Overextending Immunity: Arbitral Institutional Liability in the United States, England, and France

This Note examines the relationship between the arbitral institution and the disputing parties. Part I demonstrates the decisions parties face when choosing between traditional litigation and arbitration; it also discusses the differences between an arbitral institution and an ad hoc arbitration, as well as major arbitral institutions\u27 rules regarding their own liability. Part II introduces several nations\u27 approaches to judicial immunity, and how it is applied to arbitrators and arbitral institutions. Part II also weighs differing views on how to characterize the relationship between disputing parties and the arbitral institution. Finally, Part II discusses several key criticisms to the immunity of arbitral institutions. Part III will demonstrate the need for arbitral institutions\u27 contractual liability to disputing parties, and will address several potential criticisms and policy concerns of this approach

Genome-wide inference of ancestral recombination graphs

The complex correlation structure of a collection of orthologous DNA sequences is uniquely captured by the "ancestral recombination graph" (ARG), a complete record of coalescence and recombination events in the history of the sample. However, existing methods for ARG inference are computationally intensive, highly approximate, or limited to small numbers of sequences, and, as a consequence, explicit ARG inference is rarely used in applied population genomics. Here, we introduce a new algorithm for ARG inference that is efficient enough to apply to dozens of complete mammalian genomes. The key idea of our approach is to sample an ARG of n chromosomes conditional on an ARG of n-1 chromosomes, an operation we call "threading." Using techniques based on hidden Markov models, we can perform this threading operation exactly, up to the assumptions of the sequentially Markov coalescent and a discretization of time. An extension allows for threading of subtrees instead of individual sequences. Repeated application of these threading operations results in highly efficient Markov chain Monte Carlo samplers for ARGs. We have implemented these methods in a computer program called ARGweaver. Experiments with simulated data indicate that ARGweaver converges rapidly to the true posterior distribution and is effective in recovering various features of the ARG for dozens of sequences generated under realistic parameters for human populations. In applications of ARGweaver to 54 human genome sequences from Complete Genomics, we find clear signatures of natural selection, including regions of unusually ancient ancestry associated with balancing selection and reductions in allele age in sites under directional selection. Preliminary results also indicate that our methods can be used to gain insight into complex features of human population structure, even with a noninformative prior distribution.Comment: 88 pages, 7 main figures, 22 supplementary figures. This version contains a substantially expanded genomic data analysi

State Analysis Database Tool

The State Analysis Database Tool software establishes a productive environment for collaboration among software and system engineers engaged in the development of complex interacting systems. The tool embodies State Analysis, a model-based system engineering methodology founded on a state-based control architecture (see figure). A state represents a momentary condition of an evolving system, and a model may describe how a state evolves and is affected by other states. The State Analysis methodology is a process for capturing system and software requirements in the form of explicit models and states, and defining goal-based operational plans consistent with the models. Requirements, models, and operational concerns have traditionally been documented in a variety of system engineering artifacts that address different aspects of a mission s lifecycle. In State Analysis, requirements, models, and operations information are State Analysis artifacts that are consistent and stored in a State Analysis Database. The tool includes a back-end database, a multi-platform front-end client, and Web-based administrative functions. The tool is structured to prompt an engineer to follow the State Analysis methodology, to encourage state discovery and model description, and to make software requirements and operations plans consistent with model descriptions

Calculus variations as figured worlds for math identity development

International audienceCalculus is often an essential milestone during a students’ time at university and can be especially impactful for students wishing to pursue a math or science field. Given its relative importance, the ways in which calculus courses are delivered can have a lasting impact on a student’s trajectory and relationship with mathematics. In this study we document the ways in which three calculus course variations at the same university operate to promote different mathematics identities for students. Drawing on the framework of figured worlds (Holland et al., 1998), we showcase the ways in which these course variations act as if they are different calculus worlds that constitute socially organized and produced realms of being. We highlight the ways in which these figured worlds position or fail to position students with the opportunity to refigure themselves and others

Evolution at the Subgene Level: Domain Rearrangements in the Drosophila Phylogeny

Supplementary sections 1–13, tables S1–S10, and figures S1–S9 are available at Molecular Biology and Evolution online (http://www.mbe.oxfordjournals.org/).Although the possibility of gene evolution by domain rearrangements has long been appreciated, current methods for reconstructing and systematically analyzing gene family evolution are limited to events such as duplication, loss, and sometimes, horizontal transfer. However, within the Drosophila clade, we find domain rearrangements occur in 35.9% of gene families, and thus, any comprehensive study of gene evolution in these species will need to account for such events. Here, we present a new computational model and algorithm for reconstructing gene evolution at the domain level. We develop a method for detecting homologous domains between genes and present a phylogenetic algorithm for reconstructing maximum parsimony evolutionary histories that include domain generation, duplication, loss, merge (fusion), and split (fission) events. Using this method, we find that genes involved in fusion and fission are enriched in signaling and development, suggesting that domain rearrangements and reuse may be crucial in these processes. We also find that fusion is more abundant than fission, and that fusion and fission events occur predominantly alongside duplication, with 92.5% and 34.3% of fusion and fission events retaining ancestral architectures in the duplicated copies. We provide a catalog of ∼9,000 genes that undergo domain rearrangement across nine sequenced species, along with possible mechanisms for their formation. These results dramatically expand on evolution at the subgene level and offer several insights into how new genes and functions arise between species.National Science Foundation (U.S.) (Graduate Research Fellowship)National Science Foundation (U.S.) (CAREER award NSF 0644282

Detecting CAN Attacks on J1939 and NMEA 2000 Networks

J1939 is a networking layer built on top of the widespread CAN bus used for communication between different subsystems within a vehicle. The J1939 and NMEA 2000 protocols standardize data enrichment for these subsystems, and are used for trucks, weapon systems, naval vessels, and other industrial systems. Practical security solutions for existing CAN based communication systems are notoriously difficult because of the lack of cryptographic capabilities of the devices involved. In this paper we propose a novel intrusion detection system (IDS) for J1939 and NMEA 2000 networks. Our IDS (CANDID) combines timing analysis with a packet manipulation detection system and data analysis. This data analysis enables us to capture the state of the vehicle, detect messages with irregular timing intervals, and take advantage of the dependencies between different Electronic Control Units (ECUs) to restrict even the most advanced attacker. Our IDS is deployed and tested on multiple vehicles, and has demonstrated greater accuracy and detection capabilities than previous work

Methods and analysis of genome-scale gene family evolution across multiple species

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2010.Cataloged from PDF version of thesis.Includes bibliographical references (p. 123-136).The fields of genomics and evolution have continually benefited from one another in their common goal of understanding the biological world. This partnership has been accelerated by ever increasing sequencing and high-throughput technologies. Although the future of genomic and evolutionary studies is bright, new models and methods will be needed to address the growing and changing challenges of large-scale datasets. In this work, I explore how evolution generates the diversity of life we see in modern species, specifically the evolution of new genes and functions. By reconstructing the history of the diverse sequences present in modern species, we can improve our understanding of their function and evolutionary importance. Performing such an analysis requires a principled and efficient means of computing the most probable evolutionary scenarios. To address these challenges, I introduce a new model of gene family evolution as well as a new method SPIMAP, an efficient Bayesian method for reconstructing gene trees in the presence of a known species tree. We observe many improvements in reconstruction accuracy, achieved by modeling multiple aspects of evolution, including gene duplication and loss rates, speciation times, and correlated substitution rate variation across both species and loci. I have implemented and applied this method on two clades of fully-sequenced species, 12 Drosophila and 16 fungal genomes as well as simulated phylogenies, and find dramatic improvements in reconstruction accuracy as compared to the most popular existing methods, including those that take the species tree into account. Lastly, I use the SPIMAP method to reconstruct the evolutionary history of all gene families in 16 fungal species including several relatives of the pathogenic species C. albicans. From these reconstructions, we identify several families enriched with duplications and positive selection in pathogenic lineages. Theses reconstructions shed light on the evolution of these species as well as a better understanding of the genes involved in pathogenicity.by Matthew D. Rasmussen.Ph.D

Probabilistic framework for genome-wide phylogeny and ortholog determination

Thesis (S.M.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2006.Includes bibliographical references (leaves 63-65).Comparative genomics of multiple related species has emerged as a powerful tool for genome signal discovery. To that end, dozens of mammalian, fly, and fungal genomes have been fully sequenced. Making use of these genomes requires rigorous computational methods for determining the evolutionary history of every gene and region. In particular, comparative analysis requires the ability to distinguish between orthologous and paralogous regions. Current approaches to ortholog identification work adequately for pairs of species but are ineffective for multiple complete genomes. This thesis presents a new phylogenetic reconstruction method, SINDIR, that is designed specifically for genome-wide orthology determination. Unlike any other method, SINDIR exploits the known evolutionary history of a set of species to infer the history of their genes. This is done by learning a probabilistic model of evolution from a trusted set of unambiguous orthologs. Given this model, SINDIR can find the maximum likelihood phylogenetic tree for any set of the genes. In a novel technique, synteny maps are used to train and evaluate the evolutionary model on both simulated and real sequence data. SINDIR avoids errors commonly committed by current methods and achieves a significantly improved accuracy of orthology determination.by Matthew D. Rasmussen.S.M