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Airgap
No full textAirgap is an experimental novel of approximately 73,900 words. The fragmented, multivocal narrative explores grief, masculinity, and surveillance in a speculative future
Conditions of the Oral Cavity in Early Bronze Age Anatolia: Reconstruction of Dietary Behavior, Biological Impact, and Social Structure
No full textThe Early Bronze Age (EBA; 3000-2000 BCE) in Anatolia is recognized as a period of increased social stratification, expansive trade, urbanization, agricultural intensification, craft specialization in metallurgy, and socioeconomic shifts. This combination of sociocultural and sociopolitical changes distinguishes the EBA from the preceding Neolithic and Chalcolithic. Most research supporting these extensive changes stems from archaeological research, while more recent trends in reconstructing the EBA have followed biocultural approaches in bioarchaeology studies. Moreover, even fewer investigations seek to answer questions with evidence from the oral cavity. This dissertation intends to examine social organization from the EBA site of Karataş-Semayük (Karataş; 2700-2300 BCE) located on the Elmalı Plain of Anatolia, by combining several conditions of the oral cavity (i.e., dental caries, dental calculus, periapical lesions, periodontal disease, antemortem tooth loss, dental wear, dental chipping, and atypical dental wear). The oral cavity provides optimal biocultural evidence due to the entangled relationship between diet, food preparation, non-alimentary application of teeth, cultural modifications, trauma, hygiene, and pathological conditions of the oral cavity. The study is centered on the 2733 deciduous and permanent teeth of subadult and adult individuals (n = 274) curated at the Human Behavior Ecology and Archeometry Laboratory (IDEA Lab) at Hacettepe University in Ankara, Türkiye. To contextualize the results from Karataş, comparisons are made to sites through the Neolithic to EBA, including the sites Çayönü Tepesi, Aşıklı Höyük, Çatalhöyük, Tepecik-Çiftlik, Hakemi Use, Çamlıbel Tarlası, İkiztepe, Bakla Tepe, Titriş Höyük, and Salat Tepe. Throughout the findings, the dental conditions indicated the similarities across the intersectional identities represented at Karataş. Limited differences in dental conditions between sex and social status at Karataş suggest that the inhabitants generally shared resources and habits. Slight differences between dental chipping and dental calculus frequencies by burial location indicate the potential of very few individuals having different dietary and non-alimentary habits. While age groupings displayed differences in dental conditions, this is expected due to the progressive nature of dental conditions. In addition to the intrasite findings, the intersite comparisons on dental conditions suggest that Karataş aligns with the rise of and expansive reliance on agriculture in Anatolia following the Ceramic Neolithic. This dissertation serves and advocates as 1) a further biocultural illustration of the social organization during the EBA in Anatolia and 2) an example of the application of multiple dental conditions when studying the oral cavity to capture the entangled relationships between conditions and extrinsic factors
Decoding DNA: scalable genome annotation software, generative AI, and application to the cactus pear genome
No full textThe annotation of protein-coding genes from a raw genome assembly involves identifying the sequence regions that are transcribed into mRNA transcripts, spliced, and ultimately translated into protein. Thus, genome annotation is a fundamental task that critically supports systems level biological inquiry by providing a reference for ‘omics’ analyses including, RNA sequencing, proteomics, and comparative genomics. Despite advances in genome sequencing, which enable routine chromosome-level genome assembly, complete identification of gene structures in eukaryotes remains a significant challenge. For example, existing genome annotation pipelines suffer from a lack of automation, an inability to control precision, and from poor performance in predicting alternative splicing.The goal of this work is to develop improved computational tools for genome annotation and to apply the improved methods to annotate the genome of cactus pear (Opuntia cochenillifera). To address challenges in computational efficiency and precision, an automated bioinformatics pipeline called Sylvan was developed that computes a comprehensive genome annotation from disparate evidence sources and filters spurious gene models using a semi-supervised random forest classifier. In benchmarking trials involving Arabidopsis thaliana and Oryza sativa the pipeline outperformed current standards, such as MAKER and BRAKER, in both F1 similarity and BUSCO completeness. Sylvan was used to annotate the genome of Opuntia cochenillifera, representing the first genome sequence and assembly in the genus and a foundational tool for research into crassulacean acid metabolism (CAM) and drought tolerance in plants. To improve the capacity of genome annotation tools to predict full-length, alternatively spliced transcripts ab initio, a deep learning transformer model was developed to ‘translate’ a DNA sequence into its text-based annotation. This generative strategy provides increased flexibility to predict hierarchical and overlapping gene structures that are not possible with one dimensional segmentation models
Innovate to Elevate - AIEI in Action: North Dakota's Path to Better Performance
No full textThis document explains how the AIEI program helped North Dakota Department of Transportation turn persistent cracking and raveling into a momentum-building shift toward durable, cost-effective asphalt mixtures. The AIEI program's purpose is to address the ongoing challenges faced by the transportation community to adopt new technologies and reduce the time to implement them in business practices, specifications, and construction methods relating design, production, testing, control, construction, and investigation of asphalt pavements.United States Department of TransportationFederal Highway Administratio
Effective Practices, Lessons Learned, and Challenges When Implementing Asphalt Balanced Mix Design: Site Visits 2025 Follow-Up
No full textIn 2020, the Federal Highway Administration (FHWA) conducted virtual site visits and interviews of seven State Departments of Transportation (DOTs), and material producers, consultants and paving contractors that serviced those agencies, to learn more about the Balanced Mix Design (BMD) and mechanical tests implementation efforts in their States. During the past five years, many of these States have made considerable progress in their path towards BMD implementation. They have encountered new challenges, learned additional lessons, and updated their practices. In 2025, FHWA conducted follow-up interviews with six of these DOTs. This Technical Brief summarizes the 2025 follow-up interviews, focusing on the eight tasks towards BMD implementation.U.S Department of TransportationFederal Highway Administratio
TREK-1 confers differential effects on contractile dynamics in myometrium and the oviduct, indicating a unique role in endometriosis and labor
No full textRoughly 6-13% of reproductive age females (114-247 million) globally are affected by endometriosis, a life-altering condition with no cure causing extreme pain during periods, infertility, and even depression and anxiety. Ten percent of women undergo labor prematurely in the United States, which is a leading cause of neonatal morbidity and mortality. Both endometriosis and preterm labor are considered to be inflammation- related conditions potentially caused by hormonal and/ or immune dysregulation with a higher prevalence of interleukin 6 (IL-6), a pro-inflammatory cytokine produced by circulating immune cells including B and T-cells. IL-6 has been found to increase oxytocin receptors in the myometrium, leading to an increase in contractility. It has been established that TREK-1, a potassium channel, plays a major role in quiescing the myometrium, which is essential for maintaining pregnancy. However, the effects of IL-6 and the role of TREK-1 in the fallopian tube have yet to be fully determined. We hypothesize that an increase in IL-6 leads to reduced contractile activity in the fallopian tube and increased contractility in the myometrium, which may contribute to endometriosis and preterm labor. IL-6 leads to a decrease in TREK-1 expression in the myometrium, leading to a decrease in the ability to remain in a relaxed state. TREK-1 expression is increased in the fallopian tube as a result of IL-6 presence, leading to its dilation, allowing for retrograde movement of menses material. Though not statistically significant, the organ bath results show a trend that mouse uterine horns incubated in the presence of IL-6 result in increased contractility compared to control. In both IL-6 and control uterine tissues, contractility showed a downward trend when dosed with the TREK-1 agonist ML335. It was determined that oviducts incubated in IL-6 had a decreased contractile response after washout compared to oviducts which were not exposed to IL-6, and both groups had a similar level of contractility relative to control when exposed to ML335. TREK-1 protein expression was found to be significantly increased in oviduct samples treated with IL-6. Based on these findings we have concluded TREK-1 portrays differential effects on contractile dynamics in the myometrium and the oviduct, indicating a unique role in endometriosis and labor which will be further investigated in the future
Steady-State Infiltration Analysis in Dump Leach under Saturated Conditions Using Finite Element Modeling
No full textThis paper was presented at the Heap Leach Solutions Conference, October 19-21, 2025, Sparks, Nevada.The safe design and operation of a dump leach facility depends, among other factors, on understanding the hydraulic behavior of the leached ore, specifically under the influence of surface irrigation-induced infiltration. This study evaluates the impact of the irrigation on pore water pressure generation and phreatic level depth in a dump leach deposit, based on numerical modeling using a saturated steady-state groundwater flow approach. The main objective was to determine how flow distribution varies across representative cross-sections of the dump under different irrigation scenarios. The sections were modeled under the assumption that the system has reached hydraulic equilibrium, representing prolonged irrigation conditions that enable the assumption of internal saturation. This assumption supports the application of a steady-state analysis, which, although it does not consider the transient nature of the process, provides a representative condition for evaluating stabilized pore pressures. Results indicate that while flow tends to concentrate in localized areas within the dump, there is no significant accumulation that would compromise overall slope stability. The location of the phreatic level varies across sections, primarily influenced by internal topography and the type of surface irrigation applied. However, in all scenarios, flow lines remain confined and do not reach critical zones near the slope base. Pore water pressures remain within acceptable ranges, consistent with previous stability analyses. This analysis provides a valuable tool to complement stability assessments in leached ore dumps, enabling the visualization of how irrigation water redistributes internally through the ore, as well as guiding decisions in the optimization of high-permeability overliner materials and the implementation of efficient drainage systems
Steps to Elucidating the Competence Regulon Quorum Sensing Mechanism in Streptococcus intermedius
No full textQuorum sensing (QS) is a cell-to-cell communication system used to modulate gene expression and coordinate group behavior based on cell density. Bacteria that utilize QS secrete chemical signal molecules known as autoinducers (AIs) that will accumulate as the cells continue to divide. The cells are able to determine cell density and coordinate these group behaviors such as virulence factors, biofilm formation, and activation of competence based on the environmental concentration of AIs. Due to this, QS could be used as a novel therapeutic strategy controlling infection rates without the use of antibiotics. Although highly effective, antibiotics pose a critical health threat due to the selective pressure they pose and that result in the development of resistant strains. The economic burden resulting from treating a multi-drug resistant (MDR) infection has cost healthcare systems millions of dollars. Streptococcus intermedius is an opportunistic pathogen that appears to possess a typical comABCDE competence regulon QS circuity. In this work I set out to study the S. intermedius competence regulon QS circuitry through the creation of a cell-based reporter system. To this end, a synthetic competence stimulating peptide (CSP) was synthesized and utilized to transform an antibiotic-resistant plasmid into the bacteria. Obtaining such reporter system would allow for structure-activity relationship studies of the CSP to be conducted and consequently the development of inhibitory AI analogs that could be utilized to attenuate S. intermedius pathogenic behaviors as an alternative method to treating infections while reducing the selective pressure to develop resistance
Citing Sources
No full textCiting your sources is an important part of writing a research paper because it gives credit to others for their words and ideas. It also indicates that you have conducted thorough research and are knowledgeable about your topic. Citations identify the source of the information you are presenting, allowing the reader to locate the materials you used to verify facts or learn more about the topic
Disaster Fiction and Cultural Characteristics In Twenty-First Century America
No full textThis dissertation analyzes four twenty-first century U.S. disaster novels in order to reveal idiosyncratic cultural traits that distinguish it from the middle and late twentieth century. Disaster novels are a relatively unstudied subgenre of speculative fiction, which provides fertile ground for cultural analysis due to their focus on social disruption and cultural criticism. Works within this subgenre often distill and simplify society, cultures, and communities, providing unique insight into social norms and assumptions of certain groups during a specific period of time. Throughout my analysis, I argue that twenty-first century U.S. culture has become distinctly individualistic, embodying subjectivist attitudes. The rise of this characteristic suggests that individuals are predisposed to favor their own “good,” while rejecting collectivist or utopian ideals. This dissertation suggests that the turn toward subjectivism has become widespread throughout various aspects of U.S. culture, influencing the way(s) individuals act as a group as well as with larger social systems. This has facilitated a cultural characteristic unique to twenty-first century U.S. society—what I call subjective optimism. This trait suggests that individuals in twenty-first century U.S. society maintain a sense of social optimism by obtaining what they subjectively value (e.g., money, stability, liberty, et cetera). As a result, there is little or no concern for societal improvement. This suggests a fundamental shift in U.S. culture between the population and many social assumptions/institutions, creating a unique period differentiated from the middle and late twentieth century