Haplotype association analyses in resources of mixed structure using Monte Carlo testing

<p>Abstract</p> <p>Background</p> <p>Genomewide association studies have resulted in a great many genomic regions that are likely to harbor disease genes. Thorough interrogation of these specific regions is the logical next step, including regional haplotype studies to identify risk haplotypes upon which the underlying critical variants lie. Pedigrees ascertained for disease can be powerful for genetic analysis due to the cases being enriched for genetic disease. Here we present a Monte Carlo based method to perform haplotype association analysis. Our method, hapMC, allows for the analysis of full-length and sub-haplotypes, including imputation of missing data, in resources of nuclear families, general pedigrees, case-control data or mixtures thereof. Both traditional association statistics and transmission/disequilibrium statistics can be performed. The method includes a phasing algorithm that can be used in large pedigrees and optional use of pseudocontrols.</p> <p>Results</p> <p>Our new phasing algorithm substantially outperformed the standard expectation-maximization algorithm that is ignorant of pedigree structure, and hence is preferable for resources that include pedigree structure. Through simulation we show that our Monte Carlo procedure maintains the correct type 1 error rates for all resource types. Power comparisons suggest that transmission-disequilibrium statistics are superior for performing association in resources of only nuclear families. For mixed structure resources, however, the newly implemented pseudocontrol approach appears to be the best choice. Results also indicated the value of large high-risk pedigrees for association analysis, which, in the simulations considered, were comparable in power to case-control resources of the same sample size.</p> <p>Conclusions</p> <p>We propose hapMC as a valuable new tool to perform haplotype association analyses, particularly for resources of mixed structure. The availability of meta-association and haplotype-mining modules in our suite of Monte Carlo haplotype procedures adds further value to the approach.</p

Towards Adaptable and Adaptive Policy-Free Middleware

We believe that to fully support adaptive distributed applications, middleware must itself be adaptable, adaptive and policy-free. In this paper we present a new language-independent adaptable and adaptive policy framework suitable for integration in a wide variety of middleware systems. This framework facilitates the construction of adaptive distributed applications. The framework addresses adaptability through its ability to represent a wide range of specific middleware policies. Adaptiveness is supported by a rich contextual model, through which an application programmer may control precisely how policies should be selected for any particular interaction with the middleware. A contextual pattern mechanism facilitates the succinct expression of both coarse- and fine-grain policy contexts. Policies may be specified and altered dynamically, and may themselves take account of dynamic conditions. The framework contains no hard-wired policies; instead, all policies can be configured.Comment: Submitted to Dependable and Adaptive Distributed Systems Track, ACM SAC 200

Using User Generated Online Photos to Estimate and Monitor Air Pollution in Major Cities

With the rapid development of economy in China over the past decade, air pollution has become an increasingly serious problem in major cities and caused grave public health concerns in China. Recently, a number of studies have dealt with air quality and air pollution. Among them, some attempt to predict and monitor the air quality from different sources of information, ranging from deployed physical sensors to social media. These methods are either too expensive or unreliable, prompting us to search for a novel and effective way to sense the air quality. In this study, we propose to employ the state of the art in computer vision techniques to analyze photos that can be easily acquired from online social media. Next, we establish the correlation between the haze level computed directly from photos with the official PM 2.5 record of the taken city at the taken time. Our experiments based on both synthetic and real photos have shown the promise of this image-based approach to estimating and monitoring air pollution.Comment: ICIMCS '1

Quality of Service over Specific Link Layers: state of the art report

The Integrated Services concept is proposed as an enhancement to the current Internet architecture, to provide a better Quality of Service (QoS) than that provided by the traditional Best-Effort service. The features of the Integrated Services are explained in this report. To support Integrated Services, certain requirements are posed on the underlying link layer. These requirements are studied by the Integrated Services over Specific Link Layers (ISSLL) IETF working group. The status of this ongoing research is reported in this document. To be more specific, the solutions to provide Integrated Services over ATM, IEEE 802 LAN technologies and low-bitrate links are evaluated in detail. The ISSLL working group has not yet studied the requirements, that are posed on the underlying link layer, when this link layer is wireless. Therefore, this state of the art report is extended with an identification of the requirements that are posed on the underlying wireless link, to provide differentiated Quality of Service

Micro protocol engineering for unstructured carriers: On the embedding of steganographic control protocols into audio transmissions

Network steganography conceals the transfer of sensitive information within unobtrusive data in computer networks. So-called micro protocols are communication protocols placed within the payload of a network steganographic transfer. They enrich this transfer with features such as reliability, dynamic overlay routing, or performance optimization --- just to mention a few. We present different design approaches for the embedding of hidden channels with micro protocols in digitized audio signals under consideration of different requirements. On the basis of experimental results, our design approaches are compared, and introduced into a protocol engineering approach for micro protocols.Comment: 20 pages, 7 figures, 4 table

A Taxonomy for Congestion Control Algorithms in Vehicular Ad Hoc Networks

One of the main criteria in Vehicular Ad hoc Networks (VANETs) that has attracted the researchers' consideration is congestion control. Accordingly, many algorithms have been proposed to alleviate the congestion problem, although it is hard to find an appropriate algorithm for applications and safety messages among them. Safety messages encompass beacons and event-driven messages. Delay and reliability are essential requirements for event-driven messages. In crowded networks where beacon messages are broadcasted at a high number of frequencies by many vehicles, the Control Channel (CCH), which used for beacons sending, will be easily congested. On the other hand, to guarantee the reliability and timely delivery of event-driven messages, having a congestion free control channel is a necessity. Thus, consideration of this study is given to find a solution for the congestion problem in VANETs by taking a comprehensive look at the existent congestion control algorithms. In addition, the taxonomy for congestion control algorithms in VANETs is presented based on three classes, namely, proactive, reactive and hybrid. Finally, we have found the criteria in which fulfill prerequisite of a good congestion control algorithm

TZC: Efficient Inter-Process Communication for Robotics Middleware with Partial Serialization

Inter-process communication (IPC) is one of the core functions of modern robotics middleware. We propose an efficient IPC technique called TZC (Towards Zero-Copy). As a core component of TZC, we design a novel algorithm called partial serialization. Our formulation can generate messages that can be divided into two parts. During message transmission, one part is transmitted through a socket and the other part uses shared memory. The part within shared memory is never copied or serialized during its lifetime. We have integrated TZC with ROS and ROS2 and find that TZC can be easily combined with current open-source platforms. By using TZC, the overhead of IPC remains constant when the message size grows. In particular, when the message size is 4MB (less than the size of a full HD image), TZC can reduce the overhead of ROS IPC from tens of milliseconds to hundreds of microseconds and can reduce the overhead of ROS2 IPC from hundreds of milliseconds to less than 1 millisecond. We also demonstrate the benefits of TZC by integrating with TurtleBot2 that are used in autonomous driving scenarios. We show that by using TZC, the braking distance can be shortened by 16% than ROS