Digital Commons Network^™

Transmission Event Of Sars-Cov-2 Delta Variant Reveals Multiple Vaccine Breakthrough Infections, Timothy Farinholt, Harsha Doddapaneni, Xiang Qin, Vipin Menon, Qingchang Meng, Ginger Metcalf, Hsu Chao, Marie-Claude Gingras, Vasanthi Avadhanula, Paige Farinholt, Charu Agrawal, Donna M Muzny, Pedro A Piedra, Richard A Gibbs, Joseph Petrosino

Faculty, Staff and Students Publications

BACKGROUND: This study aims to identify the causative strain of SARS-CoV-2 in a cluster of vaccine breakthroughs. Vaccine breakthrough by a highly transmissible SARS-CoV-2 strain is a risk to global public health.

METHODS: Nasopharyngeal swabs from suspected vaccine breakthrough cases were tested for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) by qPCR (quantitative polymerase chain reaction) for Wuhan-Hu1 and alpha variant. Positive samples were then sequenced by Swift Normalase Amplicon Panels to determine the causal variant. GATK (genome analysis toolkit) variants were filtered with allele fraction ≥80 and min read depth 30x.

RESULTS: Viral sequencing revealed an infection cluster of …

Processes Used By Mothers In Opioid Recovery To Manage The Needs Of The Maternal-Infant Dyad: A Grounded Theory Study, Nicole M. Mattson

Dissertations (1934 -)

Maternal opioid use during pregnancy and the postpartum period has significant impact on the mother and infant. Maternal well-being and early maternal-infant contact can impact the early attachment and bonding of the dyad. Additionally, the stigma surrounding opioid use in pregnancy can have detrimental effects on the dyad during pregnancy and in the postpartum period. Theory driven nursing interventions to promote mother-infant dyadic care for pairs impacted by maternal opioid use disorder (OUD) are needed. First, it was necessary to understand the current processes used by mothers with OUD to manage the unique needs of their dyad. The purpose of …

Assessing Changes In Clusters Of Wildlife Road Mortalities After The Construction Of Wildlife Mitigation Structures, Thomas J. Yamashita, Trinity D. Livingston, Kevin W. Ryer, John H. Young Jr., Richard Kline

School of Earth, Environmental, & Marine Sciences Faculty Publications

Collisions with vehicles can be a major threat to wildlife populations, so wildlife mitigation structures, including exclusionary fencing and wildlife crossings, are often constructed. To assess mitigation structure effectiveness, it is useful to compare wildlife road mortalities (WRMs) before, during, and after mitigation structure construction; however, differences in survey methodologies may make comparisons of counts impractical. Location-based cluster analyses provide a means to assess how WRM spatial patterns have changed over time. We collected WRM data between 2015 and 2019 on State Highway 100 in Texas, USA. Five wildlife crossings and exclusionary fencing were installed in this area between September …

Prevention And Screening Of Hpv Malignancies, Kristina R Dahlstrom, Andrew T Day, Erich M Sturgis

Faculty, Staff and Students Publications

It is estimated that 5% of the global cancer burden, or approximately 690,000 cancer cases annually, is attributable to human papillomavirus (HPV). Primary prevention through prophylactic vaccination is the best option for reducing the burden of HPV-related cancers. Most high-income countries (HICs) have introduced the HPV vaccine and are routinely vaccinating adolescent boys and girls. Unfortunately, although they suffer the greatest morbidity and mortality due to HPV-related cancers, many lower- and middle-income countries (LMICs) have been unable to initiate and sustain vaccination programs. Secondary prevention in the form of screening has led to substantial declines in cervical cancer incidence in …

Advances In Optical Gastrointestinal Endoscopy: A Technical Review, Yubo Tang, Sharmila Anandasabapathy, Rebecca Richards-Kortum

Faculty, Staff and Students Publications

Optical endoscopy is the primary diagnostic and therapeutic tool for management of gastrointestinal (GI) malignancies. Most GI neoplasms arise from precancerous lesions; thus, technical innovations to improve detection and diagnosis of precancerous lesions and early cancers play a pivotal role in improving outcomes. Over the last few decades, the field of GI endoscopy has witnessed enormous and focused efforts to develop and translate accurate, user-friendly, and minimally invasive optical imaging modalities. From a technical point of view, a wide range of novel optical techniques is now available to probe different aspects of light-tissue interaction at macroscopic and microscopic scales, complementing …

Pancreatic Differentiation Of Stem Cells Reveals Pathogenesis Of A Syndrome Of Ketosis-Prone Diabetes, Diane Yang, Sanjeet Patel, Wojciech J Szlachcic, Jolanta Chmielowiec, Diane Scaduto, Nagireddy Putluri, Arun Sreekumar, James Suliburk, Michael Metzker, Ashok Balasubramanyam, Malgorzata Borowiak

Faculty, Staff and Students Publications

Genetic analysis of an adult patient with an unusual course of ketosis-prone diabetes (KPD) and lacking islet autoantibodies demonstrated a nucleotide variant in the 5′-untranslated region (UTR) of PDX1, a β-cell development gene. When differentiated to the pancreatic lineage, his induced pluripotent stem cells stalled at the definitive endoderm (DE) stage. Metabolomics analysis of the cells revealed that this was associated with leucine hypersensitivity during transition from the DE to the pancreatic progenitor (PP) stage, and RNA sequencing showed that defects in leucine-sensitive mTOR pathways contribute to the differentiation deficiency. CRISPR/Cas9 manipulation of the PDX1 variant demonstrated that it …

Adjuvant Platinum-Based Chemotherapy In Radically Resected Adrenocortical Carcinoma: A Cohort Study, Otilia Kimpel, Sara Bedrose, Felix Megerle, Alfredo Berruti, Massimo Terzolo, Matthias Kroiss, Knut Mai, Olaf M Dekkers, Mouhammed Amir Habra, Martin Fassnacht

Faculty, Staff and Students Publications

BACKGROUND: After radical resection, patients with adrenocortical carcinoma (ACC) frequently experience recurrence and, therefore, effective adjuvant treatment is urgently needed. The aim of the study was to investigate the role of adjuvant platinum-based therapy.

METHODS: In this retrospective multicentre cohort study, we identified patients treated with adjuvant platinum-based chemotherapy after radical resection and compared them with patients without adjuvant chemotherapy. Recurrence-free and overall survival (RFS/OS) were investigated in a matched group analysis and by applying a propensity score matching using the full control cohort (n = 268). For both approaches, we accounted for immortal time bias.

RESULTS: Of the 31 …

Cellular Regeneration As A Potential Strategy To Treat Cardiac Conduction Disorders, Satadru K Lahiri, Mohit M Hulsurkar, Xander Ht Wehrens

Faculty, Staff and Students Publications

Loss of atrioventricular conduction system (AVCS) cells due to either inherited or acquired deficits leads to conduction diseases, which can deteriorate into fatal cardiac arrhythmias and sudden death. In this issue of the JCI, Wang et al. constructed a mouse model of atrioventricular block (AVB) by inducing AVCS cell-specific injury using the Cx30.2 enhancer to drive expression of diphtheria toxin fragment A. AVCS cell ablation in adult mice led to irreversible AVB. jkjkIn contrast, AVCS cell injury in neonatal mice was followed by spontaneous recovery in a subset of mice, revealing a limited postnatal time window during which the regeneration …

Neuron-Specific Mitochondrial Oxidative Stress Results In Epilepsy, Glucose Dysregulation And A Striking Astrocyte Response, Ruth E Fulton, Jennifer N Pearson-Smith, Christopher Q Huynh, Timothy Fabisiak, Li-Ping Liang, Stefanos Aivazidis, Brigit A High, Georgia Buscaglia, Timothy Corrigan, Robert Valdez, Takahiko Shimizu, Manisha N Patel

Faculty, Staff and Students Publications

Mitochondrial superoxide (O2.−) production is implicated in aging, neurodegenerative disease, and most recently epilepsy. Yet the specific contribution of neuronal O2.− to these phenomena is unclear. Here, we selectively deleted superoxide dismutase-2 (SOD2) in neuronal basic helix-loop-helix transcription factor (NEX)-expressing cells restricting deletion to a subset of excitatory principle neurons primarily in the forebrain (cortex and hippocampus). This resulted in nSOD2 KO mice that lived into adulthood (2-3 months) with epilepsy, selective loss of neurons, metabolic rewiring and a marked mitohormetic gene response. Surprisingly, expression of an astrocytic gene, glial fibrillary acidic protein (GFAP) was significantly increased relative …

Friends And Foes: Extracellular Vesicles In Aging And Rejuvenation, Brian V Lananna, Shin-Ichiro Imai

2020-Current year OA Pubs

Extracellular vesicles (EVs) are released by many different cell types throughout the body and play a role in a diverse range of biological processes. EVs circulating in blood as well as in other body fluids undergo dramatic alterations over an organism's lifespan that are only beginning to be elucidated. The exact nature of these changes is an area of active and intense investigation, but lacks clear consensus due to the substantial heterogeneity in EV subpopulations and insufficiencies in current technologies. Nonetheless, emerging evidence suggests that EVs regulate systemic aging as well as the pathophysiology of age-related diseases. Here, we review …

Major Loss Of Coralline Algal Diversity In Response To Ocean Acidification, Viviana Peña, Ben P. Harvey, Sylvain Agostini, Lucia Porzio, Marco Milazzo, Paulo Horta, Line Le Gall, Jason Hall‐Spencer

School of Biological and Marine Sciences

Calcified coralline algae are ecologically important in rocky habitats in the marine photic zone worldwide and there is growing concern that ocean acidification will severely impact them. Laboratory studies of these algae in simulated ocean acidification conditions have revealed wide variability in growth, photosynthesis and calcification responses, making it difficult to assess their future biodiversity, abundance and contribution to ecosystem function. Here, we apply molecular systematic tools to assess the impact of natural gradients in seawater carbonate chemistry on the biodiversity of coralline algae in the Mediterranean and the NW Pacific, link this to their evolutionary history and evaluate their …

Combined Thoracic Endovascular Aortic Repair And Endovascular Aneurysm Repair And The Long-Term Consequences Of Altered Cardiovascular Haemodynamics On Morbidity And Mortality: Case Series And Literature Review, Sherif Sultan, Yogesh Acharya, Mohiey Hazima, Hiba Salahat, Juan Carlos Parodi, Niamh Hynes

2020-Current year OA Pubs

BACKGROUND: Thoracic and abdominal aortic stent grafts are firmer and more rigid than the native aorta. Aortic implanted devices have been implicated in the development of acute systolic hypertension, elevated pulse pressure, and reduced coronary perfusion.

CASE SUMMARY: We report four cases of staged thoracic endovascular aortic repair (TEVAR) and then endovascular aneurysm repair (EVAR). All patients had TEVAR first for thoracic aortic aneurysm and later on developed infra-renal abdominal aortic aneurysm (AAA) that required EVAR. There were three males and one female with a median age of 74.5 years (range 67.5-78.5). None of the patients developed aortic-related major clinical …

Simplification, Not “Tropicalization”, Of Temperate Marine Ecosystems Under Ocean Warming And Acidification, Sylvain Agostini, Ben P. Harvey, Marco Milazzo, Shigeki Wada, Koetsu Kon, Nicolas Floc’H, Kosei Komatsu, Mayumi Kuroyama, Jason Hall‐Spencer

School of Biological and Marine Sciences

Ocean warming is altering the biogeographical distribution of marine organisms. In the tropics, rising sea surface temperatures are restructuring coral reef communities with sensitive species being lost. At the biogeographical divide between temperate and tropical communities, warming is causing macroalgal forest loss and the spread of tropical corals, fishes and other species, termed “tropicalization”. A lack of field research into the combined effects of warming and ocean acidification means there is a gap in our ability to understand and plan for changes in coastal ecosystems. Here, we focus on the tropicalization trajectory of temperate marine ecosystems becoming coral-dominated systems. We …

Design And Supervision Model Of Group Projects For Active Learning, Yi Meng Lau, Kyong Jin Shim, Swapna Gottipati

Research Collection School Of Computing and Information Systems

This research paper presents a group project framework for a second-year programming course, which was conducted during the COVID-19 pandemic. The framework offers well defined stages of the group project which allow students to work on their choice of a real-world problem, integrate their learnings from previous courses, and present a working solution. In the group project, students actively participate, reflect, and contribute to achieving the goals set in the learning objectives of the course. Our framework incorporates key features from Kolb’s Experiential Learning Theory (1984) and principles of active learning from Barnes (1989) to achieve active and experiential learning …

Role Of Limonene In An Experimental Model Of Rotenone Induced Parkinson’S Disease, Lujain Mohamad Bader Eddin

Theses

Parkinson's disease (PD) is one of the prevalent neurodegenerative diseases in elderly population. The symptoms of PD often begin with motor and cognitive impairment that are attributed to the dopaminergic neurons degeneration. Rotenone (ROT) is a naturally derived pesticide that is used in agriculture to control pests. It is a neurotoxin well-established for use in resembling PD symptoms in research. Limonene (LMN) is a plant derived monoterpene extracted from citrus peel with a wide range of therapeutic effects. Due to the shortage in available therapeutic agents that can cure or halt the progressive degeneration of PD, the main aim of …

Assessment Of Heavy Metals In Sharks From The Arabian Gulf Waters, The United Arab Emirates, Noor Alali

Theses

Metals occur naturally in the environment however anthropogenic activities have contributed to their increase in the marine ecosystem. As elements have the ability to bioaccumulate, biomagnify and transfer between biological compartments throughout the food web, they pose a great threat to living biota. The characteristics of the Arabian Gulf make it a harsh environment for marine species especially when multiple stressors are acting together. Rhizoprionodon acutus (milk shark) and Carcharhinus sorrah (spot-tail shark) are essential compartments of the Arabian Gulf ecosystem. As they are found up in the food chain and considered a predator species they are under the threat …

Soliton Based All-Optical Data Processing In Waveguides, Amaria Javed

Dissertations

The growing demand for higher data processing speed and capacity motivates the replacement of the current electronic data processing by optical data processing in analogy with the successful replacement of electronic data communication by optical data communication. In a quest to achieve comprehensive optical data processing we aim at using solitons in waveguide arrays to perform all-optical data processing operations. Solitons are special nonlinear waves appreciated for their ability to conserve their shape and velocity before and after scattering. They are observed naturally in diverse fields of science, namely, nonlinear physics, mathematics, hydrodynamics, biophysics, and quantum field theory, etc. with …

Intra- And Inter-Tumoral Heterogeneity Of Liver Metastases In A Patient With Uveal Melanoma Revealed By Single-Cell Rna Sequencing, Weitao Lin, Aaron Beasley, Nima Mesbah Ardakani, Elena Denisenko, Leslie Calapre, Matthew Jones, Benjamin Woods, Lydia Warburton, Alistair R.R. Forrest, Elin S. Gray

Research outputs 2014 to 2021

Tumour heterogeneity is a major obstacle to the success of cancer treatment. An accurate understanding and recognition of tumour heterogeneity is critical in the clinical management of cancer patients. Here, we utilised single-cell RNA sequencing (scRNA-seq) to uncover the intra- and inter-tumoural heterogeneity of liver metastases from a patient with metastatic uveal melanoma. The two metastases analysed were largely infiltrated by non-cancerous cells with significant variability in the proportion of different cell types. Analysis of copy number variations (CNVs) showed gain of 8q and loss of 6q in both tumours, but loss of chromosome 3 was only detected in one …

Partnership For Empowerment And Discovering One’S Purpose, Alya Prasad

Teaching and Learning Together in Higher Education

No abstract provided.

Detecting Types Of Phobia In Contemporary Architecture, Fatima Ghosn, Loulwa Alama, Mohamad Azhari

Architecture and Planning Journal (APJ)

Phobia in its broadest sense is an irrational fear or feeling, created in a person toward an object or a certain situation that might happen around him or in his imagination and it can be related to natural elements such as animals, insects, oceans, fire and heights. Furthermore, it can be related to build environment and manmade spaces or more simply, to architecture. Unfortunately, architects shifted from the standardisation and regularity to creating innovative and irregular spaces that are reflected by the exterior and interior design of the building without having any concern of the negative consequences such as phobias …

Socio-Ecological Analysis Of Artisanal Gold Mining In West Africa: A Case Study Of Ghana, Richard Takyi, Rasha Hassan, Badr El Mahrad, Richard Adade

Journal of Sustainable Mining

The surge in artisanal gold mining (AGM) activities and the associated environmental impact in Ghana have elicited several stakeholders' attempts to curb the problem. However, due to little understanding of the underlying issues, these efforts have been ineffective. This study aims to use a socio-ecological framework to analyze drivers of AGM activities, the environmental pressures, the state change, their impact on human welfare, and the management response as measures (DAPSI(W)R(M)) to the problem. Evaluate AGM's impact on Ghana's ability to achieve the United Nations Sustainable Development Goals (SDGs). Data were collected from relevant literature on the subject and analyzed with …

Teaching Archival Research Methods Through Projects In Ethnohistory, Veronica L. Denison, Alyssa Willett, Alexandra Taitt, Medeia Csoba Dehass

Journal of Western Archives

During the spring semester of 2015 and the fall semester of 2016, two cohorts of students at the University of Alaska Anchorage learned archival research skills as part of their methodological training in the course, Ethnohistory of Alaska Natives, which subsequently led to the development of further individual research projects. As part of the course, students provided metadata to folders within an archival collection. This article explores the semester long projects, including the hardships of finding and using culturally appropriate metadata, lessons learned, and the impact the project had on students, the archivist, and instructor.

Internet Of Things Software And Hardware Architectures And Their Impacts On Forensic Investigations: Current Approaches And Challenges, Abel Alex Boozer, Arun John, Tathagata Mukherjee

Journal of Digital Forensics, Security and Law

The never-before-seen proliferation of interconnected low-power computing devices, patently dubbed the Internet of Things (IoT), is revolutionizing how people, organizations, and malicious actors interact with one another and the Internet. Many of these devices collect data in different forms, be it audio, location data, or user commands. In civil or criminal nature investigations, the data collected can act as evidence for the prosecution or the defense. This data can also be used as a component of cybersecurity efforts. When data is extracted from these devices, investigators are expected to do so using proven methods. Still, unfortunately, given the heterogeneity in …

Response Of Mixed C4 Grasses To Various Multiple Paddock Grazing Strategies, B. E. Anderson, W. H. Schacht

IGC Proceedings (1977-2023)

The botanical composition of mixed grass pastures may change during grazing due to the various grazing period/recovery period lengths associated with multiple-paddock grazing strategies. This 4-year study compared changes in relative species composition and basal plant cover of a C₄ grass mixture grazed using a nested paddock design to simulate 2, 4, 6 and 12- paddock grazing cells in eastern Nebraska. Total basal plant cover declined from 11.6% prior to grazing to 7.3% after one year of grazing and then remained nearly constant thereafter. Neither relative species composition nor basal density were affected greatly by grazing strategy. Within grazing …

Spatial And Time Distribution Of Dairy Cattle Manure In An Intensive Pasture System, S. L. White, S. P. Washburn, L. D. King, R. E. Sheffield, J. T. Green Jr.

IGC Proceedings (1977-2023)

This study determined distribution of feces and urine from dairy cattle managed in a rotationally grazed pasture. Lactating Holsteins (n=18) and Jerseys (n=18) were grazed on a .74 ha endophyte-free fescue (Festuca arundinacea)/white clover (Trifolium repens) pasture. All cows were constantly observed for 24 h 6 times over 12 mo. Cows had access to about 54% of the paddock during the first grazing period (12 h) and had access to the entire paddock during the second grazing period (8 h). Data included: (1) all feces and urine events from eight cows, observed while in the pasture, …

Test Of A Conversion Equation To Increase The Accuracy Of Microhistological Analysis Of Herbivore Diets In The Pantanal, S. A. Santos, C. Costa, A. Pott, J. M. Alvarez

IGC Proceedings (1977-2023)

Forty forage species samples were collected in September 1999, including grass, sedges, forbs, shrubs and trees. Seven hand-compounded mixtures of known botanical composition and dry weight were prepared. Five slides of each mixture were made and 20 frequency observations were recorded per slide. Two procedures were used to determine percent composition on a dry weight basis and their values were converted to correct the proportion of the unidentifiable fragments amongst species. Estimated and actual values differed significantly (P < 0.05) in 31.7%, 34.1%, 12.2% and 12.2% of the species for frequency addition (FA), density convertion (DC), frequency addition converted (FAC) and density convertion converted (DCC), respectively. The average similarity values between estimated and observed mixture were 90.2, 86.0, 94.2 and 93.3 for FA, DC, FAC and DCC, respectively. In conclusion, food habits by microscopic analysis may be described using any of the procedures tested because they rank important forage species for herbivores.

Effects Of Herbage Allowance Upon Animal Performance And Grazing Behavior Of Strip-Grazed Heifers, Claudio F. Machado, F. Di Croce, F. Gonzalez, H. Zeballos, N. J. Auza, M. H. Wade, S. T. Morris, J. Hodgson

IGC Proceedings (1977-2023)

A trial was designed to test the effect of herbage allowance (HA) on live-weight gain (LWG) and grazing behavior of heifers during spring as part of a combined field-modeling research programme. Low HA (L) and high HA (H) of 2.5 and 5.0 kg DM herbage mass 100 kg animal LW^-1day^-1 were fed respectively. H animals grazed longer and achieved a higher LWG than L (P < 0.05). H animals left a higher residual pasture (P < 0.051) with a significantly (P < 0.05) higher content of green, clover, non-lamina and petiole of a higher digestibility and NSC, with a lower NDF content. The significance of some factors involved in these results on intake and diet selection are discussed in relation to the predictability of animal performance.

Celebrating The Stories Of Black Cellular Biologists And The Path Towards Diversity, Equity, And Inclusion In Stem, Henning Schneider, Nipun Chopra, Kenneth Brown, Scott Stetson, Wendy Tomamichel, Rebecca Kinney, Valerie O'Hair

President Lori S. White Inauguration Symposium

Black scientists have made major contributions to their scientific communities, but their stories and work have not received well-deserved recognition due to systemic inequities within science and academia. By celebrating the stories of Black scientists, we aim to encourage students of color and underrepresented groups to pursue a caree in the natural sciences. Here we tell the stories of Ernest E. Just, Sandra A. Murray and Avery August, three Black cellular biologists from three different generations who have made major contributions to the scientific community using microscopy. The presented project is carried out as part of the Buehler Biomedical Imaging …

The Economic Assessment Of Factors Affecting Small Household(Tomorka) In Rural Areas And Their Income, Sh.A. Muratov

Irrigation and Melioration

In this research, the role and importance of income from small householding(tomorka) in rural areas, its specific features are analyzed. Economic factors were assessed through the tobit regression model of the factors influencing the formation of income from small households (tomorka) activities, and VIF (Variance inflation factor) test was conducted to determine their multicollinearity. Anonymous surveys of 170 landowners in 4 districts of Samarkand region have been used in the analysis. The age of landowners, the area of arable land, the consumption of organic and mineral fertilizers, the cost of seeds and seedlings, the cost of preparing the field for …

Methodology For Solving The Radiation Problem Proposed By Planck In Physics On The Basis Of The Principle Of Consistency, Raygul Khozhanazarova

Karakalpak Scientific Journal

1. www.quantumphysics.iop.org
2. М. Planck. Verhandl. Dtsch. phys. Ges., 1900, 2, 237-245. М. Planck. Ann. Phys., 1901, 4, 553-563.
3. M. Planck, Zur Theorie des Gesetzes der Energieverteilung im Normalspektrum, ibid., 237-245 (1900)/
4. M. Planck. Uber des Gesetz der Energieverteilung im Normalspektrum, Ann. d.Phys. 4, 553—563 (1901).
5. Maks Plank. 1858-1958: Sb. k stoletiyu so dnya rozhdeniya Maksa Planka / Pod red. A. F. Ioffe i A. T. Grigor'yana. M.: Izd-vo AN SSSR, 1958. 276 p.
6. L. Boltzmann. Populare Schriften. Leipzig 1905, p. 227.
7. M.Plank. Vvedeniye v teoreticheskuyu fiziku. Chast' pyataya. Teoriya teploty. Ob"yedinennoye nauchno-tekhnicheskoye izdatel'stvo NKTP SSSR. Glavnaya redaktsiya obshchetekhnicheskoy literatury i nomografii. …