VictorJuiz/thesis huggingface dataset:
Near-inertial waves in oceanic fronts [electronic resource] : from generation to dissipation

The question of how wind-forced near-inertial motions interact with strongly baroclinic upper-ocean fronts, like those occurring in wintertime western boundary current extension zones, is investigated theoretically, computationally and observationally. The investigation considers the full life cycle of near-inertial waves in this context, from generation to dissipation. Winds with frequency content near the local Coriolis frequency accelerate near-inertial motions in the ocean boundary layer. Due to the strong and variable vertical vorticity of the frontal jet, the dominant frequency of the near-inertial motion varies across the front and the horizontal length scales of the oscillations shrink with time. As a result, wave energy radiates into the upper thermocline with an e-folding time scale similar to an inertial period. In the thermocline, wave propagation is substantially modified by the presence of the background flow. Wave energy tends to pile up at turning points and slantwise critical layers where the wave group velocity goes to zero and, in the latter case, the ray tube area also goes to zero. In these regions, numerical models and observations exhibit strong, banded, and coherent wave shear nearly parallel to isopycnals oscillating at a frequency near the local minimum permitted frequency of inertia-gravity waves, which may be less than the local Coriolis frequency. Furthermore, these amplified waves are associated with banded regions of low and in some cases sub-critical Richardson numbers leading to enhanced dissipation and mixing in the thermocline. Three key results emerge from this narrative: 1) Although the dynamics of inertia-gravity wave propagation in strong fronts is qualitatively different from propagation in the absence of a background flow, the essential physics of near-inertial wave propagation can still be characterized by two conservation laws: i) conservation of absolute momentum, and ii) conservation of buoyancy. 2) The strong and variable vertical vorticity of the front facilitates energy exchange between the wave motions and the geostrophic frontal jet. In fact, a large ensemble of wind-generated near-inertial waves always extracts energy from the geostrophic flow on average. With the addition of wave dissipation, the energy loss from the geostrophic flow becomes permanent. 3) The ubiquitous banded near-inertial shear observed in the upper thermocline of the north wall front in the winter Gulf Stream over the course of a month-long observational campaign in the winter of 2012, leads to the conclusion that western boundary current fronts are undersea "surf-zones" for near-inertial waves. That is, in the presence of strong and persistent atmospheric forcing, they are regions of persistently amplified wave shear, strong vertical velocities, enhanced turbulence and mixing.

Keywords: Environmental Earth System Science.
Advisor: Thomas Leif N. primary advisor. Thesis advisor
Arrigo Kevin R. advisor. Thesis advisor
Fringer Oliver B. (Oliver Bartlett) advisor. Thesis advisor
Network and web security modeling and analysis [electronic resource]

Security modeling and analysis centers on identifying the interaction between three aspects of a system: normal operational behavior, including any security defenses, the system adversary's power, and the properties that constitute system security. In finite-state model-checking, the interactions between system operations and attacker powers can be exhaustively enumerated by an automated tool, allowing security violations to be automatically detected. We use security modeling to analyze the security of DNSSEC network protocol and to design and verify App Isolation, a Web-security technique employing browser-based isolation of web-applications to prevent common attacks such as Cross-Site Scripting, Cross-Site Request Forgery, Session Fixation, etc. We model three levels of the DNSSEC hierarchy using the Murphi model checker and discover a few weaknesses, surrounding the NSEC3 opt-out mechanism and temporal consistency of DNS records, that may allow attackers to inject their records into a DNSSEC system. App Isolation relies on two principles, State Isolation and Entry-point restriction, to provide browser-based protection for high-security web applications, such as online banking. Our modeling, done in the Alloy language, demonstrates that these two principals provided together can effectively mitigate reflected XSS, CSRF, click-jacking, session fixation, and rendering engine hijacking, and that without each other each principal alone cannot prevent attacks from a hijacked rendering engine. In addition to formal checking, we discuss our evaluation of the effectiveness of several commercial black-box Web application vulnerability scanners at detecting common Web application vulnerabilities, both on a synthetic testbed and a set of 27 Web applications built by 9 freelancers and 18 startups. We find that, as a class, black-box web application vulnerability scanners can detect textbook reflected XSS and type-1 SQL-injection vulnerabilities at about 50% success rate, but are ineffective at detected stored vulnerabilities and interpreting client-side languages such as Javascript, both for simple crawling and for vulnerability detection.

Keywords: Electrical Engineering.
Advisor: Boneh Dan
Mitchell John C. primary advisor. Thesis advisor
Dill David L.
Network function extensibility in software at round-trip timescales [electronic resource]

Networking researchers and practitioners strive for flexible network control to rapidly introduce new functionality into production networks. In this dissertation, we present a practical approach to rapidly introduce new dataplane functionality into privately owned networks such as data centers, in which both end-hosts and the network are under one administrative entity. At a high level, our approach partitions the functionality between end-hosts and the network. This separation of concerns between end-hosts and the network is useful in practice: It decouples network function extensibility from network hardware extensibility. End-hosts can deploy new network functions without having to wait for new network hardware. In the first part of the dissertation, we present a new interface between end-hosts and the network. End-hosts embed tiny programs into packets that actively query and manip- ulate a network's internal state, and execute directly in the dataplane. We then show how this single "tiny packet program" (TPP) interface gives end-hosts unprecedented visibility into network state, enabling them to work with the network with low-latency and at high throughput to realize many desirable dataplane tasks such as congestion control, measure- ment, and troubleshooting. This design requires changes both at network switches and at end-hosts, but leverages what each component does best: (a) the ASIC forwards packets at line rate, while executing a tiny program embedded within the packet (if any); and (b) end- hosts send a sequence of TPPs to query network state, and perform arbitary computation on the queried state in software. We then show that the TPP design is feasible in hardware, at a reasonable cost. We also show that TPPs are useful by implementing three different research proposals. We also outline seven other research projects that can be implemented using TPPs, highlighting that TPPs are generic, and present an architecture in which they can be made secure. In the second and third parts of this dissertation, we show how limited visibility at the access links between the network and end-hosts is sufficient to implement a quality of ser- vice network function completely at end-hosts, without requiring any changes to network switches.

Advisor: Mazières David (David Folkman)
McKeown Nick advisor. Thesis advisor
Prabhakar Balaji
Network interface design for low latency datacenter applications [electronic resource]

Ethernet network interfaces in commodity systems are designed with a focus on achieving high bandwidth at low CPU overheads, while often sacrificing latency. This approach is appropriate when software request processing is measured in milliseconds and the interface latency is not an issue. However, recent low latency software efforts in datacenters, such as memcached and RAMCloud, have lowered the software times into the microsecond range. Therefore, the network interface has been promoted into a significant contributor to the overall latency. This thesis presents NIQ: a low latency network interface design optimized for request-response based datacenter applications. NIQ features separate small and large packet interfaces that efficiently send and receive packets with a minimum number of PCIe transitions. A NIQ prototype is built on an FPGA development platform to facilitate the design space exploration and evaluation. The results demonstrate that the proposed interface is capable of 4.7 us application round trip latencies without meaningful negative impact on CPU power or throughput. The NIQ interface supports one independent transmit and receive queue per CPU core, thus enabling datacenter applications reaching higher throughput through parallelization. This thesis argues that multi-threaded multi-queue designs are prone to high latency variance which manifests itself as high tail latency. To combat the high tail latency and further improve the average latency, this thesis presents NeRD: a mechanism for dispatching arriving network requests to the appropriate processor core. NeRD is an application inspired hardware module that combined with NIQ network interface achieves low average and low tail latencies. The NIQ+NeRD combination achieves tail latency improvements by efficiently load balancing requests across processor cores. FPGA prototype results show that under the request load of 80% of maximum, the 95th percentile latency stays within a factor of two of the median latency. Additionally, NeRD provides hardware support for quickly scaling between one and multiple cores, depending on the current request load. The NIQ and NeRD prototype's latency results were found to be heavily dependent on the CPU's power management settings. To quantify the effects of modern power management, an investigation of latency-power tradeoffs was conducted. In particular, this thesis explores the tradeoffs between using interrupts and polling as notification mechanisms.

Keywords: Electrical Engineering.
Advisor: Rosenblum Mendel primary advisor. Thesis advisor
Kozyrakis Christoforos
Ousterhout John K. advisor. Thesis advisor
Neural basis of social status transition in Astatotilapia burtoni [electronic resource]

Animals display remarkable range in social behavior, despite high conservation of many neurochemicals and their receptors. Even within a species, the social behavior of an individual can vary dramatically depending on environmental and internal cues. What neural mechanisms participate in this flexibility? To investigate the neural basis of social phenotypic plasticity within a species, I used the African cichlid fish, Astatotilapia burtoni, in which adult males can reversibly transition between two strikingly different social phenotypes: subordinate and dominant. In the wild and in the laboratory, these phenotypic transitions predictably follow changes in the social environment. The speed of the behavioral transition from subordinate to dominant outpaces the development of known endocrine and neuroanatomical differences between the two phenotypes. Therefore, I hypothesized that neuromodulation by neuropeptides plays a role in this transition. To test this hypothesis, I took two approaches. First, I focused on a candidate neuropeptide, kisspeptin, a major regulator of reproductive physiology in mammals that has long been suspected to have pleiotropic functions in the brain, and showed a novel role for kisspeptin as a modulator of male social behavior. Second, I used a proxy of neural activity to guide the identification of cell populations responsive to social environment change, and show a behavioral role for the bony fish homolog of oxytocin, isotocin. Both studies indicate a role for neuropeptides in A. burtoni behavioral plasticity. Both studies also suggest my initial question does not have a single answer: neuropeptide modulation is a widespread mechanism for behavioral flexibility, but different variations on this theme have evolved across different lineages. To advance our future investigations with A. burtoni, I also developed successful transgenesis of this species. A. burtoni is not only a behavioral neuroscience model, but is also a member of a vertebrate lineage used to study evolutionary diversification. I discuss how my contribution to the understanding of the proximate mechanisms underlying social behavior within a single species and technical contribution of transgenesis opens future avenues for investigating the neural basis of social behavior variation across species.

Keywords: Biology.
Advisor: Fernald Russell D. primary advisor. Thesis advisor
Clandinin Thomas R. (Thomas Robert)
Parker Karen J.
Neural dynamics of reaching following incorrect, absent, or last-moment preparation [electronic resource]

Moving is thought to require separate preparation and execution steps. While preparing, neural activity in primary motor and dorsal premotor cortices achieves a state specific to an upcoming action, but movements are not performed until the execution phase. In this work, we investigated the interactions between motor preparation and motor execution. We first investigated whether the preparatory state (more precisely, prepare-and-hold state) is required for movement execution using two complementary experiments. We compared monkeys' neural activity during delayed and non-delayed reaches, and in a delayed reaching task in which the target switched locations on a small percentage of trials. Neural population activity bypassed the prepare-and-hold state both in the absence of a delay and if the wrong reach was prepared. However, the initial neural response to the target was similar across behavioral conditions, regardless of whether there was a delay period. This means that there are consistent neural preparatory steps which are performed prior to movement even in the absence of a delay. This suggests that the prepare-and-hold state can be bypassed if needed, but there is a short-latency preparatory step which is performed prior to movement even without a delay. We suggest that this preparatory step may be best understood as a dynamical process rather than simply a particular, static neural state. We next examined whether motor preparation and motor generation can be run in parallel. We instructed monkeys to reach to a particular target, and occasionally switched that target to a new location shortly before the monkey began initiating his reach. We found that the amount of time required to change a reach goal tends to remain constant regardless of whether that computation is being performed online (during the execution of the initially-cued reach), or offline (prior to reach initiation). Examining neural activity during this task, we found that neural activity following a switch tends to explore dimensions which are not well-represented during the course of normal reaching. Furthermore, reaches can be initiated correctly even if their neural activity has not fully recovered from the switch, as long as neural activity in dimensions which are relevant to movement output has been corrected. This work reveals a potentially important way in which neural activity can simultaneously prepare one reach while executing another, again underscoring the view that motor preparation is itself a dynamical process which is independent of but complimentary to movement generation.

Advisor: Shenoy Krishna V. (Krishna Vaughn) primary advisor. Thesis advisor
Ganguli Surya
Newsome William T. advisor. Thesis advisor
Raymond Jennifer L. advisor. Thesis advisor
The neural mechanisms of decision processes underlying memory retrieval [electronic resource]

Episodic memory retrieval can be construed as a set of decision processes in which retrieved event information guides a categorical response. Successful retrieval requires the establishment of cortical representations of event features during stimulus encoding, and the cortical reinstatement of these representations at retrieval. Additionally, retrieval requires neural mechanisms, often thought to be localized in lateral frontal and parietal cortex, to transform these representations into a decision variable that guides action selection. Finally, mnemonic decisions ultimately require the implementation of a motor response. The research described in this dissertation examines several aspects of the neural mechanisms that support mnemonic decision making, with three experiments. The first experiment examines how the strength of categorical representations during initial encoding and during retrieval influences behavioral outcomes of the mnemonic decision. The second experiment employs matched perceptual and memory tasks, to assess commonalities between the neural substrates of mnemonic and perceptual decision making. The final experiment examines retrieval acts made with oculomotor and manual responses, to assess whether lateral parietal activity associated with memory retrieval is specific to manual responses or general across response modalities. Collectively, these studies provide an account for how neural representations, decision processes, and response functions work together to support memory retrieval.

Keywords: Psychology.
Advisor: Wagner Anthony David primary advisor. Thesis advisor
McClelland James L. advisor. Thesis advisor
Norcia Anthony Matthew advisor. Thesis advisor
Neuronal MHCI function in developmental critical periods and neurological disorders [electronic resource]

Neuronal circuits dynamically strengthen or weaken through experience-regulated processes during developmental windows of synaptic plasticity. In this thesis, I test the hypothesis that two specific Major Histocompatibility Complex Class I (MHCI) genes, H2-Kb and H2-Db, restrict cortical plasticity during both developmental and adult neurological disorders. Mice lacking H2-Kb and H2-Db (KbDb KOs) have enhanced ocular dominance plasticity and excessive cortical connectivity. In a model of the autism-spectrum disorder Rett Syndrome, developmental ocular dominance plasticity is impaired, and H2-Db expression is elevated. In an adult model of stroke called middle cerebral artery occlusion, H2-Kb and H2-Db expression is elevated in the damaged hemisphere, and expression and downstream signaling of the MHCI receptor PirB are increased. KbDb and PirB KO mice have smaller infarcted regions and better motor recovery, and PirB KOs have enhanced circuit remapping in the corticospinal tract, which could contribute to improved motor function. Together, results suggest that H2-Kb and H2-Db function to constrain plasticity in juvenile and adult cerebral cortex. Moreover, an over-expression of these two MHCIs may contribute to Rett Syndrome and impede recovery following stroke. H2-Kb and H2-Db and their receptor PirB therefore may represent important therapeutic targets for disorders typified by abnormal synaptic plasticity.

Advisor: Shatz Carla J. primary advisor. Thesis advisor
Hestrin Shaul
McConnell Susan K. advisor. Thesis advisor
Raymond Jennifer L. advisor. Thesis advisor
New histories for a new state [electronic resource] : the historical narratives of textbooks and students in Northern Ireland

The three articles of this dissertation explore how the past is represented in history classrooms in Northern Ireland, and the historical understandings students develop as a result. Taken together, these articles help us to better understand the complicated position that narrative holds in the history classroom. When history first appeared on the school timetable in the UK, as elsewhere, its purpose was to communicate a shared national story to new generations. In recent decades, the centrality of the nation in historiography and history education came under attack, both from historians who wrote outside the national mode, and from educationists who argued for greater attention in schools to history as a form of knowledge rather than a body of content. These shifts appear in the changing content and structure of history textbooks in Northern Ireland, which abandon traditional narrative accounts of history in favor of inquiries into significant and controversial events. Students, for their part, also struggle to construct historical accounts that link events together into a coherent whole, and when they do often rely on sectarian templates encountered outside the school. Young people in Northern Ireland encounter multiple and competing versions of the national past. The challenge for history instruction is to provide students with the tools to adjudicate among these competing claims, and the skills to construct coherent and persuasive narratives that explain historical change.

Keywords: Education.
Advisor: Ramirez Francisco O. primary advisor. Thesis advisor
Labaree David F.
Wineburg Samuel S. advisor. Thesis advisor
A new materialist archaeology of antimarkets, power and capitalist effects in colonial Guatemala [electronic resource]

This dissertation develops an approach to the archaeology of capitalism within Spanish colonial contexts in Guatemala through the archaeology of San Pedro Aguacatepeque, a multicomponent Kaqchikel Maya community occupied from at least 900-1800 AD. I draw on new materialist and postcolonial theories to craft an archaeology of colonial capitalism that challenges classical trait-based definitions of capitalism which have proven insufficient in studying the Guatemalan colonial context. Working from Braudel and DeLanda's conception of capitalism as a system of "antimarkets", defined as power-manipulated markets, rather than the "free" markets of neoliberal models of capitalism, I attempt to move beyond the baggage-laden and uniquely 19th and 20th century definitions of capitalism that downplay how unequal power affords and sustains the practices and institutions iconic of capitalism. I do so by reorienting analyses toward the unequal power dynamics that undergird the changes in economic engagements and daily practice routinely attributed to the disembodied, abstract influence of Capitalism rather than the human actors and material configurations that catalyze these changes to the benefit of some and the detriment of others. Ceramic and lithic elemental characterization and provenance analysis, documentary research, and palynological analysis provide the bulk of data used to track changes in production and consumption at Aguacatepeque. From this data, I draw out the specific genealogy of the development and reconfiguration of production and consumption practices (namely, increasing market dependence and specialization of production), the antimarkets that afforded and sustained them, and their subsequent effects on practice and experience at Aguacatepeque. In short, this dissertation lays a groundwork for moving beyond static, global north biased models of capitalism and its effects, towards identifying the "actual details of economic history" that better explain the character and direction of change in Spanish colonial Maya economic practices.

Keywords: Anthropology.
Advisor: Voss Barbara L.
Hodder Ian advisor. Thesis advisor
Joyce Rosemary A.
Wilcox Michael V. (Michael Vincent)