RNA-DNA strand exchange by the Drosophila Polycomb complex PRC2.

Polycomb Group (PcG) proteins form memory of transient transcriptional repression that is necessary for development. In Drosophila, DNA elements termed Polycomb Response Elements (PREs) recruit PcG proteins. How PcG activities are targeted to PREs to maintain repressed states only in appropriate developmental contexts has been difficult to elucidate. PcG complexes modify chromatin, but also interact with both RNA and DNA, and RNA is implicated in PcG targeting and function. Here we show that R-loops form at many PREs in Drosophila embryos, and correlate with repressive states. In vitro, both PRC1 and PRC2 can recognize R-loops and open DNA bubbles. Unexpectedly, we find that PRC2 drives formation of RNA-DNA hybrids, the key component of R-loops, from RNA and dsDNA. Our results identify R-loop formation as a feature of Drosophila PREs that can be recognized by PcG complexes, and RNA-DNA strand exchange as a PRC2 activity that could contribute to R-loop formation

Data compression techniques applied to high resolution high frame rate video technology

An investigation is presented of video data compression applied to microgravity space experiments using High Resolution High Frame Rate Video Technology (HHVT). An extensive survey of methods of video data compression, described in the open literature, was conducted. The survey examines compression methods employing digital computing. The results of the survey are presented. They include a description of each method and assessment of image degradation and video data parameters. An assessment is made of present and near term future technology for implementation of video data compression in high speed imaging system. Results of the assessment are discussed and summarized. The results of a study of a baseline HHVT video system, and approaches for implementation of video data compression, are presented. Case studies of three microgravity experiments are presented and specific compression techniques and implementations are recommended

The analysis and synthesis of a parallel sorting engine

This thesis is concerned with the development of a unique parallel sort-merge system suitable for implementation in VLSI. Two new sorting subsystems, a high performance VLSI sorter and a four-way merger, were also realized during the development process. In addition, the analysis of several existing parallel sorting architectures and algorithms was carried out. Algorithmic time complexity, VLSI processor performance, and chip area requirements for the existing sorting systems were evaluated. The rebound sorting algorithm was determined to be the most efficient among those considered. The rebound sorter algorithm was implemented in hardware as a systolic array with external expansion capability. The second phase of the research involved analyzing several parallel merge algorithms and their buffer management schemes. The dominant considerations for this phase of the research were the achievement of minimum VLSI chip area, design complexity, and logic delay. It was determined that the proposed merger architecture could be implemented in several ways. Selecting the appropriate microarchitecture for the merger, given the constraints of chip area and performance, was the major problem. The tradeoffs associated with this process are outlined. Finally, a pipelined sort-merge system was implemented in VLSI by combining a rebound sorter and a four-way merger on a single chip. The final chip size was 416 mils by 432 mils. Two micron CMOS technology was utilized in this chip realization. An overall throughput rate of 10M bytes/sec was achieved. The prototype system developed is capable of sorting thirty two 2-byte keys during each merge phase. If extended, this system is capable of economically sorting files of 100M bytes or more in size. In order to sort larger files, this design should be incorporated in a disk-based sort-merge system. A simplified disk I/O access model for such a system was studied. In this study the sort-merge system was assumed to be part of a disk controller subsystem

Roles Of Euchromatin And Heterochromatin In Hepatocyte Maturation And Liver Fibrosis

Liver transplantation is the main treatment for acute liver failure patients; however, there is an insufficient supply of donor livers. Since transplanting hepatocytes, the main liver cell type, provides therapeutic effect and can be a bridge to transplant or recovery, scientists are working on generating replacement hepatocytes from stem cells and other cell types through reprogramming protocols. Currently, replacement hepatocytes recapitulate a subset of natural hepatocyte features, yet are still in an immature state, as they have not silenced all immature hepatocyte genes and activated all mature hepatocyte genes. Consequently, replacement hepatocytes do not perform as well as natural hepatocytes in transplant experiments. Despite these shortcomings, relatively little is known about how natural hepatic maturation is regulated, particularly at the chromatin level. We discovered extensive chromatin dynamics during hepatic postnatal maturation, including changes in H3K9me3-marked and H3K27me3-marked heterochromatin, and transcription. Heterochromatin is of particular interest, as we found that it guards cell identity by repressing lineage-inappropriate or temporally-inappropriate genes. We further classified H3K9me3- and H3K27me3-marked chromatin by compaction state with a novel assay, termed srHC-seq. In postnatal hepatocyte maturation H3K27me3-marked heterochromatin represses early maturation genes, late maturation genes, and alternative lineage genes to both regulate timing of hepatic maturation and repress alternate fates. Significantly, we identify a euchromatic H3K27me3+ promoter signature that predicts which H3K27me3-marked genes will derepress in response ablation of the enzymes that deposit H3K27me3. Disruption of either H3K9me3- or H3K27me3-marked chromatin leads to liver damage, and in the case of H3K27me3 this is likely due to the aberrant derepression of genes associated with fibrosis that normally have a euchromatic H3K27me3+ promoter signature. Our results emphasize the role of heterochromatin in regulating liver development, maturation, and fibrosis, and highlight the need to identify factors controlling heterochromatin formation and breakdown, both for the purposes of enhancing in vitro hepatic maturation and for understanding factors which predispose humans to disease

Retrieve: An Engineering Tool for Searching Remote Sensing and Environmental Engineering Databases

The design and development of a semi-automatic information retrieval system which features manual indexing, and an inverted file structure is presented. The system requires manual indexing done by an expert in the subject field to ensure high-precision searching. High-recall is achieved through the implementation of the inverted file. The system provides an interactive environment, a thesaurus for normalization of the indexing language, ranking of retrieved documents, and flexible output specifications. The purpose of this thesis is to present the design and development of in-house search-aid software for small document collections intended for Remote Sensing and Environmental Engineering users

Immune cell tracking following hematopoietic cell and gene therapy

In this project we combined standard cellular and molecular assays with a custom PCR-based technology based on high throughput sequencing to track genetically engineered cells in treated patients by means of viral integration sites (IS) analysis. We leveraged this analytical pipeline to 1) assess whether naïve T cells can still be produced for many years even in absence of any supply by multipotent progenitors in the bone marrow and 2) to investigate the origin of CAR-T cells that mediate anti-leukaemic responses or long-term immune surveillance. In a clinical trial X-linked Severe Combined Immunodeficiency patients received an infusion of autologous hematopoietic stem/progenitor cells corrected via retroviral vector encoding the interleukin-2 common cytokine receptor gamma chain. In these patients, many years after gene therapy only vector-positive T and NK cells persist while no other genetically engineered blood cell populations are detectable. By a comprehensive long-term immunophenotypic, molecular and functional characterization we demonstrated that the thymus is actively producing a new and diverse repertoire of vector-positive naïve T cells (TN). This suggests that, even if gene corrected HSC are absent, a de novo production of genetically engineered T cell is maintained by a population of gene-corrected long term lymphoid progenitors (Lt-LP). Moreover, tracking IS clonal markers overtime, we inferred that Lt-LP can support both T and NK cells production. In a separate clinical trial of CD19-CAR-T cells for the treatment of haematological malignancies, we used IS analysis to investigate the origin of short- and long-term circulating CAR-T cells that mediate early anti-leukaemic responses or long-term immune surveillance. We compared IS between the product and CAR-T cells at early/late timepoints in vivo. This analysis suggested that T memory stem cells (TSCMs) contained in the infused cell product, contributed the most to the generation of CAR-T cell clones during the peak response phase as well as to the generation of long-term persisting CAR-T cells

Leveraging Non-Volatile Memory in Modern Storage Management Architectures

Non-volatile memory technologies (NVM) introduce a novel class of devices that combine characteristics of both storage and main memory. Like storage, NVM is not only persistent, but also denser and cheaper than DRAM. Like DRAM, NVM is byte-addressable and has lower access latency. In recent years, NVM has gained a lot of attention both in academia and in the data management industry, with views ranging from skepticism to over excitement. Some critics claim that NVM is not cheap enough to replace flash-based SSDs nor is it fast enough to replace DRAM, while others see it simply as a storage device. Supporters of NVM have observed that its low latency and byte-addressability requires radical changes and a complete rewrite of storage management architectures. This thesis takes a moderate stance between these two views. We consider that, while NVM might not replace flash-based SSD or DRAM in the near future, it has the potential to reduce the gap between them. Furthermore, treating NVM as a regular storage media does not fully leverage its byte-addressability and low latency. On the other hand, completely redesigning systems to be NVM-centric is impractical. Proposals that attempt to leverage NVM to simplify storage management result in completely new architectures that face the same challenges that are already well-understood and addressed by the traditional architectures. Therefore, we take three common storage management architectures as a starting point, and propose incremental changes to enable them to better leverage NVM. First, in the context of log-structured merge-trees, we investigate the impact of storing data in NVM, and devise methods to enable small granularity accesses and NVM-aware caching policies. Second, in the context of B+Trees, we propose to extend the buffer pool and describe a technique based on the concept of optimistic consistency to handle corrupted pages in NVM. Third, we employ NVM to enable larger capacity and reduced costs in a index+log key-value store, and combine it with other techniques to build a system that achieves low tail latency. This thesis aims to describe and evaluate these techniques in order to enable storage management architectures to leverage NVM and achieve increased performance and lower costs, without major architectural changes.:1 Introduction 1.1 Non-Volatile Memory 1.2 Challenges 1.3 Non-Volatile Memory & Database Systems 1.4 Contributions and Outline 2 Background 2.1 Non-Volatile Memory 2.1.1 Types of NVM 2.1.2 Access Modes 2.1.3 Byte-addressability and Persistency 2.1.4 Performance 2.2 Related Work 2.3 Case Study: Persistent Tree Structures 2.3.1 Persistent Trees 2.3.2 Evaluation 3 Log-Structured Merge-Trees 3.1 LSM and NVM 3.2 LSM Architecture 3.2.1 LevelDB 3.3 Persistent Memory Environment 3.4 2Q Cache Policy for NVM 3.5 Evaluation 3.5.1 Write Performance 3.5.2 Read Performance 3.5.3 Mixed Workloads 3.6 Additional Case Study: RocksDB 3.6.1 Evaluation 4 B+Trees 4.1 B+Tree and NVM 4.1.1 Category #1: Buffer Extension 4.1.2 Category #2: DRAM Buffered Access 4.1.3 Category #3: Persistent Trees 4.2 Persistent Buffer Pool with Optimistic Consistency 4.2.1 Architecture and Assumptions 4.2.2 Embracing Corruption 4.3 Detecting Corruption 4.3.1 Embracing Corruption 4.4 Repairing Corruptions 4.5 Performance Evaluation and Expectations 4.5.1 Checksums Overhead 4.5.2 Runtime and Recovery 4.6 Discussion 5 Index+Log Key-Value Stores 5.1 The Case for Tail Latency 5.2 Goals and Overview 5.3 Execution Model 5.3.1 Reactive Systems and Actor Model 5.3.2 Message-Passing Communication 5.3.3 Cooperative Multitasking 5.4 Log-Structured Storage 5.5 Networking 5.6 Implementation Details 5.6.1 NVM Allocation on RStore 5.6.2 Log-Structured Storage and Indexing 5.6.3 Garbage Collection 5.6.4 Logging and Recovery 5.7 Systems Operations 5.8 Evaluation 5.8.1 Methodology 5.8.2 Environment 5.8.3 Other Systems 5.8.4 Throughput Scalability 5.8.5 Tail Latency 5.8.6 Scans 5.8.7 Memory Consumption 5.9 Related Work 6 Conclusion Bibliography A PiBenc

The Sudbury Neutrino Observatory

The Sudbury Neutrino Observatory is a second generation water Cherenkov detector designed to determine whether the currently observed solar neutrino deficit is a result of neutrino oscillations. The detector is unique in its use of D2O as a detection medium, permitting it to make a solar model-independent test of the neutrino oscillation hypothesis by comparison of the charged- and neutral-current interaction rates. In this paper the physical properties, construction, and preliminary operation of the Sudbury Neutrino Observatory are described. Data and predicted operating parameters are provided whenever possible.Comment: 58 pages, 12 figures, submitted to Nucl. Inst. Meth. Uses elsart and epsf style files. For additional information about SNO see http://www.sno.phy.queensu.ca . This version has some new reference

Database machines in support of very large databases

Software database management systems were developed in response to the needs of early data processing applications. Database machine research developed as a result of certain performance deficiencies of these software systems. This thesis discusses the history of database machines designed to improve the performance of database processing and focuses primarily on the Teradata DBC/1012, the only successfully marketed database machine that supports very large databases today. Also reviewed is the response of IBM to the performance needs of its database customers; this response has been in terms of improvements in both software and hardware support for database processing. In conclusion, an analysis is made of the future of database machines, in particular the DBC/1012, in light of recent IBM enhancements and its immense customer base