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Chemical Investigation Of Bioactive Marine Extracts, Selam Hagos

USF Tampa Graduate Theses and Dissertations

Natural products have been a fundamental source of medicinal scaffolds for decades; with sixty percent of marketed drugs. Many synthetic chemists are focused on synthesizing potent and nontoxic compounds for pharmaceutical targets, however, nature is still proving to be a source of new bioactive compounds. Produced by the host organism for defense, reproduction and communication, secondary metabolites also demonstrate promising bioactivity against human pathogens. Hence, natural product chemists continue their quest for new leads.

As a continuation of these efforts, this thesis attempts to explore fungi and sponges for new chemistry, and ultimately, new drug candidates. Antarctica is largely untapped; …

Ripple Effects Of The Belo Monte Dam: A Syndemic Approach To Addressing Health Impacts For The Downstream Community Of Gurupá, Cynthia A. Pace

USF Tampa Graduate Theses and Dissertations

This dissertation examines the public health impacts of a large dam project on a downstream community using the framework of Syndemic Theory. The particular focus is the Belo Monte Dam, located in the Brazilian Amazon, and its impact on the community of Gurupá, Pará. At the present time the Belo Monte Dam, which is nearing completion, stands out in scale as being the world’s third largest dam complex. Gurupá is a community well known (and well-studied) in the social science literature as Amazon Town. The aims of this study are to assess the pre-existing public health of Gurupá, as well …

Gesture: An Online Hand-Drawing Tool For Gene Expression Pattern Search, Chunyan Wang, Yiqing Xu, Xuelin Wang, Li Zhang, Suyun Wei, Qiaolin Ye, Youxiang Zhu, Hengfu Yin, Manoj Nainwal, Luis Tanon-Reyes, Feng Cheng, Tongming Yin, Ning Ye

Molecular Biosciences Faculty Publications

Gene expression profiling data provide useful information for the investigation of biological function and process. However, identifying a specific expression pattern from extensive time series gene expression data is not an easy task. Clustering, a popular method, is often used to classify similar expression genes, however, genes with a ‘desirable’ or ‘user-defined’ pattern cannot be efficiently detected by clustering methods. To address these limitations, we developed an online tool called GEsture. Users can draw, or graph a curve using a mouse instead of inputting abstract parameters of clustering methods. GEsture explores genes showing similar, opposite and time-delay expression patterns with …

Scalable Unsupervised Learning With Game Theory, Alireza Chakeri

USF Tampa Graduate Theses and Dissertations

Recently dominant sets, a generalization of the notion of the maximal clique to edge-weighted graphs, have proven to be an effective tool for unsupervised learning and have found applications in different domains. Although, they were initially established using optimization and graph theory concepts, recent work has shown fascinating connections with evolutionary game theory, that leads to the clustering game framework. However, considering size of today's data sets, existing methods need to be modified in order to handle massive data. Hence, in this research work, first we address the limitations of the clustering game framework for large data sets theoretically. We …

Abundance And Habitat Preferences Of Introduced Muscovy Ducks (Cairina Moschata), Jacqueline Marie Perry Cahanin

USF Tampa Graduate Theses and Dissertations

Muscovy ducks are native only to Central and South America, Mexico, and parts of southern Texas and are considered invasive in some areas outside of their native range. Although they have been introduced worldwide, they remain largely unstudied. The primary focus of this study was to relate Muscovy duck abundance to habitat characteristics of wetlands in Tampa, Florida. Muscovy abundance was measured using point count methods at 21 wetland sites that occur within an eight km radius of the University of South Florida’s main campus. Habitat features at these sites were assessed using field methods and Geographic Information Systems (GIS) …

Aposematism: An Alternative Hypothesis On How We Discover Medicinal Organisms, Nemer E. Narchi

Journal of Ecological Anthropology

The most widely accepted theories as to how primates select medicinal organisms are based on smelling-tasting bitter, and most of the times toxic, plants (Etkin & Ross, 1982; Johns, 1990). In primates, however, the senses of smell and taste are not as dominant as vision, an evolutionary trait which has been proven to be one of the most favored. I present a perspective claiming that aposematism, the conspicuous coloration displayed by toxic organisms, may play an important role in human recognition of medicinal organisms. This paper represents an open invitation for ecological anthropologists and ethnobiologists to generate empirical data that …

Full Issue 45(3)

International Journal of Speleology

No abstract provided.

Full Issue 7(4)

International Journal of Speleology

No abstract provided.

Nano-Photonic Waveguides For Chemical And Biomedical Sensing, Surya Venkatasekhar Cheemalapati

USF Tampa Graduate Theses and Dissertations

In this dissertation, advances in the fields of Photonics, and Plasmonics, and specifically, single cell analysis and waveguide sensing will be addressed. The first part of the dissertation is on Finite Difference Time Domain (FDTD) optimization and experimental demonstration of a nano-scale instrument that allows sensing at the cellular and subcellular levels. A new design of plasmonic coupler into a nanoscale waveguide is proposed and optimized using FDTD simulations. Following this, a subcellular nanoendoscope that can locally excite fluorescence in labelled cell organelles and collect the emitted fluorescent light for detailed spectrum analysis is fabricated and tested. The nanoendoscope has …

Geographically Isolated Wetlands Are Part Of The Hydrological Landscape, Mark Rains, S. G. Leibowitz, M. J. Cohen, I. F. Creed, H. E. Golden, J. W. Jawitz, P. Kalla, C. R. Lane, M. W. Lang, D. L. Mclaughlin

School of Geosciences Faculty and Staff Publications

No abstract provided.

Geographically Isolated Wetlands: Rethinking A Misnomer, David M. Mushet, Aram J. K. Calhoun, Laurie C. Alexander, Matthew J. Cohen, Edward S. Dekeyser, Laurie Fowler, Charles R. Lane, Mark C. Rains, Susan C. Walls

School of Geosciences Faculty and Staff Publications

We explore the category “geographically isolated wetlands” (GIWs; i.e., wetlands completely surrounded by uplands at the local scale) as used in the wetland sciences. As currently used, the GIW category (1) hampers scientific efforts by obscuring important hydrological and ecological differences among multiple wetland functional types, (2) aggregates wetlands in a manner not reflective of regulatory and management information needs, (3) implies wetlands so described are in some way “isolated,” an often incorrect implication, (4) is inconsistent with more broadly used and accepted concepts of “geographic isolation,” and (5) has injected unnecessary confusion into scientific investigations and discussions. Instead, we …

Inhibition Of Shp2/Ptpn11 Protein Tyrosine Phosphatase By Nsc-87877, Nsc-117199 And Their Analogs, Jie Wu, Nicholas J. Lawrence, Said M. Sebti, Harshani R. Lawrence

USF Patents

Compounds and associated methods for inhibiting a protein tyrosine phosphatase. By a combination of experimental and virtual screenings of the NCI Diversity Set chemical library, NSC-87877 and NSC-117199 have been identified as Shp2 PTP inhibitors. Significantly, NSC-87877 is active in cell-based assays and has no detectable off-target effects in the EGF-stimulated Erk 1/2 activation pathway. Additionally, a number of analogs of NSC-117199 have been produced. These analogs exhibit enhanced protein tyrosine phosphatase inhibition and are found to be potent and/or selective inhibitors of Shp1 and/or Shp2 protein tyrosine phosphatases.

Sulfidic Spring In The Gypsum Karst System Of Monte Conca (Italy): Chemistry And Microbiological Evidences, Marianna Messina, Tiziana Grech, Fiorenzo Fiorenza, Alessandro Marlettta, Pietro Valenti, Salvatore Petralia

International Journal of Speleology

Monte Conca Cave is a karst system placed in Messinian evaporites, consisting of an active cave and a resurgence located on the massif of Monte Conca, Campofranco within the "Riserva Naturale Integrale di Monte Conca". A sulfidic spring is located in the terminal gallery of the cave. To characterize the physical and chemical parameters of the Monte Conca cave and of the sulfidic spring, air temperature, relative humidity, water pH, and concentrations of dissolved sulfides, nitrates and sulfates were monitored. The high sulfide consumption rate in the sulfidic spring, evaluated by a kinetic study, suggests that biotic consumption is dominant. …

Design And Synthesis Of Bioactive Peptidomimetics, Yaogang Hu

USF Tampa Graduate Theses and Dissertations

Protein-Protein Interactions (PPIs) play a very important role in biological functions and therefore the inhibition of specific Protein-Protein Interactions has a huge therapeutic value. The most successful small molecular PPIs inhibitors do not fit with the prevalent `Rule of Five' drug profile. To overcome the disadvantages of small molecular PPIs inhibitors, peptide based PPIs inhibitors were developed. Herein we describe the development of a new class of peptidomimetics AA-peptides. The AApeptides were designed based on chiral PNA backbone. Substitution of nucleobases yields AApeptides that are resistant to proteolysis and capable of mimicking peptides. Two types of AApeptides were discussed in …

New Usfsp Grad Publishes Research In National Journal, September 12, 2014, Karlana June

USF St. Petersburg Campus News and Press Releases

No abstract provided.

Acta Carsologica, Volume 43, Issue 1, 2014, Franci Gabrovšek

KIP Articles

Contents: Interview with Andrej Kranjc -- Lower- to Middle Pleistocene Flank Margin Caves at Custonaci (Trapani, NW Sicily) and Their Relation with Past Sea Levels -- Karst in Ras Al-Khaimah, Northern United Arab Emirates -- Holocene Sedimentary Records of the Katarraktes Cave System (Northern Greece): A Stratigraphical and Environmental Magnetism Approach -- Karst Soils: Dependence of CO2 Concentrations on Pore Dimension -- Hydrochemical Response of Cave Drip Water to Snowmelt Water, a Case Study from Velika Pasica Cave, Central Slovenia -- Geothermal Potential and Sustainable Use of Karst Groundwater in Urban Areas - Belgrade, Capital of Serbia Case Study -- …

National Cave And Karst Research Institute 2013-2014 Annual Report, National Cave And Karst Research Institute

KIP Articles

No abstract provided.

Forty Years Of Epikarst: What Biology Have We Learned?, Tanja Pipan, David Culver

International Journal of Speleology

Epikarst is not only an important component of the hydrogeology of karst and an active site of speleogenesis, it is habitat for a number of species adapted to subterranean life. Water in epikarst, with a residence time of days to months, is a highly heterogeneous habitat, and the animals are primarily sampled from continuously sampling dripping water or collecting from residual drip pools. While the subterranean fauna of cracks and crevices has been known for over 100 years, it is only in the past several decades that epikarst has been recognized as a distinct habitat, with reproducing populations of stygobionts. …

2013: Proceedings Of The 16th International Congress Of Speleology, Czech Republic, Brno, July 21-28, 2013 Volume 2 International Congress Of Speleology Ics Proceedings, International Congress Of Speleology

KIP Talks and Conferences

Produced by the Organizing Committee of the 16th International Congress of Speleology. Published by the Czech Speleological Society and the SPELEO2013 and in the co-operation with the International Union of SpeleologyEdited by Michal Filippi, Pavel Bosák Contents: Preface Session: Exploration And Cave TechniquesRecent Investigations In The Gálapagos Islands, Ecuador / Aaron Addison, Theofilos Toulkeridis, Steven Taylor, Glenn Osburn, Geoffery Hoese, Vicente Delgado -- Quartz Sandstone Caves On Table Mountains Of Venezuela / Marek Audy, Richard Bouda -- Northern Velebit Deep Caves / Darko Bakšić, Dalibor Paar, Andrej Stroj, Damir Lacković -- Best-Practice Training Approaches For Mitigating Caving Hazards And Enhancing …

Species Abundance And Distribution Of Squid In The Eastern Gulf Of Mexico And Tampa Bay With A Focus On Biology, Christine Oliver

USF St. Petersburg campus Honors Program Theses (Undergraduate)

No abstract provided.

Literature Survey, Bibliographic Analysis And A Taxonomic Catalogue Of Subterranean Fauna From Portugal, Ana Sofia P.S. Reboleira, Gonçalves Fernando, Pedro Oromí

KIP Articles

A bibliographic analysis of the hypogean biological studies in Portugal is made, compiling 138 publications related to the subterranean invertebrate fauna, since its begining in 1870 until November 2012. A catalogue of hypogean endemic taxa is provided, listing 27 troglobionts and 63 stygobionts, described to be obligate hypogean and endemic from mainland Portugal (Macaronesian archipelagos excluded). The first impetus on troglobiont studies was provided by the prospections of Barros Machado during 1940’s and by an expedition of Lindberg in the spring of 1961; and the major information about stygobiont species was provided by the former Instituto de Zoologia “Dr. Augusto …

The Case For Intrinsically Disordered Proteins Playing Contributory Roles In Molecular Recognition Without A Stable 3d Structure, Vladimir N. Uversky, A. Keith Dunker

Molecular Medicine Faculty Publications

The classical ‘lock-and-key’ and ‘induced-fit’ mechanisms for binding both originated in attempts to explain features of enzyme catalysis. For both of these mechanisms and for their recent refinements, enzyme catalysis requires exquisite spatial and electronic complementarity between the substrate and the catalyst. Thus, binding models derived from models originally based on catalysis will be highly biased towards mechanisms that utilize structural complementarity. If mere binding without catalysis is the endpoint, then the structural requirements for the interaction become much more relaxed. Recent observations on specific examples suggest that this relaxation can reach an extreme lack of specific 3D structure, leading …

A Distributed Local-Leg Feedback Algorithm For Robust Walking On Uneven Terrain, Mayur Ramakant Palankar

USF Tampa Graduate Theses and Dissertations

Legged animals can traverse significantly more of the Earth's land mass than man-made wheeled and tracked vehicles~\cite{Anonymous67}. Their impressive mobility is largely due to multiple dexterous legs and the robust algorithms that coordinate and control them. A legged animal such as a squirrel can exhibit multiple locomotion modes such as walking, running and jumping and also multiple gaits or leg phase timings within each mode. A robot that could mimic this level of robust locomotion would be highly useful for planetary exploration, military reconnaissance, and time-critical search and rescue in cluttered or collapsed buildings.

A number of biological studies on …

New Perspectives On How To Discover Drugs From Herbal Medicines: Cam's Outstanding Contribution To Modern Therapeutics, Si-Yuan Pan, Shu-Feng Zhou, Si-Hua Gao, Zhi-Ling Yu, Shuo-Feng Zhang, Min-Ke Tang, Jian-Ning Sun, Dik-Lung Ma, Yi-Fan Han, Wang-Fun Fong, Kam-Ming Ko

Pharmacy Faculty Publications

With tens of thousands of plant species on earth, we are endowed with an enormous wealth of medicinal remedies from Mother Nature. Natural products and their derivatives represent more than 50% of all the drugs in modern therapeutics. Because of the low success rate and huge capital investment need, the research and development of conventional drugs are very costly and difficult. Over the past few decades, researchers have focused on drug discovery from herbal medicines or botanical sources, an important group of complementary and alternative medicine (CAM) therapy. With a long history of herbal usage for the clinical management of …

Computational Approaches For Structure Based Drug Design And Protein Structure-Function Prediction, Sai Lakshmana Kumar Vankayala

USF Tampa Graduate Theses and Dissertations

This dissertation thesis consists of a series of chapters that are interwoven by solving interesting biological problems, employing various computational methodologies. These techniques provide meaningful physical insights to promote the scientific fields of interest. Focus of chapter 1 concerns, the importance of computational tools like docking studies in advancing structure based drug design processes. This chapter also addresses the prime concerns like scoring functions, sampling algorithms and flexible docking studies that hamper the docking successes. Information about the different kinds of flexible dockings in terms of accuracy, time limitations and success studies are presented. Later the importance of Induced fit …

Ecology Of The Late Neogene Extinctions: Perspectives From The Plio-Pleistocene Of Florida, Shubhabrata Paul

USF Tampa Graduate Theses and Dissertations

The ecological impact of past extinction events is one of the central issues in paleobiology. In face of present environmental changes, a better understanding of past extinctions will enable us to identify the magnitude of biodiversity crises and their underlying processes. The Late Neogene was a time of extraordinary climatic reorganization, including Northern Hemisphere glaciation, the rise of the Central American Isthmus, and associated changes in environmental conditions. Therefore, the Late Neogene extinctions of marine molluscs of South Florida present an ideal platform to examine the interaction between environmental changes and biotic response. In the present study, three different aspects …

Assessment Of The Oxbow Morphology Of The Caloosahatchee River And Its Evolution Over Time: A Case Study In South Florida, Chloe Delhomme

USF Tampa Graduate Theses and Dissertations

The Caloosahatchee River, located in Southern Florida, was originally a meandering and relatively shallow river. During the 1920s, the Caloosahatchee River was channelized and became the C-43 canal. The channelization has significantly impacted the river ecosystem, particularly the oxbows. The oxbows are the U-shaped water bodies on each side of the river channel, which are the remnant bends of the original river. To understand how anthropogenic influence affects hydrologic systems, the proposed case study was designed to assess the geomorphic changes of the oxbows of the Caloosahatchee River, Florida. Understanding and documenting the evolution of river morphology is becoming increasingly …

Hydrophilic Polymers Of Poly (2-Hydroxy Ethyl Methacrylate) With Tunable Properties For Drug Release, Sequestration Of Blistering Agent, Preparation Of Ultra-Strong Hydrogels & Thermal Stability Of Various Organic Azides, Ramakanth Ananthoji

USF Tampa Graduate Theses and Dissertations

The design and synthesis of new finely tunable porous materials has spurred interest in developing novel uses in a variety of systems. Zeolites, inorganic materials with high thermal and mechanical stability, in particular, have been widely examined for use in applications such as catalysis, ion exchange and separation. A relatively new class of inorganic-organic hybrid materials known as metal-organic frameworks (MOFs) has recently surfaced, and many have exhibited their efficiency in potential applications such as ion exchange and drug delivery. A more recent development is the design and synthesis of a subclass of MOFs based on zeolite topologies (i.e. ZMOFs), …

Cave Research Foundation Quarterly, Volume 40, No. 1, February 2012, Laura Lexander

KIP Articles

Contents: Donkey-Mammoth Cave Connection: Eleventh Cave Joins the Longest Cave, May 28, 2011 / Roger W. Burcker -- Ave Atque Vale / Scott House -- From the President: / Charles Fox -- Regional Expedition Reports -- 2012 Expedition Calendar

Behavioral And Immunological Phenotypes Of Transgenic Mice Overexpressing Human Secreted Amyloid Precursor Protein Alpha: Implications For Autism, Antoinette R. Bailey

USF Tampa Graduate Theses and Dissertations

Autism is a heterogeneous neurodevelopmental disorder that is characterized by impaired social interaction and communication as well as restricted and repetitive behaviors and focused interests. In addition to the cardinal behavioral characteristics observed for diagnosis, autistic individuals exhibit a number of comorbid conditions as well as a variety of aberrant immunological features. Recent studies report that plasma from autistic children contained elevated levels of secreted amyloid precursor protein alpha (sAPP-á), the á-secretase cleavage product of the amyloid precursor protein (APP) which is ubiquitously expressed in the brain, spleen, thymus and other organs. Interestingly, the sAPP-á fragment functions as a neurotrophic …