VictorJuiz/thesis huggingface dataset:
A Bioarchaeological Study of Mid-Holocene Communities in the Eastern Cape, South Africa: the Interface between Foraging and Pastoralism
Keywords: bioarchaeology
South Africa
Later Stone Age
foraging
pastoralism

The late Holocene marks a period of significant population movement and subsistence change throughout much of sub-Saharan Africa. Around 3500 BP it appears that foraging populations in southernmost South Africa began to experience stress related to an increasing population and changing climatic conditions. Approximately 1500 years later a new form of subsistence - sheep herding – emerged in areas previously occupied solely by foragers, but was not exclusively adopted. The mechanisms surrounding the introduction of this new subsistence strategy – an indigenous adoption via diffusion or a foreign migration - remain unresolved. This study takes a biological approach to this significant question in southern African prehistory by exploring a collection of Later Stone Age skeletal remains that predate and postdate the appearance of pastoralism in order to determine if any significant changes in skeletal morphology indicative of population discontinuity can be identified at 2000 BP. A collection of seventy-three Later Stone Age adult skeletons (31 M, 42 F) with newly generated radiocarbon dates ranging from 8000 BP to 300 BP (uncalibrated) from the Eastern Cape Province of South Africa forms the basis of this study. Questions surrounding population continuity or discontinuity associated with the advent of sheep herding are investigated by examining metric variables collected from the cranium, post cranial skeleton and dentition, in conjunction with cranial discrete traits. Some changes in skeletal morphology are observed, but the timing, pattern and magnitude of these changes are not consistent with a foreign migration. A reduction in overall skeletal size in the absence of changes in shape corresponds with the period of forager intensification. Body size rebounds at around 2000 BP when evidence for a new form subsistence, sheep herding, is first observed in this region, suggesting that some foragers may have adopted sheep and the herding way of life as a stress relieving mechanism, while others maintained the foraging lifestyle. The timing of the observed changes in skeletal size, the absence of shape changes and the homogeneity in cranial discrete trait frequencies through time argues against the idea that sheep herding was introduced to the Cape region by outsiders. Rather, the findings of the current study suggest sheep herding was an indigenous development among existing foragers.
Understanding Community: A Comparison of Three Late Neolithic Pottery Assemblages from Wadi Ziqlab, Jordan
Keywords: archaeology
Late Neolithic
Near East
pottery
community
technology
Wadi Ziqlab
Jordan

This study presents the results of an analysis of three Late Neolithic pottery assemblages from Wadi Ziqlab, northern Jordan. These sites were occupied during the 6th millennium BC (calibrated) and are therefore contemporary with sites in other parts of the southern Levant that are attributed to the Wadi Rabah culture. The assemblages are analyzed from a stylistic perspective, broadly defined, which includes an examination of technological style in addition to a more traditional examination of vessel form and surface treatment. Different stages in the pottery production sequence are investigated using a range of analytical techniques, including thin-section petrography and xeroradiography. While there are some similarities between the assemblages, there are also some noticeable differences. The results of the pottery analysis are used to explore the nature of community in the context of the Late Neolithic. A critique of more traditional archaeological approaches to prehistoric communities leads to a re-conceptualization of community that combines interactional and ideational perspectives. Similarities in pottery among the sites, especially technological similarities, suggest that pottery producers may have comprised a dispersed community of practice. At the same time, pottery may have also been a symbolic marker of community boundaries. Differences in pottery among the sites, including surface treatment, may reflect the flexibility of these boundaries as different parts of the dispersed community negotiated their place in it. The presence of variation among contemporary pottery assemblages in a localized area suggests that social organization during the 6th millennium may have been more complex than is normally assumed for the Late Neolithic in the southern Levant. A dispersed community, with its members spread throughout the wadi, would require a sufficiently complex and flexible system of relationships to maintain it. Failing to acknowledge this has contributed to the difficulties archaeologists have encountered when trying to understand the culture-history of the 6th millennium BC in and east of the Jordan Valley.
Spatially Explicit Modeling of Hydrologically Controlled Carbon Cycles in a Boreal Ecosystem
Keywords: hydrology
ecology
soil science
carbon cycle
eco-hydrology
modelling

Current estimates of terrestrial carbon (C) fluxes overlook explicit hydrological controls. In this research project, a spatially explicit hydro-ecological model, BEPS-TerrainLab V2.0 was further developed to improve our understanding of the non-linearities associated with various hydro-ecological processes. A modeling study was conducted in a humid boreal ecosystem in north central Quebec, Canada. The sizes and nature of various ecosystem-C-pools were comprehensively reconstructed under a climate change and disturbance scenario prior to simulation in order to ensure realistic biogeochemical modeling. Further, several ecosystem processes were simulated and validated using field measurements for two years. A sensitivity analysis was also performed. After gaining confidence in the model’s ability to simulate various hydrologically controlled ecophysiological and biogeochemical processes and having understood that topographically driven sub-surface baseflow is the main process determining the soil moisture regime in humid boreal ecosystem, its influence on ecophysiological and biogeochemical processes were investigated. Three modeling scenarios were designed that represent strategies that are currently used in ecological models to represent hydrological controls. These scenarios were: 1) Explicit, where realistic lateral water routing was considered 2) Implicit, where calculations were based on a bucket-modeling approach 3) NoFlow, where the lateral sub-surface flow was turned off in the model. In general, the Implicit scenario overestimated GPP, ET and NEP, as opposed to the Explicit scenario. The NoFlow scenario underestimated GPP and ET but overestimated NEP. The key processes controlling the differences were due to the combined effects of variations in plant physiology, photosynthesis, heterotrophic respiration, autotrophic respiration and nitrogen mineralization; all of which occurred simultaneously in different directions, at different rates, affecting the spatio-temporal distribution of terrestrial C-sources or sinks (NEP). From these results it was clear that lateral water flow does play a significant role in the net terrestrial C distribution and it was discovered that non-explicit forms of hydrological representations underestimate the sizes of terrestrial C-sources rather than C-sinks. The scientific implication of this work demonstrates that regional or global scale terrestrial C estimates could have significant errors if proper hydrological constraints are not considered for modeling ecological processes due to large topographic variations of the Earth’s surface.
Design and Practical Implementation of Digital Auto-tuning and Fast-response Controllers for Low-power Switch-mode Power Supplies
Keywords: digital control
SMPS

In switched-mode power supplies (SMPS), a Controller is required for output voltage or current regulation. In low-power SMPS, processing power from a fraction of watt to several hundred watts, digital implementations of the controller, i.e. digital controllers have recently emerged as alternatives to the predominately used analog systems. This is mostly due to the better design portability, power management capability, and the potential for implementing advanced control techniques, which are not easy to realize with analog hardware. However, the existing digital implementations are barely functional replicas of analog designs, having comparable dynamic performance if not poorer. Due to stringent constraints on hardware requirements, the digital systems have not been able to demonstrate some of their most attractive features, such as parameter estimation, controller auto-tuning, and nonlinear time-optimal control for improved transient response. This thesis presents two novel digital controllers and systems. The first is an auto-tuning controller that can be implemented with simple hardware and is suitable for IC integration. The controller estimates power stage parameters, such as output capacitance, load resistance, corner frequency and damping factor by examining the amplitude and frequency of intentionally introduced limit cycle oscillations. Accordingly, a digital PID compensator is automatically redesigned and the power stage is adapted to provide good dynamic response and high power processing efficiency. Compared to state of the art analog solutions, the controller has similar bandwidth and improves overall efficiency. To break the control bandwidth limitation associated with the sampling effects of PWM controllers, the second part of the thesis develops a nonlinear dual-mode controller. In steady state, the controller behaves as a conventional PWM controller, and during transients it utilizes a continuous-time digital signal processor (CT-DSP) to achieve time-optimal response. The processor performs a capacitor charge balance based algorithm to achieve voltage recovery through a single on-off sequence of the power switches. Load transient response with minimal achievable voltage deviation and a recovery time approaching physical limitations of a given power stage is obtained experimentally.
Understanding Defloccation of Activated Sludge Under Transients of Short-term Low Dissolved Oxygen
Keywords: deflocculation
activated sludge
low oxygen
transient

Deflocculation is a common upset event in biological wastewater treatment plants and causes significant problems in biosolids discharge and environmental management. However, fundamental understanding of deflocculation is limited. The overall objective of this work was to explore the fundamentals for deflocculation under transients of short-term low dissolved oxygen (DO). The investigation was carried out in a sequence of batch and continuous experiments on activated sludge, followed by batch experiments on E. coli suspensions. Both batch and continuous experiments on activated sludge demonstrated deflocculation of bioflocs under the transients of low DO (< 0.5 mg/L). Under the short-term low DO (in hours), turbidity increased by 20 times in the batch system and by 1-2 times in the continuous system, concentrations of suspended solids increased by 1-2 times, number of small particles (< 12.5 mm) increased by 2 times, more soluble EPS (proteins and humic substances) were released into supernatant or treated effluents, the removal efficiency of organic compounds was reduced by 50-70%. A 40% of increase in bulk K+ but a 30% of decrease in bulk Ca2+ under the DO limitation were observed in the batch experiments. There were significant increases in bulk K+ and decreases in bulk Ca2+ in the continuous experiments. Reversible changes were observed within 24 hours once the DO stress was removed. Floc strength of the remaining bioflocs after deflocculation increased. Deflocculation under the short-term low DO was consistent with an erosion process. The addition of selected chemicals (i.e., Ca2+, tetraethylammonium chloride, glibenclamide, and valinomycin) did not prevent deflocculation under the short-term low DO. It is proposed that a DO stress causes an efflux of cellular K+ but an influx of extracellular Ca2+, resulting in a decreasing ratio of Ca2+/K+ in extracellular solution and thereby causing deflocculation. The E. coli tests supported that increasing bulk K+ under the DO limit was due to the release of cellular K+ and was a stress response to the DO limitation.
YETI: a GraduallY Extensible Trace Interpreter
Keywords: dynamic optimization interpretation
branch prediction

The implementation of new programming languages benefits from interpretation because it is simple, flexible and portable. The only downside is speed of execution, as there remains a large performance gap between even efficient interpreters and systems that include a just-in-time (JIT) compiler. Augmenting an interpreter with a JIT, however, is not a small task. Today, Java JITs are typically method-based. To compile whole methods, the JIT must re-implement much functionality already provided by the interpreter, leading to a ``big bang'' development effort before the JIT can be deployed. Adding a JIT to an interpreter would be easier if we could more gradually shift from dispatching virtual instructions bodies implemented for the interpreter to running instructions compiled into native code by the JIT. We show that virtual instructions implemented as lightweight callable routines can form the basis for a very efficient interpreter. Our new technique, interpreted traces, identifies hot paths, or traces, as a virtual program is interpreted. By exploiting the way traces predict branch destinations our technique markedly reduces branch mispredictions caused by dispatch. Interpreted traces are a high-performance technique, running about 25% faster than direct threading. We show that interpreted traces are a good starting point for a trace-based JIT. We extend our interpreter so traces may contain a mixture of compiled code for some virtual instructions and calls to virtual instruction bodies for others. By compiling about 50 integer and object virtual instructions to machine code we improve performance by about 30% over interpreted traces, running about twice as fast as the direct threaded system with which we started.
Gene Association Studies of Schizophrenia and Tardive Dyskinesia
Keywords: Schizophrenia Genetics
Pharmacogenetics
Tardive Dyskinesia
Dopamine
GABA

Schizophrenia (SCZ) is a severe neuropsychiatric disorder with a genetic component. Most candidate gene association studies have given mixed results. We investigated the GABAA receptor gamma2 subunit gene GABRG2, the dopamine receptor gene DRD3, and the Brain-derived neurotrophic factor gene BDNF that is required for D3 expression by genotyping polymorphisms spanning and surrounding these genes for association with SCZ, as well as suicidal behaviour. We also examined the BDNF, DRD3, as well as the dopamine receptor gene DRD2 and Protein Kinase B gene AKT1 for association with Tardive Dyskinesia (TD), a potentially irreversible motor side effect of long-term antipsychotic medication. Our analysis included single-marker tests, haplotype tests, and gene-gene interactions. We found a haplotype in the 5’ region of GABRG2 to be associated with SCZ in both families and matched case-control samples. We also found two synonymous DRD2 polymorphisms, rs6275 (C939T) and rs6277 (C957T), and their haplotypes, as well as a polymorphism 5’ of DRD3, rs905568, to be associated with TD. Further, we reviewed two putative functional DRD2 polymorphisms, -141C Ins/Del and TaqIA, in TD and found TaqIA 3’ of the gene to be associated with TD in a meta-analysis. Lastly, we found a significant interaction between AKT1 rs3730358 and DRD2 C939T in TD. Though replication studies are required, these results contribute to the future development of genetic tests to assess for the risks of SCZ and TD, leading to better outcome for patients suffering from these debilitating conditions.
Multivariate Bayesian Process Control
Keywords: multivariate process control
Bayesian control chart

Multivariate control charts are valuable tools for multivariate statistical process control (MSPC) used to monitor industrial processes and to detect abnormal process behavior. It has been shown in the literature that Bayesian control charts are optimal tools to control the process compared with the non-Bayesian charts. To use any control chart, three control chart parameters must be specified, namely the sample size, the sampling interval and the control limit. Traditionally, control chart design is based on its statistical performance. Recently, industrial practitioners and academic researchers have increasingly recognized the cost benefits obtained by applying the economically designed control charts to quality control, equipment condition monitoring, and maintenance decision-making. The primary objective of this research is to design multivariate Bayesian control charts (MVBCH) both for quality control and conditional-based maintenance (CBM) applications. Although considerable research has been done to develop MSPC tools under the assumption that the observations are independent, little attention has been given to the development of MSPC tools for monitoring multivariate autocorrelated processes. In this research, we compare the performance of the squared predication error (SPE) chart using a vector autoregressive moving average with exogenous variables (VARMAX) model and a partial least squares (PLS) model for a multivariate autocorrelated process. The study shows that the use of SPE control charts based on the VARMAX model allows rapid detection of process disturbances while reducing false alarms. Next, the economic and economic-statistical design of a MVBCH for quality control considering the control limit policy proved to be optimal by Makis(2007) is developed. The computational results illustrate that the MVBCH performs considerably better than the MEWMA chart, especially for smaller mean shifts. Sensitivity analyses further explore the impact of the misspecified out-of-control mean on the actual average cost. Finally, design of a MVBCH for CBM applications is considered using the same control limit policy structure and including an observable failure state. Optimization models for the economic and economic statistical design of the MVBCH for a 3 state CBM model are developed and comparison results show that the MVBCH performs better than recently developed CBM Chi-square chart.
Adaptive Image Quality Improvement with Bayesian Classification for In-line Monitoring
Keywords: adaptive image quality improvement
bayesian classification
in-line monitoring
case-based reasoning
automated image processing
0984
0800

Development of an automated method for classifying digital images using a combination of image quality modification and Bayesian classification is the subject of this thesis. The specific example is classification of images obtained by monitoring molten plastic in an extruder. These images were to be classified into two groups: the “with particle” (WP) group which showed contaminant particles and the “without particle” (WO) group which did not. Previous work effected the classification using only an adaptive Bayesian model. This work combines adaptive image quality modification with the adaptive Bayesian model. The first objective was to develop an off-line automated method for determining how to modify each individual raw image to obtain the quality required for improved classification results. This was done in a very novel way by defining image quality in terms of probability using a Bayesian classification model. The Nelder Mead Simplex method was then used to optimize the quality. The result was a “Reference Image Database” which was used as a basis for accomplishing the second objective. The second objective was to develop an in-line method for modifying the quality of new images to improve classification over that which could be obtained previously. Case Based Reasoning used the Reference Image Database to locate reference images similar to each new image. The database supplied instructions on how to modify the new image to obtain a better quality image. Experimental verification of the method used a variety of images from the extruder monitor including images purposefully produced to be of wide diversity. Image quality modification was made adaptive by adding new images to the Reference Image Database. When combined with adaptive classification previously employed, error rates decreased from about 10% to less than 1% for most images. For one unusually difficult set of images that exhibited very low local contrast of particles in the image against their background it was necessary to split the Reference Image Database into two parts on the basis of a critical value for local contrast. The end result of this work is a very powerful, flexible and general method for improving classification of digital images that utilizes both image quality modification and classification modeling.
Role of the Cell Adhesion Molecule L1 during Early Neural Development in Zebrafish
Keywords: zebrafish
neural development
cell adhesion molecule L1
brain ventricle formation
polarity
axonal pathfinding

The neural cell adhesion molecule L1 is a member of the immunoglobulin superfamily and it mediates many adhesive interactions during brain development. Mutations in the L1 gene are associated with a spectrum of X-linked neurological disorders known as CRASH or L1 syndrome. The objective of this thesis was to use the zebrafish model to investigate the molecular mechanisms of L1 functions and the pathological effects of its mutations. Zebrafish has two L1 homologs, L1.1 and L1.2. Inhibition of L1.1 expression by antisense morpholino oligonucleotides resulted in phenotypes that showed resemblances to L1 patients. However, knockdown of L1.2 expression did not result in notable neural defects. Furthermore, analysis of the expression pattern of L1.1 has led to the discovery of a novel soluble L1.1 isoform, L1.1s. L1.1s is an alternatively spliced form of L1.1, consisting of the first four Ig-like domains and thus a soluble secreted protein. L1.1 morphants exhibited disorganized brain structures with many having an enlarged fourth/hindbrain ventricle. Further characterization revealed aberrations in ventricular polarity, cell patterning and proliferation and helped differentiate the functions of L1.1 and L1.1s. While L1.1 plays a pivotal role in axonal outgrowth and guidance, L1.1s is crucial to brain ventricle formation. Significantly, L1.1s mRNA rescued many anomalies in the morphant brain, but not the trunk phenotypes. Receptor analysis confirmed that L1.1 undergoes heterophilic interactions with neuropilin-1a (Nrp1a). Peptide inhibition studies demonstrated further the involvement of L1.1s in neuroepithelial cell migration during ventricle formation. In the spinal cord, spinal primary motoneurons expressed exclusively the full-length L1.1, and abnormalities in axonal projections of morphants could be rescued only by L1.1 mRNA. Further studies showed that a novel interaction between the Ig3 domain of L1.1 and Unplugged, the zebrafish muscle specific kinase (MuSK), is crucial to motor axonal growth. Together, these results demonstrate that the different parts of L1.1 contribute to the diverse functions of L1.1 in neural development.