VictorJuiz/thesis huggingface dataset:
Effects of thrombin on the migration of primary osteogenic cells through fibrin-filled scaffolds

This thesis is directed towards a bone tissue engineering strategy that would maximize osteogenic cell invasion into the bony defect. Through culturing primary bone marrow cells under osteogenic culture conditions on PLGA 3-D scaffolds and examining the interface with SEM, TEM and EDS, a candidate PLGA scaffold was demonstrated to support direct bone contact. In an attempt to stimulate maximal invasion of host bone tissue in vivo, fibrin, the natural migration matrix of the blood clot, was investigated as a candidate scaffold pore-filling matrix. Scaffolds filled with fibrin, polymerized with either a low thrombin concentration (LTF) or a high thrombin concentration (HTF), were implanted into drill hole defects in the distal femurs of rats. The area of bone formed at 2, 5 and 11 days post implantation was determined histomorphometrically. After 5 days, scaffolds filled with HTF had 2.2 +/- 1.2% of their available area occupied by bone compared to 8.9 +/- 3.0% for empty scaffolds (p = 0.045, n = 3--4), but no statistical difference was found between the empty scaffolds and the scaffolds filled with LTF (p = 0.976, n = 3--4) which had 8.1 +/- 1.4% of their available area occupied by bone. However, after 11 days there was sim;50% less bone formed within the fibrin filled scaffolds compared to the empty scaffolds (p = 0.003, n = 3). Given that the thrombin, used to polymerize the fibrin, can also stimulate cell migration, the role of thrombin in osteogenic cell migration was investigated. It was shown, using a scratch wound assay, that thrombin stimulated a 2.1 +/- 0.7 (p = 0.042, n = 7) fold increase in cell migration and a common motogenic factor, PDGF-BB stimulated a 3.0 +/- 0.4 fold increase (p = 0.004, n = 3). When a modified Boyden chamber assay was combined with a bone nodule assay, primary cells that had migrated in the presence of thrombin formed 50% (p = 0.040, n = 7) more bone nodules compared to the condition without thrombin. This work has shown that the migration of osteogenic cells, through fibrin-filled PLGA scaffolds that support direct bone contact, can be modulated by altering the thrombin concentration present during fibrin polymerization, and that thrombin has the capacity to stimulate the migration of osteoprogenitor cells and increase bone formation by the migrated cells.
Exchanging experiences: knowledge-sharing through formal collaboration at BRAC and the Grameen Trust

The experiences vested in the individuals, procedures, records and actions of an organization are a valuable asset. Together they constitute an organization's knowledge. In the non-profit sector this knowledge has the potential to be shared amongst organizations wishing to learn from one another. Inter-organizational collaboration can be particularly valuable to non-profits in the social development sector and can help contribute to the achievement of the goals set out by them. This thesis examines the formal knowledge-sharing mechanisms established by two Bangladeshi organizations, BRAC and The Grameen Trust. The examination of the models established by them sheds light on the dynamics of knowledge-sharing through collaboration amongst development organizations, with a particular focus on the motivations, benefits and challenges of such collaboration. In addition it identifies key characteristics that can be learned from and that contribute to and hinder meaningful relationships amongst organizations. Finally it identifies areas where further study would be valuable.

Keywords: Nonprofit organizations, Bangladesh
Non-governmental organizations, Bangladesh
"New pressor protein (NPP)": functional relationship to coagulation factor FXII and potentiation of its cardiovascular effects by angiotensin I converting enzyme inhibitor captopril

A potent pressor activity expressed in bioassay rats has been observed in trypsin activated human and rat plasmas and attributed to a protein, “New Pressor Protein” (NPP). Purified human plasma NPP has been partially sequenced and shown to have strong homology with the βFXIIa of coagulation FXII. Intravenous (i.v.) NPP in bioassay rats exerts potent hypertensive effects that are greatly potentiated by the angiotensin I converting enzyme inhibitor, Captopril. These effects are associated with a dramatic rise in plasma adrenal medullary catecholamines. The cause of the potentiation and the mechanisms mediating the pressor effects are not fully understood. This study investigated the role of: (1) FXII and other coagulation factors in the NPP effect. (2) the mechanism by which NPP evokes its cardiovascular effects. (3) angiotensin, other peptides and adrenal medullary catecholamines in NPP potentiation by Captopril. (4) the kidneys in the NPP response. The biochemical relationship of NPP to βFXIIa is supported by studies using human plasmas deficient in coagulation FXII, which showed no NPP pressor activity. Other coagulation factor deficient plasmas showed considerable pressor effect, suggesting that NPP effect is due to FXII alone. Restoration of activity was obtained by adding highly purified active FXII to FXII deficient plasma and by direct i.v. injection of highly purified αFXIIa and βFXIIa. The potentiation of the NPP effect after Captopril is unaltered by replenishment of circulating angiotensin II (Ang II) level or inhibition of Ang II's action on its receptors, suggesting that depletion of Ang II is not the cause of potentiation. NPP appears to act enzymically via a cascade, resulting in the production of peptide(s) (e.g. bradykinin) which in turn are responsible for catecholamine release from the adrenal medulla. Enkephalins are not immediately involved, but appear to interact with NPP. Bilateral nephrectomy (2NX) alone significantly potentiated the NPP response without Captopril treatment, suggesting kidney participation in the cardiovascular effects of NPP. The present study strengthened the relationship of NPP to FXII, clarified the mechanism of Captopril's potentiation of the NPP effect, and shed new light on the relationship of NPP to the renin-angiotensin system (RAS), the sympatho-adrenal system and the kallikrein-kinin system.
A synchronization scheme based on an enhanced phase-locked loop system

This dissertation presents a synchronization method mainly for use in power electronic applications. The main building block of the system is an enhanced phase-locked loop (EPLL) system which offers structural simplicity and robustness. EPLL extracts the fundamental component of a distorted and noisy signal and estimates its amplitude, phase angle, and frequency. A number of EPLL units are added with appropriate computational blocks to build up the structure of the proposed synchronization system. The proposed system is (1) robust in performance and in structure, (2) highly immune to noise, (3) insensitive to distortions, (4) frequency-adaptive, (5) robust with respect to severe disturbances, and (6) operable in unbalanced conditions. The latter three features are the challenging requirements and are not met by conventional synchronization methods. The mathematical basis of the system is also discussed and stability issues are addressed. Several existing methods for synchronization are studied and their performances are compared with that of the proposed system by means of computer simulation case studies. Eventually, performance of the proposed system is evaluated for extracting the control signals and the synchronization signal in the context of both single-phase and three-phase power systems under steady-state and transient conditions. In both cases, the power systems are represented in the PSCAD/EMTDC power system software and the control algorithms are implemented in Matlab/Simulink/Fixed-Point Blockset. The two software environments are interfaced using link programs to operate interactively. These simulations represent models for hardware implementations such as FPGA.
In vivo characterization of ordered factor recruitment at CIITA inducible promoter IV

Chromatin may pose a major barrier to transcription of inducible genes. Previously we showed that IFN-γ induction of class II transactivator (CIITA) requires chromatin remodeling by BRG1, a component of SWI/SNF. My aim was to determine the stage at which BRG1 regulates CIITA transcription. Using ChIP and quantitative real-time PCR I detected BRG1 and acetylated histones at the promoter in untreated cells, and inducible ordered recruitment of a STAT1, USF1/c-Myc, IRF1, BRGI, CBP/p300 enhanceosome and Pol II, together with increased histone acetylation, in IFN-γ-treated cells. Analysis of a BRG1-deficient line revealed that, although transcription was totally BRG1-dependent, factor assembly and histone acetylation appeared to be only partially BRG1-dependent. My data suggest that in the absence of BRG1, transcription fails either because only incomplete enhanceosomes form, and/or because an unidentified factor, possibly involved in Pol II escape and/or elongation, cannot access the promoter.
Combined pricing and procurement decisions in stochastic inventory control theory

The classic Newsvendor Problem considers a single perishable product over a single period model. The per unit revenue, procurement, underage and overage costs are linear. Facing stochastic demand, the objective is to find the optimal procurement quantity so as to maximize the expected profit. It was shown in the literature that if the pricing decision is incorporated into the Newsvendor problem, the expected profit function loses its concavity property, but can be reduced to a single variable function. Moreover, with mild assumptions on the demand distribution, the objective function has at most two stationary points. In this thesis, by taking into account the bounds on the price that is inherent from the linear price-demand relationship, we show that the single variable expected profit function is in fact unimodal. We then extend the same result to a model that incorporates a second category of customers, who buy the end of period excess inventory in bulk and at a fixed discount price. The second extension of the basic Newsvendor with pricing model considers the launching of a new product that can be used to substitute a well-established product. Given the price of the existing product, the objective is to determine the price of the new product, and the procurement quantities of both products so as to maximize the expected profit over a single period. We show that an optimal solution can be found by solving O(n) number of single variable optimization problems, where n is the number of values the demand of the existing product can take. Moreover, under the same mild assumptions on the demand of the new product as the previous two models, each of these single variable functions has at most one stationary point that is a local maximum. We also show that, besides the expected profit, both the price and the procurement quantity of the new product are higher when it is offered as a substitute. This thesis attempts to put another building block to the bridge that connects Production/Operations Management, Marketing and Economics disciplines. We consider stochastic inventory control models that combine pricing and procurement decisions. Moreover, we specifically investigate the potential of using product substitution as a sales strategy in one of these models. Numerical studies are done to illustrate the potential profit benefit that can be achieved through integrating pricing and substitution decisions into stochastic inventory control models.
XJit: a framework for self-optimizing libraries

Code reuse is a software engineering cornerstone that has heavily influenced software language design and the software development process. However, pursuing the goal of code reuse by building software libraries causes significant optimization opportunities to elude traditional compilers. Compilers must view library calls as 'black boxes' that hold no particular semantic information. XJit is a framework for self-optimizing libraries built on top of Mono, an open-source implementation of the .NET runtime. Using XJit, library writers can express library-specific semantics with .NET metadata and an elegant graphical language that captures semantic intent using dataflow and control flow concepts. From these specifications, XJit composes high-level semantic optimizations that execute at JIT compile time, transparently optimizing end-user code. Our work shows that XJit has low overhead and a variety of software libraries can use it to achieve significant performance improvements.
Mixed-signal VLSI adiabatic array computing

Many real time signal processing algorithms require a large number of multiply-and-accumulate (MAC) operations per second to perform computationally expensive matrix transforms in real time. Implantable and wearable implementations impose an additional constraint of a small power budget. This thesis presents two adiabatic parallel processor designs satisfying both of these requirements. The processors employ a resonantly-adiabatic mixed-signal VLSI computational array, with the oscillator tank comprised of the on-chip load capacitance and an off-chip inductor. The massively parallel nature of the architecture allows to reduce adiabatic resistive losses by lowering clock frequency while maintaining high computational throughput. Energy losses are further minimized by keeping the on-chip load capacitance near its mean value for any input data, maintaining the resonance at its nominal frequency. The 256×512 resonantly-adiabatic computational array is validated in template-based face detection, and spectral analysis of neural recordings.
An investigation of attitudes towards safety in the Ontario construction industry

Safety climate research is a fundamental organizational approach to safety that entails identifying attitudes and perceptions that may be root causes of workplace incidents and injuries. This study provides a construction industry specific questionnaire that documents worker attitudes and perceptions towards a variety of organizational and physical site factors that affect safety on construction sites. A total of 275 construction workers completed the survey. Thirteen safety attitude factors were found to be consistent over the entire sample of participants. A variety of statistical methods identified numerous relationships between the factors and demographic characteristics of the participants. Most important of those were the four factors found to be statistically significant with safety performance (measured from self reported incident data). In addition to the safety climate research, attitudes towards the main causes of injuries and site safety inspections were documented. Recommendations for future construction safety climate were given.
Study of the role of endoglin in T cell development and function

Endoglin, a component of the TGF-beta receptor superfamily, has been characterized on various subsets of hematopoietic lineages. During T cell development, endoglin expression is first observed during pre-TCR signalling, and subsequently on activated CD8+ T cells. Eng+/- mice had normal viral clearance following in vivo Influenza infection. T cells from Eng+/- mice of mixed genetic background (129/Ola x C57BL/6) were hyper-responsive following mitogenic stimuli and less inhibited by TGF-beta1 than the control littermates. This was also observed in Eng+/- mice of 129/Ola but not C57BL/6 background suggesting effects of potential modifier genes in the autoimmune 129/Ola strain. Using an in vitro T cell differentiation system, we showed that generation of T cell subsets proceeded normally in cultures derived from Eng-/- ES cells. However, cells proliferated at a faster rate and were no longer inhibited by TGF-beta1, potentially implicating endoglin in T cell homeostasis via modulation of TGF-beta1 effects.
Human kallikrein 13: development of a sensitive and specific immunofluorometric assay and identification of its binding proteins

Human kallikrein gene 13, a member of the human kallikrein family, encodes a secreted serine protease (hK13). The aims of this study were to characterize hK13. Recombinant hK13 protein was produced and used as an immunogen to generate anti-hK13 antibodies in order to develop a sandwich-type immunoassay. hK13 was found in biological fluids such as seminal plasma and ovarian cancer ascites. hK13 was also found to be expressed in various tissues and appears to be overexpressed in ovarian cancer tissues. Given that several other kallikreins are sequestered by protease inhibitors present in serum, and the fact that hK13 recovery levels from hK13-spiked serum was low, we hypothesized that hK13 may also interact with similar inhibitors. Our next objective was to identify hK13 protease inhibitors. Active hK13 was shown to form complexes with alpha 1-antichymotrypsin, alpha 2-macroglobulin and alpha 2-antiplasmin. These complexes may have value in cancer diagnosis.
Characterization of gene expression profiles during differentiation, lipopolysaccharide stimulation, and heat shock repression in human U937 monocyte cells

The U937 cell line represents a class of immature monocytes capable of induced terminal differentiation, generating an immune response to lipopolysaccharide (LPS), and protecting itself from stresses brought about by heat. As it is an often used model cell line, we sought to characterize U937 gene expression profiles during the above mentioned processes as well as examining the resulting profile of LPS stimulation concomitant with heat stress, using microarray technology. Treatment with phorbol-12-myristate-13-acetate (PMA) led to the induction and downregulation of a unique set of genes that differed (but not completely) at 6h and 24h of differentiation. Similarly, microarray analyses revealed a novel set of LPS-inducible as well as downregulated genes. Concomitant heat shock and LPS exposure demonstrated the repression of almost all LPS-inducible genes. Further, heat shock treatment alone induced several novel genes in addition to the classic heat shock proteins, Hsp70 and Hsp40.
In-vitro study of the interaction between chitosan and a bovine lung surfactant

Exogenous lung surfactants are used to treat respiratory distress syndrome, and can be deactivated by serum. This study investigated the interaction between chitosan and an inhibited bovine lung extract surfactant (BLES). Dynamic surface tension measurements of surfactant formulations were conducted by Constrained Sessile Drop (CSD) device combined with Axisymmetric Drop Shape Analysis (ADSA). Zeta potential measurements and optical micrographs of surfactant aggregates were also employed. It was observed that while an initial addition of chitosan to dilute BLES was effective, an excess dosage is undesirable. Furthermore, this transition from "optimum" to "excess" chitosan-to-BLES ratios in formulations corresponded to the de-flocculation of surfactant aggregates. These observations and zeta potential measurement results suggest that chitosan, by binding to the anionic phospholipids in BLES, can change the elasticity and stability of the surface films and reduce serum-caused inhibition. These findings highlight the importance of electrostatic interactions in cationic polymer - lung surfactant systems.
Generative models for 2-D images of 3-D scenes

This thesis introduces generative models of appearance for analyzing 2D images of 3D visual scenes. Many 2D images contain multiple objects, where image components corresponding to each object undergo deformations, eg., due to changes in the shape and appearance of the object, non-uniform scaling caused by camera zoom and global transformations such as changes in the location of the object. In this thesis, we use Bayesian networks to model these sources of variability and their potentially noisy interactions while describing an image. Given an observed image, the model is used to infer the distribution over the possible explanations of the unobserved sources. But, there is an exponentially large number of combinations, so an exact search over these combinations is practically infeasible. This thesis introduces approximate inference and learning algorithms based on variational methods for inferring the underlying explanations of the observed data. In the first part of this thesis, a fast unsupervised algorithm for learning an object's appearance in a linear subspace, while being invariant to global transformations such as translations, rotations, and scalings is introduced. For modelling multiple objects in the scene, the second part of the thesis presents a generative model for explaining an image using a layered composition of "card-board cutouts". With this, each object is accounted for by a model of 2D image, including a transparency map that specifies pixels belonging to the object. Each such "layer" includes hidden variables that account for sources of variability such as changes in appearance, shape, deformation and global transformation. The model is learned using a novel unsupervised variational technique that uses a video sequence as the only input. In the final part of the thesis, a new representation of image data called the "epitome" is introduced. An epitome is useful for representing repetitive texture features in an image with both high- and low-frequency components and with a variety of spatial scales. This representation is used to account for both appearance (texture) and 2D shape (shapes of object boundaries) in a generative model of a single image containing two objects. Inference in this model enables segmenting a single image into two layers of appearance and shape. Thus, in this thesis, we advocate the use of probability models as a natural way to represent, learn and make inferences about visual data.
Quantum state manipulation and quantum chaos in an optical lattice

The effects of reversing the sinusoidal potential every q kick periods with q = 0, l, 2,3 are examined numerically with the q = 0, 1, 2 cases being verified experimentally. I have found that when considering the energy absorption of the system the q = 1 case is qualitatively and quantitatively the same as the standard kicked rotor, while the q = 2 case is qualitatively the same as the standard kicked rotor with an effective increase in the scaled dimensionless kick strength parameter, k, of k rarr; k+ p2 .In this thesis I detail the background, implementation and results of two experiments from relatively different fields of study, both of which involve ultra-cold Rubidium atoms trapped in an optical lattice. The first is an analysis of the superpositions of vibrational states of the lattice. This includes a characterization and modelling of the dephasing of the states, an effect inherent to the lattice. It is found that the lattice geometry is a primary factor in the observed dephasing. This geometry results in position-dependent energy eigenstates in the lattice. Modelling this distribution of energies allows the accurate prediction of several experimental observables and provides useful information for future experiments. Several methods of applying pulse echoes to recover the state in the face of this dephasing are demonstrated, characterized and successfully modelled. The second set of experiments centre around using the optical lattice and Rubidium atoms as a delta-kicked rotor system. First I examine quantum resonances in the delta-kicked rotor. These are characterized by a dramatically increased energy absorption rate, in stark contrast to the momentum localization generally observed. These resonances exist when the effective Planck's constant, a parameter that determines how quantum-mechanically the system behaves, has a value of plank; d5;=rs dot;4p, for integers r and s. However only for plank; d5;=r dot;2p are resonances easily observable. Here I report on the first observation of high-order quantum resonances in a non-condensed atomic sample at values of plank; d5;=r16 dot;4p for integers r = 2--6. Quantum numerical simulations suggest that this observation of high-order resonances indicates a much longer spatial coherence than expected from an initially thermal atomic sample.