Scheduling algorithms for throughput maximization in data networks

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 2007.Includes bibliographical references (p. 215-226).This thesis considers the performance implications of throughput optimal scheduling in physically and computationally constrained data networks. We study optical networks, packet switches, and wireless networks, each of which has an assortment of features and constraints that challenge the design decisions of network architects. In this work, each of these network settings are subsumed under a canonical model and scheduling framework. Tools of queueing analysis are used to evaluate network throughput properties, and demonstrate throughput optimality of scheduling and routing algorithms under stochastic traffic. Techniques of graph theory are used to study network topologies having desirable throughput properties. Combinatorial algorithms are proposed for efficient resource allocation. In the optical network setting, the key enabling technology is wavelength division multiplexing (WDM), which allows each optical fiber link to simultaneously carry a large number of independent data streams at high rate. To take advantage of this high data processing potential, engineers and physicists have developed numerous technologies, including wavelength converters, optical switches, and tunable transceivers.(cont.) While the functionality provided by these devices is of great importance in capitalizing upon the WDM resources, a major challenge exists in determining how to configure these devices to operate efficiently under time-varying data traffic. In the WDM setting, we make two main contributions. First, we develop throughput optimal joint WDM reconfiguration and electronic-layer routing algorithms, based on maxweight scheduling. To mitigate the service disruption associated with WDM reconfiguration, our algorithms make decisions at frame intervals. Second, we develop analytic tools to quantify the maximum throughput achievable in general network settings. Our approach is to characterize several geometric features of the maximum region of arrival rates that can be supported in the network. In the packet switch setting, we observe through numerical simulation the attractive throughput properties of a simple maximal weight scheduler. Subsequently, we consider small switches, and analytically demonstrate the attractive throughput properties achievable using maximal weight scheduling. We demonstrate that such throughput properties may not be sustained in larger switches.(cont.) In the wireless network setting, mesh networking is a promising technology for achieving connectivity in local and metropolitan area networks. Wireless access points and base stations adhering to the IEEE 802.11 wireless networking standard can be bought off the shelf at little cost, and can be configured to access the Internet in minutes. With ubiquitous low-cost Internet access perceived to be of tremendous societal value, such technology is naturally garnering strong interest. Enabling such wireless technology is thus of great importance. An important challenge in enabling mesh networks, and many other wireless network applications, results from the fact that wireless transmission is achieved by broadcasting signals through the air, which has the potential for interfering with other parts of the network. Furthermore, the scarcity of wireless transmission resources implies that link activation and packet routing should be effected using simple distributed algorithms. We make three main contributions in the wireless setting. First, we determine graph classes under which simple, distributed, maximal weight schedulers achieve throughput optimality.(cont.) Second, we use this acquired knowledge of graph classes to develop combinatorial algorithms, based on matroids, for allocating channels to wireless links, such that each channel can achieve maximum throughput using simple distributed schedulers. Third, we determine new conditions under which distributed algorithms for joint link activation and routing achieve throughput optimality.by Andrew Brzezinski.Ph.D

Proton-transfer pathways in the mitochondrial S. cerevisiae cytochrome c oxidase

In cytochrome c oxidase (CytcO) reduction of O2 to water is linked to uptake of eight protons from the negative side of the membrane: four are substrate protons used to form water and four are pumped across the membrane. In bacterial oxidases, the substrate protons are taken up through the K and the D proton pathways, while the pumped protons are transferred through the D pathway. On the basis of studies with CytcO isolated from bovine heart mitochondria, it was suggested that in mitochondrial CytcOs the pumped protons are transferred though a third proton pathway, the H pathway, rather than through the D pathway. Here, we studied these reactions in S. cerevisiae CytcO, which serves as a model of the mammalian counterpart. We analyzed the effect of mutations in the D (Asn99Asp and Ile67Asn) and H pathways (Ser382Ala and Ser458Ala) and investigated the kinetics of electron and proton transfer during the reaction of the reduced CytcO with O2. No effects were observed with the H pathway variants while in the D pathway variants the functional effects were similar to those observed with the R. sphaeroides CytcO. The data indicate that the S. cerevisiae CytcO uses the D pathway for proton uptake and presumably also for proton pumping

Aspirin Inhibits TGFβ2-Induced Epithelial to Mesenchymal Transition of Lens Epithelial Cells:Selective acetylation of K56 and K122 in histone H3

Posterior capsule opacification (PCO) is a complication after cataract surgery that can disrupt vision. The epithelial to mesenchymal transition (EMT) of lens epithelial cells (LECs) in response to transforming growth factor β2 (TGFβ2) has been considered an obligatory mechanism for PCO. In this study, we tested the efficacy of aspirin in inhibiting the TGFβ2-mediated EMT of human LECs, LECs in human lens capsular bags, and lensectomized mice. In human LECs, the levels of the EMT markers α-smooth muscle actin (α-SMA) and fibronectin were drastically reduced by treatment with 2 mM aspirin. Aspirin also halted the EMT response of TGFβ2 when introduced after EMT initiation. In human capsular bags, treatment with 2 mM aspirin significantly suppressed posterior capsule wrinkling and the expression α-SMA in capsule-adherent LECs. The inhibition of TGFβ2-mediated EMT in human LECs was not dependent on Smad phosphorylation or MAPK and AKT-mediated signaling. We found that aspirin significantly increased the acetylation of K56 and K122 in histone H3 of human LECs. Chromatin immunoprecipitation assays using acetyl-H3K56 or acetyl-H3K122 antibody revealed that aspirin blocked the TGFβ2-induced acetylation of H3K56 and H3K122 at the promoter regions of ACTA2 and COL1A1. After lensectomy in mice, we observed an increase in the proliferation and α-SMA expression of the capsule-adherent LECs, which was ameliorated by aspirin administration through drinking water. Taken together, our results showed that aspirin inhibits TGFβ2-mediated EMT of LECs, possibly from epigenetic down-regulation of EMT-related genes

Classification of bicovariant differential calculi on the Jordanian quantum groups GL_{g,h}(2) and SL_{h}(2) and quantum Lie algebras

We classify all 4-dimensional first order bicovariant calculi on the Jordanian quantum group GL_{h,g}(2) and all 3-dimensional first order bicovariant calculi on the Jordanian quantum group SL_{h}(2). In both cases we assume that the bicovariant bimodules are generated as left modules by the differentials of the quantum group generators. It is found that there are 3 1-parameter families of 4-dimensional bicovariant first order calculi on GL_{h,g}(2) and that there is a single, unique, 3-dimensional bicovariant calculus on SL_{h}(2). This 3-dimensional calculus may be obtained through a classical-like reduction from any one of the three families of 4-dimensional calculi on GL_{h,g}(2). Details of the higher order calculi and also the quantum Lie algebras are presented for all calculi. The quantum Lie algebra obtained from the bicovariant calculus on SL_{h}(2) is shown to be isomorphic to the quantum Lie algebra we obtain as an ad-submodule within the Jordanian universal enveloping algebra U_{h}(sl(2)) and also through a consideration of the decomposition of the tensor product of two copies of the deformed adjoint module. We also obtain the quantum Killing form for this quantum Lie algebra.Comment: 33 pages, AMSLaTeX, misleading remark remove

An Operational Overview of the EXport Processes In the Ocean From RemoTe Sensing (EXPORTS) Northeast Pacific Field Deployment

The goal of the EXport Processes in the Ocean from RemoTe Sensing (EXPORTS) field campaign is to develop a predictive understanding of the export, fate, and carbon cycle impacts of global ocean net primary production. To accomplish this goal, observations of export flux pathways, plankton community composition, food web processes, and optical, physical, and biogeochemical (BGC) properties are needed over a range of ecosystem states. Here we introduce the first EXPORTS field deployment to Ocean Station Papa in the Northeast Pacific Ocean during summer of 2018, providing context for other papers in this special collection. The experiment was conducted with two ships: a Process Ship, focused on ecological rates, BGC fluxes, temporal changes in food web, and BGC and optical properties, that followed an instrumented Lagrangian float; and a Survey Ship that sampled BGC and optical properties in spatial patterns around the Process Ship. An array of autonomous underwater assets provided measurements over a range of spatial and temporal scales, and partnering programs and remote sensing observations provided additional observational context. The oceanographic setting was typical of late-summer conditions at Ocean Station Papa: a shallow mixed layer, strong vertical and weak horizontal gradients in hydrographic properties, sluggish sub-inertial currents, elevated macronutrient concentrations and low phytoplankton abundances. Although nutrient concentrations were consistent with previous observations, mixed layer chlorophyll was lower than typically observed, resulting in a deeper euphotic zone. Analyses of surface layer temperature and salinity found three distinct surface water types, allowing for diagnosis of whether observed changes were spatial or temporal. The 2018 EXPORTS field deployment is among the most comprehensive biological pump studies ever conducted. A second deployment to the North Atlantic Ocean occurred in spring 2021, which will be followed by focused work on data synthesis and modeling using the entire EXPORTS data set

Allelic polymorphism in the T cell receptor and its impact on immune responses

In comparison to human leukocyte antigen (HLA) polymorphism, the impact of allelic sequence variation within T cell receptor (TCR) loci is much less understood. Particular TCR loci have been associated with autoimmunity, but the molecular basis for this phenomenon is undefined. We examined the T cell response to an HLA-B*3501-restricted epitope (HPVGEADYFEY) from Epstein-Barr virus (EBV), which is frequently dominated by a TRBV9*01 public TCR (TK3). However, the common allelic variant TRBV9*02, which differs by a single amino acid near the CDR2β loop (Gln55→His55), was never used in this response. The structure of the TK3 TCR, its allelic variant, and a nonnaturally occurring mutant (Gln55→Ala55) in complex with HLA-B*3501 revealed that the Gln55→His55 polymorphism affected the charge complementarity at the TCR-peptide-MHC interface, resulting in reduced functional recognition of the cognate and naturally occurring variants of this EBV peptide. Thus, polymorphism in the TCR loci may contribute toward variability in immune responses and the outcome of infection

Genome-wide association identifies ATOH7 as a major gene determining human optic disc size

Optic nerve assessment is important for many blinding diseases, with cup-to-disc ratio (CDR) assessments commonly used in both diagnosis and progression monitoring of glaucoma patients. Optic disc, cup, rim area and CDR measurements all show substantial variation between human populations and high heritability estimates within populations. To identify loci underlying these quantitative traits, we performed a genome-wide association study in two Australian twin cohorts and identified rs3858145, P = 6.2 × 10−10, near the ATOH7 gene as associated with the mean disc area. ATOH7 is known from studies in model organisms to play a key role in retinal ganglion cell formation. The association with rs3858145 was replicated in a cohort of UK twins, with a meta-analysis of the combined data yielding P = 3.4 × 10−10. Imputation further increased the evidence for association for several SNPs in and around ATOH7 (P = 1.3 × 10−10 to 4.3 × 10−11, top SNP rs1900004). The meta-analysis also provided suggestive evidence for association for the cup area at rs690037, P = 1.5 × 10−7, in the gene RFTN1. Direct sequencing of ATOH7 in 12 patients with optic nerve hypoplasia, one of the leading causes of blindness in children, revealed two novel non-synonymous mutations (Arg65Gly, Ala47Thr) which were not found in 90 unrelated controls (combined Fisher's exact P = 0.0136). Furthermore, the Arg65Gly variant was found to have very low frequency (0.00066) in an additional set of 672 controls

EXPORTS Measurements and Protocols for the NE Pacific Campaign

EXport Processes in the Ocean from Remote Sensing (EXPORTS) is a large-scale NASA-led and NSF co-funded field campaign that will provide critical information for quantifying the export and fate of upper ocean net primary production (NPP) using satellite information and state of the art technology