VictorJuiz/thesis huggingface dataset:
Mobility and Social Organization on the Ancient Anatolian Black Sea Coast: An Archaeological, Spatial and Isotopic Investigation of the Cemetery at İkiztepe, Turkey

This thesis undertakes a complete reinvestigation of the archaeology of a large Early Bronze Age cemetery at İkiztepe in northern Turkey, by utilizing oxygen and strontium isotope analysis of human remains in combination with spatial and biodistance analysis and various dating techniques to identify potential immigrants to the site and to examine larger issues of residential mobility and social organization. The occupation of the Northern Anatolian site of İkiztepe is traditionally assigned to the Late Chalcolithic and Early Bronze Ages. However, the site’s chronological framework has been challenged in recent years. These chronological issues have been addressed by applying fluoride and AMS radiocarbon dating to the skeletal remains from the İkiztepe cemetery, to develop an absolute and relative chronology for the burials. These results have shown that the cemetery dates at least a millennium earlier than previously supposed. Oxygen and strontium isotope analyses allowed the identification of individuals whose bone chemistry suggests that they were possible long distance immigrants to the site of İkiztepe, as well as suggesting the existence of a group of mobile individuals who may represent a transhumant segment of the İkiztepe population. Spatial and biodistance analyses suggest that principles of cemetery organization in this period were highly complex. Immigrant individuals and nomadic or semi-nomadic segments of the population do not appear to have been distinguished in any observable way from their sedentary local counterparts, displaying similar burial types, grave goods and spatial locations. Furthermore, burial within the İkiztepe cemetery does not appear to have been kin structured. These results suggest that assumptions about funerary practices as important indicators of cultural identity and lineage affiliation may represent an over-simplification of complex patterns of interaction and integration among and within populations and cultural groups.

Keywords: Anatolia
isotope
strontium
oxygen
Bronze Age
spatial analysis
Chalcolithic
fluoride dating
cemetery
biodistance
Advisor: Harrison, Timothy P.
Regulation of MDM2 and the p53 Family by the NEDD8 Pathway

NEDD8 is an ubiquitin-like protein sharing approximately 60% amino acid identity with ubiquitin and has biological roles in cell cycle progression, viability and development. Recently, a number of oncoproteins and tumor suppressors have been identified as NEDD8 substrates, including MDM2 and p53. MDM2 is an oncogenic E3 ligase that promotes NEDD8 modification and ubiquitin-mediated degradation of the tumor suppressor transcription factor, p53. Cellular stresses such as DNA damage lead to p53 activation due, in part, to MDM2 destabilization by mechanisms that are not completely understood. Studies in mice demonstrate the biological role of MDM2 is to negatively regulate p53 function, however, when overexpressed or amplified, MDM2 has p53-independent oncogenic functions presumably due to the regulation of additional substrates. One such substrate may be the p53 family member, p73. p73 exists as multiple isoforms and accumulating evidence suggests that the N-terminal isoforms dictate its role in tumorigenesis. The full-length pro-apoptotic TAp73 isoforms are induced by chemotherapies and are able to transactivate p53-target genes to initiate cell cycle arrest and apoptosis. Conversely, the N-terminally truncated ΔNp73 isoforms lack the transactivation domain (TAD) and consequently act as dominant-negative inhibitors for all TA isoforms of the p53 family, and are overexpressed in human tumors. Here, we report that TAp73, but not ΔNp73, is covalently modified by NEDD8 in an MDM2-dependent manner, attenuating its transactivation function and promoting cytoplasmic localization of neddylated TAp73. These results provide the first evidence of a covalent post-translational modification exclusively targeting the TA isoforms of p73, and identify the MDM2-TAp73 interaction as a promising therapeutic target. We also demonstrate that the stability of MDM2 is regulated by the NEDD8 pathway and identify NEDP1 as a chemotherapy-induced isopeptidase that deneddylates MDM2, resulting in MDM2 destabilization, concomitant with p53 activation. This study identifies a novel p53 activating mechanism in response to chemotherapy. In conclusion, the work presented herein has helped characterize the function of NEDD8 modification of MDM2 and the p53 family, and identify mechanisms by which MDM2 and the NEDD8 pathway may be targeted in the development of anti-cancer therapeutics.

Advisor: Irwin, Meredith
Ohh, Michael
Essays in Empirical Finance

This dissertation contains two essays in empirical finance. The first essay studies the mutual fund industry, and the second essay looks into the stock market. Both studies provide insights in the underlying mechanism of some asset return patterns identified from the data currently available. The first essay investigates the sources of a recently identified performance pattern in mutual funds. Specifically, actively managed mutual funds, in general, underperform a passive benchmark; however, some recent studies find they, in fact, outperform the benchmark in bad economic states. I examine whether a state dependent risk shifting behavior of mutual fund managers contributes to this performance difference across states, and find supportive evidence. As shown in prior studies, the risk shifting behavior is motivated by a non-linear flow-performance relationship. Using a piece-wise linear regression, I demonstrate that the non-linearity exists mainly in good states; whereas in bad states, the flow-performance relationship is close to linear. Thus, non-zero risk shifting incentives are only expected in good states. I empirically measure these incentives in good states, and show that managers do react to the ``gambling'' (i.e., positive) incentives. In addition, higher ``gambling'' incentives are found to be associated with lower fund performance. The second essay, based on joint work with Hai Lu and Kevin Wang, examines how stock price shocks in the absence of public announcement of firm specific news affect future stock returns. We find that both large short term price drops and hikes are followed by negative abnormal returns over the subsequent twelve months. The pattern of asymmetric drifts, the return continuation for negative shocks versus the return reversal for positive shocks, is puzzling. We explore whether investor disagreement can explain the puzzle and find that the evidence is consistent with predictions of disagreement theory. Moreover, price shocks with public news disclosures are followed by weaker drifts, suggesting that reduction of information asymmetry from public disclosures mitigates disagreement-induced overpricing.

Keywords: mutual fund
risk shifting
investor disagreement
Advisor: Kan, Raymond
The Timeliness of Accounting Write-downs by U.S. Financial Institutions during the Financial Crisis of 2007-2008

This study examines the timeliness of write-downs taken by U.S. financial institutions during the financial crisis of 2007-2008. The timeliness of write-downs is measured by benchmarking the quarterly accounting write-down schedule with the devaluation schedule implied by credit indices such as the ABX. The results show that accounting write-downs are less timely than the devaluations implied by credit indices. In a cross-sectional analysis of the determinants of the timeliness of write-downs, I document that higher corporate governance quality is positively related to timelier write-downs. Furthermore, I observe that regulatory investigations and litigation pressure are positively related to the timeliness of write-downs, whereas the write-downs by firms with more complex exposures, higher financial leverage, and tighter regulatory constraints are less timely. In addition, I control for numerous exposure-specific characteristics and document that less risky exposures, and exposures that were affected later during the financial crisis, were written down later. Regarding the consequences of timeliness, this study finds that the exposure to risky assets is reflected faster in stock returns for firms with timelier write-downs.

Keywords: Write-downs
Timeliness
Financial Crisis
Credit indices
Advisor: Callen, Jeffrey
Richardson, Gordon
Living in Two Worlds: Intentional Personal Development of Autistic Individuals

Despite an increased interest in autism over the last decades, little research exists about life outcomes of autistic adults. The earliest follow-up studies of autistic individuals suggested that self- understanding and conscious efforts to change could be crucial factors in successfully reaching good life outcomes. However, these initial suggestions have not been further investigated. Therefore, this exploratory qualitative study examined the lives of eight highfunctioning autistic adults aged 25 to 63, from their own perspectives, through in-depth, semistructured interviews, to consider the relation of self-understanding and conscious efforts to change—in this study referred to as intentional personal development—to their life outcomes. All participants demonstrated a level of self-understanding beyond what would be predicted by current theoretical models of autism. Their self-understanding was assessed through participants’ self-definitions, meaning-making of life experiences, and understanding of emotions. In their self-definitions, the participants emphasized their abilities and personality characteristics, rather than their disabilities. For their self-defining memories, as indicators of their meaning making of life experiences, most participants chose positive experiences related to their personal development. Their autobiographical accounts revealed that most participants possess a large iii repertoire of emotion words, supporting an understanding of emotions. When a good life outcome is defined traditionally—as being employed, living independently, and having social relationships—this study, contrary to expectations, did not provide overwhelming evidence for the significant role of intentional personal development in achieving this. However, when a good life outcome is defined in terms of achieving personal excellence, then the study did provide confirmation of intentionality as important to attaining good life outcomes. This study therefore suggests that traditional life outcome measures are inadequate for assessing the life outcomes of autistic individuals because such measures do not take into account the individuals’ own sense of satisfaction with themselves and with their lives.

Keywords: Autism
High-functioning autism
Asperger syndrome
Adults
Life outcomes
Life-experiences
Self-understanding
Intentional personal development
Future orientation
Meaning making
Emotional understanding
Positive psychology
Strengths and Weaknesses
First-person perspective
Life satisfaction
Advisor: Ferrari, Michel
Branch Plate-to-circular Hollow Structural Section Connections

Although branch plate connections with circular hollow section (CHS) members are simple to fabricate and cost-effective, they are generally very flexible under low load application resulting in the limit states design resistance being governed by an imposed deformation limit. Restricting the ultimate capacity of a branch plate connection by a deformation limit results in the inherent strength of the CHS member being under-utilized, highlighting the need to develop connection stiffening methods. Two methods to stiffen branch plate-to-CHS connections are examined: a through plate connection and a grout-filled CHS branch plate connection. Further, the current design guidelines of various plate-to-CHS connection types are reexamined including the effect of chord axial stress and chord length on connection behaviour. Finally, the behaviour of connections with non-orthogonal or skew plate orientation, which has not previously been examined, was studied in depth.The behaviour of these uniplanar connection types under quasi-static axial loading was studied through 16 large-scale laboratory experiments and 682 numerical finite element analyses, as well as an extensive review of all previous international experimental and numerical findings. The extensive study formed the basis for a complete set of proposed design guidelines and provided insight into plate-to-CHS connection behaviour. For all plate-to-CHS connection types, the plate thickness is shown to effect connection capacity, though previously this was thought not to have significant impact on connection behaviour. The existing ideology of using the same design recommendations for tension- and compression-loaded connections, which was developed from compression results, under-utilizes an inherent increase in capacity provided by a connection primarily loaded in tension. As such, the recommended design guidelines split the two load senses into separate expressions that reflect the difference in behaviour. Stiffened through plate connection behaviour was determined to be the summation of branch plate behaviour in compression and tension, leading to a significant increase in capacity and identical behaviour regardless of branch load sense. The skewed branch plate connection behaviour was found to relate directly to the established behaviour of longitudinal and transverse plate connections. A design function was developed that interpolates the capacities of intermediate angles by using the proposed design recommendations of the two extreme connection types. Finally, the examination of chord axial stress and chord length for plate-to-CHS connections yielded results similar to previous international studies on CHS-to-CHS connections. The effect of chord length, however, has wide-reaching implications as to how experimental and numerical FE research programs are developed.

Keywords: steel structures
hollow structural sections
connections
finite element analysis
structural engineering
welded
circular hollow sections
static loading
tubes
branch plate
stiffened connections
grout filled
Advisor: Packer, Jeffrey A.
The Physiological Ecology of C3-C4 Intermediate Eudicots in Warm Environments

The C3 photosynthetic pathway uses light energy to reduce CO2 to carbohydrates and other organic compounds and is a central component of biological metabolism. In C3 photosynthesis, CO2 assimilation is catalyzed by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), which reacts with both CO2 and O2. While competitive inhibition of CO2 assimilation by oxygen is suppressed at high CO2 concentrations, O2 inhibition is substantial when CO2 concentration is low and O2 concentration is high; this inhibition is amplified by high temperature and aridity (Sage 2004). Atmospheric CO2 concentration dropped below saturating levels 25-30 million years ago (Tipple & Pagani 2007), and the C4 photosynthetic pathway is hypothesized to have first evolved in warm, low latitude environments around this time (Christin et al. 2008a). The primary feature of C4 photosynthesis is suppression of O2 inhibition through concentration of CO2 around Rubisco. This pathway is estimated to have evolved almost 50 times across 19 angiosperm families (Muhaidat et al. 2007), a remarkable example of evolutionary convergence. In several C4 lineages, there are species with photosynthetic traits that are intermediate between the C3 and C4 states, known as C3-C4 intermediates. In two eudicot genera, Flaveria (Asteraceae) and Alternanthera (Amaranthaceae), there is evidence that these species represented an intermediate state in the evolution of the C4 pathway (McKown et al. 2005; Sanchez-del Pino 2009). The purpose of this thesis is to ascertain the specific benefits to plant carbon balance and resource-use efficiencies of the C3-C4 pathway relative to C3 species, particularly at low CO2 concentrations and high temperatures, factors which are thought to have been important in selecting for C3-C4 traits (Ehleringer et al. 1991). This will provide information on the particular advantages of the C3-C4 pathway in warm, often arid environments and how these advantages may have been important in advancing the initial stages of C4 evolution in eudicots. This thesis addresses the physiological intermediacy of previously uncharacterized C3-C4 species of Heliotropium (Boraginaceae); the water- and nitrogen-use efficiencies of C3-C4 species of Flaveria; and the photosynthetic performance and acclimation of C3, C4 and C3-C4 species of Heliotropium, Flaveria and Alternanthera grown at low and current ambient CO2 levels and high temperature.

Keywords: C4 photosynthesis
ecophysiology
Advisor: Sage, Rowan F.
Cryptography: Leakage Resilience, Black Box Separations, and Credential-free Key Exchange

We study several basic problems in cryptography: Leakage resilient cryptography: cryptographic schemes are often broken through side-channel attacks on the devices that run them. Such attacks typically involve an adversary that is within short distance from the device, and is able to measure various physical characteristics of the device such as power consumption, timing, heat, and sound emanation. We show how to immunize any cryptographic functionality against arbitrary side-channel attacks using the recently achieved fully homomorphic encryption, and a single piece of secure hardware that samples from a public distribution. Our secure hardware never touches any secret information (such as a private key) and is testable in the sense that its inputs are not influenced by user or adversarial inputs. Credential-free key exchange and sessions: One of the most basic tasks in cryptography is to allow two parties that are connected by a completely insecure channel to communicate securely. Typically, the first step towards achieving this is an exchange of a session key. Such an exchange normally requires an infrastructure, where, for example, public keys of users are stored, and can be securely retrieved. However, often such an infrastructure does not exist, or is too costly to maintain. In such a setting an adversary can always be the Man-In-The-Middle and intercept all communications. However, we argue that a meaningful level of security can still be achieved. We present a definition of secure key exchange in a setting without any infrastructure, and describe a protocol that achieves that type of security. The idea is that an adversary should either know nothing about the session key produced by the protocol, or be forced to participate in two independent instances of the protocol Black-box separations: A complementary aspect of cryptographic research is the study of the limits of cryptographic assumptions. Basing constructions on weaker assumptions gives us more confidence in their security. We therefore wish to find, for each standard cryptographic assumption, what tasks cannot be solved based solely on that assumption. In this thesis we study the limits of a very basic public key primitive: trapdoor permutations (TDPs). We show that TDPs cannot be used to construct Identity Based Encryption or a stronger type of TDPs called correlation secure TDPs. Correlation secure TDPs have been used to build chosen-ciphertext secure public key encryption scheme -- a primitive with a wide range of theoretical and practical applications.

Keywords: Cryptography
Theory
Advisor: Rackoff, Charles
Controlled Human Exposures to Concentrated Ambient Fine Particles and Ozone: Individual and Combined Effects on Cardiorespiratory Outcomes

Epidemiological studies have shown strong and consistent associations between exposure to air pollution and increases in morbidity and mortality. Key air pollutants that have been identified include fine particulate matter (PM) and ozone (O3), both major contributors to smog. However, there is a lack of understanding of the mechanisms involved and the relative contributions of individual pollutants. A controlled human exposure facility was used to carry out inhalation studies of concentrated ambient fine particles (CAP), O3, CAP+O3 and filtered air following a randomized design. Exposures were 2 hrs in duration at rest. Subjects included mild asthmatics and non-asthmatics. This thesis focuses on acute cardiovascular responses including blood pressure (BP), brachial artery reactivity (flow-mediated dilatation [FMD]) and markers of systemic inflammation (blood neutrophils and interleukin [IL]-6). Results showed that for CAP-containing exposures (CAP, CAP+O3) there were small but significant transient increases in diastolic BP (DBP) during exposures. Furthermore, neutrophils and IL-6 increased 1 - 3 hrs after and FMD decreased 20 hrs after CAP-containing exposures. Responses to O3 were smaller, comparable to filtered air. The data suggests that adverse responses were mainly driven by PM. The DBP increase was rapid-developing and quick to dissipate, which points to an autonomic irritant response. The magnitude of the DBP increase was strongly negatively associated with the high frequency component of heart rate variability, suggesting parasympathetic withdrawal as a mechanism. In comparison, IL-6, neutrophil and FMD responses were slower to develop, indicative of an inflammatory mechanism. An intriguing finding was that IL-6 increased 3 hrs after CAP, but not after CAP+O3. Further investigation revealed that exposure to CAP+O3 in some individuals may trigger a reflex inhibition of inspiration, decreasing their tidal volume and inhaled pollutant dose, leading to a reduction in systemic IL-6, a potential protective mechanism. Together the findings support the epidemiological evidence of adverse fine PM health effects. Many questions remain to be answered about the health effects of air pollution including a better understanding of how inhaled pollutants result in cardiovascular effects. It is hoped that the insights gained from this thesis will advance the understanding of air pollution health effects.

Keywords: blood pressure
air pollution
particulate matter
ozone
inflammation
vasculature
controlled human exposures
concentrated ambient particles
vascular dysfunction
heart rate variability
asthma
IL-6
cardiovascular
cardiorespiratory
neutrophils
flow-mediated dilatation
Advisor: Corey, Paul
Silverman, Frances
Abrikosov Lattice Solutions of the Ginzburg-Landau Equations of Superconductivity

In this thesis we study the Ginzburg-Landau equations of superconductivity, which are among the basic nonlinear partial differential equations of Theoretical and Mathematical Physics. These equations also have geometric interest as equations for the section and connection of certain principal bundles and are related to Seiberg-Witten equations used extensively in Differential Geometry. In 1957, Abrokosov suggested that for sufficiently high magnetic fields there exist solutions for which all physical quantities have the periodicity of a lattice, with the magnetic field penetrating the superconductor at the vertices of the lattice (Abrikosov lattice solutions). The corresponding phenomenon was confirmed experimentally and is among the most interesting aspects of superconductivity and is discussed in every book on the subject. In 2003, Abrikosov was awarded the Nobel Prize in Physics for this discovery. Building on the previous results in the subject we prove the existence of such lattices in the case where each lattice cell contains a single quantum of magnetic flux, and in the general case reduce the problem to an n-dimensional problem, where n is the number of quanta of flux. We prove that for Type II superconductors, these solutions are stable, and in the case n = 1, we show that as the external magnetic field approaches the critical value at which superconductivity first appears, the lattice which minimizes the average free energy per lattice cell is the triangular lattice.

Advisor: Sigal, Israel Michael