University at Albany, State University of New York
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Phylogenetic Analysis of Metabolic Enzymes in Hypoxic/Anoxic Conditions in Cetaceans and Cancer
Get PDFCancer cells often exhibit a Warburg-like metabolism, which includes increased fatty acid synthesis and storage that help them survive in hypoxic conditions. This shift is marked by the heightened synthesis and accumulation of fatty acids, acting as a survival mechanism in low-oxygen environments (Baumann et al., 2016). Interestingly, deep-diving whales may utilize a similar metabolic pathway to produce wax esters during their prolonged dives.
Our study focused on exploring the genetic and metabolic similarities between breast cancer cells and deep-diving whales, using computational analyses to investigate lipid metabolism genes. We looked for evolutionarily conserved variations that might reveal adaptive mechanisms enabling sperm whales to thrive in hypoxic conditions, potentially through enhanced fatty acid synthesis akin to cancer cell metabolism.
We assessed amino acid sequences from humans and various whale species, paying particular attention to variations in deep-diving compared to shallow-diving whales and other hypoxic species. Our findings identified specific amino acid changes in sperm whales that may suggest unique metabolic adaptations. However, we did not find significant differences in several candidate genes between deep-diving and shallow-diving whales.
Key enzymes like PRKAG3, ME2, and PIPOX, which show a conserved change in all deep-diving whale species, may facilitate their survival in low-oxygen environments, similar to adaptations observed in cancer. These enzymes are crucial not only in lipid synthesis and signaling but are also implicated in various cancers, reinforcing the connection between metabolic reprogramming and cancer progression.
Our analysis included 22 cetacean species, with a focus on seven deep-diving whales. We hypothesized that these adaptations would manifest at both the genomic level and the metabolite profiles. Our computational analyses indeed showed recurrent changes in amino acid composition across all deep-diving whale species, suggesting these variations represent metabolic evolutionary adaptations.
When we contrasted deep-diving whales with their shallow-diving counterparts, we noted differences in the amino acid profiles of enzymes like PRKAG3, ME2, and PIPOX. These distinctions may indicate specific adaptive strategies that enable deep-diving whales to endure extended periods in anoxic or hypoxic conditions, potentially involving metabolic mechanisms similar to those adopted by cancer cells, particularly regarding enhanced fatty acid synthesis and storage
Accuracy of Angular Displacement Measurements Using IMU
Get PDFAs a part of a larger group, this research focused on gathering data from accelerometers to gather further knowledge on how these devices could be used in further experiments. Using the Sparkfun Artemis accelerometer, angular displacement was isolated and tested to understand the parameters and abilities of the device. Simple tests were run moving the device through 90 degree angular changes. The data collected by the accelerometer was then analyzed using code written specifically to graph angular changes. The data was run through a low and a high pass filter to account for any drift experienced during the tests. An apparatus was constructed to allow the use of multiple accelerometers at once, passing through the X, Y, and Z coordinate grids. Tests were conducted moving the accelerometers through known angles, and Matlab was run to analyze the results of the experiments run with this apparatus. Graphs were obtained from Matlab to represent the angular displacement experienced by each accelerometer
Custom GPTs for STEM Student Success
No full textGenerative AI is becoming increasingly integrated within various parts of our society, with education being an important area. Students can utilize generative AI to assist with their homework and have a personalized and curated tutor. However, current models make it difficult for students to fully engage in the learning process as these models immediately give students their answers without showing the critical thinking or problem-solving skills involved in the problem. As AI slowly becomes more entangled in education, it is crucial to consider how Generative AI models can assist students in approaching their studies with a problem-solving mindset. This research narrows down on STEM students, particularly in technology-aligned classes as the problem-solving techniques vary between different disciplines. This study aims to understand how Generative AI models can be customized to help students achieve a problem-solving mindset when approaching difficulties in their studies. This study will create a customized GPT model, utilizing features that would enhance an LLM’s capabilities for better student success. An assessment criteria framework will be created to compare a standard GPT model versus this study’s customized GPT to view the effects on student success
Territory and Border Dynamics among Small Pre-Hispanic Polities in Western Chiapas, Mexico
Get PDFThis dissertation examines the concept of territory in premodern polities, challenging modern assumptions that territory is a static or obsolete notion in the face of globalization. It critiques the conventional Westphalian model of state sovereignty, emphasizing that premodern political entities often exhibited flexible, overlapping territorial arrangements rather than fixed, linear boundaries. By analyzing territorial organization in premodern societies, this research explores the historical evolution of territoriality, identifying continuities and transformations over time.
Drawing from archaeology, anthropology, and historical geography, the research investigates how different societies have defined and maintained territorial control based on factors such as political authority, economic resources, kinship, and cultural identity. As a case study, this dissertation presents archaeological research conducted in Ocozocoautla, Chiapas, Mexico. Through field surveys and material analysis, it reconstructs settlement patterns and territorial organization from the Middle Formative Period (ca. 1000-300 BCE) to the Postclassic (AD 1000-1500). The findings contribute to broader discussions on the role of space in political organization, highlighting how territoriality in premodern societies functioned at multiple scales and often diverged from modern state-based frameworks.
By proposing an alternative framework for conceptualizing territoriality, one that accounts for spatial heterogeneity and dynamic political landscapes, this study offers insights into the long-term structures of human territorial organization. The research underscores the need to reconsider the rigid, nation-state-centered perspectives on territory and to integrate historical and archaeological evidence into contemporary discussions on political geography
Backgrounds and Efficiencies for Low-Energy Searches, and Improved Calibration Techniques in the LUX-ZEPLIN Dark Matter Experiment
No full textThe full understanding of dark matter has eluded physicists for many years. While there is abundant astrophysical evidence across many scales, the exact nature of this matter, which comprises about 25% of the Universe’s energy density, remains unknown. Weakly Interacting Massive Particles (WIMPs) are one of the leading theoretical candidates, and numerous ex- periments have searched for their interactions. In recent decades, dual-phase Time Projection Chambers (TPCs) have become the leading technology in this search. The LUX-ZEPLIN (LZ) detector is one such xenon-based experiment, operating nearly a mile underground in the Black Hills of South Dakota at the Sanford Underground Research Facility (SURF). LZ contains 7 tonnes of active liquid xenon, of which about 5.5 tonnes comprise the central target within the TPC. Incoming radiation produces two signals: a prompt scintil- lation (S1) and a delayed electroluminescence (S2). By combining these two observables, LZ can reconstruct event energy and position with high precision and discriminate between signal and background. In addition to its flagship S1+S2 WIMP search, LZ also enables specialized analyses that extend its reach and refine its calibration framework. The first focus of this thesis is an S2-only analysis, which forgoes the S1 signal entirely to extend sensitivity to lower- energy depositions and lighter dark matter candidates. This approach introduces unique challenges, particularly from cathode-related backgrounds that cannot be rejected without drift-time information. My work develops data-driven methods to estimate these background rates and evaluates the efficiency of event selection cuts. The second focus of this thesis is a Doke plot analysis, which employs monoenergetic calibration sources to measure the detector gains g1 (light collection) and g2 (charge am- plification). These parameters underpin the conversion of observed signals into a common energy scale and are essential for all LZ science analyses. Here, we perform the traditional Doke analysis, extend it to include monoenergetic alpha peaks, study time-binned behavior relative to detector operational conditions, and analyze individual ER calibration sources. Together, these studies broaden LZ’s discovery reach and refine its calibration accuracy, enhancing the experiment’s overall sensitivity to rare dark matter interactions
Welfare States and Imprisonment Rates: Revisiting the Study of Public Assistance and Punishment in the United States
No full textIn the past fifty years, the United States has seen significant changes in both the criminal legal system and the welfare state. The incarceration rate surged by 475% from 1972 to 2007, driven by state-level decisions about criminal legal policy and disproportionately affecting Black Americans. Simultaneously, welfare programs became less generous, especially for those deemed “undeserving.” A long line of social science scholarship emphasizes that these two major social institutions—the welfare state and the carceral state—must be considered as complementary and alternative methods of managing marginalized groups. Quantitative research often confirms these claims, finding a durable inverse relationship between welfare generosity and imprisonment rates. However, measurement inconsistencies and methodological limitations may complicate and obfuscate prior research findings. This dissertation improves on these shortcomings and explores the theoretical and empirical connections between welfare and punishment using annual data from all fifty states from 1980 to 2019. In Study 1, I compare alternative measures of welfare generosity to determine which measure is best suited for use in analyses predicting imprisonment. In Study 2, I use the welfare measures identified in the Study 1 to determine whether welfare is associated with imprisonment after methodological limitations of prior research are addressed. Considering the gendered and racialized nature of both welfare and punishment, Study 3 decomposes the imprisonment rate by race and gender to examine if and how the relationship between welfare and imprisonment changes for different groups. On the whole, my analyses showed no significant relationship between various measures of welfare generosity and imprisonment. These findings suggest the need for future research reconceptualizing the relationship between welfare and punishment in the 21st century, as well as the importance of appropriate statistical methodology in the analysis of imprisonment rates
Essays on Technological Change and Scientific Research
No full textThe primary objective of economic science has long been to understand and promote growth, as it contributes to a more prosperous civilization and improves individual well-being. The core drivers of growth—capital accumulation, human capital development, and technological progress—are well-established. While capital deepening enables scaling of production, and human capital enhances labor productivity, technological and scientific advancements remain the most critical, as they continually redefine the efficiency frontier. Given this centrality, it is essential to understand how technological progress affects labor markets, how research resources should be allocated, and how technology relates to human capital formation.
The first part of this dissertation examines the impact of technological improvement on the labor market. Standard models based on constant elasticity of substitution (CES) production functions suggest that better technology benefits all types of labor while widening wage inequality. However, empirical evidence indicates that substitution elasticities vary over time and across countries. To address this, we employ an iso-elastic production function, where elasticity evolves with technological progress. We demonstrate that wages may respond non-monotonically to technological change. Integrating this framework with a sectoral model and a self-selective labor force, we explain sectoral transitions and “sectoral blockages”—cases where automation in one sector is not matched by sufficient progress in adjacent sectors—resulting in rising unemployment and falling wages.
The second part explores how fluctuations in science funding affect research output and human capital formation through mentoring. While prior work documents the adverse effects of budget cuts, little is known about the consequences of unsustained funding spikes. Between 1998 and 2002, the U.S. National Institutes of Health (NIH) budget doubled before returning to near-previous levels. Using this natural experiment, and datasets such as NIH ExPORTER, ProQuest, and Author-ity, we apply a staggered difference-in-differences approach at the principal investigator level. We find that the budget increase boosted output quantity but degraded output quality—including the quality of mentored students.
The third part offers a conceptual explanation for these findings. Using an overlapping generations model, we simulate the dynamics between junior and senior researchers producing knowledge. We show that in a regime shift from constrained to surplus funding, the initial gain in quantity is accompanied by a decline in quality. When funding reverts to previous levels, both quality and quantity fall, leading to overall mitigated outcomes. These results suggest that steady, linear budget increases may be more effective than short-term spikes in maximizing long-term research productivity and quality
Buoy-Based Eddy Covariance Drag Coefficient at a Near-Shore and Offshore Site
No full textAn eddy covariance (EC) flux system was integrated onto a Navy Oceanographic Meteorological Automatic Device (NOMAD) floating lidar buoy fitted for measuring the offshore wind resource. The EC flux system consisted of two sonic anemometers and an inertial measurement unit that together provided high-frequency (10 Hz) motion-corrected wind measurements. To assess possible impacts of flow distortion, EC momentum fluxes (10 min) were calculated in gravity-aligned, natural, and planar fit (PF) coordinate frames. The buoy was anchored near the Martha’s Vineyard Coastal Observatory Air-Sea Interaction Tower (ASIT; near-shore) for validation of the buoy-based EC fluxes against the fixed tower measurements before deployment within the Third Wind Forecast Improvement Project (WFIP3; offshore) zone. Drag coefficients from the direct turbulent EC flux measurements were compared to the National Oceanic and Atmospheric Administration Coupled Ocean-Atmosphere Response Experiment (NOAA COARE) bulk air-sea flux algorithm, which was run with measurements of mean (10 min) air- and ocean-side bulk variables. At both the ASIT and WFIP3 deployment locations, COARE’s wave-dependent surface roughness parameterization gave drag coefficient estimates in closer agreement with the EC-based drag than its wind-dependent roughness formulation did. There was less agreement between the EC and COARE roughness at low wind speeds, where air-sea momentum transfer and motion correction are more nuanced. The range of wind speeds with the largest differences between the EC-measured and COARE-parameterized momentum flux overlaps with the range at which turbine power curves are most sensitive to wind speed. During unstable conditions, Monin-Obukhov extrapolations of the wind profile using the PF and COARE wave-based friction velocity match the shear, shape, and magnitude of lidar observations better than when using the COARE wind-based friction velocity
How Do Young Adults with Drug Use Disorder (DUD) Utilize Treatment? Exploring and Examining Lived Experiences towards Treatment Completion in Indonesia
No full textIn Indonesia which has the highest rate of drug addiction in Southeast Asia, there is currently little knowledge about how young adults perceive the barriers faced when completing treatment or how treatment providers\u27 perspectives influence their treatment completion. Understanding and identifying barriers to treatment completion is essential to making drug treatment more effective. The purpose of this study is to explore the perspectives and live experiences of young adults with DUD and their addiction counselors to develop a deeper understanding of treatment needs. This study interviewed 33 clients and 15 counselors from the rehabilitation center of the Badan Nasional Narkotika (BNN) in Indonesia. Semi-structured interviews were recorded and transcribed verbatim, imported into N-VIVO software for coding, and then grouped and organized into relevant categories. Clients emphasized categories of family, social stigma, spiritual needs, personal values and attitudes, treatment access and drug policies as the most significant factors helping or hindering treatment success. Counselors emphasized the importance of staff attitudes, access to treatment, staffing and staff training, government policies and professional development. The findings suggest ways that changes to current policies and the addition of innovative and creative outreach may be implemented to help youth in Indonesia post-rehabilitation as well as those who have never attempted to enroll in treatment services or were unsuccessful in enrolling in treatment services. Proposals include culturally sensitive practices, accessible outreach materials, revisions to Indonesia’s drug rehabilitation quota program and preventative educational initiatives to address young adults’ lack of knowledge and attitudes that encourage experimenting with drugs
The Large-Scale Flow Dynamics and Controls on Recurving Eastern North Pacific Tropical Cyclones
No full textWhile eastern North Pacific (EPAC) tropical cyclones (TCs) most often move westward over open water, a subset deviates from this typical path, recurving toward higher latitudes or making landfall along the North American coastline. Because such events are relatively rare, they have received less attention, despite their significant contributions to rainfall and wildfire activity across the southwestern United States. This dissertation identifies and characterizes the spatial variability of EPAC TC tracks, analyzes the synoptic environments associated with TC recurvature near the North American coast, presents a detailed case study of two recurving EPAC TCs from late September to early October 2018, and constructs a climatology of upper-level interaction strength and its relationship to the relatively uncommon extratropical transition (ET) pathways observed in the basin.
EPAC TCs from 1949–2022 were grouped into four track types using k-means clustering, enabling comparison of recurving and non-recurving cases within their respective clusters. Two of the four clusters were identified as most relevant for subsequent analyses of recurvature. Composite analyses for EPAC TCs from 1979–2022 were then used to diagnose the large-scale and local dynamics associated with recurvature, employing both storm-centered and recurvature-relative frameworks to capture the evolution of environmental fields throughout the normalized TC lifecycle. Results show that recurving EPAC TCs are typically associated with long-lived upstream Rossby wave trains and enhanced dual Rossby wave breaking anomalies, which together produce a highly amplified North Pacific trough–ridge pattern. These environments can also develop under regimes characterized by local subtropical ridge amplification and an increasingly wavy upstream flow.
A detailed case study of an anomalously active sequence of recurving TCs across the western North Pacific (WPAC) and EPAC basins during late September–early October 2018 is presented. Using ERA5 reanalysis, diagnostics of layer-averaged potential vorticity advection by the irrotational wind (PVadv) and Q-vector divergence quantified TC–trough interactions, while synoptic analyses assessed Rossby wave breaking (RWB) and upper-tropospheric waveguide evolution. The ETs of WPAC TCs Trami and Kong-rey established a dynamically linked, highly amplified large-scale flow that persisted for over two weeks. Successive ETs triggered ridge amplification over the WPAC and EPAC, generated deep central Pacific troughs, and produced downstream cutoff lows that influenced the recurvature and inland decay of subsequent TCs, including Walaka, Rosa, and Sergio. These interactions indicate that coupled ET and RWB processes can sustain an anomalously amplified inter-basin flow regime, influencing precipitation and temperature extremes across North America, and may be modulated by subseasonal variability, including the Madden–Julian Oscillation (MJO).
Upper-level forcing associated with EPAC TC recurvature was systematically quantified using PVadv, while ET was classified using cyclone phase space (CPS) parameters. Composite analyses revealed that strong upper-level interactions, typically occurring for higher-latitude recurving storms embedded within amplified trough–ridge patterns, promote rapid structural asymmetrization and transition to cold-core, with enhanced divergent outflow and poleward moisture transport producing extended precipitation anomalies over North America. Lower-latitude recurving storms can undergo ET when favorably phased with an upper-level trough, highlighting the critical role of trough–storm alignment and thermodynamic structure. Comparisons of variables associated with ET and precipitation anomalies further contextualize the environmental conditions conducive to transition, establishing a physically grounded framework linking upper-level dynamics, storm structure, and downstream hydrometeorological impacts