VictorJuiz/thesis huggingface dataset:
Characterization of the role of domains and subdomains of aggrecan in post-translational processing and secretion
Keywords: molecular biology
anatomy & physiology
animals
biological sciences
proteoglycan
articular cartilage
aggrecan
secretion

Aggrecan is the major proteoglycan in the articular cartilage. This molecule is crucial to the chondroskeletal morphogenesis during development and it is also important in the proper functioning of articular cartilage by providing hydrated gel structures (via its interaction with hyaluronic acid and link protein) which endow the cartilage with load bearing properties. Aggrecan is a multimodular molecule expressed by chondrocytes. To determine the role of each aggrecan domain in its post-translational modification and secretion, we generated a number of recombinant DNA constructs bearing various aggrecan domains individually or in combinations with other domains. We observed that G1 and G2 domains inhibited product secretion and GAG chain attachment whereas, G3 domain promoted secretion and GAG chain attachment. Knowing that G1 and G2 inhibited secretion, we set to identify which region of G1 and G2 shared the inhibition of secretion properties. Utilizing recombinant genes, we demonstrated that the first tandem repeats of G1 and G2 inhibited product secretion if expressed alone or in combinations with other domains and subdomains. We next tried to isolate the amino acid residues in the first tandem repeat of G1 involved in the inhibition of secretion by mutagenesis experiments. C-terminal mutagenesis of the first tandem repeat of G1 did not promote the secretion, however, N-terminal mutagenesis (point mutations and deletions) gave rise to enhancement of secretion. We noticed that there were four N terminal residues, FHYR, which seemed to be important in inhibition of secretion, however, we next realized that these four residues were part of a stretch of 55 amino acids required for the inhibitory property. Yeast two-hybrid analyses also indicated that TR1 of G1 is interacting with ER-bound chaperones.
The Meaning of Alienation and the Struggle to Learn to Relate
Keywords: Education
alienation
relationship
Buber
Assagioli
Psychology

Alienation, a pervasive contemporary problem, has been studied for many years by scholars who represent numerous and diverse disciplines. The issue has been associated with a plethora of sociological and psychological ills. But "alienation" as a concept has not been defined clearly. Separation of some sort seems to be the only theme that binds the various usages of alienation into a single concept. Few studies of the topic have been attempted in psychology and research into interpersonal alienation hardly exists. The main intent of this dissertation has been to clarify the meaning of peoples' struggle to learn to relate. A process of understanding had to be developed to elucidate the meaning of this particular form of separateness. Mainstream psychological research stresses the differentiation between subject and object, but this kind of split, within and between people, is frequently used in the literature to define alienation. A method could not be employed that took only a traditional object stance. Relational understanding needed to be added to empirical knowledge. Thus a second goal of this study has been to further the development of intersubjective research. As an ideal model, Martin Buber's conception of an alternating dialectic between I-It and I-Thou modalities of knowing was employed. To satisfy the empirical goal, a system of interpretation was used. From this process of understanding, eighteen inter-related variables emerged. These aspects of the experience were common to each participant in the study. These variables were further clarified through reflecting on the philosophical anthropology of Martin Buber and the psychosynthetic model of Roberto Assagioli. The dissertation ends with a discussion of some implications for: an understanding of interpersonal alienation and the struggle to learn to relate, intersubjective research, work with alienated people, and education.
Analysis and processing of dark-field electron micrographs for three-dimensional reconstruction
Keywords: Biophysics
Biological sciences

Dark-field electron microscopy has the potential of providing high resolution images of biological molecules with a resolution of 5 A. The two dimensional information from dark-field electron micorgraphs may be used to generate a three dimensional structure of the molecule if the relative projection directions of the images are known. This thesis describes computational techniques aimed at recovering this three dimensional information from single images of molecules which adopt unknown orientations with respect to the imaging beam. Dark-field images contain large amounts of noise, primarily a result of structure in the carbon film used to support the specimen. The application of maximum entropy methods, in an attempt to enhance the quality of the original images by removing the noise, is described. It is seen that, to be useful, these methods require a number of other constraints. However, the additional constraints lead to significantly increased computational times which render the algorithm impractical. An algorithm is described that permits the a posteriori determination of the relative projection direction of a large number of molecules. The method uses the central section theorem to determine the relative orientations of the images. Quaternion mathematics is used to determine optimum alignments of images. A number of algorithm-specific parameters are developed to indicate the degree of success of the alignment procedure. Simulated images and dark-field electron micrographs of the Klenow Fragment of DNA Polymerase I are used to test the efficacy of the alignment algorithm. The simulations indicate, on the basis of signal-to-ratio as a measure of image quality, that the algorithm should be able to determine projection directions from dark-field micrographs of single molecules. However, application to electron micrographs provides low quality alignments. Reasons for the discrepancy between the simulations of experimental situations are discussed. Preliminary experiments indicate that visual selection of high quality images yields improved alignments. It is suggested that this improvement results from selection of particles that have retained their integrity during the imaging procedure. It is concluded that the alignment procedure will probably be successful when applied to higher quality dark-field electron micrographs.
Neuroimaging evidence for the representation of salience in the neural correlates of attention and awareness in the human brain
Keywords: Biological sciences
Neuroimaging
Attention
Awareness
Brain
Neurology

Sensory stimuli must be at the focus of attention to reach conscious awareness. Attention may serve as a mechanism for identifying salient (i.e., potentially behaviourally relevant) features of the sensory environment. Neuroimaging studies have identified a frontal-parietal-cingulate network of regions involved in attentional control and conscious sensation. The present work was designed to test the hypothesis that these regions represent the salience of sensory stimuli. Brain regions sensitive to stimulus salience across multiple sensory modalities were identified in four studies using event-related functional magnetic resonance imaging. A right-lateralized network of frontal, parietal, cingulate, and insular cortical areas responded to salient changes in visual, auditory, and tactile stimuli. These areas also showed sensitivity to both top-down and bottom-up factors affecting stimulus salience. They responded more strongly to changes in visual or auditory stimuli when the stimuli were task-relevant rather than task-irrelevant. In the absence of a task, these areas responded more strongly to novel than familiar visual, auditory, and tactile stimuli. These areas also showed prolonged responses to stimuli with prolonged salience. They responded tonically throughout the duration of a prolonged painful stimulus but only transiently to the onset and offset of a prolonged non-painful stimulus. Consistently salience-sensitive regions included the temporoparietal junction, inferior frontal gyrus, anterior insula, anterior cingulate cortex/cingulate motor area/supplementary motor area, and thalamus. These findings suggest a functional role for the frontal-parietal-cingulate networks involved in attentional control and awareness. These areas may serve as arbiters of salience, identifying currently important features of the sensory environment within the current behavioural context of the organism. The importance of these areas for subjective conscious experience may stem from their role in representing features of the external sensory environment in terms of how they relate to the intrinsically subjective needs of the organism, within the context of its current behaviour, motivations, and homeostatic requirements.
Cathode interface structure in organic semiconductor devices
Keywords: Materials Science

As organic semiconductor technology matures, enhancement requires understanding/engineering of the cathode/organic interface. In this work, using X-ray photoelectron spectroscopy (XPS) and common materials for organic light emitting diodes (OLEDs), the expected interfacial structure in conventionally fabricated devices has been described and some simple predictive methods developed. The buried electrode/active layer interface was examined by analysing: (1) both sides of the interface in conventionally fabricated devices under high vacuum with the unique peel-off technique, and (2) monolayers of one material grown atop another. Connections were drawn between the interfacial structures in devices, those observed during traditional surface science investigations, and the device behaviour. A critical insight is that no one metal or metal/interlayer combination may be used as a universal cathode. Rather, certain criteria for interfacial structure and stability must be confirmed to ensure adequate performance. This can be determined through simple material property information, such as lattice constants, or with inorganic analogues for organic molecules. For combinations of metals and 8-tris(hydroxyquinoline aluminum) (Alq 3 ), interfacial reactions can be predicted by assuming Al2 O 3 as an inorganic analogue. Using this analogue, molecular fragmentation may be described as a simple metal-exchange oxidation-reduction reaction. As cathode complexity increases, such simple descriptions lose validity. This work shows that all three components (organic/LiF/metal) are required to adequately describe the interfacial structure of bi-layer cathodes. The major conclusions regarding the role of LiF are: (1) that 5-10Å LiF changes the cathode oxidation behaviour, predicted by the lattice mismatch of the interlayer with the metal. Oxidation is suppressed for Al, which is well matched to LiF; for Mg, which has poor matching, preferential formation of carbonates occurs. Device behaviour is related to the metal oxidation, such that Al/LiF cathodes are superior to Mg/LiF ones. (2) that near the interface, LiF forms charge transfer complexes with electron transporting molecules. (3) that the cathode should be considered a metal-insulator-metal capacitor with the organic layer acting as the bottom electrode. The usable thickness of LiF is dependent on the conductivity of the layer. These insights indicate some of the conditions necessary for adequate device performance and longevity, useful for future device optimization.
Androgens reverse ovarian epithelial cell growth suppression by TGF-beta1 and regulate the expression of TGF-beta receptors and steroid receptor co-activators
Keywords: Cellular biology
Molecular biology

The objective of this thesis is to study the role of androgen in the development of ovarian cancer. My initial observation was that dihydrotestosterone (DHT) down-regulated expression of TGF-β receptors in ovarian cancer cell lines, as determined by quantitative RT-PCR. In order to relate this result to the known growth inhibitory action of TGF-β cultured ovarian surface epithelial cells derived from (1) normal women (OSE) and (2) carriers of germline BRCA1/2 mutations (OSEb), as well as cultured malignant cells from ascites of ovarian cancer patients (OVCAS) were treated with TGF-β1 in the presence or absence of DHT. TGF-β1 inhibited growth in 12/13 cultures and DHT treatment prevented this growth inhibition in 5/6 OSE, 1/2 OSEb, and 4/5 OVCAS. Remarkably, this effect of DHT was observed even though all tested cultures expressed very low levels of androgen receptor (AR) as determined by RT-PCR. Therefore the effect of DHT on the expression of TGF-β receptor types I and II as well as the AR co-activators SRC-1, ARA70, and AIB1 was also determined by quantitative RT-PCR. Unlike the results observed in ovarian cancer cell lines, DHT either up-regulated or downregulated TGF-β receptor transcripts in these primary cultures. Intriguingly, TGF-β receptors, SRC-1, and ARA70 transcripts were either up- or down-regulated synchronously in OSE, but not in OSEb or OVCAS. These studies demonstrate first that androgen can block TGF-β induced growth inhibition in malignant and non-malignant ovarian epithelial cells, in some cases by down-regulating TGF-β receptors. Second, since the steroid receptor co-activators ARA70, SRC-1 and AIB1 are not exclusive for AR, their regulation by androgen suggests a mechanism whereby androgen could influence the action of other steroid hormones such as estrogen and progesterone on ovarian epithelial cells. Third, the lack of coordinated regulation of target gene expression by androgen in OSEb and OVCAS as opposed to OSE, provides the first phenotypic link between ovarian epithelial cells bearing a BRCA1/2 mutation and ovarian cancer cells. This opens up the possibility that androgen could influence the progression of predisposed cells bearing BRCA1/2 mutations to ovarian cancer.
Androgen-dependent growth suppression and eventual death in PC-3 prostatic cell cultures expressing a full-length human androgen receptor
Keywords: Cellular biology
Oncology

Several clonal lines of PC-3 cells (human androgen-independent prostate cancer cells) transfected with an episomal vector (pCEP4) containing a full-length human androgen receptor (AR) cDNA were developed (PC-3(AR) cells). These clonal lines, expressed varying levels of a 110 kDa AR that bracketed the concentration measured in androgen-sensitive LNCaP human prostate cancer cells. The expressed ectopic receptor was viable and capable of inducing the expression of the androgen-sensitive MMTV-luciferase but not the hormone-insensitive RSV-luciferase. This activation of luciferase activity by adrogen was inhibited by the AR antagonist hydroxyflutamide. Treatment of these cells with androgen produced a paradoxical growth inhibition response and that appeared to culminate in cell death. It is hoped that the PC-3(AR) clonal cell lines established and characterized in this thesis will serve as useful models to assess AR action in prostate cancer. Work in these cell lines may establish a viable approach to the treatment of prostate cancer.
A Method for Quantitative Interpretation of Wideband, Drill-Hole EM Surveys in Mineral Exploration
Keywords: Geophysics

Drill-hole geophysical surveys are an obvious means of extending the search for massive-sulphide deposits to depths which are inaccessible to conventional surface exploration techniques. The present investigation combines field and model studies of an EM prospecting method which utilizes a large, fixed transmitter loop with a downhole axial-component magnetic field sensor. Such a system is shown to be well suited to the task of detecting deeply buried massive-sulphide conductors located in resistive host rocks at appreciable distances from the drill hole. The thesis proposes a technique whereby drill hole survey data collected with a wideband large-loop EM system can be routinely interpreted on a quantitative basis. Systems using impulse-like, step-function or frequency-domain waveforms are considered. The interpretation technique is based on forward EM modelling using two simple conductor shapes: a thin, rectangular plate and a two-layer sphere. The analysis is facilitated by "eigencurrent" decomposition of the induced current vortex into a set of non-interacting loops with simple RL-circuit behaviour. The solutions have been implemented in interactive computer programs which are fast, inexpensive and sufficiently versatile to accommodate the configurations and waveforms used in many practical EM systems. The diffusive nature of the inductive process dictates that both stationary (spatially dependent) and dynamic (time or frequency dependent) properties are important in the diagnosis of three-dimensional targets. Model fitting using the stationary characteristics of the anomaly profile allows a first estimate of target parameters such as location, shape and attitude. Direction to the conductor may be difficult to determine unambiguously. The dynamic properties of the eddy currents, which may be observed with particular sensitivity near null points in the anomaly profile, are a useful basis for refining the interpretation. As shown by scale-model experiments, the dynamic aspects of the response are affected by departures from the simple models. Mineralization which is significantly thicker away from the drill hole may reveal itself in field observations through such effects. Field studies carried out at test sites in the Sudbury and Noranda base-metal mining areas near known deposits indicate that many of the important effects predicted by the model studies are, indeed, observed in nature. The results presented in the thesis are intended to serve as guidelines during the model-fitting process and to help exploit 'the inherent advantages of the large-loop EM method. It is recommended that computer modelling be applied both at the design and at the interpretation stages of a survey. Simulation of a three-component system suggests that such measurements would be a significant improvement, as the two transverse components can help resolve ambiguities in the location of the target.
The Inductive Response of Thin Plates in a Stratified Space
Keywords: Geophysics

The equivalent source method, the method whereby conductors are replaced by induced current distributions, can be a valuable tool for solving EM problems. The method can be used to reduce problems with complex analytical solutions into ones which have a simple numerical formulation. This is accomplished by replacing conductors with predetermined source currents of unknown amplitude. The Green's functions of complex spaces can therefore be replaced with the free space Green's function or other simpler Green's functions. The choice of which conductors to replace with induced currents, and consequently which Green's function to use is merely a matter of convenience. This approach is applied to solve for the EM response of two or more plates in a stratified space by invoking the Galerkin method. The plates were replaced with predetermined current distributions and their interactions were computed using the Green's functions for a stratified space. A program was then written to demonstrate the feasibility of the method. Results of the program were compared with the results of the existing programs and with scale model experiments. Computational problems were encountered when calculating the responses of plates in a layered Earth, due to the excessive time required to calculate the Green's functions. However, the results for plates in free space agreed well enough with model experiments to confirm that the method works.
Scale Models on Transient Response of Multiple Conductors
Keywords: Geophysics

The multiple conductor model is used to explain characteristics of the transient response of extensive conductors near a large horizontal transmitter loop. The transient response of two interacting circuits can be expressed in terms of a sum of exponential decays. Scale models of two extensive conductors near a large transmitter loop show the same response characteristics as a simple sum of the two individual conductor responses. A large conductor behind the transmitter can affect the response of a conductor surveyed on a profile line. On the other hand, a conductor between a second conductor and the transmitter blanks the second conductor. Scale models with conductive solution show that a conductive medium increases the interaction between two conductors at early times. Some UTEM field survey responses are compared to results of scale models of extensive conductors. In a first case, the late time anomaly can be fitted to the response of scale models in free space. The early times characteristics are the same as observed over conductors in electrolytic solutions. The data of the second case can be fitted qualitatively to the response of scale models in free air.
Geophysical Prospecting with Electric Fields from an Inductive EM Source
Keywords: Geophysics

It is possible when carrying out EM surveys for mining exploration to measure the electric (E) as well as the magnetic (H) components. Such measurements have been made at several sites with the UTEM time-domain, fixed transmitter EM system. The object of this thesis is to provide a comprehensive basis for the interpretation of such data. It is shown that three distinct EM phenomena are involved, which have clearly separable effects on data recorded with a time-domain, step-response system such as UTEM. At low enough frequencies (in frequency domain), or at sufficiently long times after a step change in primary E field, the observed electric field consists of the divergence-free primary E field and a curl-free secondary E field that arises from charges induced in regions where the conductivity changes. The response at the limit, called the resistive limit E (RLE) field response has been calculated for a number of geologically reasonable bodies. RLE model responses can be found which fit late-time UTEM E field data in many cases. Additional geological information, particularly about resistive features is obtained from the RLE response that is not interpretable from the magnetic EM components alone. EM prospecting conventionally uses a magnetic receiver to detect the secondary fields of induced current flow, and interpretation of the conductivity structure of the ground is per-, formed using the time or frequency dependent nature of the response. The secondary induced currents create a secondary vi divergence-free electric field which through boundary interactions also contributes to the secondary curl-free E field although this latter contribution is usually small. Divergence-free E and H field anomalies (when normalized to their respective primary fields) are not of identical magnitude or form, but are related to the geometry of the induced current flow. Simple circuit estimates, together with limited scale modelling were used to predict the E field inductive anomalies for some simple models. These results were used to interpret UTEM survey data, and it was found that by including the E fields that estimates of the geometry of secondary current flow could be improved over those using H field data alone in some cases. Conventional induced polarization (IP) surveys show that many earth materials have a frequency dependent conductivity. The effects of polarizable bodies of simple shape on E fields were calculated for an inductive EM source field. The predicted effects are able to explain observed anomalous late-time UTEM E field data quantitatively. As in the case of MIP (IP surveys using a grounded transmitter and magnetic receiver) no IP anomaly is generated in the resistive limit by horizontal layers of polarizable material. Due to geometrical complications, and because the UTEM sampling times are designed to define EM time decays and do not cover a very wide time range with respect to IP effects, characterization of fundamental IP parameters can only be done in special cases.