On I/O Performance and Cost Efficiency of Cloud Storage: A Client\u27s Perspective

Cloud storage has gained increasing popularity in the past few years. In cloud storage, data are stored in the service provider’s data centers; users access data via the network and pay the fees based on the service usage. For such a new storage model, our prior wisdom and optimization schemes on conventional storage may not remain valid nor applicable to the emerging cloud storage. In this dissertation, we focus on understanding and optimizing the I/O performance and cost efficiency of cloud storage from a client’s perspective. We first conduct a comprehensive study to gain insight into the I/O performance behaviors of cloud storage from the client side. Through extensive experiments, we have obtained several critical findings and useful implications for system optimization. We then design a client cache framework, called Pacaca, to further improve end-to-end performance of cloud storage. Pacaca seamlessly integrates parallelized prefetching and cost-aware caching by utilizing the parallelism potential and object correlations of cloud storage. In addition to improving system performance, we have also made efforts to reduce the monetary cost of using cloud storage services by proposing a latency- and cost-aware client caching scheme, called GDS-LC, which can achieve two optimization goals for using cloud storage services: low access latency and low monetary cost. Our experimental results show that our proposed client-side solutions significantly outperform traditional methods. Our study contributes to inspiring the community to reconsider system optimization methods in the cloud environment, especially for the purpose of integrating cloud storage into the current storage stack as a primary storage layer

Recent Advances in Wireless Communications and Networks

This book focuses on the current hottest issues from the lowest layers to the upper layers of wireless communication networks and provides "real-time" research progress on these issues. The authors have made every effort to systematically organize the information on these topics to make it easily accessible to readers of any level. This book also maintains the balance between current research results and their theoretical support. In this book, a variety of novel techniques in wireless communications and networks are investigated. The authors attempt to present these topics in detail. Insightful and reader-friendly descriptions are presented to nourish readers of any level, from practicing and knowledgeable communication engineers to beginning or professional researchers. All interested readers can easily find noteworthy materials in much greater detail than in previous publications and in the references cited in these chapters

Simulation and design of storage area network

Master'sMASTER OF ENGINEERIN

Routing Protocols in Modern IP Networks

Τα σύγχρονα IP δίκτυα συνεχώς εξελίσσονται και μεγαλώνουν. Ο αυξανόμενος αριθμός των όλο και περισσότερο ο διασυνδεδεμένων "έξυπνων" συσκευών, υποχρεώνει τους μηχανικούς δικτύων να πρέπει να διαχειριστούν ποικίλα δίκτυα με εκατοντάδες ή χιλιάδες διασυνδεμένες συσκευές. Η δρομολόγηση του IP πρωτοκόλλου είναι ο συνδετικός κρίκος μεταξύ όλων αυτών των δικτύων. Σκοπός της παρούσας πτυχιακής εργασίας είναι να αποτελέσει ένα εργαλείο αναφοράς των πρωτόκολλων δρομολόγησης, για σπουδαστές και μηχανικούς, των οποίων κύρια δραστηριότητα είναι η διαχείριση και η εποπτεία τεχνολογιών και πρωτοκόλλων δρομολόγησης σε IP δίκτυα.Modern IP networks are continuously evolving and growing. The fact that more and more devices become “smart” and have the ability to connect to an IP network makes network engineers come across a variety of different network topologies, on a daily basis, interconnecting hundreds or thousands of different subnets. IP routing is the key link between these subnets. The purpose of this thesis is to become a reference tool for students or engineers whose main responsibility is the management or administration of core routing technologies

Decoupling User Interface Design Using Libraries of Reusable Components

The integration of electronic and mechanical hardware, software and interaction design presents a challenging design space for researchers developing physical user interfaces and interactive artifacts. Currently in the academic research community, physical user interfaces and interactive artifacts are predominantly designed and prototyped either as one-off instances from the ground up, or using functionally rich hardware toolkits and prototyping systems. During this prototyping phase, undertaking an integral design of the interface or interactive artifact’s electronic hardware is frequently constraining due to the tight couplings between the different design realms and the typical need for iterations as the design matures. Several current toolkit designs have consequently embraced component-sharing and component-swapping modular designs with a view to extending flexibility and improving researcher freedom by disentangling and softening the cause-effect couplings. Encouraged by early successes of these toolkits, this research work strives to further enhance these freedoms by pursuing an alternative style and dimension of hardware modularity. Another motivation is our goal to facilitate the design and development of certain classes of interfaces and interactive artifacts for which current electronic design approaches are argued to be restrictively constraining (e.g., relating to scale and complexity). Unfortunately, this goal of a new platform architecture is met with conceptual and technical challenges on the embedded system networking front. In response, this research investigates and extends a growing field of multi-module distributed embedded systems. We identify and characterize a sub-class of these systems, calling them embedded aggregates. We then outline and develop a framework for realizing the embedded aggregate class of systems. Toward this end, this thesis examines several architectures, topologies and communication protocols, making the case for and substantial steps toward the development of a suite of networking protocols and control algorithms to support embedded aggregates. We define a set of protocols, mechanisms and communication packets that collectively form the underlying framework for the aggregates. Following the aggregates design, we develop blades and tiles to support user interface researchers

Solving Challenging Structures using Single-Particle Cryogenic Electron Microscopy

Single-particle cryogenic electron microscopy (cryo-EM) has become a powerful mainstay tool in high resolution structural biology thanks to advances in hardware, software and sample preparation technology. In my thesis, I utilized this technique to unravel the function of various challenging biological macromolecules. My first focus was bacterial ribosomal biogenesis: understanding how bacteria assemble their ribosomes. Ribosomes are the factories of the cell, responsible for manufacturing all proteins. Ribosomes themselves are huge, with the bacterial version made of 52 proteins and 4566 RNA nucleotides. How these components assemble has long been a mystery. Early groundbreaking work sketched out a biogenesis pathway using purified components in vitro – but under non-physiological conditions. We sought to understand how the bacterial ribosome – specifically the large subunit 50S – is built inside the cell. To achieve this, we engineered a conditional knock-out bacterial strain that lacked one specific ribosomal protein (L17). This caused the cells to accumulate incomplete intermediates along the 50S biogenesis pathway. These intermediates were purified and examined with mass spectrometry and single-particle cryo-EM. Two major hurdles arose in this project: firstly, the biogenesis intermediates exhibited a preferred orientation when vitrified for cryo-EM analysis. This means that instead of showing many different views required for reconstruction of the 3D structure, the intermediates only adopted one view on the cryo-EM grid. To overcome this problem, we engineered a method to induce additional views on the microscope by tilting the stage. Using another test protein that also exhibited preferred orientation (hemagglutinin), we optimized and characterized this new tilt methodology and showed it was generally applicable to overcoming preferred orientation, regardless of type of specimen. We also created a software tool, called 3DFSC (3dfsc.salk.edu), for other microscopists to calculate the degree of directional anisotropy in their structures due to preferred orientation. Using this tilt strategy finally enabled the structural elucidation of our 50S intermediates. The second challenge in the project was the large amount of heterogeneity present in the sample. Through hierarchical 3D classification schemes using the latest software tools, we obtained 14 different 50S intermediate structures, all from imaging a single cryo-EM grid. By analyzing the missing components of each intermediate, and corroborating these observations with mass spectrometry data, we outlined the first in vivo 50S assembly pathway, and showed that ribosome assembly occurs step-wise and in parallel pathways. My second focus was on pushing the resolution limits of single-particle cryo-EM using adeno-associated virus (AAV) serotype 2 homogeneous virus-like particles (VLPs) that lack DNA. Exploiting several technical advances to improve resolution, including use of gold grids, per-particle CTF refinement, and correction for Ewald sphere curvature, we managed to obtain a 1.86 Å resolution reconstruction of the AAV2L336C variant VLP, the highest resolution icosahedral virus reconstruction solved by single-particle cryo-EM to date. Using our structure, we were able to show improvements using Ewald sphere curvature correction and shed light on the mechanistic basis as to why the L336C mutation resulted in defects in genome packaging and infectivity compared to the WT viral particles. My third focus was the understanding of small membrane proteins involved in infectious diseases. Membrane proteins are a challenge to work with due to the need for them to be extracted from the lipid bilayer for studies as compared to soluble proteins. Infectious diseases have a huge burden on society, with the top three infectious agents accounting for 2.7 million deaths in 2016. The third most deadly infectious disease is malaria, a mosquito-borne parasite which kills 450,000 people annually. One drug used early on for treating malaria was chloroquine but its usefulness waned due to development of resistance. Chloroquine resistance is mediated by the chloroquine resistance transporter (PfCRT). Although small (49 kDa) for single-particle cryo-EM, we solved its structure by using fragment antibody technology to add mass and help with image alignment and 3D reconstruction. The 3.2 Å structure resembles other drug metabolite transporters, and the chloroquine resistance mutations map to a ring around the central cavity, suggesting this central pore as the drug binding site. Tuberculosis (TB) is the top killer, above malaria and HIV/AIDS, being responsible for 1.3 million deaths. In TB, a common antibiotic target is the bacterium’s cell wall synthesis machinery. One family of such enzymes is the arabinosyltransferases, which synthesize the critical arabinose sugars. Using single-particle cryo-EM, we solved two high resolution structures of one such essential enzyme, AftD. Due to the low yield of the protein, a picoliter automated sample dispensing robot was crucial to allow for initial cryo-EM analysis. We then performed mutagenesis studies in M. smegmatis, a TB model organism, which uncovered the critical amino acid residues in the active site and determined that a bound acyl-carrier-protein was likely involved in allosteric inhibition of AftD’s active site. Another member of the family, EmbB, is the target of a widely used frontline TB drug called ethambutol. We have solved the high resolution structures of the apo and putative drug-bound states of EmbB, allowing us to map out, for the first time, both the active site and drug-resistance mutations of this crucial enzyme. The atomic structures of the functional pockets of Mycobacterial AftD and malarial PfCRT will hopefully enable structure-based drug design to improve existing drugs or potentially even develop new treatments against these infectious maladies. In conclusion, the continual and breathtaking improvements in single-particle cryo-EM methodology has been instrumental in allowing the elucidation of the aforementioned biological macromolecules from ribosome biogenesis intermediates, to AAV2 vehicle, Plasmodium drug resistance transporter to mycobacterial glycosyltransferases – structures of which help explain biological function

Mathematics & Statistics 2017 APR Self-Study & Documents

UNM Mathematics & Statistics APR self-study report, review team report, response report, and initial action plan for Spring 2017, fulfilling requirements of the Higher Learning Commission

Systems support for distributed learning environments

This thesis contends that the growing phenomena of multi-user networked "learning environments" should be treated as distributed interactive systems and that their developers should be aware of the systems and networks issues involved in their construction and maintenance. Such environments are henceforth referred to as distributed learning environments, or DLEs. Three major themes are identified as part of systems support: i) shared resource coherence in DLEs; ii) Quality of Service for the end- users of DLEs; and iii) the need for an integrating framework to develop, deploy and manage DLEs. The thesis reports on several distinct implementations and investigations that are each linked by one or more of those themes. Initially, responsiveness and coherence emerged as potentially conflicting requirements, and although a system was built that successfully resolved this conflict it proved difficult to move from the "clean room" conditions of a research project into a real world learning context. Accordingly, subsequent systems adopted a web-based approach to aid deployment in realistic settings. Indeed, production versions of these systems have been used extensively in credit-bearing modules in several Scottish Universities. Interactive responsiveness then emerged as a major Quality of Service issue in its own right, and motivated a series of investigations into the sources of delay, as experienced by end users of web-oriented distributed learning environments. Investigations into this issue provided insight into the nature of web-oriented interactive distributed learning and highlighted the need to be QoS-aware. As the volume and the range of usage of distributed learning applications increased the need for an integrating framework emerged. This required identifying and supporting a wide variety of educational resource types and also the key roles occupied by users of the system, such as tutors, students, supervisors, service providers, administrators, examiners. The thesis reports on the approaches taken and lessons learned from researching, designing and implementing systems which support distributed learning. As such, it constitutes a documented body of work that can inform the future design and deployment of distributed learning environments

EVALUATING THE ENDOPHYTIC FUNGAL COMMUNITY IN PLANTED AND WILD RUBBER TREES (Hevea brasiliensis)

The main objectives of this dissertation project were to characterize and compare the fungal endophytic communities associated with rubber trees (Hevea brasiliensis) distributed in wild habitats and under plantations. This study recovered an extensive number of isolates (more than 2,500) from a large sample size (190 individual trees) distributed in diverse regions (various locations in Peru, Cameroon, and Mexico). Molecular and classic taxonomic tools were used to identify, quantify, describe, and compare the diversity of the different assemblages. Innovative phylogenetic analyses for species delimitation were superimposed with ecological data to recognize operational taxonomic units (OTUs) or "putative species" within commonly found species complexes, helping in the detection of meaningful differences between tree populations. Sapwood and leaf fragments showed high infection frequency, but sapwood was inhabited by a significantly higher number of species. More than 700 OTUs were recovered, supporting the hypothesis that tropical fungal endophytes are highly diverse. Furthermore, this study shows that not only leaf tissue can harbor a high diversity of endophytes, but also that sapwood can contain an even more diverse assemblage. Wild and managed habitats presented high species richness of comparable complexity (phylogenetic diversity). Nevertheless, main differences were found in the assemblage's taxonomic composition and frequency of specific strains. Trees growing within their native range were dominated by strains belonging to Trichoderma and even though they were also present in managed trees, plantations trees were dominated by strains of Colletotrichum. Species of Trichoderma are known for their biocontrol properties, whereas species of Colletotrichum have been always associated with plant disease