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2016

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The Role Of The Transcription Machinery In The Remodeling Of The Promoter-Proximal Nucleosomes In Saccharomyces Cerevisiae, Michael Charles Tramantano Dec 2016

The Role Of The Transcription Machinery In The Remodeling Of The Promoter-Proximal Nucleosomes In Saccharomyces Cerevisiae, Michael Charles Tramantano

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Approximately 147 base pairs of DNA wraps almost two turns around a protein core comprised of two copies of each H2A, H2B, H3 and H4 histones to form a nucleosome—the fundamental packaging unit of chromatin. In Saccharomyces cerevisiae, nucleosomes are organized along the genome in a closely spaced and non-random manner. This compact structure blocks assembly of the transcription machinery and thus is refractory to gene expression. Surrounding the promoters of most genes, a wider nucleosome depleted region (NDR), maintained in part by the activities of chromatin remodelers, serves as the platform for assembly of the transcription preinitiation complex (PIC). …

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Stony Brook Press, V. 38, N. 05, Stony Brook University. Stony Brook Press. Dec 2016

Stony Brook Press, V. 38, N. 05, Stony Brook University. Stony Brook Press.

Stony Brook Press

v. 36,n. 4, v.:ill. ; 38 cm (original analog pub.)

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Development And Application Of An Integrated Parallel Platform On Short–Read Sequences Assembly | Development And Application Of An Integrated Parallel Platform On Short–Read Sequences Assembly, Fei He Dec 2016

Development And Application Of An Integrated Parallel Platform On Short–Read Sequences Assembly | Development And Application Of An Integrated Parallel Platform On Short–Read Sequences Assembly, Fei He

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Rapid and automated next generation sequencing (NGS) methods have emerged recently and significantly accelerated the research in biological and medical fields. The high-throughput NGS usually generates billions of shorter reads, which poses great bioinformatics challenges on extracting meaningful information from these massive data, one of which is de novo assembly. At the same time, the fast development of massive parallel processing (MPP) systems presents a substantial opportunity for processing larger datasets. Therefore, using supercomputer innovations on NGS research promises a good strategy; however, this application is not straightforward and requires new algorithms and parallel design for efficient implementations. In this …

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Exploration Of Statistical Learning Strategies And Their Applications On Medical Image Data For Computer-Aided Diagnosis, Yifan Hu Dec 2016

Exploration Of Statistical Learning Strategies And Their Applications On Medical Image Data For Computer-Aided Diagnosis, Yifan Hu

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Machine learning addresses the question of how computer make decisions and predictions automatically through existing experiences and data, which has become an increasingly important topic with the advent of modern data science and automated big data analysis. Several algorithms are widely used in machine learning. However, each classifier, inevitably, has certain inadequacy for which we hope to compensate. To address these issues, this study first introduces the necessary theoretical background and principles for machine learning and those typical classifiers. Based on these classifiers, this paper attempts to (1) use bagging/boosting to improve the simple classifier, and, (2) find some combination …

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Complexity Estimates And Reductions To Discounting For Total And Average-Reward Markov Decision Processes And Stochastic Games, Jefferson Huang Dec 2016

Complexity Estimates And Reductions To Discounting For Total And Average-Reward Markov Decision Processes And Stochastic Games, Jefferson Huang

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Recently there has been a resurgence of interest in the complexity of algorithms for Markov decision processes (MDPs) and stochastic games. Much of this work was inspired by recent groundbreaking results on the complexity of policy iteration algorithms for MDPs under the Blum-Shub-Smale (BSS) model of computation. In particular, for discounted MDPs with a fixed discount factor, Yinyu Ye showed that the number of arithmetic operations needed by two classic variants of policy iteration can be bounded above by a polynomial in the number of state-action pairs only. A natural question is whether a similar complexity estimate exists for the …

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What’S Competence Got To Do With It? The Association Between Romantic Competence And Social Support Behaviors Among Emerging Adult Couples | What’S Competence Got To Do With It? The Association Between Romantic Competence And Social Support Behaviors Among Emerging Adult Couples, Vickie Bhatia Dec 2016

What’S Competence Got To Do With It? The Association Between Romantic Competence And Social Support Behaviors Among Emerging Adult Couples | What’S Competence Got To Do With It? The Association Between Romantic Competence And Social Support Behaviors Among Emerging Adult Couples, Vickie Bhatia

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Research has consistently demonstrated that romantic relationships during emerging adulthood are salient experiences that are important to identity development and set the stage for future intimate relationships. One area of emerging research is on romantic competence, or a set of skills an individual possesses that affect how he/she approaches and negotiates romantic relationships. Although research has begun to examine the association between romantic competence and self-reported relationship behaviors and outcomes, it has not objectively assessed behavioral indicators of competence nor has it examined how romantic competence skills are enacted during couple interactions. The main goal of this dissertation was to …

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Clustering And Classification Methods For Prediction Of The Risk For Developing Disease, Hyejoo Lee Dec 2016

Clustering And Classification Methods For Prediction Of The Risk For Developing Disease, Hyejoo Lee

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The purpose of this study is to develop a statistical model to predict the risk for developing disease. In order to enrich our general understanding of schizophrenia disorder, several clustering techniques are used as a preliminary study. Schizophrenia is a heterogeneous decease with great variability in symptoms, cognition, biology and course of illness. Some of this variability may be explained by latent subgroups that differ in etiology and key features. Individuals with paternal age related schizophrenia (PARS) may represent such a subgroup as evidence suggests a distinct symptom profile. Using K-means and hierarchical clustering on a large sample of schizophrenia …

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Response To Monetary And Social Feedback During Development: Associations With Depressive Symptomatology And Risk, Jennifer Nicole Bress Dec 2016

Response To Monetary And Social Feedback During Development: Associations With Depressive Symptomatology And Risk, Jennifer Nicole Bress

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Depression represents a major public health concern, with particularly harmful effects in children. Existing interventions show relatively low response rates and high relapse rates, and there has been a recent effort to identify biomarkers of depression that may improve interventions and guide the way for novel treatments. One potential biomarker is the neural response to reward. However, existing studies typically focus on monetary reward, which may be less relevant to children and adolescents than social feedback. The current study focused on the feedback negativity (FN), an event-related potential (ERP) typically elicited by monetary feedback, in the context of a novel, …

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Estimation And Detection Of Network Variation In Intraday Stock Market, Shanshan Li Dec 2016

Estimation And Detection Of Network Variation In Intraday Stock Market, Shanshan Li

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

The last few years have witnessed an exponential growth in the collection and analysis of financial market data. Investigating the interactions between the dynamics of the financial system and extracting useful information from these multivariate data streams can help us in improving our understanding of the underlying backbone in the financial market. These massive noisy data sets require the application of suitable and efficient dependency measurements for their analysis in a real-time environment. And that is why network analysis has emerged recently, which is a plausible representation helps interpret the hidden interconnection between the elements in large datasets. However, most …

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Shifting Expectations: Medicine, Nature, And Disability In Pregnancy Texts, Laura Abbasi-Lemmon Dec 2016

Shifting Expectations: Medicine, Nature, And Disability In Pregnancy Texts, Laura Abbasi-Lemmon

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In this thesis, I consider the complex interactions between discourses of medicine, nature, and disability which determine what pregnant women can or cannot, or should or should not do to maintain an acceptable and “healthy†pregnancy that results in a desired, nondisabled child. In this thesis, I employ two interdisciplinary methods, critical discourse analysis and qualitative interviewing and ground my project in feminist disability studies and the concept of reproductive justice. I analyze interviews I conducted with five currently pregnant women from Long Island, New York and three pregnancy manuals, What to Expect When You’re Expecting, Ina May’s Guide to …

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Towards A Critical Awareness Of Worldliness: A.H. Tanpınar’S Huzur, Mahmoud Darwish’S Memory For Forgetfulness, And Virginia Woolf’S Mrs. Dalloway | Towards A Critical Awareness Of Worldliness: A.H. Tanpä±Nar’S Huzur, Mahmoud Darwish’S Memory For Forgetfulness, And Virginia Woolf’S Mrs. Dalloway, Evren Akaltun Dec 2016

Towards A Critical Awareness Of Worldliness: A.H. Tanpınar’S Huzur, Mahmoud Darwish’S Memory For Forgetfulness, And Virginia Woolf’S Mrs. Dalloway | Towards A Critical Awareness Of Worldliness: A.H. Tanpä±Nar’S Huzur, Mahmoud Darwish’S Memory For Forgetfulness, And Virginia Woolf’S Mrs. Dalloway, Evren Akaltun

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

This dissertation examines the ways in which Ahmet Hamdi Tanpınar’s novel, Huzur (1949), Mahmoud Darwish’s prose-poem Memory for Forgetfulness: August, Beirut, 1982 (1995), and Virginia Woolf’s Mrs. Dalloway (1925) manifest a cognitive landscape of crisis in discursive socio-cultural contexts that provide the reader with a critical awareness of worldliness. It argues that the crisis serves as an overarching theme and a structural and thematic principle in determining the conceptual frameworks of the critical thresholds that these works address. The three authors of my study surpass worldless thresholds designated by the crisis by moving through the idea of home, nation, culture, …

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The Graphic Memoir And The Cartoonist's Memory, Alice Claire Burrows Dec 2016

The Graphic Memoir And The Cartoonist's Memory, Alice Claire Burrows

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Graphic memoirs embrace the vibrancy and rich social and artistic history of comics, and the intimacy and imagination of autobiographies. Spanning from Justin Green’s 1972 Binky Brown Meets the Holy Virgin Mary to Riad Sattouf’s 2014 The Arab of the Future, autobiographical comics capture the fragmented, subjective, and visual nature of memory. Reacting against the Comics Code, underground comics introduced the concept of portraying oneself in comics, a practice that achieved mainstream validation in 1992 when Art Spiegelman won the Pulitzer Prize for Maus. Drawing from classic comic strips like Richard Outcault’s The Yellow Kid and comic books like the …

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Weighted-Least-Squares Based Essentially Non-Oscillatory Schemes On Unstructured Meshes, Hongxu Liu Dec 2016

Weighted-Least-Squares Based Essentially Non-Oscillatory Schemes On Unstructured Meshes, Hongxu Liu

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Essentially non-oscillatory schemes and their variants, such as ENO and WENO, are widely used high-order schemes for solving partial differential equations (PDEs), especially hyperbolic conservation laws with piecewise smooth solutions. For structured meshes, these techniques can achieve high order accuracy for smooth functions while being non-oscillatory near discontinuities. For unstructured meshes, which are needed for complex geometries, similar schemes are required but they are much more challenging to design, especially for finite different schemes. We propose a new family of non-oscillatory schemes, called WLS-ENO, in the context of solving hyperbolic conservation laws using both finite volume and finite difference methods …

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Mediating Trans/Nationalism: Japanese ‘Jun’Ai’ (Pure-Love) In Popular Media Representations | Mediating Trans/Nationalism: Japanese €˜Jun’Ai’ (Pure-Love) In Popular Media Representations, I-Te Rita Sung Dec 2016

Mediating Trans/Nationalism: Japanese ‘Jun’Ai’ (Pure-Love) In Popular Media Representations | Mediating Trans/Nationalism: Japanese €˜Jun’Ai’ (Pure-Love) In Popular Media Representations, I-Te Rita Sung

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Since the beginning of the 21st century, the jun’ai (pure-love) genre has flourished in Japan, both in works of popular literature and in film. This phenomenon coincides with a time when the country is seen by the media as being characterized by soshitsukan (sense of loss). In jun’ai films, the heroine is often the object of loss. This theme of loss in jun’ai therefore resonates with the Japanese social context, but this connection has not yet been fully elucidated. In this dissertation, I seek to explain why Japanese women, who are arguably treated as “other†within Japan, embody a transnationalism …

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Task Scheduling In Modern Data Center: Task Placement And Resource Allocation, Li Shi Dec 2016

Task Scheduling In Modern Data Center: Task Placement And Resource Allocation, Li Shi

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In modern data centers, the wide use of virtualization techniques has enabled dynamic resource allocation in the form of virtual machines and virtual networks. With such an ability, scheduling tasks, including both computing tasks and data transfer tasks, comprises (a) placing tasks on servers or network paths and (b) allocating a certain amount of resources to each task. In such a context, minimizing the completion time of the tasks, as a critical goal on many task processing platforms, requires joint consideration of both task placement and resource allocation. While many approaches have been proposed in the area of scheduling tasks …

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Multi-Source Image Integration Towards Solar Forecast, Zhenzhou Peng Dec 2016

Multi-Source Image Integration Towards Solar Forecast, Zhenzhou Peng

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Accurate prediction of solar energy in short-term and mid-term horizons becomes increasingly important for harvesting solar energy and improving its viability in comparing with fossil fuels. Because clouds are the primary cause of large fluctuations in solar radiation, estimating cloud movements and correlating cloud activities and the variability of solar irradiance are the essential components in short-term or mid-term solar predictions and play a vital role in the subsequent mitigation in responding to potential solar power fluctuations. However cloud detecting and tracking is very challenging due to the volatility and complexity of clouds and expensive meteorological instruments or remote sensing …

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Investigating Interdomain Routing In The Wild, Ruwaifa Anwar Dec 2016

Investigating Interdomain Routing In The Wild, Ruwaifa Anwar

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Models of Internet routing are critical for studies of Internet security, reliability and evolution, which often rely on simulations of the Internet’s routing system. Accurate models are difficult to build and suffer from a dearth of ground truth data, as ISPs often treat their connectivity and routing policies as trade secrets. In this environment, researchers rely on a number of simplifying assumptions and models proposed over a decade ago, which are widely criticized for their inability to capture routing policies employed in practice. This thesis makes the following two contributions: â— Investigating Interdomain Routing Policies. First we put Internet topologies …

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Verification Of Probabilistic Branching Time Systems, Andrey Gorlin Dec 2016

Verification Of Probabilistic Branching Time Systems, Andrey Gorlin

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

This thesis deals with verification of complex systems, which involve probabilistic choices. In total, we explore three interrelated problems. First, we explore probabilistic extensions of mu-calculus. GPL extends mu-calculus by having all the probabilistic choices made first; this keeps the model checking procedure decidable for any property. We extend GPL to a logic, XPL, which is undecidable, in general. We define a syntactic property of an XPL formula, separability, as a sufficient condition for model checking. Second, we can frame the problem of probabilistic model checking as query evaluation over probabilistic logic programs. We have developed an inference algorithm, PIP, …

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Measuring Internet Traffic Manipulation, Anke Li Dec 2016

Measuring Internet Traffic Manipulation, Anke Li

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Traffic differentiation---giving better or worse performance to certain classes of Internet traffic---is a well-known but poorly understood traffic management policy. There is active discussion on whether and how ISPs should be allowed to differentiate Internet traffic, but little data about current practices to inform this discussion. Previous work attempted to address this problem for fixed line networks, but at the time of the publication of our work, there was no solution that works in the more challenging mobile environment. In terms of censorship measurement, despite the high perceived value and increasing severity of online information controls, a data-driven understanding of …

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Using Locality To Tackle Modern Algorithmic Challenges, Samuel Mccauley Dec 2016

Using Locality To Tackle Modern Algorithmic Challenges, Samuel Mccauley

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

As computers become faster and more parallel, the number of computations a process executes is becoming too simplistic a predictor of performance. In many circumstances, modern algorithmic research can no longer rely on the assumption that each computation roughly corresponds to a set amount of time. For example, large-scale computers may spend far more time moving data around than performing computation, in which case minimizing data transfers is the best way to improve wall-clock performance. Similarly, manufacturing plants may need to focus on minimizing maintenance costs. While they must still guarantee good throughput, the maintenance costs are what most impact …

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Automatic Discovery Of Efficient Divide-&-Conquer Algorithms For Dynamic Programming Problems, Pramod Ganapathi Dec 2016

Automatic Discovery Of Efficient Divide-&-Conquer Algorithms For Dynamic Programming Problems, Pramod Ganapathi

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

This dissertation is an excursion into computer-discovered algorithms and computer-aided algorithm design. In our vision of the not-so-distant future of computing, machines will take the responsibility of designing and implementing most, if not all, machine-specific highly efficient nontrivial algorithms with provable correctness and performance guarantees. Indeed, as the complexity of computing hardware grows and their basic architectures keep changing rapidly, manually redesigning and reimplementing key algorithms for high performance on every new architecture is quickly becoming an impossible task. Automation is needed. We design algorithms that can design other algorithms. Our focus is on auto-generating algorithms for solving dynamic programming …

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Securing Web Applications, Riccardo Pelizzi Dec 2016

Securing Web Applications, Riccardo Pelizzi

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Over the past decade, web application vulnerabilities have become far more common than vulnerabilities in conventional applications. To mitigate them, we approach the problem from two extremes: one that requires no changes to existing applications but is limited to a few well-defined vulnerability classes, and the second that provides a comprehensive solution but requires a re-thinking of web applications. Our first approach mitigates specific vulnerabilities using policies that do not depend on the application logic, and thus require no developer involvement or effort. We target two of the most common high-profile vulnerabilities, namely, cross-site scripting (XSS) and cross-site request forgery …

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Local Modeling Of Attributed Graphs: Algorithms And Applications, Bryan Perozzi Dec 2016

Local Modeling Of Attributed Graphs: Algorithms And Applications, Bryan Perozzi

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

It is increasingly common to encounter real-world graphs which have attributes associated with the nodes, in addition to their raw connectivity information. For example, social networks contain both the friendship relations as well as user attributes such as interests and demographics. A protein-protein interaction network may not only have the interaction relations but the expression levels associated with the proteins. Such information can be described by a graph in which nodes represent the objects, edges represent the relations between them, and feature vectors associated with the nodes represent the attributes. This graph data is often referred to as an attributed …

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The Computational Complexity Of The Provision-After-Wait Problem In Healthcare, Gowtham Srinivasan Dec 2016

The Computational Complexity Of The Provision-After-Wait Problem In Healthcare, Gowtham Srinivasan

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

In Provision-after-Wait in Healthcare (PaW), a social planner operating on a constrained budget is required to sponsor medical treatments to a population of patients. Specifically, each patient is allocated to any of the k hospitals to receive a single unit of medical treatment. The cost of treatment depends upon the hospital and is paid for by the planner. Associated with every patient is a set of k non-negative numbers which denote the patients’ preference or intrinsic value towards getting treated in each of the k hospitals. Since the patients do not pay for the treatment and the planner cannot afford …

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To Fuse Or Not To Fuse? Analysis And Performance Characterization Of The Fuse User-Space File System Framework, Bharath Kumar Reddy Vangoor Dec 2016

To Fuse Or Not To Fuse? Analysis And Performance Characterization Of The Fuse User-Space File System Framework, Bharath Kumar Reddy Vangoor

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Traditionally, file systems were implemented as part of operating systems kernels, which provide a limited set of tools and facilities to a programmer. As complexity of file systems grew, many new file systems began being developed in user space. Low performance is considered the main disadvantage of user-space file systems but the extent of this problem has never been explored systematically. As a result, the topic of user-space file systems remains rather controversial: while some consider user-space file systems a ``toy'' not to be used in production, others develop full-fledged production file systems in user space. In this thesis we …

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Enhancing Operating Systems With Network Provenance Based Policies For Systematic Malware Defense, Wai Kit Sze Dec 2016

Enhancing Operating Systems With Network Provenance Based Policies For Systematic Malware Defense, Wai Kit Sze

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Todays OSes adopt users as the basic unit of trust. Every file and process owned by the same user has the same userid as the user. This design stems from the very first multi-user OS created, a time when computers were self-contained, and file contents were under the control of users. Today, users frequently download data and code from the Internet, without fully understanding their content or consequences. However, existing desktop OSes reuse the same old trust model and treat downloaded files as if users are fully responsible for them. This trust is exploited by today’s malware. In this dissertation, …

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Corporate Torts: International Human Rights And Superior Officers, Jennifer M. Green Dec 2016

Corporate Torts: International Human Rights And Superior Officers, Jennifer M. Green

Chicago Journal of International Law

Recent decisions by U.S. courts have attacked the ability of human rights victims to hold corporations accountable for their complicity in atrocities around the world. This Article argues that in the face of this attack, advocates and scholars have given insufficient attention to a potent strategy—holding corporate officers liable. It examines the corporate officer liability question through the lens of tort liability, focusing on those officers with superior responsibility over their subordinates who physically commit the violations. It is the first to provide a systematic analysis of how superior officer liability under tort and international law approaches to superior responsibility …

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The Limits Of Isomorphism: Global Investment Law And The Asean Investment Regime, Sungjoon Cho, Jürgen Kurtz Dec 2016

The Limits Of Isomorphism: Global Investment Law And The Asean Investment Regime, Sungjoon Cho, Jürgen Kurtz

Chicago Journal of International Law

This Article probes the unique ontogenetic path of ASEAN’s regulation of foreign investment by juxtaposing global investment law with the ASEAN investment regime. While the former delivers a powerful heuristic on isomorphism that ASEAN exhibits in its strong reflection of global investment norms, the latter sheds critical light on ideological and analytical blind spots by exploring distinct heterogeneities in ASEAN’s investment regulation. Those heterogeneities, especially preferences towards non-legal forms of cooperation and tailored flexibilities to pursue public and development outcomes, are not simply outliers, but reflect important historical and cultural values inherent to ASEAN and its members. The insights uncovered …

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Research News Newsletter, Winter 2016, Research News Newsletter, Stony Brook University. Dec 2016

Research News Newsletter, Winter 2016, Research News Newsletter, Stony Brook University.

Research News

Quarterly newsletter from the Office of the Vice President for Research

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Justices Of The Peace, Lawyers And The People: Local Courts And The Contested Professionalization Of Law In Late Colonial New York, Sung Yup Kim Dec 2016

Justices Of The Peace, Lawyers And The People: Local Courts And The Contested Professionalization Of Law In Late Colonial New York, Sung Yup Kim

Stony Brook Theses and Dissertations Collection, 2006-2020 (closed to submissions)

Legal professionalization in New York was a contested social process entailing myriad local struggles over the use of land and credit. New York’s legal professionalization gained momentum in the mid-eighteenth century, as provincial lawyers pursued a collective mission to monopolize doctrinal interpretation and procedural application of English common law in the colony. The on-the-ground application of that mission frequently pitted lawyers against commoners, many of whom preferred the informal resolutions provided by lay justices, jurors, arbitrators, and town meetings. Professionalized law determined cases with doctrines and procedures alien to most laypeople. It disrupted the local communities’ means of equitable dispute …

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