. Coultrap, K. Robinson, N. Vaillant, A. Reiner, T. Norman. 2015. 2013 Rim Fire Stanislaus National Forest and Yosemite National Park Fire Behavior Assessment Team Summary Report. Each video was started based on a thermocouple trigger when the fire reached it.

Marginal Beta Probability Density Functions For Predator-Prey Diet Linkages For The Gulf Of Mexico Fitted Using Maximum Likelihood Method, April 2013-May 2015, Cameron Ainsworth

C-IMAGE data

This is a dataset of the marginal beta probability density functions (PDFs) representing the percent contribution of prey to predator diet. Predator and prey are provided at the level of functional groups, where functional groups correspond to those used in an Atlantis biogeochemical ecosystem model of the Gulf of Mexico published by Ainsworth et al. 2015 (NOAA Tech. Memo. NMFS-SEFSC-676). The PDFs have been provided in a CSV file, and also graphically (Fig1.tif, Fig2.tif, Fig3.tif, Fig4.tif). This data set only deals with predator groups that are fish. Note that this data is also provided in a summarized form (mode and …

The Genome-Wide Analysis Of Carcinoembryonic Antigen Signaling By Colorectal Cancer Cells Using Rna Sequencing, Olga Bajenova, Anna Gorbunova, Igor Evsyukov, Michael Rayko, Svetlana Gapon, Ekaterina Bozhokina, Alexander Shishkin, Stephen J. O'Brien

Biology Faculty Articles

Carcinoembryonic antigen (CEA, CEACAM5, CD66) is a promoter of metastasis in epithelial cancers that is widely used as a prognostic clinical marker of metastasis. The aim of this study is to identify the network of genes that are associated with CEA-induced colorectal cancer liver metastasis. We compared the genome-wide transcriptomic profiles of CEA positive (MIP101 clone 8) and CEA negative (MIP 101) colorectal cancer cell lines with different metastatic potential in vivo. The CEA-producing cells displayed quantitative changes in the level of expression for 100 genes (over-expressed or down-regulated). They were confirmed by quantitative RT-PCR. The KEGG pathway analysis identified …

Discrete Chlorophyll Data For The Northeastern Gulf Of Mexico And West Florida Shelf: June 2012 – August 2014, Kendra L. Daly

C-IMAGE data

This dataset contains seasonal and interannual discrete chlorophyll data collected from the northeastern Gulf of Mexico and the west Florida shelf. The contents of the dataset are an assessment of the seasonal and interannual changes in distributions of chlorophyll after the Deepwater Horizon oil spill.

Pah Analysis: Muscle And Liver Pah Concentrations In Longline Captured Fish, Northern Gulf Of Mexico, 2011-2013, Steven Murawski

C-IMAGE data

The data contained in the two spreadsheets in this dataset represent biliary PAH metabolite concentrations from selected species collected in the northern Gulf of Mexico (NGOM) during longline sampling. The 2011 data were analyzed at the Northwest Fisheries Science Center (NWFSC). All data from 2012 on were analyzed at Mote Marine Laboratory (MML). Sample collection and methods are described in Snyder et al. 2015, PAH-exposure in Gulf of Mexico Demersal Fishes, Post-Deepwater Horizon. Environmental Science and Technology, DOI 10.1021/acs.est.5b01870.

Lesion Data From Fish Collected Off Terrebonne Bay, La To The Dry Tortugas, Fl, 2011-2014, Steven Murawski

C-IMAGE data

This data set represents collections taken by demersal longline fishing gears in the northern Gulf of Mexico and West Florida Shelf. They include station location information, standardized fish catch data (numbers, weights, sex, length), PAH contamination levels determined from sub-samples, and photographs of fishes with unusual external skin conditions that were observed in longline cruises undertaken between 2011 and 2014. The 2012-2014 data were collected during GoMRI/C-IMAGE sponsored cruises. Data from 2011 are included because they are the subject of two papers published with data from them: Murawski, S.A., W. T. Hogarth, E.B. Peebles, L. Barbieri. 2014. Prevalence of External …

Ctd And Other Environmental Data For The Northeastern Gulf Of Mexico And West Florida Shelf: June 2012 – August 2014, Kendra L. Daly

C-IMAGE data

This dataset contains seasonal and interannual CTD data collected from the northeastern Gulf of Mexico and the west Florida shelf. The contents of the dataset are an assessment of the seasonal and interannual changes in distributions of temperature, salinity, density, oxygen, chlorophyll and CDOM fluorescence, turbidity, and Photosynthetically Active Radiation (PAR) after the Deepwater Horizon oil spill.

Toxicity And Mutagenicity Of The Gulf Of Mexico Waters During And After The Deepwater Horizon Oil Spill, July 2010 To August 2012, Jonelle Basso

C-IMAGE data

The dataset is representative of 13 research cruises spanning from July 2010 to August 2012. Five cruises set to observe the West Florida shelf, while eight cruises were employed to assess the impact of the BP Oil spill on impacted North Florida shelf sites. West Florida Shelf samples sites (10 sampling sites total) comprised of Southern Transect (ST) line (stations ST03, ST06, ST12, ST18 and ST24), and the Northern Transect (NT) (stations NT31, NT25, NT19, NT13, and NT07). NE Gulf of Mexico sites included 16 sampling sites; DHS01, DSH07-10, Deepwater Horizon (DWH) station, FT1, PCB01-06, PCB11-12, and PCB14. Also included …

Zooplankton Biomass On The West Florida Shelf, July 2010 – August 2014, Kendra L. Daly

C-IMAGE data

Zooplankton have high temporal and spatial variability. Therefore, they need to be assessed before oil impact and regularly thereafter, to interpret what changes are causally related to oil spills. We surveyed plankton using bongo net tows and the USF SIPPER imaging system to evaluate the variation in plankton abundance on the west Florida shelf and the northern Gulf of Mexico. Seasonal CTD, chlorophyll, nutrient, and zooplankton abundance data from the northeastern Gulf of Mexico and the west Florida shelf. Developed new algorithms for data mining SIPPER (Shadow Imaging Particle Profiler and Evaluation Recorder) camera particle imaging data.

Land Cover Data For The Mississippi-Alabama Barrier Islands, 2010-2011 Arcgis V10.3 Geodatabase, Gregory A. Carter, Carlton P. Anderson, Kelly L. Lucas, Nathan L. Hopper

Land Cover Data for the Mississippi-Alabama Barrier Islands, 2010-2011

Land cover on the Mississippi-Alabama barrier islands was surveyed in 2010-2011 as part of continuing research on island geomorphic and vegetation dynamics following the 2005 impact of Hurricane Katrina. Results of the survey include sub-meter GPS location, a listing of dominant vegetation species and field photographs recorded at 375 sampling locations distributed among Cat, West Ship, East Ship, Horn, Sand, Petit Bois and West Dauphin Islands. The survey was conducted in a period of intensive remote sensing data acquisition over the northern Gulf of Mexico by federal, state and commercial organizations in response to the 2010 Macondo Well (Deepwater Horizon) …

Predator-Prey Diet Linkages With Error Range For The Gulf Of Mexico Fitted Using Maximum Likelihood Method, April 2013- May 2015, Cameron Ainsworth

C-IMAGE data

Data is from Tarnecki, J.H., Wallace, A., Simons, J. and Ainsworth, C.H. 2016. Progression of a Gulf of Mexico Food Web Supporting Atlantis Ecosystem Model Development. Fisheries Research (doi:10.1016/j.fishres.2016.02.023). This is a dataset representing predator-prey linkages with associated error ranges for Gulf of Mexico fish functional groups. The data will be used in an Atlantis biogeochemical trophic ecosystem model of the Gulf of Mexico described by Ainsworth et al. 2015 (NOAA Technical Memorandum NMFS-SEFSC-676). This diet dataset is based on data previously published in Masi, M.D., Ainsworth, C.H., Chagaris, D., 2014. (Ecol. Model. 284, 60-74) and expanded to include new …

Effectiveness Of The Toxicant Drc-1339 In Reducing Populations Of Common Ravens In Wyoming, Luke W. Peebles, Michael R. Conover

Wildland Resources Faculty Publications

Common raven (Corvus corax) populations have increased several-fold in the western United States during the past century; these birds cause problems when they kill new-borne lambs and calves and depredate nests of greater sage-grouse (Centrocercus urophasianus). The toxicant DRC-1339 is used by U.S. Department of Agriculture/Animal and Plant Health Inspection Service Wildlife Services to manage common raven populations and reduce the severity of these problems, but it is difficult to determine how many ravens are killed by an application because carcasses are rarely found. We examined the effectiveness of DRC-1339 applications for preventative control of ravens at 3 landfills and …

Making Sense Of Self Harm, Sandra H. Sulzer

Kinesiology and Health Science Faculty Publications

In Making Sense of Self-harm: The Cultural Meaning and Social Context of Nonsuicidal Self-injury, Dr. Peter Steggals slowly and carefully circles around self-harm as a social construct. His book gathers up the underlying meanings and contradictions inherent in the practice and inspects them in turn. He makes a case that self-harm as we see it today in the form of skin cutting, picking, and other related phenomenon is unique to our time period and is not universally present across cultures— regardless of other mutilation, cutting, or piercing practices that may exist. And importantly, he starts by addressing our aversion to …

Sipper Plankton And Marine Snow Abundance And Distribution Data For The Northeastern Gulf Of Mexico: June 2012 – August 2014, Kendra L. Daly

C-IMAGE data

This dataset contains seasonal and interannual marine snow, phytoplankton, zooplankton, and larval fish abundance and distributions collected from the northeastern Gulf of Mexico using the Shadowed Image Particle Profiling Evaluation Recorder (SIPPER). The purpose of the dataset is to assess the seasonal and interannual zooplankton abundance and distribution after the Deepwater Horizon oil spill.

Zooplankton Dry Weight Biomass Data For The Northeastern Gulf Of Mexico And West Florida Shelf: June 2012 – August 2014, Kendra L. Daly

C-IMAGE data

This dataset contains zooplankton dry weight biomass calculated from samples collected during RV Weatherbird II and RV Bellows cruises from June 2012 to August 2014. Zooplankton was collected using towed bongo nets from the northeastern Gulf of Mexico and the west Florida shelf. The contents of the dataset are an assessment of the seasonal and interannual changes in zooplankton biomass after the Deepwater Horizon oil spill.

2016-01-A3dsrinp-Csc-Sta-Cmb-522-Bps-542, Raymond Pulver, Neal Buxton, Xiaodong Wang, John Lucci, Jean Yves Hervé, Lenore Martin

Bioinformatics Software Design Projects

Cholesterol is carried and transported through bloodstream by lipoproteins. There are two types of lipoproteins: low density lipoprotein, or LDL, and high density lipoprotein, or HDL. LDL cholesterol is considered “bad” cholesterol because it can form plaque and hard deposit leading to arteries clog and make them less flexible. Heart attack or stroke will happen if the hard deposit blocks a narrowed artery. HDL cholesterol helps to remove LDL from the artery back to the liver.

Traditionally, particle counts of LDL and HDL plays an important role to understanding and prediction of heart disease risk. But recently research suggested that …

Response To Comment By Faurby, Werdelin And Svenning, Stephen J. O'Brien, Klaus Peter Koepfli, Eduardo Eizirik, Warren Johnson, Carlos Driscoll, Agostinho Antunes, Anne Schmidt-Kuntzel, Laurie Marker, Pavel Dobrynin

Biology Faculty Articles

No abstract provided.

Microhabitat Conditions In Wyoming’S Sage-Grouse Core Areas: Effects On Nest Site Selection And Success, Jonathan B. Dinkins, Kurt T. Smith, Jeffrey L. Beck, Christopher P. Kirol, Aaron C. Pratt, Michael R. Conover

Wildland Resources Faculty Publications

The purpose of our study was to identify microhabitat characteristics of greater sage-grouse (Centrocercus urophasianus) nest site selection and survival to determine the quality of sage-grouse habitat in 5 regions of central and southwest Wyoming associated with Wyoming’s Core Area Policy. Wyoming’s Core Area Policy was enacted in 2008 to reduce human disturbance near the greatest densities of sage-grouse. Our analyses aimed to assess sage-grouse nest selection and success at multiple micro-spatial scales. We obtained microhabitat data from 928 sage-grouse nest locations and 819 random microhabitat locations from 2008–2014. Nest success was estimated from 924 nests with survival data. Sage-grouse …

Benthic Foraminifera Abundance, Stable Isotopes, Desoto Canyon Sediments, 2010-2012, Patrick Schwing

C-IMAGE data

Spatial and temporal compilation of benthic foraminiferal abundance based on individually counted foraminifera from washed sediment samples, del13C measurements from Cibicidoides sp. measured by the SIRMS instrument at USF, CMS, all presented in the context of depth in each sediment core as well as by short-lived radioisotope age models. Spreadsheet: Benthic Foram Taxonomy, Foram Abundance Manuscript title: Quantifying the ecological impact of the Deepwater Horizon event on benthic foraminifera and subsequent rates of recovery Spreadsheet: Benthic Foram Stable Carbon Isotopes Manuscript title: Persistent δ13C depletion in benthic foraminiferal carbonate following the Deepwater Horizon event

Satellite, Glider Data, And Field Measurements To Study Harmful Algae On The West Florida Shelf During 2011 And 2012, Chuanmin Hu

C-IMAGE data

Satellite Oceanography is a sub-task under Task 4. It relies primarily on satellite-collected data, processed using either NASA standard algorithms or customized algorithms to produce data and imagery products specifically tailored for this project.

Predator-Prey Diet Linkages With Error Range For The Gulf Of Mexico Fitted Using Maximum Likelihood Method, Cameron H. Ainsworth

C-IMAGE data

Data is from Masi, M and Ainsworth, C. (in press) A Probabilistic Representation of Fish Diet Compositions from Multiple Data Sources: A Gulf of Mexico Case Study. Ecological Modelling. April 2014. Trophic ecosystem models are interactive tools that allow decision makers to analyze how a management decision can impact an ecosystem on a multi-species level, and are increasingly being used as a supplement to the current single species approach to fisheries management. The functionality of such a model is dependent upon an accurate representation of the trophic interactions occurring within a study area. Typical methods for developing a diet matrix …

Spatial Distributions Of Fish And Invertebrates In The Gulf Of Mexico For 2010-01-01 Estimated Using A Statistical Model, Michael Drexler

C-IMAGE data

A generalized additive modelling (GAM) approach is used to describe the abundance of 40 species groups (i.e. functional groups) across the Gulf of Mexico (GoM) using a large fisheries independent data set (SEAMAP) and climate scale oceanographic conditions. Predictor variables included in the model are chlorophyll a, sediment type, dissolved oxygen, temperature, and depth. The GAM approach was shown to be robust despite zero-inflated data. article: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0064458

West Florida Shelf Beach Sediment Pah And Dioctyl Sodium Sulfosuccinate Concentrations, Microtox Luminescence And Microscreen Mutagenicity Data, 2010 To 2013, Lauren D. Mcdaniel

C-IMAGE data

Six cohesive sand patty sediments were collected on a West Florida Shelf beach in St. Petersburg Florida, January, 2013. These were analyzed for presence of PAH compounds and the composition compared to measurements from known Deepwater Horizon contaminated beach sediments. Known contaminated samples were collected from Santa Rosa Florida in July 2010 and January 2011, and from Gulf Shores Alabama in December 2012. The same samples were also analyzed for biological activity and the presence of Corexit dispersant (DOSS). This dataset includes concentration data for PAHs and DOSS in these samples. The biological activity in the water accommodated fraction of …