The Relationship Between First Case On-Time Starts, Turnover Times, And Operating Room Productivity,
2022
Walden University
The Relationship Between First Case On-Time Starts, Turnover Times, And Operating Room Productivity, Rhafia Bucoy
Walden Dissertations and Doctoral Studies
Operating room (OR) managers struggle to manage day-to-day surgical operations while meeting and exceeding organizational productivity amid the COVID-19 pandemic. The deferral of surgeries contributes to millions of backlogs of surgical case volume and unintended negative consequences. Grounded in the proposition that first-case on-time starts (FCOTS) and turnover time (TOT) are correlates of OR productivity, the purpose of this quantitative correlational study was to examine the relationship between FCOTS, TOT, and OR productivity. Archival data from 136 electronic surgical records were collected from two free-standing ambulatory surgery centers and analyzed using multiple regression. The results of the one-service, eye-specialized, ambulatory …
Conservation And Prevalence Of Sequence Paired Sites In Humans,
2022
San Jose State University
Conservation And Prevalence Of Sequence Paired Sites In Humans, Punit Sundar
Master's Projects
The completion of the Human Genome Project in 2003 made it possible to leverage the power of computers to quicken biological discoveries. The human genome contains rich information relevant to the proper functions of cells that is computationally arduous and costly to investigate in a laboratory setting. Specifically, gene expression levels in cells can be impacted when functionally relevant motifs in the DNA are mutated preventing proper transcription factor binding. To study the consequences of such mutations, it is necessary to first identify such functionally relevant regions of the genome using computational approaches. A signaling pathway that is of particular …
The Impact Of Bisphenol A And Its Analogues On Neurodevelopmental Transcriptomes In Drosophila Melanogaster,
2022
San Jose State University
The Impact Of Bisphenol A And Its Analogues On Neurodevelopmental Transcriptomes In Drosophila Melanogaster, An Nguyen
Master's Projects
Bisphenol A (BPA) is an endocrine-disrupting compound (EDC) that can act as an agonist or antagonist to interfere with multiple signaling pathways, including neurological pathways. The impact of BPA related to neurodevelopmental disorders (NDDs) is one of the biggest concerns in BPA exposure in humans. Therefore, BPA analogues are used to replace BPA in manufacturing and BPA-free products. However, most BPA analogues, including Bisphenol F (BPF) and Bisphenol S (BPS), act the same way as BPA on estrogen and androgen receptors. RNASequencing (RNA-seq) analysis was used to investigate the impact of BPA, BPF, and BPS on neurodevelopmental transcriptomes in Drosophila …
Comparative Transcriptomic Analysis Of Cancer Testis Genes In Ovarian Cancer,
2022
Michigan Technological University
Comparative Transcriptomic Analysis Of Cancer Testis Genes In Ovarian Cancer, Zayne Knuth
Dissertations, Master's Theses and Master's Reports
Cancer testis genes are common targets for the development of immunotherapy for cancer treatment. Ovarian cancer is one of the leading causes of death in women cancer patients. Cancer testis genes play a role in tumorigenesis, but it is not clear how these genes are activated. This study utilized differential expression analysis between The Cancer Genome Atlas (TCGA) ovarian cancer data, Genotype-Tissue Expression (GTEx) non-cancerous ovary and testis data, and cell line data to identify a list of cancer testis genes that have a novel expression profile. To identify ovarian cancer testis genes, we obtained normal ovary tissue data and …
Population Structure Of The Lizard Ecpleopus Gaudichaudii Coincides With A Biogeographic Barrier - The Doce River,
2022
CUNY City College
Population Structure Of The Lizard Ecpleopus Gaudichaudii Coincides With A Biogeographic Barrier - The Doce River, Alexander J. Garretson
Dissertations and Theses
Intraspecific genetic variation is an integral component of diversification and the accumulation of biodiversity. The degree to which isolated populations of the same species are genetically structured in geographical space is impacted by a variety of mechanisms. In this study, I document patterns and discuss possible drivers of genetic structure within Ecpleopus gaudichaudii, a lizard species endemic to the Atlantic Forest of Brazil. For that, I assembled ddRadseq sequences from 48 individuals across much of the range of the E. gaudichaudii and analyzed its population structure. I created an intraspecific phylogeny for this group utilizing RAxML and conducted a …
Multilevel Computational Investigation Into The Dynamics And Reaction Mechanisms Of Non-Heme Iron And 2-Oxoglutarate Dependent Enzymes,
2022
Michigan Technological University
Multilevel Computational Investigation Into The Dynamics And Reaction Mechanisms Of Non-Heme Iron And 2-Oxoglutarate Dependent Enzymes, Shobhit Sanjeev Chaturvedi
Dissertations, Master's Theses and Master's Reports
Computational chemistry methods have been extensively applied to investigate biological systems. This dissertation utilizes a multilevel computational approach to explore the dynamics and reaction mechanisms of two groups of enzymes belonging to non-heme Fe(II) and 2-oxoglutarate (2OG) dependent superfamily – histone lysine demethylases from class 7 and ethylene forming enzyme (EFE). Chapter 2 uncovers the role of conformational dynamics in the substrate selectivity of histone lysine demethylases 7A and 7B. The molecular dynamics (MD) simulations of the two enzymes revealed the importance of linker flexibility and dynamics in relative orientations of the reader (PHD) and the catalytic (JmjC) domains. Chapter …
Development Of Genomic Resources In Vitis Riparia For Discoveries On Pre- And Post-Transcriptional Molecular Regulators Of Early Induction Into Endodormancy,
2022
South Dakota State University
Development Of Genomic Resources In Vitis Riparia For Discoveries On Pre- And Post-Transcriptional Molecular Regulators Of Early Induction Into Endodormancy, Michael Robben
Electronic Theses and Dissertations
Grapevine is one of the most important fruit crops in the world, responsible for billions in global sales annually. The largest threat to grapevine and other crop production is global climate change resulting human activities. This brings unpredictable and drastic changes in ambient air temperatures to many climates in which grapes are grown. Lower temperatures and inclement weather are already responsible for millions in lost revenue due to tissue damage of established plants. Thus, protecting grapevine crops from weather-related damage is the biggest concern to growers aside from pathogen- and diseaserelated crop damage. The primary mechanism for winter survival in …
Framework For The Evaluation Of Perturbations In The Systems Biology Landscape And Inter-Sample Similarity From Transcriptomic Datasets — A Digital Twin Perspective,
2022
University of South Dakota
Framework For The Evaluation Of Perturbations In The Systems Biology Landscape And Inter-Sample Similarity From Transcriptomic Datasets — A Digital Twin Perspective, Mariah Marie Hoffman
Dissertations and Theses
One approach to interrogating the complexities of human systems in their well-regulated and dysregulated states is through the use of digital twins. Digital twins are virtual representations of physical systems that are descriptive of an individual's state of health, an object fundamentally related to precision medicine. A key element for building a functional digital twin type for a disease or predicting the therapeutic efficacy of a potential treatment is harmonized, machine-parsable domain knowledge. Hypothesis-driven investigations are the gold standard for representing subsystems, but their results encompass a limited knowledge of the full biosystem. Multi-omics data is one rich source of …
Determining Haplotype Specific X Chromosome Inactivation State And Related Epigenetic Features In Female X-Linked Genes,
2022
Cal Poly Humboldt
Determining Haplotype Specific X Chromosome Inactivation State And Related Epigenetic Features In Female X-Linked Genes, Ariah Dawn Mackie
Cal Poly Humboldt theses and projects
Females with heterozygous X-linked mutations are prone to pseudo-haploinsufficiency because random X chromosome inactivation (XCI) silences one of their two X chromosomes. A prior study explored the theory that reactivating the silenced healthy allele could be a treatment for pseudo-haploinsufficient females. The next step was to evaluate this approach in a clinically relevant stem cell model of the rare neurological disease CDKL5 Deficiency Disorder (CDD). It was necessary to validate X-inactivation state with respect to CDKL5 allele expression in one of these models. We explored CDKL5 allele expression in two populations of CDD female patient-derived induced pluripotent stem cells (iPSCs) …
Catalytic Mechanism And Inhibition Of Plasmodium Sp. Serine Hydroxymethyltransferase By Computational Simulations,
2022
Graduate School
Catalytic Mechanism And Inhibition Of Plasmodium Sp. Serine Hydroxymethyltransferase By Computational Simulations, Pitchayathida Mee-Udorn
Chulalongkorn University Theses and Dissertations (Chula ETD)
Malaria has spread in many countries with a 12% increase in death cases after the COVID-19 pandemic. Over the Greater Mekong subregion, the clinical efficacy of antimalarial drugs has been reduced due to resistance. Target-based approaches on attractive drug targets, such as Plasmodium serine hydroxymethyltransferases (SHMTs) exhibiting distinct structure and function as well as kinetic mechanisms from the human enzyme homologue, are highly useful methods to be used for bypassing the present resistance in the field. In this study, the catalytic mechanism of Plasmodium SHMT was investigated following the retro-aldol proposed scheme by the combined quantum mechanics/molecular mechanics molecular dynamics …
From Thermal Springs To Subway Benches: Exploring The Diversity Of Carbon Monoxide Dehydrogenases Through Metagenomes, Phylogenetics, And Machine Learning,
2022
Michigan Technological University
From Thermal Springs To Subway Benches: Exploring The Diversity Of Carbon Monoxide Dehydrogenases Through Metagenomes, Phylogenetics, And Machine Learning, Isaac Bigcraft
Dissertations, Master's Theses and Master's Reports
Carbon monoxide is well known as a toxic gas but can also be an important input and intermediary for microbial metabolisms. Carbon monoxide dehydrogenases (CODHs) serve as key enzyme complexes for a variety of microbial carbon monoxide (CO) utilization pathways. Such pathways include the Wood-Ljungdahl pathway, which is important in methanogenesis and acetogenesis, metal and sulfate reduction pathways, hydrogen production, and others. The CODH enzymes allow microbes to turn the traditionally toxic waste gas of CO into a useful carbon and energy source. Despite the flexibility of CODH enzymes, the use of carbon monoxide is still believed to be a …
Characterizing Drought Adaptations, Phenotypic Plasticity, And Fixed Gene Expression Patterns Within Quercus,
2022
Michigan Technological University
Characterizing Drought Adaptations, Phenotypic Plasticity, And Fixed Gene Expression Patterns Within Quercus, James K. Rauschendorfer
Dissertations, Master's Theses and Master's Reports
This dissertation was written on topics related to the genus Quercus with a primary focus on Quercus ellipsoidalis (northern pin oak) and Quercus rubra (northern red oak). Within this dissertation are chapters related to the setup of experimental common gardens within the Ford and Kellogg experimental forest, a literature review describing drought adaptations of Quercus sect. Lobatae (red oak group), identification of transcription factors within the Q. robur (English oak) and Q. rubra genomes, a study comparing leaf trait phenotypic plasticity of Q. ellipsoidalis and Q. rubra, and an RNA-seq experiment studying ecological speciation between Q. ellipsoidalis and Q. …
Evolutionary Conservation Of The Dream Subcomplex Muvb,
2022
Michigan Technological University
Evolutionary Conservation Of The Dream Subcomplex Muvb, Spencer Snider
Dissertations, Master's Theses and Master's Reports
As the publications of annotated genomes from species representing most domains of life continue to grow exponentially, we are gaining more insight into how proteins, cellular pathways, and protein complexes evolved. We are interested in understanding how each protein in the 8-subunit transcriptional repressor complex called DREAM interacts with each other. DREAM is comprised of 3 main components: an E2F-DP transcription factor heterodimer, a pocket protein, and the highly conserved 5-subunit subcomplex called MuvB. We hypothesize that the mechanism of DREAM’s formation on chromatin dictates how DREAM functions to turn off target gene expression. Unfortunately, many interaction surfaces remain unknown, …
Bone Marrow Stroma-Induced Transcriptome Signatures Of Multiple Myeloma As Modulated By Junb,
2022
West Virginia University
Bone Marrow Stroma-Induced Transcriptome Signatures Of Multiple Myeloma As Modulated By Junb, Jasleen Kaur Gandhi
Graduate Theses, Dissertations, and Problem Reports
The bone marrow (BM) microenvironment acts as a breeding ground for drug resistance in multiple myeloma (MM). The interaction with bone marrow stromal cells (BMSCs) confer environment-mediated drug resistance (EMDR) to multiple myeloma. We investigated BM stroma-induced transcriptome signatures of MM cells through a sophisticated analysis of gene expression. In particular, we defined transcription program modulated by JunB, an emerging regulator of MM pathogenesis and a member of the transcription factor superfamily activator protein 1 (AP-1), in response to BM stimulation. The data and results lay down a foundation for future studies to illustrate the regulatory role of JunB in …
A Novel Computational Network Methodology For Discovery Of Biomarkers And Therapeutic Targets,
2022
West Virginia University
A Novel Computational Network Methodology For Discovery Of Biomarkers And Therapeutic Targets, Qing Ye
Graduate Theses, Dissertations, and Problem Reports
Lung cancer has the second highest cancer incidence rate and the top cancer-related mortality worldwide. An estimate from the American Cancer Society shows that, in 2022, there will be about 236,740 lung cancer cases (117,910 men and 118,830 women) in the US. To date, there are no prognostic/predictive biomarkers to select chemotherapy, immunotherapy, and radiotherapy in individual non-small cell lung cancer (NSCLC) patients. There is an unmet clinical need to identify patients with early-stage NSCLC who are likely to develop recurrence and to predict their therapeutic responses. This dissertation developed a novel computational methodology for modeling molecular gene association networks …
Getting To The Root Cause: The Genetic Underpinnings Of Root System Architecture And Rhizodeposition In Sorghum,
2022
West Virginia University
Getting To The Root Cause: The Genetic Underpinnings Of Root System Architecture And Rhizodeposition In Sorghum, Farren Smith
Graduate Theses, Dissertations, and Problem Reports
Plants are some of the most diverse organisms on earth, consisting of more than 350,000 different species. To understand the underlying processes that contributed to plant diversification, it is fundamental to identify the genetic and genomic components that facilitated various adaptations over evolutionary history. Most studies to date have focused on the underlying controls of above-ground traits such as grain and vegetation; however, little is known about the “hidden half” of plants. Root systems comprise half of the total plant structure and provide vital functions such as anchorage, resource acquisition, and storage of energy reserves. The execution of these key …
Computational Approaches For Identifying Bioactive Compounds Inhibiting Sars-Cov-2 Main Protease,
2022
Graduate School
Computational Approaches For Identifying Bioactive Compounds Inhibiting Sars-Cov-2 Main Protease, Piyatida Pojtanadithee
Chulalongkorn University Theses and Dissertations (Chula ETD)
The infectious disease caused by the novel coronavirus 2019 has devastatingly affected the global economy and society. However, the drug discovery process from concept to approval requires a significant investment of time and resources. To address these challenges, we employed structure-based virtual screening techniques, including drug-likeness screening, pharmacophore-based virtual screening, molecular docking, molecular dynamics simulation, and fragment molecular orbital calculation. The protein target of this investigation was the main protease or 3-chymotrypsin-like-protease (3CLpro) of the coronavirus, given its pivotal role in the viral replication process. Using our in-house database of natural products and their derivatives, we aimed to identify potent …
Enhanced Triacylglycerol Production In Chlorella Vulgaris By Flux Balance Analysis On Metabolic Network,
2022
Graduate School
Enhanced Triacylglycerol Production In Chlorella Vulgaris By Flux Balance Analysis On Metabolic Network, Issalapap Kaothong
Chulalongkorn University Theses and Dissertations (Chula ETD)
Triacylglycerol (TAG) is a type of lipid that can be produced by a microalga called Chlorella vulgaris, which is a promising source of biodiesel. However, there is a lack of research and models explaining how to directly produce this lipid. To address this, we propose using linear minimization of metabolic adjustment (LMOMA), which predicts gene manipulation effects based on Flux Balance Analysis (FBA), to enhance TAG production. We conducted single-gene deletion experiments on the genome-scale metabolic model of C. vulgaris UTEX 395 (iCZ843) under different growth conditions: heterotrophy, photoautotrophy, and mixotrophy conditions. We found that the TAG production increased by …
Comparative Analysis Of Mutational Landscapes Identified From Exome Sequencing Of Tumor Tissues And Circulating Tumor Dna,
2022
Graduate School
Comparative Analysis Of Mutational Landscapes Identified From Exome Sequencing Of Tumor Tissues And Circulating Tumor Dna, Julanee Leenanitikul
Chulalongkorn University Theses and Dissertations (Chula ETD)
Next-generation sequencing of circulating tumor DNA (ctDNA) has been used as a noninvasive alternative for cancer diagnosis and characterization of tumor mutational landscape. However, low ctDNA fraction and other factors can limit the ability of ctDNA analysis to capture tumor-specific and actionable variants. In this study, whole-exome sequencings (WES) were performed on paired ctDNA and tumor biopsy in 15 cancer patients to assess the extent of concordance between mutational profiles derived from the two source materials. We found that up to 16.4% ctDNA fraction can still be insufficient for detecting tumor-specific variants and that high concordance with tumor biopsy is …
Analysis Of Expression Patterns Of Brassinosteroid-Responsive Genes In Arabidopsis Root Using Single-Cell Rna Sequencing Datasets,
2022
Graduate School
Analysis Of Expression Patterns Of Brassinosteroid-Responsive Genes In Arabidopsis Root Using Single-Cell Rna Sequencing Datasets, Thanaporn Wongkham
Chulalongkorn University Theses and Dissertations (Chula ETD)
Brassinosteroid (BR) plays a complex role in root growth and development by regulating the expression of downstream target genes through the BR signaling pathway. In this scRNA-seq study of Arabidopsis roots, tissue- and developmental-specific roles of BR were identified. Atrichoblast, an epidermal cell that develops into a non-hair cell, displayed the highest enrichment of BR-induced genes in the elongation and maturation zones among all cell types. Trajectory analysis revealed distinct expression patterns of BR biosynthesis and signaling genes between atrichoblasts and trichoblasts. Atrichoblasts exhibited higher expression levels of BR biosynthesis genes (DET2 and ROT3) and BR signaling genes (BRI1 and …
