Digital Commons Network^™

Chromomap: An R Package For Interactive Visualization Of Multi-Omics Data And Annotation Of Chromosomes, Lakshay Anand, Carlos M. Rodriguez Lopez

Horticulture Faculty Publications

BACKGROUND: The recent advancements in high-throughput sequencing have resulted in the availability of annotated genomes, as well as of multi-omics data for many living organisms. This has increased the need for graphic tools that allow the concurrent visualization of genomes and feature-associated multi-omics data on single publication-ready plots.

RESULTS: We present chromoMap, an R package, developed for the construction of interactive visualizations of chromosomes/chromosomal regions, mapping of any chromosomal feature with known coordinates (i.e., protein coding genes, transposable elements, non-coding RNAs, microsatellites, etc.), and chromosomal regional characteristics (i.e. genomic feature density, gene expression, DNA methylation, chromatin modifications, etc.) of organisms …

Evaluation Of The Availability And Utilization Status Of Texts In Core Subjects In Primary Schools’ Libraries, Valentine Joseph Owan, Daniel Clement Agurokpon, Abahcham V. Owan

Library Philosophy and Practice (e-journal)

The study evaluated primary texts' availability and utilisation status in core subjects (English Language, Mathematics, Social Studies and Basic Science) in primary schools’ libraries in Obubra Local Government Area of Cross River State. The researchers formulated six null hypotheses to guide the study. The study adopted the descriptive survey research design. The target population of this study comprised a total of 30,036 teachers and pupils, distributed across the 73 public primary schools. A proportionate stratified sampling technique was used to select 30% and 5% of the available teachers and pupils in each school, resulting in a sample of 270 respondents. …

Tracking Spatial Regimes In Animal Communities: Implications For Resilience-Based Management, Caleb P. Roberts, Daniel R. Uden, Craig R. Allen, David G. Angeler, Larkin A. Powell, Brady W. Allred, Matthew O. Jones, Jeremy D. Maestas, Dirac L. Twidwell Jr

Department of Agronomy and Horticulture: Faculty Publications

Spatial regimes (the spatial extents of ecological states) exhibit strong spatiotemporal order as they expand or contract in response to retreating or encroaching adjacent spatial regimes (e.g., woody plant invasion of grasslands) and human management (e.g., fire treatments). New methods enable tracking spatial regime boundaries via vegetation landcover data, and this approach is being used for strategic management across biomes. A clear advancement would be incorporating animal community data to track spatial regime boundaries alongside vegetation data. In a 41,170-hectare grassland experiencing woody plant encroachment, we test the utility of using animal community data to track spatial regimes via two …

Use Of Tocilizumab, Remdesivir, And High-Dose Methylprednisolone Prevents Intubation In An Esrd Patient With Covid-19 Pneumonia, Ramzan Judge, Stephanie Kolaski, Farhan Qadeer

College of Pharmacy Faculty Papers

Coronavirus disease 2019 (COVID-19) has affected over 200 million patients worldwide. COVID-19 is transmitted through respiratory droplets from patient to patient or by touching a surface that has been contaminated by an infected patient. Many COVID-19 patients have other comorbidities, such as end-stage renal disease. Currently, management of COVID-19 in patients with end-stage renal disease is unclear. Some studies have shown improvement in this population with the use of tocilizumab, a humanized interleukin-6 monoclonal antibody, in addition to the standard therapy as per guidelines published by the National Institutes of Health. In this case report, we present a patient case …

Accuracy And Practical Considerations For Doubly Labeled Water Analysis In Nutrition Studies Using A Laser-Based Isotope Instrument (Off-Axis Integrated Cavity Output Spectroscopy), Linda M Reynard, William W Wong, Noreen Tuross

Children’s Nutrition Research Center Staff Publications

Background: Given the utility of the doubly labeled water (DLW) method for determination of energy expenditure, additional techniques for isotope analysis of the samples are welcome. Laser-based instruments are one such new analytical tool, but their accuracy and feasibility for DLW studies are grossly understudied.

Objectives: We assessed the accuracy of laser-based isotope ratio measurements as part of the DLW method for estimation of carbon dioxide production rate (rCO2) and total energy expenditure (TEE), in between-group comparison study designs.

Methods: Urine samples from a previous study were analyzed with a laser-based instrument [off-axis integrated cavity output spectroscopy (OA-ICOS)]. In that …

Pressure-Mediated Reflection Spectroscopy Criterion Validity As A Biomarker Of Fruit And Vegetable Intake: A 2-Site Cross-Sectional Study Of 4 Racial Or Ethnic Groups, Stephanie B Jilcott Pitts, Nancy E Moran, Qiang Wu, Lisa Harnack, Neal E Craft, Neil Hanchard, Ronny Bell, Stacey G Moe, Nevin Johnson, Justice Obasohan, Pamela L Carr-Manthe, Melissa N Laska

Children’s Nutrition Research Center Staff Publications

Background: Valid biomarkers of fruit and vegetable (FV) intake are needed for field-based nutrition research.

Objectives: To examine criterion-related validity of pressure-mediated reflection spectroscopy as a proxy measure of FV intake, using plasma carotenoids and self-reported FV and carotenoid intake as primary and secondary criterion measures, respectively.

Methods: Healthy adults 18-65 y of age, self-identifying as African American/black (n = 61), Asian (n = 53), white (n = 70), or Hispanic (n = 29), in North Carolina and Minnesota were recruited. Skin carotenoids were assessed via pressure-mediated reflection spectroscopy (Veggie Meter), skin melanin via spectrophotometer, and total plasma carotenoid concentration …

Astrocytic 4r Tau Expression Drives Astrocyte Reactivity And Dysfunction, Lubov A. Ezerskiy, Kathleen M. Schoch, Chihiro Sato, Mariana Beltcheva, Kanta Horie, Frank Rigo, Ryan Martynowicz, Celeste M. Karch, Randall J. Bateman, Timothy M. Miller

Open Access Publications

The protein tau and its isoforms are associated with several neurodegenerative diseases, many of which are characterized by greater deposition of the 4-repeat (4R) tau isoform; however, the role of 4R tau in disease pathogenesis remains unclear. We created antisense oligonucleotides (ASOs) that alter the ratio of 3R to 4R tau to investigate the role of specific tau isoforms in disease. Preferential expression of 4R tau in human tau-expressing (hTau-expressing) mice was previously shown to increase seizure severity and phosphorylated tau deposition without neuronal or synaptic loss. In this study, we observed strong colocalization of 4R tau within reactive astrocytes …

Fasn-Dependent De Novo Lipogenesis Is Required For Brain Development, Daniel Gonzalez-Bohorquez, Isabel M Gallego López, Baptiste N Jaeger, Sibylle Pfammatter, Megan Bowers, Clay F Semenkovich, Sebastian Jessberger

Open Access Publications

Fate and behavior of neural progenitor cells are tightly regulated during mammalian brain development. Metabolic pathways, such as glycolysis and oxidative phosphorylation, that are required for supplying energy and providing molecular building blocks to generate cells govern progenitor function. However, the role of de novo lipogenesis, which is the conversion of glucose into fatty acids through the multienzyme protein fatty acid synthase (FASN), for brain development remains unknown. Using Emx1Cre-mediated, tissue-specific deletion of

Epigenetic Silencing Of Tumor Suppressor Lncrna Nkila: Implication On Nf-Κb Signaling In Non-Hodgkin’S Lymphoma, Min-Yue Zhang, George Calin, Ming-Dan Deng, Rex K H Au-Yeung, Lu-Qian Wang, Chor-Sang Chim

Faculty, Staff and Student Publications

The long non-coding RNA (lncRNA) NKILA, localized to 20q13.31, is a negative regulator of NF-κB signaling implicated in carcinogenesis. As a CpG island is embedded in the promoter region of NKILA, it is hypothesized as a tumor suppressor lncRNA silenced by promoter DNA methylation in non-Hodgkin’s lymphoma (NHL). By pyrosequencing-verified methylation-specific PCR, NKILA methylation was detected in 1/10 (10%) NHL cell lines, but not in normal peripheral blood buffy coats or tonsils. NKILA methylation correlated with the repression of NKILA in cell lines. Hypomethylation treatment with 5-Aza-2′-deoxycytidine resulted in promoter demethylation and the re-expression of NKILA. In 102 …

Cxcl10 Chemokine Regulates Heterogeneity Of The Cd8+ T Cell Response And Viral Set Point During Chronic Infection, Aleksandra J Ozga, Melvyn T Chow, Mateus E Lopes, Rachel L Servis, Mauro Di Pilato, Philippe Dehio, Jeffrey Lian, Thorsten R Mempel, Andrew D Luster

Faculty, Staff and Student Publications

CD8+ T cells responding to chronic infection adapt an altered differentiation program that provides some restrain on pathogen replication yet limits immunopathology. This adaptation is imprinted in stem-like cells and propagated to their progeny. Understanding the molecular control of CD8+ T cell differentiation in chronic infection has important therapeutic implications. Here, we found that the chemokine receptor CXCR3 was highly expressed on viral-specific stem-like CD8+ T cells and that one of its ligands, CXCL10, regulated the persistence and heterogeneity of responding CD8+ T cells in spleens of mice chronically infected with lymphocytic choriomeningitis virus. CXCL10 was produced by inflammatory monocytes …

The Rise And Fall Of Dopamine: A Two-Stage Model Of The Development And Entrenchment Of Anorexia Nervosa, Jeff A. Beeler, Nesha S. Burghardt

Publications and Research

Dopamine has long been implicated as a critical neural substrate mediating anorexia nervosa (AN). Despite nearly 50 years of research, the putative direction of change in dopamine function remains unclear and no consensus on the mechanistic role of dopamine in AN has been achieved. We hypothesize two stages i n AN– corresponding to initial development and entrenchment– characterized by opposite changes in dopamine. First, caloric restriction, particularly when combined with exercise, triggers an escalating spiral of increasing dopamine that facilitates the behavioral plasticity necessary to establish and reinforce weight-loss behaviors. Second, chronic self-starvation reverses this escalation to reduce or impair …

Translatina Immigrant Mental Health Wellness: Suggestive Intervention Strategies The City Of San Francisco Should Consider Adopting, Valeria Vera

Master's Theses

Translatina immigrants in the United States often suffer from intersectional traumas due to their race, gender, sexual orientation, religion, and immigration status — putting them in a vulnerable position socially, psychologically, economically, and medically. Due to their positionality in the intersections of migration, criminalization, cissexism, and mental health, they are often more marginalized and have greater needs than communities with privileged sociocultural identities. As a particularly vulnerable group, they need guaranteed access to gender-affirming healthcare that is inclusive of mental health services. Despite Translatinas’ need for mental health services, there exist many barriers making services inaccessible and insufficient in San …

Fabrication And Characterization Of A Ph-Sensitive Intelligent Film Incorporating Dragon Fruit Skin Extract, Nurnabila Afiqah Azlim, Abdorreza Mohammadi Nafchi, Nazila Oladzadabbasabadi, Fazilah Ariffin, Pantea Ghalambor, Shima Jafarzadeh, A. A. Al-Hassan

Research outputs 2022 to 2026

A novel intelligent pH-sensing indicator based on gelatin film and anthocyanin extracted from dragon fruit skin (Hylocereus polyrhizus) (DFSE) as a natural dye was developed to monitor food freshness by the casting method. Anthocyanin content of DFSE was 15.66 ± 1.59 mg/L. Dragon fruit bovine gelatin films were characterized by Fourier transform infrared spectroscopy (FTIR) and observed by a scanning electron microscope (SEM). Moisture content, mechanical properties, water solubility, water vapor permeability (WVP), light transmittance, color, and pH-sensing evaluations were evaluated for potential application. FTIR spectroscopy revealed that the extracted anthocyanin could interact with the other film components through hydrogen …

Mapk4 Promotes Triple Negative Breast Cancer Growth And Reduces Tumor Sensitivity To Pi3k Blockade, Wei Wang, Dong Han, Qinbo Cai, Tao Shen, Bingning Dong, Michael T Lewis, Runsheng Wang, Yanling Meng, Wolong Zhou, Ping Yi, Chad J Creighton, David D Moore, Feng Yang

Faculty, Staff and Students Publications

About 15-20% of breast cancer (BCa) is triple-negative BCa (TNBC), a devastating disease with limited therapeutic options. Aberrations in the PI3K/PTEN signaling pathway are common in TNBC. However, the therapeutic impact of PI3K inhibitors in TNBC has been limited and the mechanism(s) underlying this lack of efficacy remain elusive. Here, we demonstrate that a large subset of TNBC expresses significant levels of MAPK4, and this expression is critical for driving AKT activation independent of PI3K and promoting TNBC cell and xenograft growth. The ability of MAPK4 to bypass PI3K for AKT activation potentially provides a direct mechanism regulating tumor sensitivity …

P300 Or Cbp Is Required For Insulin-Stimulated Glucose Uptake In Skeletal Muscle And Adipocytes, Vitor F. Martins, Gretchen A. Meyer, Et Al.

2020-Current year OA Pubs

While current thinking posits that insulin signaling to glucose transporter 4 (GLUT4) exocytic translocation and glucose uptake in skeletal muscle and adipocytes is controlled by phosphorylation-based signaling, many proteins in this pathway are acetylated on lysine residues. However, the importance of acetylation and lysine acetyltransferases to insulin-stimulated glucose uptake is incompletely defined. Here, we demonstrate that combined loss of the acetyltransferases E1A binding protein p300 (p300) and cAMP response element binding protein binding protein (CBP) in mouse skeletal muscle caused a complete loss of insulin-stimulated glucose uptake. Similarly, brief (i.e., 1 hour) pharmacological inhibition of p300/CBP acetyltransferase activity recapitulated this …

Don’T You Know That They’Re Toxic: Parasocial Attachments And Fictional Relationships, Morgan Macke, Jana Hackathorn

Posters-at-the-Capitol

Problem or Major Purpose. Parasocial relationships are one-sided interactions individuals have with fictional characters or famous celebrities (Derrick et al., 2008). Parasocial relationships can be beneficial for the exploration and development of one’s own romantic emotions, sexuality, or ideal self (Derrick et al., 2008; Erikson & Dal Cin, 2018). Conversely, there may be drawbacks such as unrealistic expectations and dysfunctional beliefs (Spiranec, 2018). For example, the young adult genre often contains harmful tropes that expose the audience to dysfunctional relationship behaviors such as portraying abuse as romantic, normalizing slut shaming, and fetishizing virginity (Spiranec, 2018). The current study examines the …

C2c Stem Collaboration, Mary Andrea Parish, Angela Renee Rowe, Annette Hines, Hannah Elizabeth Brewer

Posters-at-the-Capitol

Campus to Classroom is a STEM collaboration effort brought about by the brainstorming and continued efforts of Ms. Angela Rowe (MSUTeach), Ms. Annette Hines (Talent Search), MSUTeach STEM Ambassadors, and MSUExplore (MSUTeach student group).

The goal is an educational, collaborative partnership with cross-campus departments and both pre-service and in-service teachers, with a main focus on students from underserved population and communities.

Continued steps will be planned to develop a multi-level partnership with the end goals of increased usage of project-based instruction, incorporate research that increases STEM knowledge/skill, and encourage career exploration while building bridges from “campus and classroom”.

A Perusal On Preservation And Conservation Techniques In The Government Aided College Libraries Of Diamond Harbour And Alipore Subdivision In South 24 Parganas, Bibhash Ram Singha, Bikash Kumar Halder

Library Philosophy and Practice (e-journal)

The present study is exhibited the preservation and conservation techniques in the college libraries of Diamond Harbour and Alipore subdivisions in the district of South 24parganas. It also discusses degradation problems of print and non-print materials, causes of deterioration of library documents, and different obstacles to using preservation techniques. To secure the library materials in a good manner need to apply the preservation and conservation techniques which include cleaning and dusting, use of insecticides and insect repellent such as Thymol, Dichlorovos, Dursban, Naphthalene balls, Neem leaf, etc., besides that there is a provision for security systems of the college libraries …

Pilgering Researchers Or Researching Pilgrims: Experiences From Four Student Projects On The Camino De Santiago 2016-2019, Andreas Braun

International Journal of Religious Tourism and Pilgrimage

Between 2016 and 2019, I accompanied four student groups on the Camino de Santiago - however the planned 2020 project was cancelled due to the coronavirus epidemic. In this article, I describe the project, its planning, its implementation, and its conclusion, as well as some experiences and impressions of the participating students on the basis of an ethnographical approach. The projects presented have two objectives: on the one hand, to teach the students qualitative and quantitative research methods in a delimited, protected environment, and on the other hand, to introduce the students to the fascination of pilgrimage and the Camino …

Walking On The Camino Paths: A Spiritual And Biopsychosocial Journey, Ofra Walter

International Journal of Religious Tourism and Pilgrimage

The Camino de Santiago is an ancient network of pilgrimage routes that lead to Santiago de Compostela in Spain. This qualitative study was conducted to explore contemporary pilgrims’ experiences on the route. I walked the route for 14 days, interviewing other pilgrims about their reasons for taking the journey and their experiences while on it. The methodology thus involved gaining wisdom on two levels: the researcher’s level and the participants’ level. Nineteen people from various counties and of different ages consented to an interview. The participants expressed an interesting mix of biopsychosocial experiences. They mentioned self contemplation and spiritual experiences. …

Local Knowledge On The Changes In Vegetation Composition And Abundance In Rusinga Island, Homa Bay County, Kenya, M. N. Nyaga, S. M. Mureithi, V. O. Wasonga, O. K. Koech

IGC Proceedings (1977-2023)

Local communities have been coping with environmental dynamics since time immemorial, and they often possess considerable knowledge about environmental change, as well as mechanisms of coping with the consequences of such changes. Local knowledge on the changes in vegetation composition and abundance is therefore fundamental for the development of management strategies aimed at sustainable use and conservation of natural vegetation resources. Household interviews (n=150), Key informant interviews (n=30) and Focus group discussions (n=4) were used in this study to extract information on the communities’ perceptions on the status of vegetation in Rusinga Island of …

Cloud Computing Solution For Monitoring Arid Rangeland Dynamics: Case Of Moroccan Highlands And Southern Acacia Ecosystems, Said Lahssini, Said Moukrim, H. Mharzi-Alaoui, N. Rifai, L. El Mansouri, F. El Wahidi

IGC Proceedings (1977-2023)

The wide availability of free satellite imagery, the recent development of cloud platforms dedicated to big spatial data (Big Data) that integrates both image archives from different providers, processing algorithms, distributed processing capabilities as well as an application programming interface (API) that facilitate scripting and automation process opened new perspectives for the use of vegetation observation time series over long timestamps and over large spatial scales (almost planetary).

This work aims at harnessing these technologies and building up an automated solution to monitor rangeland rehabilitation dynamics in arid lands and to assess the effectiveness of stakeholder’s management strategies. Such solution …

Characterizing Invasiveness Through A Descriptive Study Of Guinea Grass (Megathyrsus Maximus) Growing In Three Habitat Types And Differing Herbivore Assemblages In Both Kenya And Texas, A. C. Rhodes, R. M. Plowes, D. J. Martins, I. Ng'iru, L. E. Gilbert

IGC Proceedings (1977-2023)

Guinea grass (Megathyrsus maximus syn. Panicum maximum) is an important pasture grass that has been introduced pantropically, yet in many cases has escaped cultivation and is invading native rangelands – threatening biodiversity at multiple trophic levels. An increasing challenge of rangeland management is balancing the importance of pasture grasses with their negative impact on ecosystem processes. Given this challenge, it is critical to understand the mechanisms that underlie grass invasion. In this descriptive study, our objective was to assess the ecological stress release hypothesis by comparing the relative abundance and functional traits of Guinea grass in Kenya's home …

Physics Learning For Non-Physical Specialists In High School System, Utkir Mirzaqobilovich Farmonov, Nizom Abdurazzakovich Taylanov

Mental Enlightenment Scientific-Methodological Journal

This article is devoted to the learning process of physics for non-physics specialists in high schools. When training specialists studying in the relevant specialties of higher professional education, the university has the right to use the specified structure, content and procedure for implementing a cycle of general mathematical and natural science disciplines, changing the depth of elaboration of individual sections of the programs. This can lead to a redistribution of educational material between lectures, seminars and laboratory workers, a change in their nature and focus

Conversion Of Food Waste Into 2,3-Butanediol Via Thermophilic Fermentation: Effects Of Carbohydrate Content And Nutrient Supplementation, Dajun Yu, Joshua O'Hair, Nicholas Poe, Qing Jin, Sophia Pinton, Yanhong He, Haibo Huang

Biology Faculty Research

Fermentation of food waste into 2,3-butanediol (2,3-BDO), a high-value chemical, is environmentally sustainable and an inexpensive method to recycle waste. Compared to traditional mesophilic fermentation, thermophilic fermentation can inhibit the growth of contaminant bacteria, thereby improving the success of food waste fermentation. However, the effects of sugar and nutrient concentrations in thermophilic food waste fermentations are currently unclear. Here, we investigated the effects of sugar and nutrients (yeast extract (YE) and peptone) concentrations on 2,3-BDO production from fermenting glucose and food waste media using the newly isolated thermophilic Bacillus licheniformis YNP5-TSU. When glucose media was used, fermentation was greatly affected …

Introduction To Epigenetics, Yevgeniy Grigoryev

Open Educational Resources

Syllabus for Bio481 Introduction to Epigenetics

Investigating The Effects Of Climate Change On The Phenology Of Achillea Millefolium, Aquilegia Coerulea, And Penstemon Cyanocaulis, Hannah O’Toole, Kailey Hicks, Lisa Long, Jackson Garske, Anna Sher

DU Undergraduate Research Journal Archive

As the effects of climate change are starting to unearth themselves, the impacts can be observed by tracking the patterns of cyclical natural phenomena also known as phenology, and monitoring how they have changed over time. These cycles are at the crux of making ecosystems viable for their local biodiversity, and understanding the ongoing change allows for further understanding of the ecosystem’s change over time. In this study, we look at the ordinal flowering dates of the Achillea millefolium, Aquilegia coerulea, and Penstemon cyanocaulis over the past century. Our data give insight into how warmer temperatures occurring earlier in …

Du Research Grants Fuel Undergraduate Student Creativity And Academic Projects, Anit Tyagi

DU Undergraduate Research Journal Archive

The University of Denver has several funding options for undergraduate students seeking to carry out research under the tutelage of experienced faculty members, present their findings on a national or international stage, and implement scholarly community outreach initiatives. These funding options have helped defray the costs associated with conducting and presenting research for thousands of students and faculty and are an important facet of the research experience at DU. Here the Editorial Board explores the various funding options undergraduate students have access to throughout their research experience(s) at DU.

Natural History Of The Guatemalan Copper Iophanus Pyrrhias (Godman And Salvin, 1887) (Lepidoptera: Lycaenidae) In Guatemala, José Monzón-Sierra, Gregory C. Ballmer

The Taxonomic Report of the International Lepidoptera Survey

Abstract

Detailed information including photographs about the natural history of Iophanus pyrrhias (Godman and Salvin 1887) in Guatemala is presented. Information includes geographic and altitudinal distribution and phenology. We reconfirm the immatures stages use Muehlenbeckia tamnifolia (Kunth) Meisn., 1841 (Polygonaceae) as the host plant.

Reusmen

Se presenta información detallada incluyendo fotografías de la historia natural de Iophanus pyrrhias (Godman y Salvin 1887) en Guatemala. La información incluye distribución geográfica y altitudinal y fenología. Confirmamos que los estados inmaduros se alimentan de Muehlenbeckia tamnifolia (Kunth) Meisn., 1841 (Polygonaceae).

Feature Papers In Horticulturae, Douglas D. Archbold

Horticulture Faculty Publications

No abstract provided.