Rapid compensatory evolution promotes the survival of conjugative plasmids

Conjugative plasmids play a vital role in bacterial adaptation through horizontal gene transfer. Explaining how plasmids persist in host populations however is difficult, given the high costs often associated with plasmid carriage. Compensatory evolution to ameliorate this cost can rescue plasmids from extinction. In a recently published study we showed that compensatory evolution repeatedly targeted the same bacterial regulatory system, GacA/GacS, in populations of plasmid-carrying bacteria evolving across a range of selective environments. Mutations in these genes arose rapidly and completely eliminated the cost of plasmid carriage. Here we extend our analysis using an individual based model to explore the dynamics of compensatory evolution in this system. We show that mutations which ameliorate the cost of plasmid carriage can prevent both the loss of plasmids from the population and the fixation of accessory traits on the bacterial chromosome. We discuss how dependent the outcome of compensatory evolution is on the strength and availability of such mutations and the rate at which beneficial accessory traits integrate on the host chromosome.

An Examination of a Church-Based Recovery Program on the Quality of Physical and Spiritual Life of Mentally Ill Persons in Korea

This study explores the effectiveness of a Church-based recovery program for the mentally ill in Korea where many Christian communities view mental illness as evidence of sin. Building on theological and psychological literature, an empirical study was conducted with participants in the alternative program of the Han-ma-um community. Data analysis revealed that this program, which views mental disorders as illness rather than sin, helps participants build self-respect and enables families to provide support as they move toward recovery. Based on this empirical examination, recommendations for refinement and expansion of the program and avenues for future research are proposed.

A Bayesian Approach for TCP to Distinguish Congestion from Wireless Losses

(This Technical Report revises TR-BUCS-2003-011) The Transmission Control Protocol (TCP) has been the protocol of choice for many Internet applications requiring reliable connections. The design of TCP has been challenged by the extension of connections over wireless links. In this paper, we investigate a Bayesian approach to infer at the source host the reason of a packet loss, whether congestion or wireless transmission error. Our approach is "mostly" end-to-end since it requires only one long-term average quantity (namely, long-term average packet loss probability over the wireless segment) that may be best obtained with help from the network (e.g. wireless access agent).Specifically, we use Maximum Likelihood Ratio tests to evaluate TCP as a classifier of the type of packet loss. We study the effectiveness of short-term classification of packet errors (congestion vs. wireless), given stationary prior error probabilities and distributions of packet delays conditioned on the type of packet loss (measured over a larger time scale). Using our Bayesian-based approach and extensive simulations, we demonstrate that congestion-induced losses and losses due to wireless transmission errors produce sufficiently different statistics upon which an efficient online error classifier can be built. We introduce a simple queueing model to underline the conditional delay distributions arising from different kinds of packet losses over a heterogeneous wired/wireless path. We show how Hidden Markov Models (HMMs) can be used by a TCP connection to infer efficiently conditional delay distributions. We demonstrate how estimation accuracy is influenced by different proportions of congestion versus wireless losses and penalties on incorrect classification.

TCP-friendly SIMD Congestion Control and Its Convergence Behavior

The increased diversity of Internet application requirements has spurred recent interests in flexible congestion control mechanisms. Window-based congestion control schemes use increase rules to probe available bandwidth, and decrease rules to back off when congestion is detected. The parameterization of these control rules is done so as to ensure that the resulting protocol is TCP-friendly in terms of the relationship between throughput and packet loss rate. In this paper, we propose a novel window-based congestion control algorithm called SIMD (Square-Increase/Multiplicative-Decrease). Contrary to previous memory-less controls, SIMD utilizes history information in its control rules. It uses multiplicative decrease but the increase in window size is in proportion to the square of the time elapsed since the detection of the last loss event. Thus, SIMD can efficiently probe available bandwidth. Nevertheless, SIMD is TCP-friendly as well as TCP-compatible under RED, and it has much better convergence behavior than TCP-friendly AIMD and binomial algorithms proposed recently.

Open Issues on TCP for Mobile Computing

We discuss the design principles of TCP within the context of heterogeneous wired/wireless networks and mobile networking. We identify three shortcomings in TCP's behavior: (i) the protocol's error detection mechanism, which does not distinguish different types of errors and thus does not suffice for heterogeneous wired/wireless environments, (ii) the error recovery, which is not responsive to the distinctive characteristics of wireless networks such as transient or burst errors due to handoffs and fading channels, and (iii) the protocol strategy, which does not control the tradeoff between performance measures such as goodput and energy consumption, and often entails a wasteful effort of retransmission and energy expenditure. We discuss a solution-framework based on selected research proposals and the associated evaluation criteria for the suggested modifications. We highlight an important angle that did not attract the required attention so far: the need for new performance metrics, appropriate for evaluating the impact of protocol strategies on battery-powered devices.

A Spectrum of TCP-Friendly Window-Based Congestion Control Algorithms

The increased diversity of Internet application requirements has spurred recent interests in transport protocols with flexible transmission controls. In window-based congestion control schemes, increase rules determine how to probe available bandwidth, whereas decrease rules determine how to back off when losses due to congestion are detected. The parameterization of these control rules is done so as to ensure that the resulting protocol is TCP-friendly in terms of the relationship between throughput and loss rate. In this paper, we define a new spectrum of window-based congestion control algorithms that are TCP-friendly as well as TCP-compatible under RED. Contrary to previous memory-less controls, our algorithms utilize history information in their control rules. Our proposed algorithms have two salient features: (1) They enable a wider region of TCP-friendliness, and thus more flexibility in trading off among smoothness, aggressiveness, and responsiveness; and (2) they ensure a faster convergence to fairness under a wide range of system conditions. We demonstrate analytically and through extensive ns simulations the steady-state and transient behaviors of several instances of this new spectrum of algorithms. In particular, SIMD is one instance in which the congestion window is increased super-linearly with time since the detection of the last loss. Compared to recently proposed TCP-friendly AIMD and binomial algorithms, we demonstrate the superiority of SIMD in: (1) adapting to sudden increases in available bandwidth, while maintaining competitive smoothness and responsiveness; and (2) rapidly converging to fairness and efficiency.

STAIR: Practical AIMD Multirate Congestion Control

Existing approaches for multirate multicast congestion control are either friendly to TCP only over large time scales or introduce unfortunate side effects, such as significant control traffic, wasted bandwidth, or the need for modifications to existing routers. We advocate a layered multicast approach in which steady-state receiver reception rates emulate the classical TCP sawtooth derived from additive-increase, multiplicative decrease (AIMD) principles. Our approach introduces the concept of dynamic stair layers to simulate various rates of additive increase for receivers with heterogeneous round-trip times (RTTs), facilitated by a minimal amount of IGMP control traffic. We employ a mix of cumulative and non-cumulative layering to minimize the amount of excess bandwidth consumed by receivers operating asynchronously behind a shared bottleneck. We integrate these techniques together into a congestion control scheme called STAIR which is amenable to those multicast applications which can make effective use of arbitrary and time-varying subscription levels.

Effectiveness of Loss labeling in Improving TCP Performance in Wired/Wireless Networks

The current congestion-oriented design of TCP hinders its ability to perform well in hybrid wireless/wired networks. We propose a new improvement on TCP NewReno (NewReno-FF) using a new loss labeling technique to discriminate wireless from congestion losses. The proposed technique is based on the estimation of average and variance of the round trip time using a filter cal led Flip Flop filter that is augmented with history information. We show the comparative performance of TCP NewReno, NewReno-FF, and TCP Westwood through extensive simulations. We study the fundamental gains and limits using TCP NewReno with varying Loss Labeling accuracy (NewReno-LL) as a benchmark. Lastly our investigation opens up important research directions. First, there is a need for a finer grained classification of losses (even within congestion and wireless losses) for TCP in heterogeneous networks. Second, it is essential to develop an appropriate control strategy for recovery after the correct classification of a packet loss.

Smooth Multirate Multicast Congestion Control

A significant impediment to deployment of multicast services is the daunting technical complexity of developing, testing and validating congestion control protocols fit for wide-area deployment. Protocols such as pgmcc and TFMCC have recently made considerable progress on the single rate case, i.e. where one dynamic reception rate is maintained for all receivers in the session. However, these protocols have limited applicability, since scaling to session sizes beyond tens of participants necessitates the use of multiple rate protocols. Unfortunately, while existing multiple rate protocols exhibit better scalability, they are both less mature than single rate protocols and suffer from high complexity. We propose a new approach to multiple rate congestion control that leverages proven single rate congestion control methods by orchestrating an ensemble of independently controlled single rate sessions. We describe SMCC, a new multiple rate equation-based congestion control algorithm for layered multicast sessions that employs TFMCC as the primary underlying control mechanism for each layer. SMCC combines the benefits of TFMCC (smooth rate control, equation-based TCP friendliness) with the scalability and flexibility of multiple rates to provide a sound multiple rate multicast congestion control policy.

A Spectrum of TCP-friendly Window-Based Congestion Control Algorithms

The increasing diversity of Internet application requirements has spurred recent interest in transport protocols with flexible transmission controls. In window-based congestion control schemes, increase rules determine how to probe available bandwidth, whereas decrease rules determine how to back off when losses due to congestion are detected. The control rules are parameterized so as to ensure that the resulting protocol is TCP-friendly in terms of the relationship between throughput and loss rate. This paper presents a comprehensive study of a new spectrum of window-based congestion controls, which are TCP-friendly as well as TCP-compatible under RED. Our controls utilize history information in their control rules. By doing so, they improve the transient behavior, compared to recently proposed slowly-responsive congestion controls such as general AIMD and binomial controls. Our controls can achieve better tradeoffs among smoothness, aggressiveness, and responsiveness, and they can achieve faster convergence. We demonstrate analytically and through extensive ns simulations the steady-state and transient behavior of several instances of this new spectrum.

3D Trajectory Recovery for Tracking Multiple Objects and Trajectory Guided Recognition of Actions

A mechanism is proposed that integrates low-level (image processing), mid-level (recursive 3D trajectory estimation), and high-level (action recognition) processes. It is assumed that the system observes multiple moving objects via a single, uncalibrated video camera. A novel extended Kalman filter formulation is used in estimating the relative 3D motion trajectories up to a scale factor. The recursive estimation process provides a prediction and error measure that is exploited in higher-level stages of action recognition. Conversely, higher-level mechanisms provide feedback that allows the system to reliably segment and maintain the tracking of moving objects before, during, and after occlusion. The 3D trajectory, occlusion, and segmentation information are utilized in extracting stabilized views of the moving object. Trajectory-guided recognition (TGR) is proposed as a new and efficient method for adaptive classification of action. The TGR approach is demonstrated using "motion history images" that are then recognized via a mixture of Gaussian classifier. The system was tested in recognizing various dynamic human outdoor activities; e.g., running, walking, roller blading, and cycling. Experiments with synthetic data sets are used to evaluate stability of the trajectory estimator with respect to noise.

TCP Control Groups: Aggregated Congestion Control for TCP (MA Thesis)

This thesis presents a framework for aggregated congestion management for TCP flows and shows how to integrate such an approach in an existing TCP protocol stack. The thesis presents an initial implementation of this congestion management scheme in Linux, with performance evaluation in ns as well.

Facial Feature Tracking and Occlusion Recovery in American Sign Language

Facial features play an important role in expressing grammatical information in signed languages, including American Sign Language(ASL). Gestures such as raising or furrowing the eyebrows are key indicators of constructions such as yes-no questions. Periodic head movements (nods and shakes) are also an essential part of the expression of syntactic information, such as negation (associated with a side-to-side headshake). Therefore, identification of these facial gestures is essential to sign language recognition. One problem with detection of such grammatical indicators is occlusion recovery. If the signer's hand blocks his/her eyebrows during production of a sign, it becomes difficult to track the eyebrows. We have developed a system to detect such grammatical markers in ASL that recovers promptly from occlusion. Our system detects and tracks evolving templates of facial features, which are based on an anthropometric face model, and interprets the geometric relationships of these templates to identify grammatical markers. It was tested on a variety of ASL sentences signed by various Deaf native signers and detected facial gestures used to express grammatical information, such as raised and furrowed eyebrows as well as headshakes.

Fuzzy ART: An Adaptive Resonance Algorithm for Rapid, Stable Classification of Analog Patterns

The Fuzzy ART system introduced herein incorporates computations from fuzzy set theory into ART 1. For example, the intersection (n) operator used in ART 1 learning is replaced by the MIN operator (A) of fuzzy set theory. Fuzzy ART reduces to ART 1 in response to binary input vectors, but can also learn stable categories in response to analog input vectors. In particular, the MIN operator reduces to the intersection operator in the binary case. Learning is stable because all adaptive weights can only decrease in time. A preprocessing step, called complement coding, uses on-cell and off-cell responses to prevent category proliferation. Complement coding normalizes input vectors while preserving the amplitudes of individual feature activations.

ART 2-A: An Adaptive Resonance Algorithm for Rapid Category Learning and Recognition

This article introduces ART 2-A, an efficient algorithm that emulates the self-organizing pattern recognition and hypothesis testing properties of the ART 2 neural network architecture, but at a speed two to three orders of magnitude faster. Analysis and simulations show how the ART 2-A systems correspond to ART 2 dynamics at both the fast-learn limit and at intermediate learning rates. Intermediate learning rates permit fast commitment of category nodes but slow recoding, analogous to properties of word frequency effects, encoding specificity effects, and episodic memory. Better noise tolerance is hereby achieved without a loss of learning stability. The ART 2 and ART 2-A systems are contrasted with the leader algorithm. The speed of ART 2-A makes practical the use of ART 2 modules in large-scale neural computation.