Congestion control, energy efficiency and virtual machine placement for data centers

Data centers, facilities with communications network equipment and servers for data processing and/or storage, are prevalent and essential to provide a myriad of services and applications for various private, non-profit, and government systems, and they also form the foundation of cloud computing, which is transforming the technological landscape of the Internet. With rapid deployment of modern high-speed low-latency large-scale data centers, many issues have emerged in data centers, such as data center architecture design, congestion control, energy efficiency, virtual machine placement, and load balancing. The objective of this thesis is multi-fold. First, an enhanced Quantized Congestion Notification (QCN) congestion notification algorithm, called fair QCN (FQCN), is proposed to improve rate allocation fairness of multiple flows sharing one bottleneck link in data center networks. Detailed analysis on FQCN and simulation results is provided to validate the fair share rate allocation while maintaining the queue length stability. Furthermore, the effects of congestion notification algorithms, including QCN, AF-QCN and FQCN, are investigated with respect to TCP throughput collapse. The results show that FQCN can significantly enhance TCP throughput performance, and achieve better TCP throughput than QCN and AF-QCN in a TCP Incast setting. Second, a unified congestion detection, notification and control system for data center networks is designed to efficiently resolve network congestion in a uniform solution and to ensure convergence to statistical fairness with “no state” switches simultaneously. The architecture of the proposed system is described in detail and the FQCN algorithm is implemented in the proposed framework. The simulation results of the FQCN algorithm implemented in the proposed framework validate the robustness and efficiency of the proposed congestion control system. Third, a two-level power optimization model, namely, Hierarchical EneRgy Optimization (HERO), is established to reduce the power consumption of data center networks by switching off network switches and links while still guaranteeing full connectivity and maximizing link utilization. The power-saving performance of the proposed HERO model is evaluated by simulations with different traffic patterns. The simulation results have shown that HERO can reduce the power consumption of data center networks effectively with reduced complexity. Last, several heterogeneity aware dominant resource assistant heuristic algorithms, namely, dominant residual resource aware first-fit decreasing (DRR-FFD), individual DRR-FFD (iDRR-FFD) and dominant residual resource based bin fill (DRR-BinFill), are proposed for virtual machine (VM) consolidation. The proposed heuristic algorithms exploit the heterogeneity of the VMs’ requirements for different resources by capturing the differences among VMs’ demands, and the heterogeneity of the physical machines’ resource capacities by capturing the differences among physical machines’ resources. The performance of the proposed heuristic algorithms is evaluated with different classes of synthetic workloads under different VM requirement heterogeneity conditions, and the simulation results demonstrate that the proposed heuristics achieve quite similar consolidation performance as dimension-aware heuristics with almost the same computational cost as those of the single dimensional heuristics

Photoacoustic microscopy

Photoacoustic microscopy (PAM) is a hybrid in vivo imaging technique that acoustically detects optical contrast via the photoacoustic effect. Unlike pure optical microscopic techniques, PAM takes advantage of the weak acoustic scattering in tissue and thus breaks through the optical diffusion limit (∼1 mm in soft tissue). With its excellent scalability, PAM can provide high-resolution images at desired maximum imaging depths up to a few millimeters. Compared with backscattering-based confocal microscopy and optical coherence tomography, PAM provides absorption contrast instead of scattering contrast. Furthermore, PAM can image more molecules, endogenous or exogenous, at their absorbing wavelengths than fluorescence-based methods, such as wide-field, confocal, and multi-photon microscopy. Most importantly, PAM can simultaneously image anatomical, functional, molecular, flow dynamic and metabolic contrasts in vivo. Focusing on state-of-the-art developments in PAM, this Review discusses the key features of PAM implementations and their applications in biomedical studies

Cooking shapes the structure and function of the gut microbiome

Diet is a critical determinant of variation in gut microbial structure and function, outweighing even host genetics1-3. Numerous microbiome studies have compared diets with divergent ingredients1-5, but the everyday practice of cooking remains understudied. Here, we show that a plant diet served raw versus cooked reshapes the murine gut microbiome, with effects attributable to improvements in starch digestibility and degradation of plant-derived compounds. Shifts in the gut microbiota modulated host energy status, applied across multiple starch-rich plants, and were detectable in humans. Thus, diet-driven host-microbial interactions depend on the food as well as its form. Because cooking is human-specific, ubiquitous and ancient6,7, our results prompt the hypothesis that humans and our microbiomes co-evolved under unique cooking-related pressures

Evaluation of Antigens for Development of a Serological Test for Human African Trypanosomiasis

BACKGROUND: Control and elimination of human African trypanosomiasis (HAT) can be accelerated through the use of diagnostic tests that are more accurate and easier to deploy. The goal of this work was to evaluate the immuno-reactivity of antigens and identify candidates to be considered for development of a simple serological test for the detection of Trypanosoma brucei gambiense or T. b. rhodesiense infections, ideally both. METHODOLOGY/PRINCIPAL FINDINGS: The reactivity of 35 antigens was independently evaluated by slot blot and ELISA against sera from both T. b. gambiense and T. b. rhodesiense infected patients and controls. The antigens that were most reactive by both tests to T. b. gambiense sera were the membrane proteins VSG LiTat 1.3, VSG LiTat 1.5 and ISG64. Reactivity to T. b. rhodesiense sera was highest with VSG LiTat 1.3, VSG LiTat 1.5 and SRA, although much lower than with T. b. gambiense samples. The reactivity of all possible combinations of antigens was also calculated. When the slot blot results of 2 antigens were paired, a VSG LiTat 1.3- ISG75 combination performed best on T. b. gambiense sera, while a VSG LiTat 1.3-VSG LiTat 1.5 combination was the most reactive using ELISA. A combination of SRA and either VSG LiTat 1.3 or VSG LiTat 1.5 had the highest reactivity on T. b. rhodesiense sera according to slot blot, while in ELISA, pairing SRA with either GM6 or VSG LiTat 1.3 yielded the best results. CONCLUSIONS: This study identified antigens that were highly reactive to T. b. gambiense sera, which could be considered for developing a serological test for gambiense HAT, either individually or in combination. Antigens with potential for inclusion in a test for T. b. rhodesiense HAT were also identified, but because their reactivity was comparatively lower, a search for additional antigens would be required before developing a test for this form of the disease.Support was provided by Bill & Melinda Gates Foundation (http://www.gatesfoundation.org/), grant 39524 (JMN); National Institutes of Health (https://www.nih.gov/), grant 2R37AI034432 (MAP); National Institute of Allergy and Infectious Diseases (https://www.niaid.nih.gov/), grants AI035739 and AI056866 (JB); Wellcome Trust (https://wellcome.ac.uk/), grant 101842 (MF); The Sandler Foundation to University of California (JMK); Agence nationale de la recherche (http://www.agence-nationale-recherche.fr/), grant ANR-11-LABX-0024 (DRR); Wellcome Trust Centre for Molecular Parasitology (http://www.gla.ac.uk/researchinstitutes/iii/wtcmp/), grant 104111/Z/14/Z (MPB, RMC and JCM). The funders provided support in the form of salaries for authors JMN, SB, AA, GM, MR, MAP, JB, MF, JMK, DRR, MPB, RMC and JCM, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. HW is an employee of MicroCoat Biotechnologie GmbH. This company was contracted by FIND to evaluate the reactivity of the antigens by slot blot and ELISA against sera. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Managing the Risks of Extreme Events and Disasters to Advance Climate Change Adaptation: Special Report of the Intergovernmental Panel on Climate Change

This Special Report on Managing the Risks of Extreme Events and Disasters to Advance Climate Change Adaptation (SREX) has been jointly coordinated by Working Groups I (WGI) and II (WGII) of the Intergovernmental Panel on Climate Change (IPCC). The report focuses on the relationship between climate change and extreme weather and climate events, the impacts of such events, and the strategies to manage the associated risks. The IPCC was jointly established in 1988 by the World Meteorological Organization (WMO) and the United Nations Environment Programme (UNEP), in particular to assess in a comprehensive, objective, and transparent manner all the relevant scientific, technical, and socioeconomic information to contribute in understanding the scientific basis of risk of human-induced climate change, the potential impacts, and the adaptation and mitigation options. Beginning in 1990, the IPCC has produced a series of Assessment Reports, Special Reports, Technical Papers, methodologies, and other key documents which have since become the standard references for policymakers and scientists.This Special Report, in particular, contributes to frame the challenge of dealing with extreme weather and climate events as an issue in decisionmaking under uncertainty, analyzing response in the context of risk management. The report consists of nine chapters, covering risk management; observed and projected changes in extreme weather and climate events; exposure and vulnerability to as well as losses resulting from such events; adaptation options from the local to the international scale; the role of sustainable development in modulating risks; and insights from specific case studies

An interdisciplinary study of the hazards associated with an AD1754 style eruption of Taal Volcano, Philippines

Taal Volcano, 60 km south of Metro Manila in Batangas Province, is one of the most active volcanoes in the Philippines. With 33 known eruptions, Taal has caused tremendous impacts on lives, property, economy and environment. The exposure of people and assets around Taal has increased greatly in recent years with around two million people living within a 35 km radius all at risk to volcanic hazards. The risk from Taal poses multiple challenges for local volcano disaster risk reduction (DRR) efforts. This interdisciplinary study combines a synthesis and critical review of historical eruptions of Taal; physical studies (geologic mapping, stratigraphic analyses and grain size measurements of the AD1754 tephra deposit); reconstruction of tephra dispersal for the AD1754 Plinian event using TEPHRA2 inversion modelling; and consideration of the social aspects of volcanic hazard and risk (e.g. socio-economic, political and DRR contexts for Batangas Province, and a pilot study assessing the knowledge, education, awareness and preparedness of Barangay Captains who are responsible for local level volcano disaster preparedness and response). Key outputs of the research include: 1) the first single, comprehensive chronology of identified historical eruptions of Taal; 2) discovery, mapping and sampling of 41 suspected AD1754 tephra outcrops; 3) first detailed field-based verification of two of the four identified phases of this event; 4) determination of likely eruption source parameters for the AD1754 event and new tephra dispersal isopachs through inversion modelling; and 5) preliminary insights into the knowledge, awareness and preparedness of the Barangay Captains, which show that while they do take volcanic risk seriously, they are ill-prepared to effectively support their communities in the case of a major volcanic crisis at Taal. The results and recommendations are aimed at strengthening volcano disaster risk management plans for Batangas Province

An Integrated Approach for Including Social Capacities, and Economic Valuation in Risk Assessment of Water Related Hazards in Uncertain Scenarios

We propose a conceptual framework, KR-FWK (i.e. KULTURisk Framework from the name of the European project within which it originated) and its implementation methods SERRA (Socio-Economic Regional Risk Assessment) for integrated (physical and economical) risk assessment, and economic valuation of risk prevention benefits on multiple receptors. The KR-FWK and the SERRA approach are characterised by: (i) integration of physical-environmental dimensions and the socio-economic ones in risk assessment; (ii) consideration of the role of social capacities (adaptive and coping capacity) in reducing risk and related costs, (iii) quantitative (even monetary) assessment of risks and of the benefits of risk reduction measures, and (iv) solutions to deal with multiple sources of uncertainty in view of including the change dimension in decision support. Building on a widely adopted conceptual model, Risk is here considered as the combination of Hazard, Vulnerability and Exposure. In turn, Vulnerability is the result of the interactions between physical characteristics (susceptibility) and the capacities of the socio-economic system to adapt and cope with a given natural hazard. Exposure quantifies the natural and anthropogenic assets, which may be subject to the hazard. Whenever possible and desirable, exposure can be assessed in monetary terms, and thus the multiplicative combination of two indices ranging between 0 and 1 (H and V) with a third one (E) expressed in monetary terms produces a monetary quantification of risk. KR-FWK and SERRA have been applied to a series of case studies to test and consolidate the approach in various contexts of data availability, scale, etc

Managing Network Delay for Browser Multiplayer Games

Latency is one of the key performance elements affecting the quality of experience (QoE) in computer games. Latency in the context of games can be defined as the time between the user input and the result on the screen. In order for the QoE to be satisfactory the game needs to be able to react fast enough to player input. In networked multiplayer games, latency is composed of network delay and local delays. Some major sources of network delay are queuing delay and head-of-line (HOL) blocking delay. Network delay in the Internet can be even in the order of seconds. In this thesis we discuss what feasible networking solutions exist for browser multiplayer games. We conduct a literature study to analyze the Differentiated Services architecture, some salient Active Queue Management (AQM) algorithms (RED, PIE, CoDel and FQ-CoDel), the Explicit Congestion Notification (ECN) concept and network protocols for web browser (WebSocket, QUIC and WebRTC). RED, PIE and CoDel as single-queue implementations would be sub-optimal for providing low latency to game traffic. FQ-CoDel is a multi-queue AQM and provides flow separation that is able to prevent queue-building bulk transfers from notably hampering latency-sensitive flows. WebRTC Data-Channel seems promising for games since it can be used for sending arbitrary application data and it can avoid HOL blocking. None of the network protocols, however, provide completely satisfactory support for the transport needs of multiplayer games: WebRTC is not designed for client-server connections, QUIC is not designed for traffic patterns typical for multiplayer games and WebSocket would require parallel connections to mitigate the effects of HOL blocking

Release of insulin from PLGA-alginate dressing stimulates regenerative healing of burn wounds in rats

Burn wound healing involves a complex set of overlapping processes in an environment conducive to ischemia, inflammation, and infection costing $7.5 billion/year in the US alone, in addition to the morbidity and mortality that occur when the burns are extensive. We previously showed that insulin, when topically applied to skin excision wounds, accelerates re-epithelialization, and stimulates angiogenesis. More recently, we developed an alginate sponge dressing (ASD) containing insulin encapsulated in PLGA microparticles that provides a sustained release of bioactive insulin for >20days in a moist and protective environment. We hypothesized that insulin-containing ASD accelerates burn healing and stimulates a more regenerative, less scarring, healing. Using a heat-induced burn injury in rats, we show that burns treated with dressings containing 0.04mg insulin/cm2, every three days for 9 days, have faster closure, faster rate of disintegration of dead tissue, and decreased oxidative stress.In addition, in insulin-treated wounds the pattern of neutrophil inflammatory response suggests faster clearing of the burn dead tissue. We also observe faster resolution of the pro-inflammatory macrophages. We also found that insulin stimulates collagen deposition and maturation with the fibers organized more like a basket weave (normal skin) than aligned and crosslinked (scar tissue). In summary , application of ASD-containing insulin-loaded PLGA particles on burns every three days stimulates faster and more regenerative healing. These results suggest insulin as a potential therapeutic agent in burn healing and, because of its long history of safe use in humans, insulin could become one of the treatments of choice when repair and regeneration are critical for proper tissue function.This work was supported by the National Natural Science Fund of China [grant numbers 81170761 and 81270909 (to Y.L.)]; the Natural Sciences and Engineering Research Council of Canada [grant numbers 204794-2011 (to M.H.) and private donor (to M.M.-G.)]