Thesis (M.S.)--Villanova University, 2008. / Chemistry Dept. Includes bibliographical references.

Thesis (M.S.)--Villanova University, 2009. / Chemistry Dept. Includes bibliographical references.

The long stated vision of persistent memory is set to be realized with the release of 3D XPoint memory by Intel and Micron. Persistent memory, as the name suggests, amalgamates the persistence (non-volatility) property of storage devices (like disks) with byte-addressability and low latency of memory. These properties of persistent memory coupled with its accessibility through the processor load/store interface enable programmers to design in-memory persistent data structures. An important challenge in designing persistent memory systems is to provide support for maintaining crash consistency of these in-memory data structures. Crash consistency is necessary to ensure the correct recovery of program state after a crash. Ordering is a primitive that can be used to design crash consistent programs. It provides guarantees on the order of updates to persistent memory. Atomicity can also be used to design crash consistent programs via two primitives. First, as an atomic durability primitive which guarantees that in the presence of system crashes updates are made durable atomically, which means either all or none of the updates are made durable. Second, in the form of ACID transactions that guarantee atomic visibility and atomic durability. Existing systems do not support ordering, let alone atomic durability or ACID. In fact, these systems implement various performance enhancing optimizations that deliberately reorder updates to memory. Moreover, software in these systems cannot explicitly control the movement of data from volatile cache to persistent memory. Therefore, any ordering requirement has to be enforced synchronously which degrades performance because program execution is stalled waiting for updates to reach persistent memory. This thesis aims to provide the design principles and efficient implementations for three crash consistency primitives: ordering, atomic durability and ACID transactions. A set of persistency models have been proposed recently which provide support for the ordering primitive. This thesis extends the taxonomy of these models by adding buffering, which allows the hardware to enforce ordering in the background, as a new layer of classification. It then goes on show how the existing implementation of a buffered model degenerates to a performance inefficient non-buffered model because of the presence of conflicts and proposes efficient solutions to eliminate or limit the impact of these conflicts with minimal hardware modifications. This thesis also proposes the first implementation of a buffered model for a server class processor with multi-banked caches and multiple memory controllers. Write ahead logging (WAL) is a commonly used approach to provide atomic durability. This thesis argues that existing implementations ofWAL in software are not only inefficient, because of the fine grained ordering dependencies, but also waste precious execution cycles to implement a fundamentally data movement task. It then proposes ATOM, a hardware log manager based on undo logging that performs the logging operation out of the critical path. This thesis presents the design principles behind ATOM and two techniques that optimize its performance. These techniques enable the memory controller to enforce fine grained ordering required for logging and to even perform logging in some cases. In doing so, ATOM significantly reduces processor stall cycles and improves performance. The most commonly used abstraction employed to atomically update persistent data is that of durable transactions with ACID (Atomicity, Consistency, Isolation and Durability) semantics that make updates within a transaction both visible and durable atomically. As a final contribution, this thesis tackles the problem of providing efficient support for durable transactions in hardware by integrating hardware support for atomic durability with hardware transactional memory (HTM). It proposes DHTM (durable hardware transactional memory) in which durability is considered as a first class design constraint. DHTM guarantees atomic durability via hardware redo-logging, and integrates this logging support with a commercial HTM to provide atomic visibility. Furthermore, DHTM leverages the same logging infrastructure to extend the supported transaction size, from being L1-limited to the LLC, with minor changes to the coherence protocol.

The persistent organic pollutants (POPs) refer to many different chemicals that, upon release into the environment, remain intact for several decades. These contaminants travel long distances through repeated cycles of deposition and evaporation, and eventually deposit in the Arctic regions. The purpose of this work was to examine the potential human health implications of POP exposures among the Canadian Inuit, using modelling and epidemiological approaches. Blood guideline values were developed for the organochlorine pesticides, chlordane and toxaphene, and the polychlorinated biphenyls (PCBs) using the concept of biomonitoring equivalents (BEs), which are based on toxicity endpoints and toxicokinetic modelling to convert an oral reference dose to an equivalent blood concentration. The biomonitoring data from the Adult Inuit Health Survey (2007-2008) and the Canadian Health Measures Survey (CHMS, Cycle 1 2007-2009) were compared with the derived guideline values to assess population-level risks of exposures for the Inuit and the general Canadian population, respectively. Epidemiological analyses were also conducted to explore if POPs were associated with diabetes and high cholesterol, using data from the Inuit Health Survey. A set of BE values were derived for chlordane isomers and metabolite, three abundant toxaphene isomers, and the PCBs. The derived values are in a similar range of the BEs of other POPs in the literature. Among the Inuit, a large percentage exceeded the trans-nonachlor guideline value, particularly among the elderly. Fewer exceedances were observed for cis-nonachlor and oxychlordane, none for toxaphene, and minimally for the PCBs. In comparison, no exceedances for any of the POPs were observed in the general Canadian population. Highest vs. lowest quartile exposures to PCBs and p,p’-DDE were associated with increased risk of diabetes and an increase in fasting glucose among the Inuit. In addition, PCBs were associated with increased risk of high cholesterol, and higher levels of serum triglycerides, total cholesterol, and low-density lipoprotein cholesterol (LDL-C), but not high-density lipoprotein cholesterol (HDL-C). The results of this work suggest that exposures to POPs remain a potential health concern among the Canadian Inuit. Future research efforts should be devoted to collecting updated contaminant concentrations for the Inuit, measuring contaminants in prepared food samples, conducting cohort studies on contaminant exposures and health outcomes, and assessing the effects of chemical mixtures using statistical approaches and toxicokinetic modelling.

No description available.

No description available.

Hemorrhagic enteritis is a disease of turkeys caused by virulent strains of Turkey Hemorrhagic Enteritis Virus (THEV) resulting in depression, splenomegaly, intestinal hemorrhage, immunosuppression, and mortality. Avirulent strains that do not produce intestinal lesions and mortality are used in live-virus vaccines that protect turkeys from virulent field challenge. The cause for the difference in phenotype between virulent and avirulent strains is unknown. The full-length genome of the Virginia Avirulent Strain (VAS) of THEV was sequenced and compared to the genome sequence of a virulent field isolate from Israel. Genetic differences were found in seven viral genes. Further sequencing narrowed the focus from seven genes to three: ORF1, E3, and Fiber. Consistent variation in these genes between strains of THEV with different phenotypes strongly indicates these genes as key factors affecting virulence. THEV is an officially recognized member of the viral family Adenoviridae, genus Siadenovirus. The genomes of the members of the genus, THEV and Frog Adenovirus 1, are not well-characterized. The genome sequences of both members were compared for the prediction of genetic and structural elements. Common features were found that distinguish this genus from all other adenoviruses, and differences were found that possibly contribute to host specificity of the members. The VAS is known to stimulate a life-long protective antibody response, though viral replication is only of short duration. Several studies were undertaken to determine changes in virus location and serology over time. Viral DNA was detected in various tissues through 15 weeks post-infection in the presence of high antibody titers. THEV infection was found to be similar to the non-lytic persistent infections seen with human adenoviruses. Regardless of the mechanism involved in the persistent stimulation of antibodies in infected turkeys, the VAS was shown to be an ideal vector for use in a recombinant live-virus vaccine. The next step in THEV research should be the creation of a full-length infectious DNA clone, which could be used in the creation of a recombinant vaccine. The infectious clone would also allow for the systematic testing of genes that are suspected to be involved in virulence. / Ph. D.

No description available.

This thesis presents several descriptor selection schemes for video content pairwise-matching tasks. Those proposed schemes attempt to leverage two significant properties of videos, temporal correlation and motion information. Aiming to find an efficient and descriptive representation for a video sequence, the concept of descriptor persistency is defined. Those descriptors that satisfy this definition are called persistent descriptors. In order to exploit descriptor persistency, an encoder is proposed. The proposed encoder consists of five main components. First, keyframe labelling is introduced to reduce complexity and ensure a reasonable size of persistent sets. After that, persistent descriptor detection is performed on each group of pictures (GOP) separately. The second component is the standard SIFT descriptor extraction. The third part is to identify persistent descriptors from each GOP, called persistent descriptors extraction. In this stage, three different methods are proposed: The direct method and two approximation approaches. Persistent descriptors selection, which is the fourth stage, is carried out to control the size of the persistent set. For this stage, three selection methods are proposed. All of them attempt to utilize the motion information to select more descriptive descriptors among all the persistent descriptors in the GOP. In order to perform pairwise-matching, in this thesis, a simple but efficient pairwise-matching method is proposed. Experiments are carried out to evaluate the performance of the proposed schemes. The datasets used for performance evaluation are subsets from the categories that describe in [1]. Two metrics de ned in [2], namely false positive rate (FPR) and true positive rate (TPR), are used for the performance evaluation. / Thesis / Master of Applied Science (MASc)

The current thesis aims to address the prognosis and management of patients who have injuries necessitating orthopaedic surgery. In Chapter 1 I introduce the thesis, and in Chapter 5 I offer conclusions and summarize the contribution of the work. In Chapter 5, I address the scope, rationale, key findings, limitations and implications. Chapter 2 is a systematic review and meta-analysis investigating the effectiveness of antibiotic prophylaxis in patients with open fracture of the extremities. The results demonstrate moderate quality evidence of an important reduction in the infection rate in patients receiving, versus not receiving, antibiotic prophylaxis. We found no difference in infection rate with longer (3 to 5 days) versus shorter (1 day) duration of antibiotics – this finding warrants only low confidence. Chapter 3 is a systematic survey of current practice and recommendations regarding antibiotic prophylaxis in open fracture management. Authors of publications over the last decade strongly support early systemic antibiotics prophylaxis for patients with open fractures of extremities. In practice, most used systemic antibiotics with both gram-positive and gram-negative coverage, and continued the administration for 2 to 3 days. Most recommendations suggested gram-positive coverage for less severe injuries, and administration duration of no more than 3 days (half suggested 1 day). For more severe injuries, most recommendations suggested broad antimicrobial coverage continued for 2 to 3 days. Chapter 4 is a longitudinal study investigating predictors of persistent post-surgical pain after tibia fracture. We found significant independent associations between resolution of pain and male sex, non-smoking and alcohol consumption. Age, obesity, type of fracture (closed versus open), additional injuries, and post-operative weight-bearing status did not predict resolution of pain. Our findings suggest that clinicians should be particularly alert to the possibility of troublesome post-operative pain in female smokers who do not drink alcohol. Clinicians may consider counselling patients to discontinue smoking, inform them that they are at nearly double the risk of incidence of troublesome post-operative pain (in addition to the long-term adverse health consequences of smoking). / Thesis / Doctor of Philosophy (PhD) / Antibiotic prophylaxis reduces infection with 10% fewer event rate than the group without antibiotic prophylaxis (low to moderate confidence in estimates). The optimal antibiotic regimens and duration remain uncertain. There is a higher risk of persistent post-surgical pain in female smokers who do not use alcohol, following tibia fractures.