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A Primate Model for Studying the Importance of Environment and Family Lineage on Development, Health, and Aging
No full textThe Cayo Santiago rhesus macaques are one of the most intensely studied primate colonies in the world. They are associated with a rare skeletal collection that is contextualized with known sex, age, and familial information. The purpose of this dissertation is to elucidate environmental and genetic contributions of bone health, evolution, and development. In doing so, this will become a translational resource for human disease and variation. This study departs from previous endeavors by extracting almost all development and pathological data from the derived skeletal collection and stratifying it with known life-history and demographic information to produce reliable biomedical models of health. The backbone of the proposed model is derived from the skeletal collections housed at the Caribbean Primate Research Center University of Puerto Rico, Medical Sciences Campus and New York University, Department of Anthropology. Statistical analysis such as relative risk ratios, and multivariate regression were employed to test for the relative roles of environment and genetics on bone health in the population. The Cayo Santiago population were found to exhibit secular trends in congruence with ecogeographic rules. Specifically, body weights declined, and limb dimensions became slenderer, increasing surface area/volume ratios of individuals and heightening heat expenditure in a more homogeneously warm climate than the one they were adapted to over evolutionary timescales. In contrast to the gradual impacts of climate, major hurricane events precipitated increased levels of systemic disease, bone mineral density (BMD) reductions, and delayed dental eruption timings. Greater rheumatic disease, lower BMD, and delayed dental eruption are believed to relate to immune dysregulation, low grade chronic inflammation, and early-adversity. Further analysis indicated that disease is also patterned across families indicating that a genetic susceptibility to disease can be observed within the matrilines of the Cayo population. Lastly, the neurosurgical landmark, the pterion, exhibited strong support for inheritance of pattern. This work suggests craniotomies using the pterional approach may benefit from taking or making use of family history of pterion type and subsequently benefit from aspects of its variatio
Cryo-Em Structures of Single-Strand RNA Pepeviruses and the Interaction with Their Host Receptor, Type IV Pilus
No full textPositive-sense single-stranded RNA bacteriophages (ssRNA phages) have recently been reclassified because of the increase in the number of genomes discovered in metagenomes and metatranscriptomes. ssRNA phages infect gram-negative bacteria and are known to be structurally and genetically simple RNA viruses. Their infectivity is dependent on host retractile pili. Despite the discovery of ssRNA phages since 1960, only the structures of mature virions for F-pilus-specific E. coli phage (coliphage) MS2 and Q�� were solved by cryo-electron microscopy (cryo-EM). Mature virions of coliphages are composed of a single copy of maturation protein (Mat) and a capsid containing a single strand of genomic RNA (gRNA). Mat is an essential protein required for phage adsorption onto pili. However, ssRNA phages are diverse, as they infect several gram-negative bacteria and target different types of pili. Pseudomonas aeruginosa pepeviruses, PP7 and LeviOr01, infect their hosts through type IV pili (T4P). Here, we present the cryo-EM structures of pepevirus PP7 and LeviOr01, which are distinct from those of coliphages. These T4P targeting phages unexpectedly contain two Mat proteins in mature virions. One of the Mat proteins is internalized (MatIN) inside the virion, whereas the other is exposed (MatEX) for T4P binding. LeviOr01 exhibits plasticity in its assembly through Mat, in which particles with defined gRNA containing only a single MatIN and no Mat proteins are observed. Although mature PP7 virions always consist of two Mat proteins, a region of PP7-gRNA surprisingly displays high plasticity by adopting several conformations. This discovery underlines the importance of structural studies in mature virions and suggests that the structural simplicity of ssRNA phages might require reconsideration. We also solved the complex structure of PP7 bound to purified T4P from PAO1 to better understand host recognition and the entry mechanism. These findings provide insights into the exploitation of pepeviruses for phage therapy and biotechnological applications
John Bickham field notebook: AK18001-AK18500.pdf
No full textBound book, each page corresponds to a karyotype slide data.Data pages for AK18501-AK19000 corresponding to unique identifiers of specimens/samples examined for biological research. Specimens are primarily housed at Texas A&M University; Biodiverstiy Research and Teaching Collection
A mm-Wave Concurrent Dual-Band Dual-Beam Phased Array Receiver Front-End in 22 nm FDSOI CMOS
No full textA mm-Wave concurrent dual-band (28 and 39 GHz) dual-beam phased array multi-input���multi output (MIMO) receiver front end with mid-band rejection was designed and fabricated in 22 nm Fully Depleted Silicon on Insulator (FDSOI) CMOS process. This phased array receiver front end has 4 inputs and 2 output streams with fully connected configuration where takes advantage of sharing LNA and quadrature network and using a unique PS structure which allows power and area saving. The measured 3-dB gain bandwidth is from 23 to 30 GHz for the lower bandwidth a peak gain of 21 dB at 29 GHz, and 36 to 40 GHz for the upper bandwidth a peak gain of 18 dB at 38.5 GHz, and a NF minimum of 6 and 7 dB at 28 and 37 GHz, respectively. The 21 dB mid-band rejection at 33.5 GHz is provided by the LNA to attenuate the out-of-band unwanted interference helping the relaxing the linearity requirement. The entire single-channel receiver front end achieves IIP3 varying from -18 dBm to -11 dBm, and input 1-dB compression point varying from -25 dBm to -18 dBm. The front end has 5-bit phase control and 7-dB gain control achieving the RMS phase and gain errors less than 6 deg and 1.2 dB, respectively, enabling orthogonality. This array demonstrates the concurrent functionality, and carrier aggregation for over-the-air beam steering and EVM measurements. The chip has a length of 2738 ��m, a width of 1808 ��m, and an area of 4.95 mm2 including all DC, RF pads, and decoupling capacitors
Essays in Behavioral and Experimental Economics
No full textMy dissertation consists of three independent essays on the topics of behavioral economics, experimental economics, and information economics.
In Chapter 1, we investigate how rule enforcers leverage the options to hide or reveal their privately-informed detection ability and how agents respond utilizing a disclosure game of verifiable information with either transparent or opaque enforcement objectives. When governing entities levy financial penalties for rule violation, they may aim to maximize compliance or revenues. Agents may be uncertain of these objectives; further they may also not know enforcers��� detection ability for rule violation. Our model derives multiple equilibria. To examine the selection among those equilibria, we conduct laboratory experiments where the enforcer���s objective is known to the agent in transparent treatments, but unknown to the agent in the opaque treatment. In transparent treatments, unraveling occurs. However, under the opaque treatment, only compliance-maximizing enforcers with strong detection ability reveal their detection ability, and agents violate the rule when enforcers hide. Our results outline that when the enforcement objective is opaque to agents, strategic withholding information related to the detection ability benefits revenue-maximizing enforcers.
In Chapter 2, we provide the means to have the largest comprehensive standardized test of all such elicitation mechanisms that are strategically-equivalent but cognitively-simpler than the Becker-Degroot-Marschak (BDM) mechanism. The dominant-strategy BDM mechanism is the prevailing mechanism for eliciting individuals��� valuations within economic research. However, recent research has highlighted systematic bidding mistakes under the BDM mechanism. We examine a BDM design for induced-value sellers in a controlled, laboratory environment. Treatments vary across three additional formats of elicitation mechanisms: (1) a descending price clock mechanism that satisfies refinements of dominant strategy, namely obviousness; (2) a BDM mechanism with additional contingent protocols that improves subjects��� understanding of the payoff function; and (3) a dynamic multiple price list with descending prices that simplifies the structure of the game. Our experimental results show that (3) appears to improve the game form misconceptions of the BDM mechanism but cannot improve overall accuracy of bids. Meanwhile, contrary to previous theoretical findings and online experiments, neither (1) nor (2) provides more accurate elicited values than the BDM mechanism in the laboratory.
In Chapter 3, we experimentally examine of two distinct channels influencing market behavior in a post-price mechanism of experienced goods: (1) whether there is a mandatory return option that the buyer can utilize or not, and (2) the degree to which buyers share different perceptions for the range of the random distribution that draws the experienced good���s true value. Previous literature has documented that a mandatory return option increases seller���s uniform price and buyer���s purchasing tendency in online sales platforms. However, limited attention has been given to its effect on experience goods���where the good���s true value is drawn from a random distribution, and only the buyer can learn it after purchase. Our results show that a mandatory return option decreases the seller���s uniform price for the experienced good. Conversely, for experienced goods with more heterogeneous perceptions, such heterogeneity benefits the buyer but hurts the seller. Our findings provide insights regarding the potential negative impacts of a mandatory return option on market behavior, particularly when buyer���s perception about the experienced good���s value varies in terms of its possible range
Characteristics of Atomic Mirrors in Waveguide QED
No full textThis thesis presents a detailed study of photon-atom interactions in one-dimensional waveguide systems, exploring the dynamics of photon decay in atomic cavities and the emission characteristics of single photons from two-level emitters. The study focuses on the decay dynamics of single-photon pulses in cavities formed by atomic mirrors coupled to waveguides and reveals strategies to increase photon storage times by optimizing system parameters such as coupling strength, cavity length, and atomic separation. In addition, the emission of single photons from two-level emitters in atomic cavities is investigated, demonstrating the potential for frequency combing and spectral narrowing through appropriate control of atomic separations. The results of this work contribute to the understanding of light-matter interactions in waveguide quantum electrodynamics and provide insight into the design of novel photonic devices for quantum information processing and communication
The Economic and Financial Potential of Vineyards in the Texas Hill Country
No full textThere has been a substantial increase in the population of the Texas Hill Country over the last
decade (Hill Country Alliance 2008). Currently, the population in the Texas Hill Country is 3.1
million and is projected to increase to 4.3 million by the year 2030 (Hill Country Alliance 2008).
With respect to agricultural production activities in the area, a major downside of the population influx occurring is that property values have increased at a rapid rate in association with the resulting high demand (American Society of Farm Managers and Rural Appraisers 2019, p. 54). With the rapid influx of people into this region of the state expected to continue, many rural property owners are looking for sources of income that could help offset the increase in property taxes associated with the steadily increasing land prices. In this regard, the potential that vineyards have in the Texas Hill Country, due to their proximity to wineries, presents an interesting question, ���Are vineyards economically and financially feasible for current and potential vineyard operators as well as investors?���
While the concept of growing wine grapes to offset the cost of land and associated property taxes is intriguing, there are several questions that present themselves. Potential producers, and investors, do not have all the necessary information needed to make an informed decision as to if growing grapes is a sound financial endeavor. This thesis is an investigation of a series of scenarios that consider the relative effects of several factors on the potential profitability of a hypothetical Texas Hill Country vineyard operation. Evaluation of these projections allows economic and financial evaluation of the potential of self-sustaining vineyards in the Texas Hill Country, providing information to producers and investors interested in growing grapes in the Texas Hill Country.
This thesis includes a detailed documentation of the assumptions and parameters for three
vineyards of varied sizes as well as the economic and financial results for each size for the
specified scenarios. High land prices contribute to substantial initial capital investment
requirements which places an immediate financial strain on the vineyard from day one. Based
on the established parameters for this thesis, the potential for vineyards in the Texas Hill Country to be economically and financially attractive to potential investors and producers is unlikely. The limitations of this thesis and suggestions for future research are identified, with intentions of identifying pathways for further evaluating the potential of vineyard investments and the value of vineyards in complementing winery operations
Functional Analyses of TMTC-Type O-Mannosyltransferases in Drosophila
No full textOxygen-linked mannosylation, also known as Protein O-mannosylation, is a type of glycosylation, obstruction of which has been shown to cause severe phenotypes in humans, from neurological abnormalities to congenital muscular dystrophies. O-mannose modifications are of special interest due to their essential role in nervous system development. Protein O-mannosyltransferases (POM) are the enzymes responsible for O-mannosylation. They are highly conserved in metazoans. A majority of human O-mannosyltransferase enzymes have homologs present in Drosophila, including canonical protein O-mannosyltransferases, POMT1 and 2, (designated as Rt and Tw in Drosophila), and recently discovered non-canonical O-mannosyltransferases, transmembrane O-mannosyltransferases targeting cadherins 1-4 (TMTC1- TMTC4), all of which share conserved sequence, and structure with their human counterparts. TMTCs have been shown to selectively modify cadherins and protocadherins in humans. Yet the functions of the O-mannose modifications from individual TMTCs in humans and Drosophila are not well understood. In order to address this, we focus on elucidating the molecular mechanisms and functions of O-mannosylation mediated by TMTC1 & 2 in Drosophila. Using the advantages of the Drosophila model, I investigate the effect of TMTC-mediated modifications on the development of the nervous system, behavior, and neurological functions. In my project, I focus on a deeper understanding of how O-mannose modifications affect cadherin function at the molecular, cellular, and organismal levels. Investigating the localization, expression levels, and functional effects of TMTC targets in TMTC mutants will shed light on the function of O-mannose. I analyzed mutant alleles of TMTC1 and TMTC2 and employed rescue constructs to restore functions using both Drosophila and human constructs. I investigated possible redundancy and collaboration within the TMTC gene family by combining the downregulation of different TMTCs and using various transgenic approaches. My results revealed that TMTC1 & TMTC2 function in a partially redundant manner to establish sensory axon connections in the larval brain. My results shed light on the in vivo functions of TMTCs, their role in the regulation of cadherin functions, and have built a Drosophila model for further elucidation of the mechanism of thus highly conserved non-canonical O-mannosylation pathway in animals, including the role of TMTC genes in human biology and pathological conditions
San Giacomo di Galizia: The Digital Reconstruction of a Galleon of the Anglo-Spanish War of 1585 ��� 1604
No full textThe San Giacomo di Galizia was a late-16th century galleon employed by Spain during the Anglo-Spanish War that took place between 1585 and 1604. After a failed attempt to capture the English port of Falmouth, the ship returned to Ribadeo on the north coast of Spain, where it sunk due to the damage received in foul weather. The purpose of the thesis was to digitally reconstruct the vessel based on the archaeological evidence, primary historical sources, and contemporary naval treatises in order to analyze the hydrostatic features of the galleon to comprehend the seagoing performance of similar ships of this period. Likewise, the project aimed to determine the efficiency of this new methodology as a digital tool for nautical archaeology and historical research
Advancing Stress Detection: Towards Real-Time, Naturalistic, and Personalized Artificial Intelligence Approaches for Stress and Mental Disorder Detection
No full textThis dissertation presents a comprehensive exploration of Machine Learning (ML) and Deep Learning (DL) methodologies for the detection, prediction, and analysis of stress and stress-related mental disorders (MDs). The research begins with a systematic review of existing ML algorithms, preprocessing techniques, and data types used in stress detection, highlighting the superior performance of Support Vector Machine (SVM), Neural Network (NN), and Random Forest (RF) models. The review also underscores the prevalent use of physiological parameters, such as heart rate measurements, as stress predictors, and identifies significant research gaps, including model interpretability, personalization, the incorporation of naturalistic settings, and real-time processing capabilities.
Addressing these gaps, the dissertation presents a series of studies. The first study explores a machine learning-based method for continuous monitoring and identification of stress in a naturalistic setting among college students, using a mobile health (mHealth) application and wearable wrist-worn sensors. The XGBoost model was found to be the most reliable in this context, with an accuracy of 84.5%.
The second study proposes a stress detection methodology that utilizes an array of deep learning models, including feedforward neural networks (FFDNN), Conv1D, long short-term memory (LSTM), hybrid Conv1D-LSTM, and Conv1D-LSTM with attention mechanism. The hybrid Conv1D-LSTM model augmented with an attention mechanism outperformed the other models, achieving a cross-validation accuracy of 0.89 and an area under the curve (AUC) score of 0.94. The final study explores the potential of individualized ML and DL algorithms in accurately identifying stress responses in individuals afflicted with Post-Traumatic Stress Disorder (PTSD). The findings demonstrate that individualized models, particularly advanced deep learning models such as LSTM and hybrid CNN-RNN models, consistently surpass standard models in accurately identifying stress in PTSD patients.
In conclusion, this dissertation underscores the importance of employing advanced ML and DL techniques, such as hybrid models and attention mechanisms, and individualized approaches to improve stress detection performance. The findings contribute significantly to the field of digital health, suggesting innovative strategies for monitoring and managing stress in various populations