Transmission Bottleneck Research Articles

Vertex data compression through vector quantization

Rendering geometrically detailed 3D models requires the transfer and processing of large amounts of triangle and vertex geometry data. Compressing the geometry bit stream can reduce bandwidth requirements and alleviate transmission bottlenecks. In this paper, we show vector quantization to be an effective compression technique for triangle mesh vertex data. We present predictive vector quantization methods using unstructured code books as well as a product code pyramid vector quantizer. The technique is compatible with most existing mesh connectivity encoding schemes and does not require the use of entropy coding. In addition to compression, our vector quantization scheme can be used for complexity reduction by accelerating the computation of linear vertex transformations. Consequently, an encoded set of vertices can be both decoded and transformed in approximately 60 percent of the time required by a conventional method without compression.

Estimating population size and transmission bottlenecks in maternally transmitted endosymbiotic bacteria.

Many species of bacterial endosymbionts are acquired by animal hosts before birth, through direct transmission from mothers to eggs or embryos. This vertical transmission imposes a reduction in numbers or "bottleneck," and the size of this bottleneck affects the population structure and evolution of symbiotic lineages. We have estimated the size of the transmission bottleneck in Buchnera, the bacterial symbiont of aphids, using basic light and electron microscopy techniques. By serial-sectioning whole aphid abdomens, their eggs, and embryos, we determined the following parameters: (i) The average size of a Buchnera cell is 2.9 mm in diameter. (ii) The total number of Buchnera in an Acyrthosiphon pisum embryo was around 36700 whereas a first instar nymph contained more than 119000. (iii) The number of symbionts per bacteriocyte was around 800 in an embryo and 3200 in a first instar nymph. (iv) The total number of Buchnera transmitted to each sexual egg ranged from 850 in Nasonovia to 1800 in A. pisum to more than 8000 in Uroleucon ambrosiae. (v) The total number of secondary endosymbionts in A. pisum was 12170 for an embryo and 18360 for a first instar nymph. Secondary symbionts were arranged both extracellularly and in clusters of 2000-8000 bacteria inside bacteriocytes. These numbers are consistent with the few previous estimates of symbiont population sizes based on counts of gene copies.

HIV/host interactions: new lessons from the Red Queen's country.

HIV/host interactions: new lessons from the Red Queen's country.

Transmission bottlenecks and the evolution of fitness in rapidly evolving RNA viruses

We explored the evolutionary importance of two factors in the adaptation of RNA viruses to their cellular hosts, size of viral inoculum used to initiate a new infection, and mode of transmission (horizontal versus vertical). Transmission bottlenecks should occur in natural populations of viruses and their profound effects on viral adaptation have been previously documented. However, the role of transmission mode has not received the same attention. Here we used a factorial experimental design to test the combined effects of inoculum (bottleneck) size and mode of transmission in evolution of vesicular stomatitis virus (VSV) in tissue culture, and compared our results to the predictions of a recent theoretical model. Our data were in accord with basic genetic principles concerning the balance between mutation, selection and genetic drift. In particular, attenuation of vertically transmitted viruses was a consequence of the random accumulation of deleterious mutations, whereas horizontally transmitted viruses experiencing similar bottlenecks did not suffer the same fitness losses because effective bottleneck size was actually determined by the number of host individuals. In addition, high levels of viral fitness in horizontally transmitted populations were explained by competition among viral variants.

Three Distinct Mechanisms Facilitate Genetic Isolation of Sympatric Wheat Streak Mosaic Virus Lineages

Cross-protection and vector transmission bottlenecks have been proposed as mechanisms facilitating genetic isolation of sympatric viral lineages. Molecular markers were used to monitor establishment and resolution of mixed infections with genetically defined strains of wheat streak mosaic virus (WSMV). Two closely related WSMV strains from the U.S. (Type and Sidney 81) exhibited reciprocal cross-protection in wheat, confirming this classic phenomenon as a mechanism of genetic isolation. In contrast, cross-protection between either U.S. strain and the divergent El Batán 3 strain from Mexico was unilateral, erratic, and only partially effective. Distribution of WSMV strains within individual leaves of plants supporting a mixed infection of Type and Sidney 81 was spatially nonuniform. Strain distribution among individual tillers of coinfected plants also was heterogeneous, with some containing either Type or Sidney 81 alone and some containing both. Transmission by wheat curl mites, acquiring virus from source plants simultaneously infected with both Type and Sidney 81, often resulted in test plants bearing only a single WSMV strain. Spatial subdivision of virus strains within coinfected plants likely contributed to vector transmission bottlenecks during acquisition. Collectively, these three distinct mechanisms enhance genetic isolation of individual viral lineages, and together with stochastic processes, may explain generation and maintenance of genetic diversity in field populations.

An architecture for packet-striping protocols

Link-striping algorithms are often used to overcome transmission bottlenecks in computer networks. Traditional striping algorithms suffer from two major disadvantages. They provide inadequate load sharing in the presence of variable-length packets, and may result in non-FIFO delivery of data. We describe a new family of link-striping algorithms that solves both problems. Our scheme applies to any layer that can provide multiple FIFO channels. We deal with variable-sized packets by showing how fair-queuing algorithms can be transformed into load-sharing algorithms. Our transformation results in practical load-sharing protocols, and shows a theoretical connection between two seemingly different problems. The same transformation can be applied to obtain load-sharing protocols for links with different capacities. We deal with the FIFO requirement for two separate cases. If a sequence number can be added to each packet, we show how to speed up packet processing by letting the receiver simulate the sender algorithm. If no header can be added, we show how to provide quasi FIFO delivery. Quasi FIFO is FIFO except during occasional periods of loss of synchronization. We argue that quasi FIFO is adequate for most applications. We also describe a simple technique for speedy restoration of synchronization in the event of loss. We develop an architectural framework for transparently embedding our protocol at the network level by striping IP packets across multiple physical interfaces. The resulting stripe protocol has been implemented within the NetBSD kernel. Our measurements and simulations show that the protocol offers scalable throughput even when striping is done over dissimilar links, and that the protocol synchronized quickly after packet loss. Measurements show performance improvements over conventional round-robin striping schemes and striping schemes that do not resequence packets. Some aspects of our solution have been implemented in Cisco's router operating system (IOS 11.3) in the context of Multilink PPP striping.

Transmission bottlenecks as determinants of virulence in rapidly evolving pathogens.

Transmission bottlenecks occur in pathogen populations when only a few individual pathogens are transmitted from one infected host to another in the initiation of a new infection. Transmission bottlenecks can dramatically affect the evolution of virulence in rapidly evolving pathogens such as RNA viruses. Characterizing pathogen diversity with the quasispecies concept, we use analytical and simulation methods to demonstrate that severe bottlenecks are likely to drive down the virulence of a pathogen because of stochastic loss of the most virulent pathotypes, through a process analogous to Muller's ratchet. We investigate in this process the roles of host population size, duration of within-host viral replication, and transmission bottleneck size. We argue that the patterns of accumulation of deleterious mutation may explain differing levels of virulence in vertically and horizontally transmitted diseases.

Founder virus population related to route of virus transmission: a determinant of intrahost human immunodeficiency virus type 1 evolution?

We and others have shown that in individual human immunodeficiency virus type 1 (HIV-1) infection, the adaptive evolution of HIV-1 is influenced by host immune competence. In this study, we tested the hypothesis that in addition to selective forces operating within the host, transmission bottlenecks have an impact on HIV-1 intrahost evolution. Therefore, we studied the intrahost evolution of the V3 region of the external glycoprotein gp120 of HIV-1 during the 3- and 5-year periods following seroconversion after parenteral versus sexual (male-to-male) transmission in 41 participants of the Amsterdam prospective cohorts of homosexual men (n = 31) and intravenous drug users (IVDUs; n = 10) who were AIDS free and had comparable numbers of CD4+ cells. We observed that HIV-1 strains in homosexual men accumulated over 5 years more nonsynonymous substitutions within the V3 loop than HIV-1 strains in IVDUs as a result of lower rates of nonsynonymous evolution in both the initial 3-year period from seroconversion and the following 2-year period as well as a larger proportion of nonsynonymous back substitutions in IVDUs. The mean numbers of synonymous substitutions did not differ between the two risk groups. Since HIV-1 strains in IVDUs could be distinguished from the viruses of homosexual men based on several nucleotide substitutions of which the most conserved is a synonymous substitution at the tip of the V3 loop (GGC pattern), we studied whether the founder virus population itself has an impact on the intrahost evolution of HIV-1. The mean number of nonsynonymous substitutions accumulated over 5 years within the V3 loop was lower in 10 IVDUs infected by the HIV-1 strains with the GGC signature than in 4 IVDUs infected by HIV-1 strains lacking this pattern, while the mean numbers of synonymous substitutions were similar in the two groups.

A reliable and scalable striping protocol

Link striping algorithms are often used to overcome transmission bottlenecks in computer networks. Traditional striping algorithms suffer from two major disadvantages. They provide inadequate load sharing in the presence of variable length packets, and may result in non- FIFO delivery of data. We describe a new family of link striping algorithms that solves both problems. Our scheme applies to any layer that can provide multiple FIFO channels.We deal with variable sized packets by showing how fair queuing algorithms can be transformed into load sharing algorithms. Our transformation results in practical load sharing protocols, and shows a theoretical connection between two seemingly different problems. The same transformation can be applied to obtain load sharing protocols for links with different capacities. We deal with the FIFO requirement for two separate cases. If a sequence number can be added to each packet, we show how to speed up packet processing by letting the receiver simulate the sender algorithm. If no header can be added, we show how to provide quasi- FIFO delivery. Quasi- FIFO is FIFO except during occasional periods of loss of synchronization. We argue that quasi- FIFO is adequate for most applications. We also describe a simple technique for speedy restoration of synchronization in the event of loss.We develop an architectural framework for transparently embedding our protocol at the network level by striping IP packets across multiple physical interfaces. The resulting strIPe protocol has been implemented within the NetBSD kernel. Our measurements and simulations show that the protocol offers scalable throughput even when striping is done over dissimilar links, and that the protocol synchronizes quickly after packet loss. Measurements show performance improvements over conventional round robin striping schemes and striping schemes that do not resequence packets.

Active Narrow-Band Vibration Isolation Of Machinery Noise From Resonant Substructures

Machinery noise and vibration is an important issue in many applications, including spacecraft, aircraft and naval vessels. A classic approach to ameliorating the effect of such disturbances is isolation at a vibration transmission bottleneck, the machinery mounts. Passive approaches are widespread, and introduce no risk of instability. Active techniques promise increased isolation performance, but introduce the risk of unstable interaction with system dynamics, particularly resonant vibrations of the machine or of the supporting structure.This paper focuses upon a specialization of active isolation, isolation of nearly time-periodic disturbances with feedback control. In this situation one can achieve significant isolation performance with minimal risk of instability. The paper demonstrates, with the aid of a simple case study, that the safely achievable performance is limited by three important factors. (1) The level of passive damping present in the unmodeled resonant response of the mechanical system (supporting structure and machine): the importance of passive damping is most concisely quantified by the modal overlap, the ratio of modal bandwidth to modal spacing. (2) The pole-zero structure of the transfer function from the actuators to sensors at frequencies near the disturbance frequency: for rigid machines, the single most important parameter is machine mass relative to effective modal mass. (3) The spectral bandwidth of the offending disturbance: slowly time-varying quasi-periodic disturbances are easiest to isolate by the techniques studied. For the case study, attention is restricted to a rigid "machine" and single axis motion. The paper develops modeling analyses, discusses sensor and actuator choices, discusses control algorithms, and presents the results of an experimental study.

Massively parallel architectures for large scale neural network simulations

A toroidal lattice architecture (TLA) and a planar lattice architecture (PLA) are proposed as massively parallel neurocomputer architectures for large-scale simulations. The performance of these architectures is almost proportional to the number of node processors, and they adopt the most efficient two-dimensional processor connections for WSI implementation. They also give a solution to the connectivity problem, the performance degradation caused by the data transmission bottleneck, and the load balancing problem for efficient parallel processing in large-scale neural network simulations. The general neuron model is defined. Implementation of the TLA with transputers is described. A Hopfield neural network and a multilayer perceptron have been implemented and applied to the traveling salesman problem and to identity mapping, respectively. Proof that the performance increases almost in proportion to the number of node processors is given.

Summary of panel: long term impact of third-party transmission use

The comments made by the five panel participants at the winter 1989 IEEE Power Engineering Society meeting are summarized. The speakers emphasized the changing role of transmission as a delivery mechanism for power belonging to many users. The increased competition between owners of transmission, which also happen to be owners of generation, make sharing of information, which is necessary to understand transmission bottlenecks, more difficult. The transmission aspects of electric utility planning are becoming more challenging because they are more complex.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

Optimal economic power transfers

The mathematical models used in a computer program for the analysis of economic power transfers are presented. The program computes fuel-to-fuel transfers between explicitly identified utilities in an interconnected power system. The computational procedure used by the program is carried out by four basic modules: (1) bus grouping to reduce the size of the network for computational purposes (since the entire network is modeled, any interface in the network can be specified, not just the company/pool ties, thus allowing all potential transmission bottlenecks to be considered); (2) initial economic dispatch, including allocation of hydraulic generation; (3) dispatch adjustment, reflecting company operating policies in the event of transmission overloads caused by the initial economic dispatch; and (4) economic transaction optimization superimposed on the operating conditions arrived at in (3). Results obtained for a realistic test case demonstrate the ability of the program to select an optimal power transfer pattern.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>