I have invented "Internet Fish," a novel class of resource-discovery tools designed to help users extract useful information from the Internet. Internet Fish (IFish) are semi-autonomous, persistent information brokers; users deploy individual IFish to gather and refine information related to a particular topic. An IFish will initiate research, continue to discover new sources of information, and keep tabs on new developments in that topic. As part of the information-gathering process the user interacts with his IFish to find out what it has learned, answer questions it has posed, and make suggestions for guidance. Internet Fish differ from other Internet resource discovery systems in that they are persistent, personal and dynamic. As part of the information-gathering process IFish conduct extended, long-term conversations with users as they explore. They incorporate deep structural knowledge of the organization and services of the net, and are also capable of on-the-fly reconfiguration, modification and expansion. Human users may dynamically change the IFish in response to changes in the environment, or IFish may initiate such changes itself. IFish maintain internal state, including models of its own structure, behavior, information environment and its user; these models permit an IFish to perform meta-level reasoning about its own structure. To facilitate rapid assembly of particular IFish I have created the Internet Fish Construction Kit. This system provides enabling technology for the entire class of Internet Fish tools; it facilitates both creation of new IFish as well as additions of new capabilities to existing ones. The Construction Kit includes a collection of encapsulated heuristic knowledge modules that may be combined in mix-and-match fashion to create a particular IFish; interfaces to new services written with the Construction Kit may be immediately added to "live" IFish. Using the Construction Kit I have created a demonstration IFish specialized for finding World-Wide Web documents related to a given group of documents. This "Finder" IFish includes heuristics that describe how to interact with the Web in general, explain how to take advantage of various public indexes and classification schemes, and provide a method for discovering similarity relationships among documents.

This thesis studies the intrinsic disorder effects and the transport and magnetic properties of ring-shaped epitaxial thin films and superconducting tunnel junctions (STJs) of the high temperature superconductor YBa$_2$Cu$_3$O$_{7-delta}$. We used an unconventional contactless technique that allows us to directly measure the persistent current of superconducting rings. In order to study the disorder effects on the persistent current, we slowly increased oxygen vacancies in YBa$_2$Cu$_3$O$_{7-delta}$ by changing $delta$ from 0.03 to 0.55 in steps of $sim$0.021. Monitoring the corresponding changes in the temperature dependence of the persistent current revealed an anomaly in its flow within a certain range of disorder. We found that this anomaly is directly related to the occurrence of a spinodal decomposition of oxygen vacancies in YBCO, which we explain as a competition between two coexisting phases, oxygen rich and oxygen deficient. The analysis of the time dependence of the persistent current revealed that increasing oxygen vacancies transforms the vortex structure from quasi-lattice into a glass and subsequently into a pinned liquid phase. Our results also exhibited the first evidence of self-organization of the vortex structure with increasing disorder. We also performed the first direct measurement of the temperature dependence of the $c$-axis persistent current ($J_c$) that is purely due to tunnelling Cooper-pairs through intrinsic Josephson junctions (IJJs) of YBCO. This is made possible by incorporating IJJs of YBCO into ring-shaped films. Then, we studied the temperature dependence of the persistent current of YBCO nanowires embedded in SrTiO$_3$-barrier integrated between two semi-ring-shaped YBCO thin films and systematically varied the nanowires length. Our observations revealed that $J_c$ has two different temperature dependences: a GL-dependence ($J_c propto (T_c - T)^{3/2}$) at low temperatures which we found the same in all studied samples, and another power law dependence ($J_c propto (T_c - T)^{alpha > 3/2}$) at high temperatures which turned out to depend on the length of the nanowires. We attribute the cross-over between these two temperature dependences to the depinning and the dissipative motion of vortices. These experimental approaches and findings not only provide new information, but more importantly open new avenues of investigating the transport and magnetic properties of superconducting films, junctions, and nanowires.

A vast number of sites that have been contaminated by industrial activities have been identified worldwide. Many such sites now pose serious risks to humans and the environment. Given the large number of contaminated sites there is a great need for efficient, cost-effective  remediation methods. Extensive research has therefore been focused on the development of such methods. However, the remediation of old industrial sites is challenging, for several reasons. One major  problem is that organic contaminants become increasingly strongly sequestered as they persist in the soil matrix for a long period of time. This process is often referred to as ‘aging’, and leads to decreasing availability of the contaminants, which also affects the remediation efficiency. In the work underlying this thesis, the influence of soil and contaminant properties on the efficiency of various physical and chemical soil remediation methods was investigated. The investigated contaminants were polycyclic aromatic hydrocarbons (PAHs), polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs). Briefly, the results show that as the size of soil particles decreases the contaminants become more strongly sorbed to the soil’s matrix, probably due to the accompanying increases in specific surface area. This affected the efficiency of the removal of organic pollutants by both a process based on solvent washing and processes based on chemical oxidation. The sorption strength is also affected by the hydrophobicity of the contaminants. However, for a number of the investigated PAHs their chemical reactivity was found to be of greater importance for the degradation efficiency. Further, the organic content of a soil is often regarded as the most important soil parameter for adsorption of hydrophobic compounds. In these studies the effect of this parameter was found to be particularly pronounced for the oxidation of low molecular weight PAHs, but larger PAHs were strongly adsorbed even at low levels of organic matter. However, for these PAHs the degradation efficiency was positively correlated to the amount of degraded organic matter, probably due to the organic matter being oxidized to smaller and less hydrophobic forms. The amount of organic matter in the soil had little effect on the removal efficiency obtained by the solvent-washing process. However, it had strong influence on the performance of a subsequent, granular activated carbon-based post-treatment of the washing liquid. In conclusion, the results in this thesis show that remediation of contaminated soils is a complex process, the efficiency of which will be affected by the soil matrix as well as the properties of the contaminants present at the site. However, by acquiring thorough knowledge of the parameters affecting the treatability of a soil it is possible to select appropriate remediation methods, and optimize them in terms of both remediation efficiency and costs for site- and contaminant-specific applications.

This thesis describes the development and the use of quantitative deuterium Nuclear Magnetic Resonance spectroscopy (NMR) as a tool in two areas of environmental research: the study of long term climate-plant interactions and the source tracking of persistent organic pollutant. Long-term interactions between plants and climate will influence climate change during this century and beyond, but cannot be studied in manipulative experiments. We propose that long tree rings series can serve as records for tracking such interactions during past centuries. The abundance of the stable hydrogen isotope deuterium (D) is influenced by physical and biochemical isotope fractionations. Because the overlapping effects of these fractionations are not understood, studies of the D abundance of tree rings led to conflicting results. We hypothesized that both types of fractionations can be separated if the D abundance of individual C-H groups of metabolites can be measured, that is if individual D isotopomers are quantified. The first paper describes a technique for quantification of D isotopomers in tree-ring cellulose by NMR. The technique showed that the D isotopomers distribution (DID) was non-random. Therefore, the abundance of each isotopomer potentially contains individual information which suggests an explanation for the conflicting results obtained by measuring the overall D abundance (dD). In the second paper, this technique was used to study hydrogen isotope exchange during cellulose synthesis in tree rings. This revealed that some C-H positions exchange strongly with xylem water, while others do not. This means that the exchanging C-H positions should acquire the D abundance of source water, which is determined by physical fractionations, while non-exchanging C-H positions of tree-ring cellulose should retain biochemical fractionations from the leaf level. Therefore, the abundance of the corresponding D isotopomers should contain information about climate and physiology. When analysing tree-ring series, the DIDs should reflect information about temperature, transpiration and regulation of photosynthesis. In the third paper, we showed that CO2 concentration during photosynthesis determines a specific abundance ratio of D isotopomers. This dependence was found in metabolites of annual plants, and in tree-ring cellulose. This result shows that D isotopomers of tree-ring series may be used to detect long-term CO2 fertilisation effects. This information is essential to forecast adaptations of plants to increasing CO2 concentrations on time scales of centuries. In the fourth paper, the source of persistent organic pollutants in the environment was tracked using DID measurements. The dD values of two compounds of related structures were not enough to show indisputably that they did not originate from the same source. However, the DIDs of the common part between the two compounds proved that they did not originate from the same source. These results underline the superior discriminatory power of DIDs, compared to dD measurements. The versatility of DID measurements makes them a precious tool in addressing questions that can not be answered by dD measurements. / Betson, Tatiana R

<p>This dissertation extends the theory of persistent homology to time varying systems. Most of the previous work has been dedicated to using this powerful tool in topological data analysis to study static point clouds. In particular, given a point cloud, we can construct its persistence diagram. Since the diagram varies continuously as the point cloud varies continuously, we study the space of time varying persistence diagrams, called vineyards when they were introduced by Cohen-Steiner, Edelsbrunner, and Morozov.</p><p>We will first show that with a good choice of metric, these vineyards are stable for small perturbations of their associated point clouds. We will also define a new mean for a set of persistence diagrams based on the work of Mileyko et al. which, unlike the previously defined mean, is continuous for geodesic vineyards. </p><p>Next, we study the sensor network problem posed by Ghrist and de Silva, and their application of persistent homology to understand when a set of sensors covers a given region. Giving each of these sensors a probability of failure over time, we show that an exact computation of the probability of failure of the whole system is NP-hard, but give an algorithm which can predict failure in the case of a monitored system.</p><p>Finally, we apply these methods to an automated system which can cluster agents moving in aerial images by their behaviors. We build a data structure for storing and querying the information in real-time, and define behavior vectors which quantify behaviors of interest. This clustering by behavior can be used to find groups of interest, for which we can also quantify behaviors in order to determine whether the group is working together to achieve a common goal, and we speculate that this work can be extended to improving tracking algorithms as well as behavioral predictors.</p> / Dissertation

Background and objective: Major risk factors for congestive heart failure (CHF) are myocardial infarction, hypertension, diabetes, atrial fibrillation, smoking, left ventricular hypertrophy (LVH) and obesity. However, since these risk factors only explain part of the risk of CHF, we investigated whether persistent organic pollutants (POPs) might also play a role. Methods: In the Prospective Investigation of the Vasculature in Uppsala Seniors (PIVUS) study, left ventricular ejection fraction, (EF), E/A-ratio and isovolumic relaxation time (IVRT), were determined by echocardiography and serum samples of 21 POPs were analyzed in serum measured by high-resolution chromatography coupled to high-resolution mass spectrometry (HRGC/HRMS) in 998 subjects all aged 70 years. Results: In this cross-sectional analysis, high levels of several of the polychlorinated biphenyls (PCB congeners 99, 118, 105, 138, 153, and 180) and octachlorodibenzo-p-dioxin (OCDD) were significantly related to a decreased EF. Some POPs were also related to a decreased E/A-ratio (PCBs 206 and 209). All the results were adjusted for gender, hypertension, diabetes, smoking, LVH and BMI, and subjects with myocardial infarction or atrial fibrillation were excluded from the analysis. Conclusions: Circulating levels of POPs were related to impairments in both left ventricular systolic and diastolic function independently of major congestive heart failure risk factors, suggesting a possible role of POPs in heart failure.

This imaginative work of fiction depicts the lives of the Foley family. After a brutal car accident, Kate Foley has lived for the past fourteen years at Gregg Catastrophic Care Center in a persistent vegetative state, leaving her daughter Grace and husband Tom to reconstruct their lives around her. Aside from her mother’s condition, life is relatively normal for Grace; she worries about school, boys, her friends. Then her mother slowly regains consciousness. The family gathers around Kate’s bedside. Grandmother Helen arrives along with Aunt Liz, family that Grace cannot remember, and their stories of her mother’s past are vastly different from the ones her father has told her. Over the next emotional months, secrets are revealed, new alliances forged and others broken as each member of the family grapples with their own issues of memory, self and what it means to be fully present.

Wikipedia is a free, web-based, collaborative, multilingual encyclopedia project supported by the non-profit Wikimedia Foundation. Due to the free nature of Wikipedia and allowing open access to everyone to edit articles the quality of articles may be affected. As all people don’t have equal level of knowledge and also different people have different opinions about a topic so there may be difference between the contributions made by different authors. To overcome this situation it is very important to classify the articles so that the articles of good quality can be separated from the poor quality articles and should be removed from the database. The aim of this study is to classify the articles of Wikipedia into two classes class 0 (poor quality) and class 1(good quality) using the Adaptive Neuro Fuzzy Inference System (ANFIS) and data mining techniques. Two ANFIS are built using the Fuzzy Logic Toolbox [1] available in Matlab. The first ANFIS is based on the rules obtained from J48 classifier in WEKA while the other one was built by using the expert’s knowledge. The data used for this research work contains 226 article’s records taken from the German version of Wikipedia. The dataset consists of 19 inputs and one output. The data was preprocessed to remove any similar attributes. The input variables are related to the editors, contributors, length of articles and the lifecycle of articles. In the end analysis of different methods implemented in this research is made to analyze the performance of each classification method used.

<p>In this thesis we explore and extend the theory of persistent homology, which captures topological features of a function by pairing its critical values. The result is represented by a collection of points in the extended plane called persistence diagram.</p><p>We start with the question of ridding the function of topological noise as suggested by its persistence diagram. We give an algorithm for hierarchically finding such epsilon-simplifications on 2-manifolds as well as answer the question of when it is impossible to simplify a function in higher dimensions.</p><p>We continue by examining time-varying functions. The original algorithm computes the persistence pairing from an ordering of the simplices in a triangulation and takes worst-case time cubic in the number of simplices. We describe how to maintain the pairing in linear time per transposition of consecutive simplices. A side effect of the update algorithm is an elementary proof of the stability of persistence diagrams. We introduce a parametrized family of persistence diagrams called persistence vineyards and illustrate the concept with a vineyard describing a folding of a small peptide. We also base a simple algorithm to compute the rank invariant of a collection of functions on the update procedure.</p><p>Guided by the desire to reconstruct stratified spaces from noisy samples, we use the vineyard of the distance function restricted to a 1-parameter family of neighborhoods of a point to assess the local homology of a sampled stratified space at that point. We prove the correctness of this assessment under the assumption of a sufficiently dense sample. We also give an algorithm that constructs the vineyard and makes the local assessment in time at most cubic in the size of the Delaunay triangulation of the point sample.</p><p>Finally, to refine the measurement of local homology the thesis extends the notion of persistent homology to sequences of kernels, images, and cokernels of maps induced by inclusions in a filtration of pairs of spaces. Specifically, we note that persistence in this context is well defined, we prove that the persistence diagrams are stable, and we explain how to compute them. Additionally, we use image persistence to cope with functions on noisy domains.</p> / Dissertation

In this work the interactions between neighboring superconducting thin film and ferromagnetic structures, i.e. superconductor-ferromagnet hybrid systems, were studied. A type-II superconducting thin film (Pb82Bi12), was deposited in close proximity to various ferromagnetic structures. These magnetic structures include: (i) alternating iron-brass shims of 275 mu m period, (ii) an array of 4 mu m wide Co stripes with smaller period (9 mu m), (iii) a square array of 50nm diameter, high aspect ratio (5-7) Ni rods with 250nm period. Measurements of critical transport current (IC), resistance (RH(T)) and second critical field (HC2) are reported. A variety of novel effects (enhancement of (IC) and (HC2), matching field effect, field compensation effect, and large hysteresis) are also reported. Using measurements on thin superconducting films atop a Co stripe array with a 9 mu m period, a superconductor-ferromagnet hybrid device (a mechanical superconducting persistent switch) is proposed. In addition, scanning Hall probe microscopy (SHPM) and other imaging techniques were used to characterize the magnetic properties of the systems mentioned. The SHPM was also used to acquire B-H and M-H curves. An additional sharp magnetic needle and electromagnetic coil assembly intended for micromanipulation of small magnetic particles and individual cells was also characterized.