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The Effects Of Effluent Discharge Into The Santa Fé River, João Vito Bezerra Dragone

Undergraduate Journal of Mathematical Modeling: One + Two

The discharge of effluents into rivers is something that has occurred a lot throughout our history, rivers like the Mississippi River and the Tiete River (São Paulo, Brazil) have been targets for many years. Therefore, in this paper I choose to show, through hard data and some assumptions, the impact of sewage dumping in water bodies, in this case the Santa Fé River, Florida and the reason why we should avoid dumping these effluents into the rivers.

Hymnal Of Teeth: Southern Stories Of Folk And Fey, James E. Phillips Iii

Honors Undergraduate Theses

We are the stories we tell. Folk and fairy tales are reflections of the cultures that pass them down. Contemporary literary traditions, such as the Southern Gothic and tales of magical realism, also provide unique ways of responding to concerns within our society. This thesis attempts to merge these literary traditions to create a collection of Southern folk and fairy tales. These stories vary in style from very traditional fairy tales to more modern styles of magical realism and lyrical poetry. This collection was crafted after studying an extensive reading list of novels and short story collections written by masters …

The Importance Of Emotional And Physical Safety In The Success And Development Of Public Spaces, Isabella Wilhelm

Honors Undergraduate Theses

Our day-to-day lives consist of formal and informal settlements in the built environment. As humans, we gravitate towards successful informal settlements (public spaces) to conduct activities such as socializing and recharging. Previous research has highlighted the importance of distinct factors in determining the success of public spaces. Still, research has failed to develop the foundation that makes all public places prosper. Through examining successful and unsuccessful public places through case studies, this research analyses the success and importance of our emotional and physical safety in public spaces through the presence or absence of sound, light, nature, boundaries, and order.

On Your Painted Wings, Sandra M. Ford

Honors Undergraduate Theses

The intent of this thesis is to explore historical issues of Cuban restrictions on emigration through a magical realism lens. Drawing inspiration from Cuban-American writer Ana Menéndez and Columbian writer Gabriel García Márquez, this thesis focuses on family relationships, especially how grief shapes those relationships and the people in them. The thesis approaches these issues of family, grief, and Cuban emigration by weaving a more grounded central narrative with an original fairytale.

Good Patients, Susan Mesler-Evans

Honors Undergraduate Theses

This thesis is the first 21 chapters (approximately 150 pages) of a novel, Good Patients, accompanied by a complete synopsis. Good Patients is a social satire which seeks to touch on the flaws of the American healthcare system and social media culture, and how these two intersect for many people. To prepare for writing, I spent my first semester completing a guided reading list and preparing the synopsis, both of which were approved by my thesis chair. While writing, I consulted several medical articles to make my work as accurate as possible. The novel explores the way social media …

Revealing The Black Form: Black Bodies In Nineteenth-Century French Orientalist Visual Art, Nathanael Amir Justin Lapierre

Honors Undergraduate Theses

In the nineteenth century, Orientalism functioned as a Western tool for dominating and restructuring the perception of the Orient. In France, where Orientalism found favor amongst artists, Orientalist works were produced in the literary and visual arts to inform and control the narrative about the East. Influenced by the Napoleonic imperial conquests and an increased French presence in the East, Orientalism became an integral movement in the French visual arts. The relationship between France and the Orient was one of power and domination, which was mirrored in that between the French and the Blacks.

As a part of the Western …

Everything But The Smell: The Ethics Of The “Connective Turn” In Argentinian Memory Activism, Megan L. Corbin

Languages & Cultures Faculty Publications

This chapter interrogates what is lost and what is gained in [the] turn toward cyberspace as a new venue for interacting with a traumatic past. It will first examine the discussions and debates that took place in Argentina as former detention centres were converted into sites of memory, using the debate about the recovery of Escuela Mecánica de la Armada [ESMA] (the Navy School of Mechanics) as an illustrative example. Then, it will compare the features of some of actual memory sites in Buenos Aires with the interactive documentary features on the website, specifically focusing on the narrative logic and …

Learning From The Collective Space In Making Culture And Making Space : A Case Study From Yogyakarta City, Indonesia, Zita Wahyu Larasati, Pinurba Parama Pratiyudha, Galih Prabaningrum, Devy Dhian Cahyati, Krisdyatmiko Krisdyatmiko

Journal of Urban Culture Research

The contestation of urban space is a dialectical process in defining space by stakeholders in urban areas. We will explain the efforts of city citizens to form a collective space by promoting a making culture. With the spirit of Do It Yourself and Do It With Others, the collective space produces shared knowledge and democratizes data to increase the capacity of urban citizens. This study is grounded on empirical research in Yogyakarta through in-depth interviews, focus group discussions, and participant observation. We discuss the formation of collective space in urban informality to encourage urban communities. This study finds that the …

2021 Kentucky River Watershed Watch: Annual Report, Malissa Mcalister, Steven Evans

Kentucky River Watershed Watch

No abstract provided.

Investigating The Impact Of Unlimited Sucrose During Adolescence On Flex Maze Performance In Rats, Emma Klopatek, Emily Tobolski, Bailey Harvey, Danielle Frances, Taylor Garrels, Gillian Lado

Science University Research Symposium (SURS)

As depression continues to impact many people, there are important considerations to be taken in how depression impacts people's learning and motivations. The objective of this study is to examine the effects of unlimited sucrose consumption during adolescence, which can mimic symptoms of depression, on spatial memory and motivation in rats. The flex maze is used in the present study to assess these behaviors. Before initial training on the flex maze, 6 male rats were separated into two groups: an experimental group with unlimited access to 5% sucrose (and water) for approximately 3 weeks and a control group with free …

Bowling Online: Introduction To Social Worlds In Second Life, Hope Mac Donald

Graduate Research Theses & Dissertations

During the ongoing covid pandemic, people with underlying conditions that could become comorbidities were forced to retreat into their homes and were banned from social spaces if they wanted to survive. Those with capital could participate in online social spaces. With the push towards considering Covid an endemic disease, which by definition means repeated outbreaks, immunocompromised people will be forced to continually withdraw from social spaces. Virtual worlds and other digital communities may be helpful in dealing with the social isolation and anxiety caused by having to distance oneself in order to protect themselves. Virtual worlds are not a perfect …

Editorial: Emerging And Re-Emerging Viral Zoonoses, Naveen Kumar, Vladimir N. Uversky, Shailly Tomar, Kenneth S. M. Li, Keith Chappell, Susanna K. P. Lau

Molecular Medicine Faculty Publications

No abstract provided.

An Ayurgenomics Approach: Prakriti-Based Drug Discovery And Development For Personalized Care, Zoufang Huang, Vivek P. Chavda, Rajashri Bezbaruah, Vladimir N. Uversky, Sucharitha Palagati, Aayushi B. Patel, Zhe-Sheng Chen

Molecular Medicine Faculty Publications

Originating in ancient India, Ayurveda is an alternative medicinal approach that provides substantial evidence for a theoretical-level analysis of all aspects of life. Unlike modern medicine, Ayurveda is based upon tridoshas (Vata, pitta, and Kapha) and Prakriti. On the other hand, the research of all the genes involved at the proteomics, metabolomics, and transcriptome levels are referred to as genomics. Geoclimatic regions (deshanupatini), familial characteristics (kulanupatini), and ethnicity (jatiprasakta) have all been shown to affect phenotypic variability. The combination of genomics with Ayurveda known as ayurgenomics provided new insights into tridosha that may pave the way for precision medicine (personalized …

Msh3 Homology And Potential Recombination Link To Sars-Cov-2 Furin Cleavage Site, Balamurali K. Ambati, Akhil Varshney, Kenneth Lundstrom, Giorgio Palù, Bruce D. Uhal, Vladimir N. Uversky, Adam M. Brufsky

Molecular Medicine Faculty Publications

Among numerous point mutation differences between the SARS-CoV-2 and the bat RaTG13 coronavirus, only the 12-nucleotide furin cleavage site (FCS) exceeds 3 nucleotides. A BLAST search revealed that a 19 nucleotide portion of the SARS-CoV-2 genome encompassing the furin cleavage site is a 100% complementary match to a codon-optimized proprietary sequence that is the reverse complement of the human mutS homolog (MSH3). The reverse complement sequence present in SARS-CoV-2 may occur randomly but other possibilities must be considered. Recombination in an intermediate host is an unlikely explanation. Single stranded RNA viruses such as SARS-CoV-2 utilize negative strand RNA templates in …

Bmi1 Silencing Induces Mitochondrial Dysfunction In Lung Epithelial Cells Exposed To Hyperoxia, Helena Hernández-Cuervo, Ramani Soundararajan, Sahebgowda Sidramagowda Patil, Mason T. Breitzig, Matthew Alleyn, Lakshmi Galam, Richard Lockey, Vladimir N. Uversky, Narasaiah Kolliputi

Molecular Medicine Faculty Publications

Acute Lung Injury (ALI), characterized by bilateral pulmonary infiltrates that restrict gas exchange, leads to respiratory failure. It is caused by an innate immune response with white blood cell infiltration of the lungs, release of cytokines, an increase in reactive oxygen species (ROS), oxidative stress, and changes in mitochondrial function. Mitochondrial alterations, changes in respiration, ATP production and the unbalancing fusion and fission processes are key events in ALI pathogenesis and increase mitophagy. Research indicates that BMI1 (B cell-specific Moloney murine leukemia virus integration site 1), a protein of the Polycomb repressive complex 1, is a cell cycle and survival …

What Is Parvalbumin For?, Eugene A. Permyakov, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Parvalbumin (PA) is a small, acidic, mostly cytosolic Ca2+-binding protein of the EF-hand superfamily. Structural and physical properties of PA are well studied but recently two highly conserved structural motifs consisting of three amino acids each (clusters I and II), which contribute to the hydrophobic core of the EF-hand domains, have been revealed. Despite several decades of studies, physiological functions of PA are still poorly known. Since no target proteins have been revealed for PA so far, it is believed that PA acts as a slow calcium buffer. Numerous experiments on various muscle systems have shown that PA accelerates the …

Shell Disorder Models Detect That Omicron Has Harder Shells With Attenuation But Is Not A Descendant Of The Wuhan-Hu-1 Sars-Cov-2, Gerard Kian-Meng Goh, A. Keith Dunker, James A. Foster, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Before the SARS-CoV-2 Omicron variant emergence, shell disorder models (SDM) suggested that an attenuated precursor from pangolins may have entered humans in 2017 or earlier. This was based on a shell disorder analysis of SARS-CoV-1/2 and pangolin-Cov-2017. The SDM suggests that Omicron is attenuated with almost identical N (inner shell) disorder as pangolin-CoV-2017 (N-PID (percentage of intrinsic disorder): 44.8% vs. 44.9%—lower than other variants). The outer shell disorder (M-PID) of Omicron is lower than that of other variants and pangolin-CoV-2017 (5.4% vs. 5.9%). COVID-19-related CoVs have the lowest M-PIDs (hardest outer shell) among all CoVs. This is likely to be …

Peptidoglycan-Free Bacterial Ghosts Confer Enhanced Protection Against Yersinia Pestis Infection, Svetlana V. Dentovskaya, Anastasia S. Vagaiskaya, Mikhail E. Platonov, Alexandra S. Trunyakova, Sergey A. Kotov, Ekaterina A. Krasil’Nikova, Galina M. Titareva, Elizaveta M. Mazurina, Tat’Yana V. Gapel’Chenkova, Rima Z. Shaikhutdinova, Sergey A. Ivanov, Tat’Yana I. Kombarova, Vladimir N. Gerasimov, Vladimir N. Uversky, Andrey P. Anisimov

Molecular Medicine Faculty Publications

To develop a modern plague vaccine, we used hypo-endotoxic Yersinia pestis bacterial ghosts (BGs) with combinations of genes encoding the bacteriophage ɸX174 lysis-mediating protein E and/or holin-endolysin systems from λ or L-413C phages. Expression of the protein E gene resulted in the BGs that retained the shape of the original bacterium. Co-expression of this gene with genes coding for holin-endolysin system of the phage L-413C caused formation of structures resembling collapsed sacs. Such structures, which have lost their rigidity, were also formed as a result of the expression of only the L-413C holin-endolysin genes. A similar holin-endolysin system from phage …

Α-Synuclein Fibrils As Penrose Machines: A Chameleon In The Gear, Francesca De Giorgi, Vladimir N. Uversky, François Ichas

Molecular Medicine Faculty Publications

In 1957, Lionel Penrose built the first man-made self-replicating mechanical device and illustrated its function in a series of machine prototypes, prefiguring our current view of the genesis and the proliferation of amyloid fibrils. He invented and demonstrated, with the help of his son Roger, the concepts that decades later, would become the fundamentals of prion and prion-like neurobiology: nucleation, seeding and conformational templating of monomers, linear polymer elongation, fragmentation, and spread. He published his premonitory discovery in a movie he publicly presented at only two conferences in 1958, a movie we thus reproduce here. By making a 30-year-jump in …

Arrow Of Time, Entropy, And Protein Folding: Holistic View On Biochirality, Victor V. Dyakin, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Chirality is a universal phenomenon, embracing the space–time domains of non-organic and organic nature. The biological time arrow, evident in the aging of proteins and organisms, should be linked to the prevalent biomolecular chirality. This hypothesis drives our exploration of protein aging, in relation to the biological aging of an organism. Recent advances in the chirality discrimination methods and theoretical considerations of the non-equilibrium thermodynamics clarify the fundamental issues, concerning the biphasic, alternative, and stepwise changes in the conformational entropy associated with protein folding. Living cells represent open, non-equilibrium, self-organizing, and dissipative systems. The non-equilibrium thermodynamics of cell biology are …

Fundamental Clock Of Biological Aging: Convergence Of Molecular, Neurodegenerative, Cognitive And Psychiatric Pathways: Non-Equilibrium Thermodynamics Meet Psychology, Victor V. Dyakin, Nuka V. Dyakina-Fagnano, Laura B. Mcintire, Vladimir N. Uversky

Molecular Medicine Faculty Publications

In humans, age-associated degrading changes, widely observed in molecular and cellular processes underly the time-dependent decline in spatial navigation, time perception, cognitive and psychological abilities, and memory. Cross-talk of biological, cognitive, and psychological clocks provides an integrative contribution to healthy and advanced aging. At the molecular level, genome, proteome, and lipidome instability are widely recognized as the primary causal factors in aging. We narrow attention to the roles of protein aging linked to prevalent amino acids chirality, enzymatic and spontaneous (non-enzymatic) post-translational modifications (PTMs SP), and non-equilibrium phase transitions. The homochirality of protein synthesis, resulting in the steady-state non-equilibrium condition …

Intrinsically Disordered Proteins Play Diverse Roles In Cell Signaling, Sarah E. Bondos, A. Keith Dunker, Vladimir N. Uversky

Molecular Medicine Faculty Publications

Signaling pathways allow cells to detect and respond to a wide variety of chemical (e.g. Ca2+ or chemokine proteins) and physical stimuli (e.g., sheer stress, light). Together, these pathways form an extensive communication network that regulates basic cell activities and coordinates the function of multiple cells or tissues. The process of cell signaling imposes many demands on the proteins that comprise these pathways, including the abilities to form active and inactive states, and to engage in multiple protein interactions. Furthermore, successful signaling often requires amplifying the signal, regulating or tuning the response to the signal, combining information sourced from multiple …

Limosilactobacillus Fermentum Strain 3872: Antibacterial And Immunoregulatory Properties And Synergy With Prebiotics Against Socially Significant Antibiotic-Resistant Infections Of Animals And Humans, Vyacheslav M. Abramov, Igor V. Kosarev, Andrey V. Machulin, Tatiana V. Priputnevich, Irina O. Chikileva, Eugenia I. Deryusheva, Tatiana N. Abashina, Almira D. Donetskova, Alexander N. Panin, Vyacheslav G. Melnikov, Natalia E. Suzina, Ilya N. Nikonov, Marina V. Selina, Valentin S. Khlebnikov, Vadim K. Sakulin, Raisa N. Vasilenko, Vladimir A. Samoilenko, Vladimir N. Uversky, Andrey V. Karlyshev

Molecular Medicine Faculty Publications

Limosilactobacillus fermentum strain 3872 (LF3872) was originally isolated from the breast milk of a healthy woman during lactation and the breastfeeding of a child. The high-quality genome sequencing of LF3872 was performed, and a gene encoding a unique bacteriocin was discovered. It was established that the bacteriocin produced by LF3872 (BLF3872) belongs to the family of cell-wall-degrading proteins that cause cell lysis. The antibacterial properties of LF3872 were studied using test cultures of antibiotic-resistant Gram-positive and Gram-negative pathogens. Gram-positive pathogens (Staphylococcus aureus strain 8325-4 and S. aureus strain IIE CI-SA 1246) were highly sensitive to the bacteriolytic action of LF3872. …

A Study On The Nature Of Sars-Cov-2 Using The Shell Disorder Models: Reproducibility, Evolution, Spread, And Attenuation, Gerard Kian-Meng Goh, A. Keith Dunker, James A. Foster, Vladimir N. Uversky

Molecular Medicine Faculty Publications

The basic tenets of the shell disorder model (SDM) as applied to COVID-19 are that the harder outer shell of the virus shell (lower PID—percentage of intrinsic disorder—of the membrane protein M, PIDM) and higher flexibility of the inner shell (higher PID of the nucleocapsid protein N, PIDN) are correlated with the contagiousness and virulence, respectively. M protects the virion from the anti-microbial enzymes in the saliva and mucus. N disorder is associated with the rapid replication of the virus. SDM predictions are supported by two experimental observations. The first observation demonstrated lesser and greater presence of the Omicron particles …

Bayesian Molecular Dating Analyses Combined With Mutational Profiling Suggest An Independent Origin And Evolution Of Sars-Cov-2 Omicron Ba.1 And Ba.2 Sub-Lineages, Naveen Kumar, Rahul Kaushik, Ashutosh Singh, Vladimir N. Uversky, Kam Y. J. Zhang, Upasana Sahu, Sandeep Bhatia, Aniket Sanyal

Molecular Medicine Faculty Publications

The ongoing evolution of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has resulted in the recent emergence of a highly divergent variant of concern (VOC) defined as Omicron or B.1.1.529. This VOC is of particular concern because it has the potential to evade most therapeutic antibodies and has undergone a sustained genetic evolution, resulting in the emergence of five distinct sub-lineages. However, the evolutionary dynamics of the initially identified Omicron BA.1 and BA.2 sub-lineages remain poorly understood. Herein, we combined Bayesian phylogenetic analysis, mutational profiling, and selection pressure analysis to track the virus’s genetic changes that drive the early evolutionary dynamics of …

Insights Into The Structural Properties Of Sars-Cov-2 Main Protease, Ibrahim Y. Akbaryak, Sule I. Caglayan, Lukasz Kurgan, Vladimir N. Uversky, Orkid Coskuner-Weber

Molecular Medicine Faculty Publications

SARS-CoV-2 is the infectious agent responsible for the coronavirus disease since 2019, which is the viral pneumonia pandemic worldwide. The structural knowledge on SARS-CoV-2 is rather limited. These limitations are also applicable to one of the most attractive drug targets of SARS-CoV-2 proteins – namely, main protease Mpro, also known as 3C-like protease (3CLpro). This protein is crucial for the processing of the viral polyproteins and plays crucial roles in interfering viral replication and transcription. In fact, although the crystal structure of this protein with an inhibitor was solved, Mpro conformational dynamics in aqueous solution is usually studied by molecular …

Fight Fire With Fire: The Need For A Vaccine Based On Intrinsic Disorder And Structural Flexibility, Vladimir N. Uversky

Molecular Medicine Faculty Publications

The absence of advancement in finding efficient vaccines for several human viruses, such as hepatitis C virus (HCV), human immunodeficiency virus type 1 (HIV-1), and herpes simplex viruses (HSVs) despite 30, 40, and even 60 years of research, respectively, is unnerving. Among objective reasons for such failure are the highly glycosylated nature of proteins used as primary vaccine targets against these viruses and the presence of neotopes and cryptotopes, as well as high mutation rates of the RNA viruses HCV and HIV-1 and the capability to establish latency by HSVs. However, the lack of success in utilization of the structure-based …

An Optimal Lysis Time Maximizes Bacteriophage Fitness In Quasi-Continuous Culture, Sherin Kannoly, Abhyudai Singh, John J. Dennehy

Publications and Research

Optimality models have a checkered history in evolutionary biology. While optimality models have been successful in providing valuable insight into the evolution of a wide variety of biological traits, a common objection is that optimality models are overly simplistic and ignore organismal genetics. We revisit evolutionary optimization in the context of a major bacteriophage life history trait, lysis time. Lysis time refers to the period spanning phage infection of a host cell and its lysis, whereupon phage progenies are released. Lysis time, therefore, directly determines phage fecundity assuming progeny assembly does not exhaust host resources prior to lysis. Noting that …

Bio-Inspired Sutures: Using Finite Element Analysis To Parameterize The Mechanical Response Of Dovetail Sutures In Simulated Bending Of A Curved Structure, Melissa M. Gibbons, Diana A. Chen

School of Engineering: Faculty Scholarship

Many animals have protective anatomical structures that allow for growth and flexibility; these structures contain thin seams called sutures that help the structure to absorb impacts. In this study, we parameterized the stiffness and toughness of a curved archway structure based on three geometric properties of a suture through finite element, quasi-static, three-point bending simulations. Each archway consisted of two symmetric pieces linked by a dovetail suture tab design. The three parameters included suture tab radii (1–5 mm), tangent lengths (0–20 mm), and contact angles (0–40◦). In the simulations, a steel indenter was displaced 6.5 mm to induce progressive tab …

Concerning A Requirement That The Ballot Title And Fiscal Summary For Any Ballot Initiative That Increases Or Decreases State Income Tax Rates Include A Table Showing The Average Tax Change For Tax Filers In Different Income Categories, Colorado General Assembly

Session Laws 2001-Present

No abstract provided.