Digital Commons Network^™

Hydrogen Bond Arrangement Is Shown To Differ In Coexisting Phases Of Aqueous Two-Phase Systems, Pedro P. Madeira, Amber R. Titus, Luisa A. Ferreira, Alexander I. Belgovskiy, Elizabeth K. Mann, Jay Adin Mann Jr., William V. Meyer, Anthony E. Smart, Vladimir N. Uversky, Boris Zaslavsky

Molecular Medicine Faculty Publications

Analysis by attenuated total reflection–Fourier transform infrared spectroscopy shows that each coexisting phase in aqueous two-phase systems has a different arrangement of hydrogen bonds. Specific arrangements vary for systems formed by different solutes. The hydrogen bond arrangement is shown to correlate with differences in hydrophobic and electrostatic properties of the different phases of five specific systems, four formed by two polymers and one by a single polymer and salt. The results presented here suggest that the arrangement of hydrogen bonds may be an important factor in phase separation.

Urgent Need For Field Surveys Of Coronaviruses In Southeast Asia To Understand The Sars-Cov-2 Phylogeny And Risk Assessment For Future Outbreaks, Murat Seyran, Sk. Sarif Hassan, Vladimir N. Uversky, Pabitra Pal Choudhury, Bruce D. Uhal, Kenneth Lundstrom, Diksha Attrish, Nima Rezaei, Alaa A. A. Aljabali, Shinjini Ghosh, Damiano Pizzol, Parise Adadi, Tarek Mohamed Abd El-Aziz, Ramesh Kandimalla, Murtaza M. Tambuwala, Amos Lal, Gajendra Kumar Azad, Samendra P. Sherchan, Wagner Baetas-Da-Cruz, Giorgio Palù, Adam M. Brufsky

All publications

No abstract provided.

The Highly Flexible Disordered Regions Of The Sars-Cov-2 Nucleocapsid N Protein Within The 1–248 Residue Construct: Sequence-Specific Resonance Assignments Through Nmr, Marco Schiavina, Letizia Pontoriero, Vladimir N. Uversky, Isabella C. Felli, Roberta Pierattelli

All publications

The nucleocapsid protein N from SARS-CoV-2 is one of the most highly expressed proteins by the virus and plays a number of important roles in the transcription and assembly of the virion within the infected host cell. It is expected to be characterized by a highly dynamic and heterogeneous structure as can be inferred by bioinformatics analyses as well as from the data available for the homologous protein from SARS-CoV. The two globular domains of the protein (NTD and CTD) have been investigated while no high-resolution information is available yet for the flexible regions of the protein. We focus here …

Dcaf14 Promotes Stalled Fork Stability To Maintain Genome Integrity, Arik Townsend, Gabriella Lora, Justin Engel, Neysha Tirado-Class, Huzefa Dungrawala

Molecular Biosciences Faculty Publications

No abstract provided.

Deep Learning For Supervised Classification Of Temporal Data In Ecology, César Capinha, Ana Ceia-Hasse, Andrew M. Kramer, Christiaan Meijer

Integrative Biology Faculty and Staff Publications

Temporal data is ubiquitous in ecology and ecologists often face the challenge of accurately differentiating these data into predefined classes, such as biological entities or ecological states. The usual approach consists of transforming the time series into user-defined features and then using these features as predictors in conventional statistical or machine learning models. Here we suggest the use of deep learning models as an alternative to this approach. Recent deep learning techniques can perform the classification directly from the time series, eliminating subjective and resource-consuming data transformation steps, and potentially improving classification results. We describe some of the deep learning …

Usf School Of Architecture And Community Design, Hillsborough County Sustainability Action Plan, 2021, Taryn Sabia, Maggie Winter

School of Architecture and Community Design

The Hillsborough County Sustainability Action Plan outlines a five-year strategy to advance environmental sustainability through data-driven goals and community collaboration. The plan addresses clean energy, water, waste, mobility, and housing. Contributors

Record Of A Red-Rumped Agouti (Dasyprocta Leporina) In Miami-Dade County, Florida, Bill Pranty, Valeri Ponzo

Florida Field Naturalist

No abstract provided.

Least Bittern Nesting In Pinal County, Az, Doug Jenness, Steve West

Arizona Birds

No abstract provided.

A Scopus-Based Bibliometric Study Of Maritime Research Involving The Automatic Identification System, Steven D. Meyers, Laura Azevedo, Mark E. Luther

Marine Science Faculty Publications

Vessel traffic records from the Automatic Identification System (AIS) are a useful source of information for maritime data analytics, and of training data for maritime artificial intelligence systems. Researchers utilizing these data are developing the foundations for operational maritime tools essential to economic expansion and security. The global growth and distribution of this research effort from 1997 to 2019 was examined through a bibliometric study of 817 Scopus-listed publications. Indications of both collaboration and accelerating competition were found by examining the number of publications and authors, national and institutional affiliations of the authors, and number of citations received. Prior …

Neuroprotective Effects Of Human Amniotic Fluid Stem Cells-Derived Secretome In An Ischemia/Reperfusion Model, Vanessa Castelli, Ivana Antonucci, Michele D'Angelo, Alessandra Tessitore, Veronica Zelli, Elisabetta Benedetti, Claudio Ferri, Giovambattista Desideri, Cesar Borlongan, Liborio Stuppia, Annamaria Cimini

Neurosurgery and Brain Repair Faculty Publications

Stem cells offer the basis for the promotion of robust new therapeutic approaches for a variety of human disorders. There are still many limitations to be overcome before clinical therapeutic application, including a better understanding of the mechanism by which stem cell therapies may lead to enhanced recovery. In vitro investigations are necessary to dissect the mechanisms involved and to support the potential development in stem cell-based therapies. In spite of growing interest in human amniotic fluid stem cells, not much is known about the characteristics of their secretome and regarding the potential neuroprotective mechanism in different pathologies, including stroke. …

National Identity And Integration Challenges Of Deferred Action For Childhood Arrivals (Daca) Recipients, Sofia Paschero, Jody Mcbrien

School of Interdisciplinary Global Studies Sarasota Manatee Campus Faculty Publications

Approximately 650,000 children and young adults currently reside in the United States with Deferred Action for Childhood Arrivals (DACA) status, providing them with temporary legal status to reside in the country. We explored the phenomenon of how five DACA recipients experienced their national identities and how it contributed to their acculturation patterns using in-depth semi-structured interviews. We interpreted their comments through the theoretical lens of Berry’s (1997) acculturation theory and Edensor’s (2002) emphasis on everyday life as a critical factor of national identity. Although the participants had the desire to remain in the United States and be a part of …

Multilevel Factors Associated With Length Of Stay For Neonatal Abstinence Syndrome In Florida’S Nicus: 2010–2015, Chinyere N. Reid, Tara R. Foti, Alfred K. Mbah, Mark L. Hudak, Maya Balakrishnan, Russell S. Kirby, Roneé E. Wilson, William M. Sappenfield

College of Public Health Faculty Publications

To investigate potential factors influencing initial length of hospital stay (LOS) for infants with neonatal abstinence syndrome (NAS) in Florida. The study population included 2984 term, singleton live births in 33 Florida hospitals. We used hierarchical linear modeling to evaluate the association of community, hospital, and individual factors with LOS. The average LOS of infants diagnosed with NAS varied significantly across hospitals. Individual-level factors associated with increased LOS for NAS included event year (P <  0.001), gestational age at birth (P <  0.001), maternal age (P = 0.002), maternal race and ethnicity (P <  0.001), maternal education (P = 0.032), and prenatal care adequacy (P <  0.001). Average annual hospital NAS volume (P = 0.022) was a significant hospital factor. NAS varies widely across hospitals in Florida. In addition to focusing on treatment regimens, to reduce LOS, public health and quality improvement initiatives should identify and adopt strategies that can minimize the prevalence and impact of these contributing factors.

A Whale Of A Tale: Gaming Disorder And Spending And Their Associations With Ad Watching In Role-Playing And Loot-Box Gaming, Samuel M. Tham, Gregory P. Perreault

School of Advertising & Mass Communications Faculty Publications

Mobile games featuring the loot-box design are associated with gambling because of the uncertainty in the value of the purchase and the propensity for gamers to keep spending. Role-playing games (RPGs) have been associated with gaming disorders because of the addictiveness and immersion experienced by gamers. Advertisers have capitalized on this gaming trend by having gamers watch advertisements, often in return for earning in-game currency. In this study, we explored the intersection of role-playing and loot-box mobile gaming, in particular examining the association with gaming disorders and ad watching and the role of game spending. An online survey was conducted …

The Gamification Of Gambling: A Case Study Of The Mobile Game Final Fantasy Brave Exvius, Gregory P. Perreault, Emory Daniel Jr., Samuel M. Tham

School of Advertising & Mass Communications Faculty Publications

The present study seeks to understand the 'loot box' gamer--gamers who play games in which real money is spent in order to gamble for the chance at digital game content. Prior research has found loot box gaming associated with problematic gaming behaviors and gambling. This study seeks to understand the players themselves through a case study of players of the loot box game Final Fantasy Brave Exvius. Examined through the lens of Social Identity Theory and Social Comparison Theory, this study examines the phenomenon through two data sets: a survey of participants on the Final Fantasy Brave Exvius subreddit …

How Journalists Think About The First Amendment Vis-À-Vis Their Coverage Of Hate Groups, Gregory P. Perreault, Jonathan Peters, Brett Johnson, Leslie Klein

School of Advertising & Mass Communications Faculty Publications

This study, based on in-depth interviews with U.S.-based journalists (n = 18), explores the increasingly fraught circumstances of reporting on hate groups. We examine how journalists think about the First Amendment vis-à-vis their coverage of such groups. Through the lens of media ecology and First Amendment principles and theories, we argue ultimately that journalists who cover hate groups use the First Amendment to identify their place in the journalistic environment.

A Synthesis Of Deepwater Horizon Impacts On Coastal And Nearshore Living Marine Resources, Steven A. Murawski, Joshua P. Kilborn, Adriana C. Bejarano, David Chagaris, David Donaldson, Frank J. Hernandez, Timothy C. Macdonald, Craig Newton, Ernst Peebles, Kelly L. Robinson

Marine Science Faculty Publications

The 2010 Deepwater Horizon (DWH) oil blowout in the Gulf of Mexico began on April 20, originating in the deep sea 66 km off the Louisiana coast. By early June, DWH oil had spread to coastal Louisiana, Mississippi, Alabama and western Florida. An estimated 2,113 km of shoreline were oiled, making DWH the largest marine oil spill in global history by length of affected shoreline. Additionally, a series of oil spill response measures were deployed, including diversions of Mississippi River discharge to forestall oil coming ashore, and the establishment of large-scale fishery closures, with both affecting coastal resources to varying …

The Gulf Of Mexico: An Overview, Larry D. Mckinney, John G. Shepherd, Charles A. Wilson, William T T. Hogarth, Jeff Chanton, Steven A. Murawski, Paul A. Sandifer, Tracey Sutton, David Yoskowitz, Katya Wowk, Tamay M. Özgökmen, Samantha B. Joye, Rex Caffey

Marine Science Faculty Publications

The Gulf of Mexico is a place where the environment and the economy both coexist and contend. It is a resilient large marine ecosystem that has changed in response to many drivers and pressures that we are only now beginning to fully understand. Coastlines of the states that border the Gulf comprise about half of the US southern seaboard, and those states are capped by the vast Midwest. The Gulf drains most of North America and is both an economic keystone and an unintended waste receptacle. It is a renowned resource for seafood markets, recreational fishing, and beach destinations and …

Analytic Hierarchy Process: An Innovative Technique For Culturally Tailoring Evidence-Based Interventions To Reduce Health Disparities, Jaime A. Corvin, Isabella Chan, Claudia X. Aguado, Ian Dollman, Junius Gonzales

Global Health Faculty Publications

Latinos in the United States represent a disproportionate burden of illness and disease and face barriers to accessing health care and related resources. Culturally tailored, evidence-based interventions hold promise in addressing many of these challenges. Yet, ensuring patient voice is vital in the successful development and implementation of such interventions. Thus, this paper examines the application of analytic hierarchy process (AHP) to inform the augmentation and implementation of an evidence-based chronic disease self-management programme for underserved Latinos living with both minor depression and chronic illness. The process of AHP allows for direct input from the individuals that would utilize such …

Advancing Gerontological Nursing At The Intersection Of Age-Friendly Communities, Health Systems, And Public Health, Jane Carmody, Kathy Black, Alice Bonner, Megan Wolfe, Terry Fulmer

Aging Studies Sarasota Manatee Campus Faculty Publications

Mounting efforts to improve care and promote healthy aging throughout society and across the care continuum have created unique opportunities for gerontological nursing practice. Population aging has invoked a multitude of responses among all levels of international and national organizations, foundations, health care, and government to meet the needs and promote preferences of older adults. Large-scale programs by the World Health Organization, The John A. Hartford Foundation, Institute for Health-care Improvement, and Trust for America's Health have galvanized to advance the momentum of age-friendly communities, health care, and public health. Gerontological nurses can leverage this growing interest in aging by …

Journalists On Covid-19 Journalism: Communication Ecology Of Pandemic Reporting, Mildred F. Perreault, Gregory P. Perreault

School of Advertising & Mass Communications Faculty Publications

In the midst of the COVID-19 pandemic, journalists have the challenging task of gathering and distributing accurate information. Journalists exist as a part of an ecology in which their work influences and is influenced by the environment that surrounds it. Using the framework of disaster communication ecology, this study explores the discursive construction of journalism during the COVID-19 crisis. To understand this process in the field of journalism, we unpacked discourses concerning the coronavirus pandemic collected from interviews with journalists during the pandemic and from the U.S. journalism trade press using the Discourses of Journalism Database. Through discourse analysis, we …

Perceptions Of Scientists Held By Us Students Can Be Broadened Through Inclusive Classroom Interventions, Sarah L. Sheffield, Meghan L. Cook, Victor J. Ricchezza, Guizella A. Rocabado, Fenda A. Akiwumi

School of Geosciences Faculty and Staff Publications

More diverse representation in undergraduate classrooms may be an important step towards turning science, technology, engineering, and mathematics (STEM) disciplines into more inclusive communities. In the United States of America, the individuals whose work is discussed in typical introductory science courses collectively do not represent the diversity of students’ identities in the classroom and further reinforce existing stereotypes of scientists as male, white, and aged. Here we report on the implementation of a semester-long intervention in an introductory-level geoscience course at the University of South Florida, USA. We introduced students to individuals with marginalized identities who are either scientists or …

Designing A Flexible Outreach Program For Scholarly Communication And Copyright Services: A Modular Roadshow For The University Of South Florida, Leetta Schmidt, Jason Boczar

Tampa Library Faculty and Staff Publications

Much the same as many other academic libraries, the University of South Florida (USF) developed scholarly communication and copyright services in response to community demand and to fulfill perceived institutional needs. The services initially established connections through liaison librarians and referral, when faculty patrons intuitively approached the library with a query. Growth of the services was slow. A new method of outreach for copyright and scholarly communication services was needed. The DSS Roadshow, named after the library department Digital Scholarship Services, aimed at providing a menu of modularly configured presentations to faculty and graduate students at the university. Based on …

Chemical Synthesis Of Peptidoglycan Mimetic–Disaccharide-Tetrapeptide Conjugate And Its Hydrolysis By Bacteriophage T5, Rb43 And Rb49 L-Alanyl-D-Glutamate Peptidases, Viatcheslav Azev, Alexey Chulin, Maxim Molchanov, Dmitry Prokhorov, Galina Mikoulinskaia, Vladimir N. Uversky, Viktor Kutyshenko

Molecular Medicine Faculty Publications

Endolysins of a number of bacteriophages, including coliphages T5, RB43, and RB49, target the peptidoglycans of the bacterial cell wall. The backbone of these bacterial peptidoglycans consist of alternating N-acetylglucosamine and N-acetylmuramic acid residues that is further “reinforced” by the peptide subunits. Because of the mesh-like structure and insolubility of peptidoglycans, the processes of the peptidoglycan binding and hydrolysis by enzymes cannot be studied by spectral methods. To overcome these issues we synthesized and analyzed here one of the simplest water soluble peptidoglycan mimetics.

A compound has been synthesized that mimics the peptidoglycan fragment of the bacterial cell wall, N-acetylglucosaminyl-β(1-4)-N-acetylmuramoyl-l-alanyl-γ-d-glutamyl-l-alanyl-d-alanine. …

Structural Protein Analysis Of Driver Gene Mutations In Conjunctival Melanoma, Mak B. Djulbegovic, Vladimir N. Uversky, J. William Harbour, Anat Galor, Carol L. Karp

Molecular Medicine Faculty Publications

In recent years, there has been tremendous enthusiasm with respect to detailing the genetic basis of many neoplasms, including conjunctival melanoma (CM). We aim to analyze five proteins associated with CM, namely BRAF, NRAS, c-KIT, NF1, and PTEN. We evaluated each protein for its intrinsically disordered protein regions (IDPRs) and its protein-protein interactions (PPI) with the Predictor of Natural Disordered Protein Regions (PONDR®) and the Search Tool for the Retrieval of Interacting Genes (STRING®). Our PONDR® analysis found high levels of IDPRs in all five proteins with mutations linked to CM. The highest levels of IDPRs were in BRAF (45.95%), …

The Finite Size Effects And Two-State Paradigm Of Protein Folding, Artem Badasyan, Matjaz Valant, Jože Grdadolnik, Vladimir N. Uversky

Molecular Medicine Faculty Publications

The coil to globule transition of the polypeptide chain is the physical phenomenon behind the folding of globular proteins. Globular proteins with a single domain usually consist of about 30 to 100 amino acid residues, and this finite size extends the transition interval of the coil-globule phase transition. Based on the pedantic derivation of the two-state model, we introduce the number of amino acid residues of a polypeptide chain as a parameter in the expressions for two cooperativity measures and reveal their physical significance. We conclude that the 𝑘2 measure, defined as the ratio of van ’t Hoff and calorimetric …

On The Roles Of Intrinsically Disordered Proteins And Regions In Cell Communication And Signaling, Sarah E. Bondos, A. Keith Dunker, Vladimir N. Uversky

Molecular Medicine Faculty Publications

For proteins, the sequence → structure → function paradigm applies primarily to enzymes, transmembrane proteins, and signaling domains. This paradigm is not universal, but rather, in addition to structured proteins, intrinsically disordered proteins and regions (IDPs and IDRs) also carry out crucial biological functions. For these proteins, the sequence → IDP/IDR ensemble → function paradigm applies primarily to signaling and regulatory proteins and regions. Often, in order to carry out function, IDPs or IDRs cooperatively interact, either intra- or inter-molecularly, with structured proteins or other IDPs or intermolecularly with nucleic acids. In this IDP/IDR thematic collection published in Cell Communication …

Predicting Associations Of Mirnas And Candidate Gastric Cancer Genes For Nanomedicine, Aigul Akimniyazova, Anna Pyrkova, Vladimir N. Uversky, Anatoliy Ivashchenko

Molecular Medicine Faculty Publications

Nanoscale miRNAs regulate the synthesis of most human proteins involved in differentiation, proliferation, cell cycle, apoptosis, and other processes associated with the growth and the development of an organism. miRNAs also play a number of important roles in the development of gastric cancer. In this work, we studied the quantitative characteristics of miRNA interactions with 69 candidate gastric cancer genes using bioinformatics approaches. To this end, the MirTarget program was used, which determines the characteristics of miRNA binding to mRNA in the 5′UTR, CDS, and 3′UTR. Associations of miRNAs with alternative target genes and associations of genes with alternative miRNAs …

Protein Intrinsic Disorder And Evolvability Of Mers-Cov, Vladimir N. Uversky, Elrashdy M. Redwan, Abdullah A. Aljadawi

Molecular Medicine Faculty Publications

No abstract provided.

Evolutionary Signatures Governing The Codon Usage Bias In Coronaviruses And Their Implications For Viruses Infecting Various Bat Species, Naveen Kumar, Rahul Kaushik, Chandana Tennakoon, Vladimir N. Uversky, Anamika Mishra, Richa Sood, Pratiksha Srivastava, Meghna Tripathi, Kam Y. J. Zhang, Sandeep Bhatia

Molecular Medicine Faculty Publications

Many viruses that cause serious diseases in humans and animals, including the betacoronaviruses (beta-CoVs), such as SARS-CoV, MERS-CoV, and the recently identified SARS-CoV-2, have natural reservoirs in bats. Because these viruses rely entirely on the host cellular machinery for survival, their evolution is likely to be guided by the link between the codon usage of the virus and that of its host. As a result, specific cellular microenvironments of the diverse hosts and/or host tissues imprint peculiar molecular signatures in virus genomes. Our study is aimed at deciphering some of these signatures. Using a variety of genetic methods we demonstrated …

Analysis Of The Dark Proteome Of Chandipura Virus Reveals Maximum Propensity For Intrinsic Disorder In Phosphoprotein, Nishi R. Sharma, Kundlik Gadhave, Prateek Kumar, Mohammad Saif, Md. M. Khan, Debi P. Sarkar, Vladimir N. Uversky, Rajanish Giri

Molecular Medicine Faculty Publications

Chandipura virus (CHPV, a member of the Rhabdoviridae family) is an emerging pathogen that causes rapidly progressing influenza-like illness and acute encephalitis often leading to coma and death of the human host. Given several CHPV outbreaks in Indian sub-continent, recurring sporadic cases, neurological manifestation, and high mortality rate of this infection, CHPV is gaining global attention. The ‘dark proteome’ includes the whole proteome with special emphasis on intrinsically disordered proteins (IDP) and IDP regions (IDPR), which are proteins or protein regions that lack unique (or ordered) three-dimensional structures within the cellular milieu. These proteins/regions, however, play a number of vital …