236 research outputs found

    Organic Phosphorus Dynamics and Contributions to Eutrophication in a Shallow, Freshwater Bay

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    Indiana University-Purdue University Indianapolis (IUPUI)Phosphorus (P) is essential for aquatic life; cycling between both inorganic and organic forms to maintain an ecological balance. Its addition into P-scarce freshwaters, either through terrestrial (external) or sedimentary (internal) loading, may disrupt this balance causing blooms of phytoplankton to flourish, often resulting in harmful environmental and anthropogenic consequences. Accordingly, reduction of external P loading has been commonly implemented with a recent focus on sediment-bound legacy P that is mobilized into the water column during dynamic redox conditions. Mobile P species have been identified as both inorganic and organic, with the former representing the most bioavailable fraction, and the latter serving as a source for labile P in freshwaters when in high demand, particularly during blooms. Missisquoi Bay in Lake Champlain, VT experiences harmful cyanobacterial blooms driven by internal P loading and has been the target of numerous geochemical and hydrological studies. This thesis describes a high-resolution investigation of both the organic P and organic matter compositions of the bay with respect to mobility, reactivity, and bioavailability using Fourier Transform-Ion Cyclotron Mass Spectrometry (FT-ICR MS). Sediment from Missisquoi Bay was extracted with a diverse set of reagents, resulting in fractionation of both organic matter and organic P, and illustrating the distribution of various labile and recalcitrant compounds. Many of these molecules are associated with porewater or easily extractable mineral surfaces providing a link to the benthic organic matter and phosphorus fractions available to microorganisms. Additionally, the organic chemistry of the bay was investigated seasonally from May 2017 to January 2018 revealing biological processing from the spring runoff season through the post-bloom summer season. The transition from late summer to under ice conditions in winter was less severe with a higher commonality between both organic matter and organic P compounds, suggesting reduced biological and abiotic degradation. Moreover, short-term anoxic incubations of sediment cores from each season revealed the presence of diverse organic signatures from sorption processes, and a significant contribution of benthic microbial activity to the benthic organic geochemistry

    Reducing the Computational Effort Associated with Evolutionary Optimisation in Single Component Design

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    The dissertation presents innovative Evolutionary Search (ES) methods for the reduction in computational expense associated with the optimisation of highly dimensional design spaces. The objective is to develop a semi-automated system which successfully negotiates complex search spaces. Such a system would be highly desirable to a human designer by providing optimised design solutions in realistic time. The design domain represents a real-world industrial problem concerning the optimal material distribution on the underside of a flat roof tile with varying load and support conditions. The designs utilise a large number of design variables (circa 400). Due to the high computational expense associated with analysis such as finite element for detailed evaluation, in order to produce "good" design solutions within an acceptable period of time, the number of calls to the evaluation model must be kept to a minimum. The objective therefore is to minimise the number of calls required to the analysis tool whilst also achieving an optimal design solution. To minimise the number of model evaluations for detailed shape optimisation several evolutionary algorithms are investigated. The better performing algorithms are combined with multi-level search techniques which have been developed to further reduce the number of evaluations and improve quality of design solutions. Multi-level techniques utilise a number of levels of design representation. The solutions of the coarse representations are injected into the more detailed designs for fine grained refinement. The techniques developed include Dynamic Shape Refinement (DSR), Modified Injection Island Genetic Algorithm (MiiGA) and Dynamic Injection Island Genetic Algorithm (DiiGA). The multi-level techniques are able to handle large numbers of design variables (i.e. > 100). Based on the performance characteristics of the individual algorithms and multi-level search techniques, distributed search techniques are proposed. These techniques utilise different evolutionary strategies in a multi-level environment and were developed as a way of further reducing computational expense and improve design solutions. The results indicate a considerable potential for a significant reduction in the number of evaluation calls during evolutionary search. In general this allows a more efficient integration with computationally intensive analytical techniques during detailed design and contribute significantly to those preliminary stages of the design process where a greater degree of analysis is required to validate results from more simplistic preliminary design models

    A Framework for File Format Fuzzing with Genetic Algorithms

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    Secure software, meaning software free from vulnerabilities, is desirable in today\u27s marketplace. Consumers are beginning to value a product\u27s security posture as well as its functionality. Software development companies are recognizing this trend, and they are factoring security into their entire software development lifecycle. Secure development practices like threat modeling, static analysis, safe programming libraries, run-time protections, and software verification are being mandated during product development. Mandating these practices improves a product\u27s security posture before customer delivery, and these practices increase the difficulty of discovering and exploiting vulnerabilities. Since the 1980\u27s, security researchers have uncovered software defects by fuzz testing an application. In fuzz testing\u27s infancy, randomly generated data could discover multiple defects quickly. However, as software matures and software development companies integrate secure development practices into their development life cycles, fuzzers must apply more sophisticated techniques in order to retain their ability to uncover defects. Fuzz testing must evolve, and fuzz testing practitioners must devise new algorithms to exercise an application in unexpected ways. This dissertation\u27s objective is to create a proof-of-concept genetic algorithm fuzz testing framework to exercise an application\u27s file format parsing routines. The framework includes multiple genetic algorithm variations, provides a configuration scheme, and correlates data gathered from static and dynamic analysis to guide negative test case evolution. Experiments conducted for this dissertation illustrate the effectiveness of a genetic algorithm fuzzer in comparison to standard fuzz testing tools. The experiments showcase a genetic algorithm fuzzer\u27s ability to discover multiple unique defects within a limited number of negative test cases. These experiments also highlight an application\u27s increased execution time when fuzzing with a genetic algorithm. To combat increased execution time, a distributed architecture is implemented and additional experiments demonstrate a decrease in execution time comparable to standard fuzz testing tools. A final set of experiments provide guidance on fitness function selection with a CHC genetic algorithm fuzzer with different population size configurations

    Requiem banana man: banana farming in the commonwealth of Dominica

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    Computational Methods for the Identification of Statistically Significant Genes: Applications to Gene Expression Data of Various Human Diseases

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    Σε αυτή την διατριβή αντιμετωπίσαμε το πρόβλημα της επιλογής γονιδίων από ταξινομημένες λίστες. Προτείναμε μια νέα υβριδική μέθοδο επιλογής χαρακτηριστικών (mAP-KL) που συνδυάζει με επιτυχία μια μέθοδο πολλαπλού ελέγχου υποθέσεων και μια μέθοδο συσταδοποίησης (Affinity Propagation) μαζί με έναν δείκτη ποιότητας συστάδων των Krzanowski & Lai, για την επιλογή ενός μικρού αλλά αντιπροσωπευτικού υποσυνόλου γονιδίων. Υποβάλαμε τη μέθοδό μας σε διάφορες αξιολογήσεις με δεδομένα προσομοίωσης μικροσυστοιχιών καθώς και με πραγματικά δεδομένα μικροσυστοιχιών. Τα συνολικά αποτελέσματα της αξιολόγησης δείχνουν ότι η mAP-KL παράγει συνοπτικά υποσύνολά από -υπογραφές γονιδιακής έκφρασης οι οποίες σχετίζονται βιολογικά και μπορούν να χρησιμεύσουν ως ένα πολύτιμο διακριτικό εργαλείο για διαγνωστικούς και προγνωστικούς σκοπούς, με τον εντοπισμό πιθανών βιοδεικτών της νόσου σε ένα ευρύ φάσμα ασθενειών. Τέλος, προκειμένου να δώσουμε στην ερευνητική κοινότητα με τη δυνατότητα να εφαρμόσει την mAP-KL σε οποιοδήποτε σύνολο δεδομένων γονιδιακής έκφρασης, αναπτύξαμε τη μεθοδολογία μας σε ένα Bioconductor/R- πακέτο το οποίο συνοδεύεται και από άλλες επιπλέον λειτουργίες.In this dissertation, we address the problem of gene selection from ranked gene lists. We propose a new hybrid feature selection method (mAP-KL) that combines successfully multiple hypothesis testing and affinity propagation clustering algorithm along with the Krzanowski & Lai cluster quality index, to select a small yet informative subset of genes. We subject our method across a variety of validation tests on simulated microarray data as well as on real microarray data. The overall evaluation results suggest that mAP-KL generates concise yet biologically relevant and informative n-gene expression signatures, which can serve as a valuable discrimination tool for diagnostic and prognostic purposes, by identifying potential disease biomarkers in a broad range of diseases. Finally, to provide the research community with the capability to apply mAP-KL in any given gene expression dataset, we have implemented this methodology to a Bioconductor/R-package accompanied with extra functionalities

    A STUDY OF THE THERMAL CYCLING PERFORMANCE OF SOLDER JOINTS IN AREA ARRAY PACKAGING

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    For both the electronics manufacturer and consumer, reliability is an essential characteristic defining the quality of the electronic component and system. Gradual degradation of the electronic components decreases efficiency of the system, and lack of reliability can lead to a significant loss. Efforts at achieving better quality and reliability of electronic components involve the inspection of solder joints in area array packaging. It is of note that solder interconnections are the vulnerable parts of circuit board assemblies (CBA), because they are mainly subjected to various assembly process during electronic manufacturing as well as environmental exposure failures during service. Therefore, the reliability of solder joints is a major concern during the entire life of an area array packaging in order to minimize the electronic failure rate that may lead to large losses. This thesis aims to provide a solution that helps to overcome some of the challenges that can occur during the reliability inspection of solder joints in area array packaging. Firstly, by successfully developing a non-destructive monitoring methodology to study the performance of solder joints under thermal cycling test. The quality of the solder joints in this research work from growth to failure was monitored by using a type of ultrasonic inspection called acoustic micro imaging (AMI). Results indicate that provided a suitable AMI parameters is applied, one can generate a 3D reconstruction of the solder joints images to allow and assess the solder joints’ behaviour in flip chip packages. AMI inspection of solder joints show good agreement with the results obtained that was used to examine how the reliability was affected by the geometry and position of the joints. An automatic segmentation technique was developed that allow to characterize and extract distinctive features of solder joints on different area array packages; such features include mean intensity, structural similarities model and histogram intensity of the region of interest of solder joints. The validation experimental results have been statistically implemented using novel geometrical and time domain features extraction methods like area, form factor and standard deviation. The result from these methods were used to extrapolate the solder joint’s fatigue life at normal operating conditions. Moreover, the analysis of variance (ANOVA) was employed to determine the percentage contribution of solder joints parameters on the acquired images. The results indicated that the thickness of the printed circuit board can affect solder joint reliability

    Bacillus sp. strains and their inducible in vitro antagonism : a biochemical and molecular study

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    Discovering novel antibiotic substances from natural sources and revitalizing the pipeline for screenings of naturally sourced substances that could render new bioactive compounds, is a priority nowadays in the face of a world crisis of antimicrobial resistance. This research was focused on disclosing an observed antagonism system composed of Bacillus sp. strains producing inducible antimicrobial activity against the plant pathogen Ralstonia solanacearum, a widespread bacterium that causes bacterial wilt disease to a great variety of plant species, including many agriculturally important ones as are bananas. The inducible phenomenon was discovered during the screening of 1493 aerobic endospore forming bacteria against plant pathogens. It was observed that in the presence of the chemical compound Triphenyl Tetrazolium Chloride (TTC), which belongs to the group of synthetic compounds known as tetrazolium salts used to monitor cell respiration, Bacillus sp. strains produced inhibition zones against the bacterial plant pathogen and other pathogenic bacterial species, while in the absence of the compound they did not have any bioactivity. During biochemical characterization, it was evidenced that although the phenomenon was observable across several species of the order Bacillales, strains belonging to B. cereus, B. pumilus and B. subtilis were outstanding in their inducible antagonism potential, among other species tested. Besides, relevant traits revealed that other tetrazolium salts did not induce antagonistic activity and that the addition of antioxidant compounds did not reduce the inducible antagonistic activity. Also, R. solanacearum sensitivity to antibiotics was not increased by the addition of TTC and the inducible activity was independent of the presence of the pathogenic strain. In order to determine genes and pathways that were activated under TTC conditions, transcriptomic and metabolomics analysis were performed. Transcriptomic results revealed that specific pathways of the nitrogen metabolism, such as pyrimidines, purines and histidine biosynthetic routes, were 2 to 5 fold up-regulated in B. subtilis NCIB-3610 cells growing under TTC presence. On the other hand, metabolomic analysis showed that 28 specific compounds were either unique or 3 to 5 fold more abundant in active extracts obtained from inducible conditions, compared to non-induced controls. Data mining on public chemical databases, using intrinsic properties of the selected compounds, suggests that they mostly belong to chemical families of carbamates, imidazoles, pyrrolidines, pyrimidines, dipeptides and oligopeptides, all of which are part of the nitrogen metabolism. Results suggest that Bacillus cells reduction of TTC into triphenyl formazan (TPF) and its further accumulation inside the cells, induces the production of nitrogen-derived compounds, either by activation of nitrogen metabolism biosynthetic pathways or by a biotransformation of TPF into derivatives. Once produced, the compounds are secreted into the medium and act as antimicrobials against other bacteria

    Non-destructive evaluation of solder joint reliability

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    A through life non-destructive evaluation technique is presented in which a key solder joint feature, nucleating at the bump to silicon interface and propagating across a laminar crack plane is captured and tracked using acoustic microscopy imaging (AMI). The feasibility of this concept was successfully demonstrated by employing the measurement technique in combination with Finite Element Analysis (FEA) to study the impact of component floor plan layout on the reliability of electronics systems subjected to thermal cycling. A comprehensive review of current and emerging packaging and interconnect technologies has shown increasingly a move from conventional 2D to 3D packaging. These present new challenges for reliability and Non Destructive Evaluation (NDE) due to solder joints being hidden beneath the packaging, and not ordinarily visible or accessible for inspection. Solutions are developed using non-destructive testing (NDT) techniques that have the potential to detect and locate defects in microelectronic devices. This thesis reports on X-ray and Acoustic Micro Imaging (AMI) which have complementary image discriminating features. Gap type defects are hard to find using X-ray alone due to low contrast and spot size resolution, whereas AMI having better axial resolution has allowed cracks and delamination at closely spaced interfaces to be investigated. The application of AMI to the study of through life solder joint behaviour has been achieved for the first time. Finite Element Analysis and AMI performance were compared to measure solder joint reliability for several realistic test cases. AMI images were taken at regular intervals to monitor through- life behaviour. Image processing techniques were used to extract a diameter measurement for a laminar crack plane, within a solder joint damage region occurring at the bump to silicon interface. FEA solder joint reliability simulations for flip-chip and micro-BGA (mBGA) packages placed on FR4 PCB's were compared to the AMI measurement performance, with a reasonable level of correlation observed. Both techniques clearly showed significant reliability degradation of the critical solder joints located furthest from the neutral axis of the package, typically residing at the package corners. The technique also confirmed that circuit board thickness can affect interconnect reliability, as can floor plan. Improved correlation to the real world environment was achieved when simulation models considered the entire floor plan layout and constraints imposed on the circuit board assembly. This thesis established a novel through life solder joint evaluation method crucial to the development of better physics of failure models and the advancement of model based prognostics in electronics systems
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