VictorJuiz/thesis huggingface dataset:
Development and testing of mono- and multimeric hammerhead ribozymes for HIV-1 gene therapy

Moloney murine leukemia virus (MoMuLV)-derived retroviral vectors were developed to allow delivery and expression of five monomeric hammerhead ribozymes targeted against conserved sites within HIV-1 gag, pro, RT, tat and env coding regions. The susceptibility to ribozyme-mediated cleavage of these five highly conserved sites within HIV-1 RNA was compared both in vitro and in vivo . These retroviral vectors were tested in a human CD4+ T lymphoid cell line (MT4) for their anti-HIV-1 efficacy using the pool of stably transduced MT4 cells. While the ribozymes differed both in their ability to cleave HIV-1 sequences in vitro and their efficacy to inhibit HIV-1 replication in vivo, no direct correlation could be found between the two. Next, a multimeric ribozyme strategy was adopted as a second approach to improve on the anti-HIV-1 efficacy of hammerhead ribozymes. A retroviral vector expressing a multimeric ribozyme (RzEnv1-9) targeting several conserved sites within HIV-1 RNA was developed and compared with a monomeric ribozyme (RzEnv) for its anti-HIV-1 potential in MT4 cells. Although in MT4 cells, the monomeric ribozyme could only delay viral replication and the virus eventually escaped ribozyme inhibition, almost no virus could be detected in cells expressing the multimeric ribozyme for up to sixty days post-infection. PCR analysis of HIV-1 infected RzEnv1-9-expressing cells at days three and sixty post-infection confirmed the presence of HIV-1 and RzEnv1-9 sequences within the genome of MT4 cells. RT-PCR analysis of the above cells at day sixty post-infection confirmed the presence of Rz Env1-9 RNA, whereas, no HIV-1 RNA could be detected. To further study the anti-HIV-1 potential of RzEnv and Rz Env1-9 in a more clinically relevant setting, hu-PBLs were obtained from healthy donors, stably transduced with retroviral vectors expressing RzEnv and RzEnv1-9 and challenged with a laboratory strain and a primary clinical isolate of HIV-1. Upon HIV-1 challenge, both RzEnv and RzEnv1-9-expressing cells demonstrated significant inhibition of HIV-1 replication, with better inhibition of virus replication obtained by RzEnv1-9-expressing cells. (PsycINFO Database Record (c) 2016 APA, all rights reserved)
Trace-based optimization for precomputation and prefetching

Memory latency is an important barrier to performance in computing applications. With the advent of Simultaneous Multithreading, it is now possible to use idle thread contexts to execute code that prefetches data, thereby reducing cache misses and improving performance. TOPP is a system that completely automates the process of detecting delinquent loads, generating prefetch slices and executing prefetch slices in a synchronized manner to achieve speedup by data prefetching. We present a detailed description of the components of TOPP and their interactions. We identify tradeoffs and significant overheads associated with TOPP and the process of prefetching. We evaluate TOPP on memory-intensive benchmarks and demonstrate drastic reductions in cache misses in all tested benchmarks, leading to significant speedups in some cases, and negligible benefits in others.
Gigabit/second clock and data recovery circuits for local area networks

The demand for high data rate information at the subscriber terminal has increased the need for inexpensive high-speed serial data receivers. The most challenging part in the receiver is the design of the clock and data recovery (CDR), which defines the performance of the overall transceiver system. This thesis deals with the integration of high speed PLL-based CDR circuits for serial receiver applications. A 5Gb/s CDR implemented in a 0.18mum CMOS process with a supply voltage of 1.8V was designed and characterized. Extensive isolation and decoupling techniques in the layout of the CDR are used to reduce the effect of cross-talk and the power supply and ground noise. The CDR area was 0.3mm2 and the total power dissipation was 80mW. The total generated jitter was 4.8ps (rms). The CDR achieved a bit error rate of 10-12 with a data eye opening of 35%. This thesis proposes and implements a design methodology for an economical, fully integrated and high speed PLL-based CDR with a bang-bang phase detector in a CMOS process without the use of integrated inductors and off-chip capacitors. To overcome the problems associated with the use of an on-chip loop filter capacitor, a novel four-step bang-bang phase detector is proposed and used in the CDR design to meet the requirements of a short serial link in local area networks (LAN) applications. A 10Gb/s CDR was also implemented in a 0.13mum CMOS process. The challenge of designing the CDR in such a process is to overcome the limitations imposed by the 1.2V power supply voltage. A 10Gb/s random pattern generator with a random sequence of 211-1 was implemented on the same chip to eliminate testing problems associated with transferring off-chip high speed test patterns to the CDR. The CDR area was 0.6mm2 and the total power dissipation was 140mW The maximum generated jitter was 3ps (rms). A data eye opening of 50% was necessary for the CDR to achieve the 10 -12 bit error rate.
Expression of heat shock proteins 70 and 90 in tissues of the western painted turtle following bacterial infection and anoxia

Hsp73, 72 and 90 expression was investigated in the western painted turtle following bacterial infection, forced dive and reoxygenation. Following infection, Hsp73 expression increased in brain, liver and heart; Hsp72 in brain and liver; Hsp90 in brain, heart and skeletal muscle. Following a 30h forced dive, Hsp73, 72 and 90 expression remained at control levels for at least 12h in all tissues but the liver. Brain and liver Hsp73, 72 and 90 expression increased 3-fold by 18, 24 and 30h dive. Heart and muscle Hsp73 and heart Hsp90 expression did not change throughout the entire dive, while heart and muscle Hsp72 and muscle Hsp90 increased 4-fold by 24 and 30h dive. Following reoxygenation, Hsp expression increased in all tissues. I conclude that increased Hsp expression is not critical to early anoxic survival but could play a role in promoting long-term anoxia tolerance.
Abjection, sublimity, and the question of the unpresentable in Poe, Baudelaire, and Lovecraft

Edgar Allan Poe, Charles Baudelaire, and Howard Phillips Lovecraft: what do these three authors have in common, aside from superficial similarities prevalent to the "damned artist" type, such as a turbulent life marked by social alienation and an early death? Their respective statuses at the margins of the literary establishment during their lifetimes and their espousals of reactionary social and political perspectives (Poe championed slavery, Baudelaire was a misanthrope and an anti-Semite, and Lovecraft was, during the first part of his adult life, a proponent of Nazi eugenics) point to affinities than run deeper than merely biographical coincidences: all three were beholden to, yet distanced themselves from, the widespread currents of thought of their respective epochs. This tension that characterizes their worldviews informs their art: in defying the status quo, Poe and Baudelaire were committed to uncovering a new way of seeing that would radically change our relation to the world; Lovecraft, on the other hand, adopted a reactionary aesthetics in an attempt to ward off the horrors of modern life. In examining the critical and literary works of each author, this thesis argues that Poe's, Baudelaire's, and Lovecraft's common ground is aesthetic: each bases his critical theory on the sublime and engages aspects of sublimity in his literature. However, the subjective position conveyed in the poetry of Baudelaire and the fiction of Poe and Lovecraft is conditioned by the abject. In other words, a tension arises between the sublime that defines their poetics and the abjection that founds their fictional personae. Ultimately, by outlining the limits of the sublime experience by means of the abject, their literature explores the question of the unpresentable and enlists them as contributors to the modernist avant-garde project. Unless otherwise indicated, emphasis in citations is present in the original source. All citations are unadulterated except for typographic symbols, which have been modified for consistency. In parenthetical references Poe's complete works are cited as CW; Baudelaire's are identified as OC. When quoting or paraphrasing critical works, parenthetical references provide the title of the scholarly text the first time it is cited; all other entries contain only the name of the author and the page number, except for cases in which I cite more than one work for a given writer. In such instances, in addition to the author's name and the page number, the abbreviated title of the work appears in parentheses in all subsequent entries.
Two-dimensional finite element analysis of confined concrete columns and beams

A two-dimensional non-linear finite element program, named Confine4.1, was developed to analyze the confining effects in columns and beams. The constitutive material model was selected and slightly modified from other models available in the literature. The program was verified against 18 columns tested under concentric compression and two columns tested under eccentric compression. The program was able to accurately predict the load-strain response and the moment curvature response of the columns, including the post-peak response. The use of a triaxial failure criterion allows the prediction of cover spalling to be made. The program was able to distinguish the effects of varying concrete strengths, transverse yield strength and the amount of transverse reinforcement. Confine4.1 is a research tool and further work is needed before can be used in day-to-day engineering.
Segmented ring-oscillator based 8-bit digital pulse width modulator power controller IC

The purpose of this thesis is to develop a complete Digital Pulse Width Modulator (DPWM) solution for high-frequency dc-dc Switch-Mode Power Supply (SMPS) that is well-suited for integration in power management systems of portable devices. The DPWM is required to have low-power and low-area consumption, whilst having high resolution and high switching frequency operation. The proposed architecture consists of a DPWM based on a segmented ring-oscillator structure to time-quantize the resolution steps. It also includes a digitally programmable switching frequency capability, in addition to having the option of matching the switching frequency to that of an external clock reference. The proposed architecture has been implemented on a standard TSMC 0.18 mum CMOS process and has been verified through simulation and experiments. The mostly digital content of this design has made this design very portable, and so it has been prototyped on an FPGA system.
Evaluation of Gliricidia Sepium provenances in an alley cropping system with maize in Sri Lanka using vector competition analysis

The productivity of an alley cropping system comparing three provenances of Gliricidia sepium, originating from Sri Lanka and each of the wet and dry zones of Guatemala was evaluated in sole and mixed crop combinations in the intermediate zone of Sri Lanka. The objectives were to investigate growth and nutrient interactions in the alley cropping system of G. sepium provenances with maize using Vector Competition Analysis (VCA), and recommend the most effective G. sepium provenance to improve crop productivity and soil fertility. Yield measurements revealed that the growth interactions were synergistic except in alleys with the dry provenance of Guatemala. Both crop and tree yields exceeded sole cropping yields, and the major limiting factors of productivity were identified as nutrients, particularly nitrogen on VCA. The wet provenance of Guatemala was recommended for use because of its superiority in biomass production and soil fertility enrichment, and low underground competition.
Cloning and characterization of the insulin receptor-related receptor (IRR) reveals that it is closely associated with trkA in the genome and maps to human chromosome 1q22, A type 2 diabetes susceptibility locus

The insulin receptor-related receptor (IRR) is structurally and functionally related to the insulin receptor and IGF-IR, but its physiological ligand and role are unknown. Cloning of the mouse IRR gene in this study has revealed that the IRR gene is positioned extremely close to the trkA gene in the genome; this genomic orientation is conserved in humans. The IRR and trkA genes are arranged head-to head, with their transcription start only ∼1.6 kb apart. This close proximity raises the interesting possibility that this intergenic region functions as a bidirectional (divergent) promoter, responsible for the temporal and spatial coordinate expression of these genes seen in specific neurons. This observation also supports the possible existence of other members of these receptor tyrosine kinase families, and provides considerations for the development and analysis of knockout mice. Cross-species promoter analysis in this study identifies several well conserved motifs, (including a putative insulin response element (IRE)), supporting their potential involvement in the regulation of gene expression The identification of a polymorphic marker within the first intron of IRR allowed the precise mapping of this gene to human chromosome 1q22, with respect to several known polymorphic markers. This revealed that IRR lies in a region that has been shown to be linked to the development of type 2 diabetes in several populations, indicating that IRR is a candidate gene for the development of this disease. A human genomic clone carrying IRR was identified in the high throughput genome sequencing database, providing the full genomic sequence of IRR, to allow for investigations of polymorphisms within this gene. Other candidate genes, including hypothetical genes, within this chromosomal region have been identified, and a novel mathematical model to help evaluate coding regions of DNA and colon reading frames has been developed. This model has been used as a tool to further investigate hypothetical genes in the IRR chromosomal region, showing that this tool can be applied to further predict the validity and accuracy of these potential coding regions, which are additional candidate genes for the development of type 2 diabetes.
Mate selection, social monogamy and pair bond behaviour in the big-clawed snapping shrimp, Alpheus heterochelis

Monogamous systems without biparental care have evolved in many taxa, even though they seem particularly costly to males, as they likely reduce a male's mating access to multiple females. In these cases, physiological and environmental factors play an important role in making monogamy selectively advantageous to males and females. The big-clawed snapping shrimp, Alpheus heterochelis, is found in male-female pairs in the field. In this thesis, its monogamous mating system was analyzed with regard to mate recognition, the social processes underlying the evolution of monogamy, pair bond behaviour, size assortative pairing, and the role of mate selection in pair formation and its possible implications for sexual selection. Recognition of mates is usually expected in pair-forming species. It was found that A. heterochelis can discriminate former mates from other, unknown conspecifics. In species exhibiting social monogamy, mate guarding and shared resource defense are common behaviour patterns. It was found that success in the defense of shared territory did not confer a significant advantage to animals in a pair bond. Extended mate guarding by the male, however, contributed importantly to monogamy. Males were unable to assess the female's pre-moult stage. Females are only receptive for a brief period of time after their moult, and engage in only one copulation. This makes searching for receptive females a costly strategy for males. These two factors support the monogamous reproductive system. Contrary to initial assumptions, male-male competition for females did not play a role in pair formation. In contrast, females chose, and competed for, access to larger males, who are most likely to be successful in shelter defense, probably to have a male reliably present in order to avoid eviction or injury by conspecifics. Males were more successful than females in obtaining high quality shelters from conspecifics, which might contribute to the sexual dimorphism in snapping claw size between males and females. Those males that competed successfully with other males for access to shelters were preferred by females. A female needs a reliable male present at the time of her moult to ensure fertilization, and protection when she broods the eggs.
The northeastern Ontario men's health study: test-retest reliability of the Physical Activity Questionnaire

The test-retest reliability sub-study of Northeastern Ontario Men's Health Study (NEOMHS) was conducted on the physical activity section of the questionnaire (see Appendix A). A random sample of controls who had previously responded to the questionnaire participated in the reliability sub-study (n = 95, response rate = 66%). The weighted kappa statistic and intraclass correlation coefficients (ICC) were used to assess reliability. ICC for average lifetime activity was 0.63. For occupational activity, weighted kappas ranged from 0.56 (early 20s) to 0.65 (5 years ago). Leisure-time activity was less reliably recalled: kappa = 0.10 (strenuous, leisure-time activity in the mid-teens) to 0.49 (strenuous, leisure-time activity 5 years ago). Since the reliability of physical activity is imperfect, there may be misclassification of exposure to physical activity. Bias in the association of physical activity and prostate cancer, may occur especially if the age-period of interest is during youth (mid-teens to early 30s).
A longitudinal study on the effect of mucoid Pseudomonas aeruginosa on the course of lung disease in pediatric cystic fibrosis patients

Mixed model regression analysis was employed in order to evaluate the relationship between Pseudomonas aeruginosa infectious status (PA; PA free, nonmucoid PA, and mucoid PA) and percent predicted forced expiratory volume in one second (ppFEVI) in 481 pediatric CF patients followed from 1991 to 2003. The annual rate of decline in ppFEV1 was 1.29% per year in PA free patients, 1.90% per year following nonmucoid PA culture, and 2.00% per year following culture of mucoid PA (p = 0.0004 and 0.0001 for PA free vs. nonmucoid and mucoid PA respectively). This difference in ppFEV1 slopes due to PA culture status was only significant in males. There was no statistically significant difference between ppFEV1 slopes of subjects with nonmucoid PA and mucoid PA (p = 0.99). The previously reported finding of increased decline in lung function following mucoid conversion of PA in young CF patients is not supported by this study.
The theoretical modeling of large aggregate telechelic gels with site-bond percolation theory

A unique site-bond percolation model was developed to describe the formation of gels by telechelic polymers in the large aggregate limit. This was accomplished by assigning a discrete number of bonding segments per site to mediate the formation of high-multiplicity bonds. For this model, the percolation threshold, and the scaling exponents for: the correlation length, weight average cluster size and gel fraction were calculated. These results were correlated with physical observations of the critical gelation concentration and the erodible fraction of a poly(ethylene glycol)-co-poly(N-isopropylacrylamide) telechelic gel. The model predictions of the percolation threshold agreed, within experimental error, with the experimental measurements of the critical gelation concentration. However, the gel fraction predictions of the model could not be compared with the experimental erosion data, because the erosion data indicated that the gel eroded through the dissolution of the network, rather than through the diffusion of sols from the gel network.
A study of organometallic block copolymer "nanobarrels" using electron microscopy and scattering techniques

Samples of asymmetric poly(ferrocenyldimethylsilane-b-dimethylsiloxane) (PFS-b-PDMS) copolymers with narrow polydispersity indices were synthesized by sequential anionic polymerization. Usually asymmetric block copolymers form star-like micelles when dissolved in a solvent selective for the longer block, but in this case nanotubes were formed in selective solvents for the longer PDMS block. The formation of the cylindrical morphology is likely due to the crystalline character of the short PFS block. These assemblies were viewed by transmission electron microscopy (TEM). PFS-b-PDMS nanotubes in n-decane were also studied in detail by static and dynamic light scattering. Since the refractive index of n-decane is similar to that of PDMS, the corona was contrast-matched. At 25°C, the PFS shell of the nanotubes behaves like a thin rigid rod with lengths of ca. 450 nm. If samples for TEM analysis are prepared by dipping the carbon-coated grid into the solution or by blotting the solvent with a piece of filter paper, the nanotubes fuse to form wormlike structures with lengths exceeding 10 mum. When the micelle solutions are heated to 50°C, the nanotubes dissociate and rearrange into dense rod-like micelles with lengths of ca. 150 nm. Here, the PFS core behaves like a "short" rigid rod. If the solutions are cooled back to room temperature, the nanotubes form again. This result establishes that both the dense rods and the nanotubes are equilibrium structures. Small angle neutron scattering measurements were performed on a series of PFS-b-PDMS micelle solutions. Although we still have not found the best form factor models to describe the micelles, we have obtained important information about their structure (the number of molecules per nanometer and the radii of gyration of the cross section). Finally, we explored the microphase segregation in the bulk state of an asymmetric PFS-b -PDMS sample (volume fraction of PFS = 0.20). We discovered the formation of a hexagonal periodic structure, where part of the major component forms the core of concentric cylinders surrounded by a shell of PFS. The remaining PDMS fills the interstitial spaces. The morphology was elucidated by small angle X-ray scattering, as well as by scanning and conventional TEM.
Modelling density variation due to phase change during droplet impact

A three-dimensional model of droplet impact and solidification has been modified to include the effects of density variation during phase change. The governing equations for conservation of mass, momentum, and energy, and a volume of fluid (VOF) equation are derived by assuming different but constant solid and liquid densities. A fixed-grid control volume discretization of the momentum and energy equations, combined with a volume-tracking algorithm to track free surfaces, has been developed. The numerical model was validated against the Stefan problem and a planar solidification problem, for which analytical solutions are available. The numerical and analytical solutions were in good agreement. The numerical model was then applied to simulate solidification shrinkage of molten tin in a rectangular mold. Finally, the effects of density variation during phase change were studied during the impact and solidification of a tin droplet impinging onto a stainless steel substrate.