Digital Commons Network^™

Undergraduate Biology Lecture Courses Predominantly Test Facts About Science Rather Than Scientific Practices, Crystal Uminski, Sara M. Burbach, Brian A. Couch

School of Biological Sciences: Faculty Publications

Scientific practices are the skills used to develop scientific knowledge and are essential for careers in science. Despite calls from education and government agencies to cultivate scientific practices, there remains little evidence of how often students are asked to apply them in undergraduate courses. We analyzed exams from biology courses at 100 institutions across the United States and found that only 7% of exam questions addressed a scientific practice and that 32% of biology exams did not test any scientific practices. The low occurrence of scientific practices on exams signals that undergraduate courses may not be integrating foundational scientific skills …

Dissection, Histological Processing, And Gene Expression Analysis Of Murine Supraclavicular Brown Adipose Tissuejove: Peer Reviewed Scientific Video Journal Article Protocols, Mark G Waterstraat, Ziyi Wang, Mari Kogiso, Rommel Caballero-Juarez, Miao-Hsueh Chen

Faculty, Staff and Students Publications

Brown adipose tissue (BAT)-mediated thermogenesis plays an important role in the regulation of metabolism, and its morphology and function can be greatly impacted by environmental stimuli in mice and humans. Currently, murine interscapular BAT (iBAT), which is located between two scapulae in the upper dorsal flank of mice, is the main BAT depot used by research laboratories to study BAT function. Recently, a few previously unknown BAT depots were identified in mice, including one analogous to human supraclavicular brown adipose tissue. Unlike iBAT, murine supraclavicular brown adipose tissue (scBAT) is situated in the intermediate layer of the neck and thus …

Dissection, Histological Processing, And Gene Expression Analysis Of Murine Supraclavicular Brown Adipose Tissue, Mark G Waterstraat, Ziyi Wang, Mari Kogiso, Rommel Caballero-Juarez, Miao-Hsueh Chen

Children’s Nutrition Research Center Staff Publications

Brown adipose tissue (BAT)-mediated thermogenesis plays an important role in the regulation of metabolism, and its morphology and function can be greatly impacted by environmental stimuli in mice and humans. Currently, murine interscapular BAT (iBAT), which is located between two scapulae in the upper dorsal flank of mice, is the main BAT depot used by research laboratories to study BAT function. Recently, a few previously unknown BAT depots were identified in mice, including one analogous to human supraclavicular brown adipose tissue. Unlike iBAT, murine supraclavicular brown adipose tissue (scBAT) is situated in the intermediate layer of the neck and thus …

Gut Microbiota And Blood Metabolites Related To Fiber Intake And Type 2 Diabetes, Zheng Wang, Brandilyn A Peters, Bing Yu, Megan L Grove, Tao Wang, Xiaonan Xue, Bharat Thyagarajan, Martha L Daviglus, Eric Boerwinkle, Gang Hu, Yasmin Mossavar-Rahmani, Carmen R Isasi, Rob Knight, Robert D Burk, Robert C Kaplan, Qibin Qi

Faculty, Staff and Student Publications

BACKGROUND: Consistent evidence suggests diabetes-protective effects of dietary fiber intake. However, the underlying mechanisms, particularly the role of gut microbiota and host circulating metabolites, are not fully understood. We aimed to investigate gut microbiota and circulating metabolites associated with dietary fiber intake and their relationships with type 2 diabetes (T2D).

METHODS: This study included up to 11 394 participants from the HCHS/SOL (Hispanic Community Health Study/Study of Latinos). Diet was assessed with two 24-hour dietary recalls at baseline. We examined associations of dietary fiber intake with gut microbiome measured by shotgun metagenomics (350 species/85 genera and 1958 enzymes; n=2992 at …

Stereotyped Non-Stereotypicality: Exploring Positive Effects Of Non-Stereotypical Gender Portrayals On Consumer Perceptions, Veronika Ponomarenko

USF Tampa Graduate Theses and Dissertations

This research attempts to identify contexts where non-stereotypical gender portrayals may have positive effects on consumer perceptions. It tests the perceived self-expressiveness of non-stereotypical gender portrayals as the mediating mechanism behind these effects as well as other alternative mechanisms in a comprehensive experiment. The analysis results show that an interpretation of gender through the theoretical lens of extravagance rather than self-expressiveness seems to be more appropriate. This study also introduces an overarching theoretical framework of metacognitive experiences that may explain the processes driving the effects of non-stereotypical gender portrayals on consumer perceptions. Finally, this research explores different types of gender …

Blocking The Dimerization Of Polyglutamine-Expanded Androgen Receptor Protects Cells From Dht-Induced Toxicity By Increasing Ar Turnover, Allison Lisberg, Yuhong Liu, Diane E. Merry

Department of Biochemistry and Molecular Biology Faculty Papers

Spinal and bulbar muscular atrophy (SBMA) is a neuromuscular degenerative disease caused by a polyglutamine expansion in the androgen receptor (AR). This mutation causes AR to misfold and aggregate, contributing to toxicity in and degeneration of motor neurons and skeletal muscle. There is currently no effective treatment or cure for this disease. The role of an interdomain interaction between the amino- and carboxyl-termini of AR, termed the N/C interaction, has been previously identified as a component of androgen receptor-induced toxicity in cell and mouse models of SBMA. However, the mechanism by which this interaction contributes to disease pathology is unclear. …

Thermal Ecology And Swimming Performance Of Native Tadpoles Dryophytes Femoralis In Central Florida, Jessalyn Aretz

USF Tampa Graduate Theses and Dissertations

Urbanization and climate warming have contributed to global amphibian declines in recent decades. Amphibians are particularly vulnerable to climate and urban-induced warming because their physiological processes are dependent on temperature across all life stages, but few studies have been done on tadpole responses to warming in comparison to adult responses. The study objective was to determine how the thermal ecology and swimming performance of a native Florida tadpole varied with rearing temperature and urban level, and whether these traits are plastic or adaptive. We collected eggs from wild populations of pine woods treefrog (Dryophytes femoralis) tadpoles at an urban and …

An Ecofeminist Ontological Turn: Preparing The Field For A New Ecofeminist Project, M. Laurel-Leigh Meierdiercks

USF Tampa Graduate Theses and Dissertations

Ecofeminists have predominantly refuted oppressive conceptual frameworks by rejecting dualistic logic and value hierarchies, despite the foundational view of ontology that underlies our logic and value systems. I argue that ecofeminists must engage in the creative process of articulating an ecofeminist ontology. I demonstrate that the omission of ontological discourse in ecofeminist scholarships is primarily due to the time period during which ecofeminism gained peak traction and their concerns with essentialism. I also show that feminists experienced an ontological turn in the 2000s that produced a new model for ontological theories that would be beneficial for ecofeminists to embrace. In …

Making The Invisible Visible: (Re)Envisioning The Black Body In Contemporary Adaptations Of Nineteenth-Century Fiction, Urshela Wiggins Mckinney

USF Tampa Graduate Theses and Dissertations

A trend in neo-Victorian adaptations -- both novels and films-- that reimage, and at times reinterpret, canonical Victorian texts is the inclusion of nonwhite, mainly Black, perspectives, which has gained considerable traction in recent years. A vital aspect of this trend is the purposeful attempt to re-establish iconic Victorian characters through Black characterizations. In doing so, filmmakers and authors are reinvigorating familiar texts to provide an inclusionary space for the Black experience previously ignored in the original texts. These adaptations, which revisit and often reinterpret Victorian fiction, have undergone notable transformations by incorporating Black characters to fill voids in traditional …

Band Members’ Attitudes Toward The Queer Community And Perception Of Band As A Safe Space, Brian J. Panetta

USF Tampa Graduate Theses and Dissertations

Using Bronfenbrenner’s ecological framework of human development and Yuval-Davis’ analytical framework of belonging as a lens to explain how the band environment might cultivate positive attitudes toward the queer community, this study investigated band members’ attitudes toward the queer community and their perception of the band as a safe space. Utilizing adapted inventories with established reliability and validity, the following research questions were addressed: 1) What are queer and non-queer band members’ attitudes toward the queer community? 2) What are queer and non-queer band members’ attitudes toward the band as a safe space? 3) What differences exist between the independent …

‘In This Prison We Have Our Main Meal At 11:30 Am’. The Significance Of ‘Time’ For Food Among People Serving Custodial Sentences In England And Wales, Julie M. Parsons

School of Law, Humanities and Social Sciences

In this article, I am thinking through the social life of time for food in prison from a practice theory perspective. I draw upon empirical data from in-depth qualitative interviews with people serving custodial sentences or recently released from prison in England and Wales who have been on placement at a prisoner resettlement charity (RC). These support findings from Her Majesty’s Inspectorate for Prisons report on Life Inside: Food from 2016, and I consider two aspects from the report, (i) an exploration of the standards and conditions in which food is consumed and (ii) the timings of mealtimes. For people …

Visual Analysis Of Bone Malignancies Immunotherapy: A Bibliometric Analysis From 2010 To 2023, Kaiyu Shen, Liu Yang, Shuaiyi Ke, Wencang Gao

Faculty, Staff and Student Publications

Background: Bone malignancies (BM), including osteosarcoma, Ewing's sarcoma, chondrosarcoma, and chordoma, are characterized by high rates of recurrence and mortality, despite the availability of diverse treatment approaches. Immunotherapy has gained increasing importance in cancer treatment. However, there is a lack of comprehensive studies that utilize bibliometric analysis to explore immunotherapy for BM.

Methods: A literature search of English studies on BM and immunotherapy from 2010 to 2023 was conducted in the Web of Science Core Collection database. Bibliometric analysis tools such as VOSviewer, CiteSpace, and R Studio were utilized to examine global trends and research hotspots in this field.

Results: …

Admix-Kit: An Integrated Toolkit And Pipeline For Genetic Analyses Of Admixed Populations, Kangcheng Hou, Stephanie Gogarten, Joohyun Kim, Xing Hua, Julie-Alexia Dias, Quan Sun, Ying Wang, Taotao Tan, Elizabeth G Atkinson, Alicia Martin, Jonathan Shortt, Jibril Hirbo, Yun Li, Bogdan Pasaniuc, Haoyu Zhang

Faculty, Staff and Students Publications

SUMMARY: Admixed populations, with their unique and diverse genetic backgrounds, are often underrepresented in genetic studies. This oversight not only limits our understanding but also exacerbates existing health disparities. One major barrier has been the lack of efficient tools tailored for the special challenges of genetic studies of admixed populations. Here, we present admix-kit, an integrated toolkit and pipeline for genetic analyses of admixed populations. Admix-kit implements a suite of methods to facilitate genotype and phenotype simulation, association testing, genetic architecture inference, and polygenic scoring in admixed populations.

AVAILABILITY AND IMPLEMENTATION: Admix-kit package is open-source and available at https://github.com/KangchengHou/admix-kit. …

Challenges And Considerations Of Preclinical Development For Ipsc-Based Myogenic Cell Therapy, Congshan Sun, Carlo Serra, Brianna Harley Kalicharan, Jeffrey Harding, Mahendra Rao

Faculty, Staff and Students Publications

Cell therapies derived from induced pluripotent stem cells (iPSCs) offer a promising avenue in the field of regenerative medicine due to iPSCs' expandability, immune compatibility, and pluripotent potential. An increasing number of preclinical and clinical trials have been carried out, exploring the application of iPSC-based therapies for challenging diseases, such as muscular dystrophies. The unique syncytial nature of skeletal muscle allows stem/progenitor cells to integrate, forming new myonuclei and restoring the expression of genes affected by myopathies. This characteristic makes genome-editing techniques especially attractive in these therapies. With genetic modification and iPSC lineage specification methodologies, immune-compatible healthy iPSC-derived muscle cells …

Arch: Improving The Performance Of Clonal Hematopoiesis Variant Calling And Interpretation, Irenaeus C C Chan, Alex Panchot, Evelyn Schmidt, Brian J Wiley, Jie Liu, Kimberly Turner, Duc Tran, J Scott Beeler, Armel Landry Batchi-Bouyou, Daniel C Link, Kelly L Bolton, Et Al.

2020-Current year OA Pubs

MOTIVATION: The acquisition of somatic mutations in hematopoietic stem and progenitor stem cells with resultant clonal expansion, termed clonal hematopoiesis (CH), is associated with increased risk of hematologic malignancies and other adverse outcomes. CH is generally present at low allelic fractions, but clonal expansion and acquisition of additional mutations leads to hematologic cancers in a small proportion of individuals. With high depth and high sensitivity sequencing, CH can be detected in most adults and its clonal trajectory mapped over time. However, accurate CH variant calling is challenging due to the difficulty in distinguishing low frequency CH mutations from sequencing artifacts. …

Ndrgs In Breast Cancer: A Review And In Silico Analysis, Emilly S Villodre, Anh P N Nguyen, Bisrat G Debeb

Faculty, Staff and Student Publications

Simple Summary

Breast cancer is the most common cancer in women and one of the deadliest. While survival rates for patients with breast cancer have seen notable improvements in recent decades, current treatment strategies still face significant limitations, especially for patients with aggressive, therapy-resistant, and metastatic breast cancers. For this reason, it is important to identify new targets in order to develop more effective therapeutic strategies. The N-myc downstream regulated gene family (NDRGs), comprising NDRG1, NDRG2, NDRG3, and NDRG4, has been previously described as tumor suppressors. However, recent findings challenge this perception, particularly for NDRG1, …

Regional Analysis To Delineate Intrasample Heterogeneity With Regionalst, Yue Lyu, Chong Wu, Wei Sun, Ziyi Li

Faculty, Staff and Student Publications

MOTIVATION: Spatial transcriptomics has greatly contributed to our understanding of spatial and intra-sample heterogeneity, which could be crucial for deciphering the molecular basis of human diseases. Intra-tumor heterogeneity, e.g. may be associated with cancer treatment responses. However, the lack of computational tools for exploiting cross-regional information and the limited spatial resolution of current technologies present major obstacles to elucidating tissue heterogeneity.

RESULTS: To address these challenges, we introduce RegionalST, an efficient computational method that enables users to quantify cell type mixture and interactions, identify sub-regions of interest, and perform cross-region cell type-specific differential analysis for the first time. Our simulations …

Structure Of Alpha-Synuclein Fibrils Derived From Human Lewy Body Dementia Tissue, Dhruva D Dhavale, Katherine Basore, Isabelle R Gordon, Jialu Liu, Jennifer Y O'Shea, Michael J Rau, Zachary Smith, Brock Summers, Richard J Perrin, Joel S Perlmutter, James A J Fitzpatrick, Paul T Kotzbauer, Et Al.

2020-Current year OA Pubs

The defining feature of Parkinson disease (PD) and Lewy body dementia (LBD) is the accumulation of alpha-synuclein (Asyn) fibrils in Lewy bodies and Lewy neurites. Here we develop and validate a method to amplify Asyn fibrils extracted from LBD postmortem tissue samples and use solid state nuclear magnetic resonance (SSNMR) studies to determine atomic resolution structure. Amplified LBD Asyn fibrils comprise a mixture of single protofilament and two protofilament fibrils with very low twist. The protofilament fold is highly similar to the fold determined by a recent cryo-electron microscopy study for a minority population of twisted single protofilament fibrils extracted …

It's In The "Weeds" : 'Pesky' Plants As Teachers In Imagining Decolonial Futures, Sofia Ahmad Cook

Tapestries: Interwoven voices of local and global identities

As a category of plant species, “weeds” are often thought of as ‘pesky’ nuisances and treated with absolute disdain. But what are “weeds” and how did they become “pests” that homeowners, gardeners, and conservationists alike seek to control and/or eliminate? My inquiry into “weeds” reveals that the designation of “weeds” is not scientific so much as it is socially and culturally constructed. The categorization of “weeds,” shaped by evolving notions of place, space, and belonging, provides a window into underlying social and cultural norms that structure our relationships with one another and the more-than-human world. Situated within settler colonial contexts, …

Abolish R(Ice): (Dis)Ability, Immigration, And Asian American Resistance, Vivian S. Tran

Tapestries: Interwoven voices of local and global identities

In 2021, Minneapolis-based Khmer artist, Kat Eng designed the “Abolish r(ICE)” t-shirt as part of a fundraiser for Southeast Asians and their families experiencing deportation. Inspired by the iconic Three Ladies Brand jasmine rice bag, Eng re-imagined the three ladies as freedom fighters in response to heightened immigration policing and detention of Southeast Asian communities. In this paper, I unpack and contextualize the Abolish r(ICE) t-shirt campaign within immigration debates, the contemporary abolitionist movement, and Asian American resistance. The Abolish r(ICE) shirts also function as a form of political education and an invitation specifically to Asian American youth to learn …

Pursuing The Exemption: The Makah's White Whale, Sarah Van Voorhis

Washington Journal of Social & Environmental Justice

No abstract provided.

Chemical Composition And Physico-Chemical Properties Of Lithium-Containing Water Resources, Murodjon Samadiy, Ilkham Usmanov, Shafoat Namazov

CHEMISTRY AND CHEMICAL ENGINEERING

The aim of the study is determination of chemical composition, physicochemical and biological properties of the Aral Sea water for further selection of the most economical and environmentally friendly method of lithium extraction. It is shown that the content of lithium in water is 0,11 g/l, which is 3-4 times higher than in those used in industry at Chinese enterprises. The chemical oxygen demand is 677,76 mg O2/l, the biological oxygen demand is 120,50 mg O2/l.

Detection And Identification Of Microorganisms - Oil Destructors In Oil-Contaminated Soils Of Turkmenistan, Durdymurad Gadamov, Dunyagozel Amannazarova, Ludmila Gulmamedova

CHEMISTRY AND CHEMICAL ENGINEERING

In this article, samples of soils contaminated with oil and oil sludge from the Seydi and Turkmenbashi oil refineries were studied. In order to identify the native microflora, as well as hydrocarbon-oxidizing microorganisms of oil destructors, microbiological and mycological analyzes were carried out. The identification of microorganisms was carried out using the VITEC MS apparatus, the principle of which is based on the colorimetric method. As a result, samples of soil studies, at the Seydi oil refinery, have been identified 3 strains of bacteria, 14 actinomycetes and 9 strains of hydrocarbon-oxidizing microorganisms. On the oil-contaminated soils of the Turkmenbashi oil …

Synthesis Of The New Heterocyclic Derivatives Of Alkaloids, Gulim Mukusheva, Madina Aliyeva, Marzhan Kaiyrbayeva, Alisher Mazhitov

CHEMISTRY AND CHEMICAL ENGINEERING

The aim of the study is the synthesis of heterocyclic derivatives of alkaloids. A convenient method has been developed for obtaining natural alkaloid derivatives of anabazine and cytisine by the acylation reaction of 1,2-azole-3-, pyridine-3-, pyridine-4- and adamantane-1-carbonyl chlorides. A number of N-acyl derivatives of anabazine and cytisine have been obtained for the discovery of new medicines based on natural products. Molecular docking of the studied compounds was carried out on a model of hemagglutinin (1 RAY 1930 Swine H1 Hemagglutinin) and neuraminidase (neuraminidase 3BEQ strain A/Brevig Mission/1/1918 H1N1) proteins. It was found that all the studied compounds are able …

Complex Formation In Solution Of Chitosan And Bombyx Mori Protein, Oynavod Avazova, Sayyora Rashidova

CHEMISTRY AND CHEMICAL ENGINEERING

The purpose of the study is to identify the reaction conditions for the complex formation of chitosan and the Bombyx mori protein at pH and to determine the structure and properties of the obtained samples.The properties of Bombyx mori chitosan (Xs) and protein in solutions and their interaction under various reaction conditions (concentration and pH 4,88-6,7) were studied. The analysis of the obtained results was studied and the fundamental possibilities of obtaining complexes based on Bombyx mori chitosan and protein were determined. Conductometric titration showed that the COO- groups in the protein chain of Bombyx mori accounted for 4.95%, and …

Obtaining A Composition Of Emulsifiers To Increase The Durability Of Margarine Emulsion, Sarvar Khodjaev

CHEMISTRY AND CHEMICAL ENGINEERING

The aim of the study is to obtain a composition of emulsifiers from local raw materials for the production of margarine. The article presents the results of the influence of the composition of the resulting emulsifiers on the stability of the margarine emulsion. The main components of the resulting emulsifier compositions were soy lecithin, mono- and diglycerides obtained from cottonseed oil and beef fat by glycerolysis with glycerin. At the same time, three different margarine recipes were selected to determine the effect of the developed emulsifier compositions on the stability of the obtained products. Lecithin, in addition to emulsifying abilities, …

Essential Oils Incorporation Technology To Improve Shelflife And Stability Of Yoghurt, Mohamed Rifky, Kamar Serkayev, Murodjon Samadiy

CHEMISTRY AND CHEMICAL ENGINEERING

The purpose of this study is to develop a technology for incorporating essential oils (EOs) into yogurt. Various essential oils such as cinnamon oil, garlic oil, caraway oil and clove oil in yogurt are used as antimicrobial and stabilizing agents to increase shelf life and stability. Three hundred μl/kg of essential oil was added to the yogurt after pasteurization to prevent deterioration of functional properties when heated. To determine the antibacterial activity of the main bacterial pathogens, such as total aerobic count of bacteria, yeasts and molds, the total number of bacteria on plates (pour method), the total number of …

Synthesis Of Binary Acrylonitrile Copolymers, Latofat Mahkamova, Shukhrat Mutalov, Oytura Maksumova

CHEMISTRY AND CHEMICAL ENGINEERING

The aim of this work is to study the radical copolymerization of acrylonitrile with 1-chloro-3-piperidin-2-propylacrylate and to study the structure and properties of the synthesized copolymers. Ammonium persulfate was used as the radical initiator. Water and dimethylformamide were used as solvents. Under these conditions the process proceeds heterogeneously in water, and homogeneously with high speed in dimethylformamide. The synthesis rate of the 1-chloro-3-piperidino-2-propylacrylate and acrylonitrile copolymers increases with increasing temperature in the studied solvents. Experimental studies have shown that copolymerization does not proceed in the absence of the initiator and this indicates a radical nature of the reaction. The structure …

Hplc Method For The Quantitative Determination Of Aconitine Alkaloid And Comparison With The Titrating Method, Dilnoza Mutalova, Obidjon Juraev, Alimjan Sadikov, Shomansur Sagdullaev

CHEMISTRY AND CHEMICAL ENGINEERING

The aim of this study was to develop and validate the quantitative determination of titration and HPLC methods and compare them in terms of reproducibility. The development of new approaches to quality control requires the standardization of pharmaceutical products using modern methods of quantitative analysis. An HPLC method for the quantitative analysis of akonitin alkaloids has been developed and validated. Statistical processing of the obtained results showed that all the studied validation parameters are within the selected acceptance criteria, therefore, the developed method is included in the regulatory technical document Ts 03535440-017:2020 and is used in quantitative analyzes in production …

Synthesis Of Arylpropargyl Esters With Dialkylamines And Investigation Of Some Of Their Physicochemical Properties, Dilshod Akhtamov, Bakhodir Mukhiddinov, Abduhamid Makhsumov, Abdulahad Djalilov

CHEMISTRY AND CHEMICAL ENGINEERING

The aim of the work is the synthesis and study of aryloxyalkylamines used as corrosion inhibitors. As a result of aminomethylation of arylproporgyl ethers, phenoxybutin-2-dimethylamine and phenoxy-butin-2-diethylamine were synthesized against metal corrosion. Based on the research, various factors affecting the synthesis process have been studied: temperature, the nature and concentration of the catalyst, the nature of solvents and the duration of time. As a result, the best solvent for the synthesis process, the catalytic system, the temperature and the duration of the synthesis time were determined. The mechanism of the reaction of aminomethylation of arylpropargyl esters is proposed. The structure …