published_or_final_version / Statistics and Actuarial Science / Master / Master of Philosophy

No description available.

No description available.

No description available.

No description available.

DNA fingerprinting was applied for the molecular elucidation of taxonomic relationships within a genus of orchids which have previously been based on morphological characteristics. Phragmipediwn consists of 15-20 species native to Central and South America. This research project included two studies. In the first study DNA was isolated from 11 samples (including two unidentified ones). These individuals, which were mostly hybrids, were found in the Wheeler Orchid Collection and Species Bank at Ball State University. In order to position Phragmipediwn within the orchid family fingerprinting was also performed on individuals in the sister taxa, Cypripedium and Paphiopedium, which are members of the same subfamily, and on a member of the outgroup taxon Vanda. The polymerase chain reaction (PCR) was employed to yield fingerprints resulting from the use of random primers. Fifty nine random amplified polymorphic DNA (RAPD) bands were obtained using 5 different primers to yield 107 polymorphic bands. As many as 75% of genetic loci were found to be shared between hybrids that resulted from a cross of more than one individual in the same section. However the percentage dropped to 35-65 % when only one parent was shared in the cross. Furthermore, the sister group taxa Cypripedium and Paphilopedium shared from 12 % -35 % of their polymorphic loci with the members of the genus Phragmipedium. The outgroup taxon Vanda shared 17% of its polymorphic loci with the rest of the samples.In a second study DNA was isolated from one member of each of the five sections of the genus Phragmipedium, and RAPD-PCR fingerprinting was used to compare their genetic similarities to that of the two sister taxa and the outgroup taxon. It was found that individuals in different genera shared 25% or less of their polymorphic bands. Between sections of the same genus 20-50% of genetic loci were shared. Two sections, Platypetalwn and Phragmipedium showed the highest degree of genetic relatedness (41-53%). Again the outgoup taxon shared less than 20% Phragmipediwn samples on the phenograms produced but the percentage was again insignificant. However, genetic analyses of the members of the section Lorifolia gave conflicting results: 46% genetic identity was observed in the first trial and 20% in the second.In conclusion, RAPD-PCR fingerprinting results appeared to be effective in the positioning of sections within a genus indicating the degree of similarity of closely related taxa. Also RAPD-PCR was able to place an unknown individual within a specific section of the genus. However, it could not be employed to determine the identity of unknown species due to the high degree of genetic diversity observed between even closely related individuals. / Department of Biology

Audio fingerprinting is a highly specific content-based audio retrieval technique. Given a short audio fragment as query, an audio fingerprinting system can identify the particular file that contains the fragment in a large library potentially consisting of millions of audio files. In this thesis, we investigate the possibility and feasibility of applying audio fingerprinting to do speech recognition in noisy environments based on speech reconstruction. To reconstruct noisy speech, the speech is divided into small segments of equal length at first. Then, audio fingerprinting is used to find the most similar segment in a large dataset consisting of clean speech files. If the similarity is above a threshold, the noisy segment is replaced with the clean segment. At last, all the segments, after conditional replacement, are concatenated to form the reconstructed speech, which is sent to a traditional speech recognition system. In the above procedure, a critical step is using audio fingerprinting to find the clean speech segment in a dataset. To test its performance, we build a landmark-based audio fingerprinting system. Experimental results show that this baseline system performs well in traditional applications, but its accuracy in this new application is not as good as we expected. Next, we propose three strategies to improve the system, resulting in better accuracy than the baseline system. Finally, we integrate the improved audio fingerprinting system into a traditional speech recognition system and evaluate the performance of the whole system. / Graduate

Thesis advisor: Noah P. Snyder / Centuries-long intensive land use change in the northeastern U.S. provides the opportunity to study the response timescale of geomorphic processes to anthropogenic perturbations. In this region, deforestation and the construction of dams following European settlement drastically altered the landscape, leading to the impoundment of sediment in mill ponds. This legacy sediment continues to be released into transport decades after a dam has been removed or breached. Geochemical tracers can help distinguish sediment sources and understand how sediment moves through a watershed. The South River in western MA is located in a formerly glaciated watershed, and these surficial deposits compose 98% of the area. It experienced two generations of damming, beginning with smaller mill dams in the 18th-19th centuries, followed by the construction of the Conway Electric Dam (CED), a 17 m tall hydroelectric dam in the early 20th century. Legacy sediment deposits from sediment stored behind mill dams cover 1.5% of the watershed area. The CED is located near the outlet of the river, providing a century-long depositional record for the watershed, during reforestation. I hypothesize that sediment mobilized from human activity will contain a different geochemical signature than glacial material, that recent erosion in the watershed is primarily from anthropogenic legacy deposits rather than from glacial age landforms, and channel widening is occurring in reaches of the channel composed of legacy sediment, rather than in glacially confined reaches. These hypotheses were tested through a two part investigation, consisting of a sediment tracing study using Hg, and a Geographic Information Systems (GIS) analysis of channel changes using aerial photographs from 1940 and 2014. Samples were collected from river bank exposures of 11 glacial deposits and four mill pond legacy sites. Two vibracores measuring 476 and 500 cm were collected in reservoir sediment stored behind the CED in 2013 and 2017, respectively. Hg concentrations range from 1-4 ppb in glacial sediment, 3-380 ppb in legacy sediment, and 2-18 ppb and 7-50 ppb in the two CED cores. I used Hg as a tracer to estimate percent contributions to the CED reservoir from each watershed source during the 20th century. Results from a sediment mixing model suggest glacial sources contributed 32 ± 15%, and legacy sediment deposits contributed 68 ± 15% during the 20th century. Based on 137Cs dates on the cores, high amounts of legacy sediment filled in behind the CED prior to 1953 (74 ± 35 %), and background erosion from glacial deposits dominated from 1953 until the reservoir was filled in the 1980s (63 ± 14%). GIS analyses using aerial photographs from 1940 and 2014 indicate that the channel did not significantly widen along any section of the river, however, increases in sinuosity (up to 12%) occurred in the legacy sediment dominated reaches of the channel, and minor increases (1-2%) occurred in the glacial reaches. Overall, these analyses show an increase in the amount of sediment released in the channel as a result of mill dams breaching through the mid-19th to early 20th centuries, and suggest a short recovery timescale response from this land-use change. / Thesis (MS) — Boston College, 2018. / Submitted to: Boston College. Graduate School of Arts and Sciences. / Discipline: Earth and Environmental Sciences.

Degree awarded with distinction on 6 December l995. A dissertation submitted to the Faculty of Science, University the Witwatersrand, in fulfilment of the requirements for the degree of Master of Science. March. 1995 / Hepatitis B virus (HBV) infection resulting in integration of the viral DNA into host liver cell DNA is associated with the development of hepatocellular carcinoma (HCC). This is indicated by epidemiological trends, molecular studies and studies of animal models infected with viruses closely related to HBv. However, little is known about the mechanism by which the integrated HBV DNA includes HCC despite continuing analysis of the integrated HBV DNA and its surrounding cellular sequences. [Abbreviated Abstract. Open document to view full version]

Concerns about increased stratospheric ozone depletion increasing ambient levels of ultraviolet-B radiation (UV-B), and the fact that some ecosystems are naturally exposed to high levels, has resulted in an increased interest in the effects of UV-B on plant communities. Despite this, there has been a paucity of studies into its effects on plant competition. Artificial plant communities consisting of Lolium perenne and Lotus corniculatus and a sub-montane community consisting of Agrostis tenuis, Festuca ovina and Galium saxatile (also including different nitrogen levels) were created using the response surface approach. The long-term effects of UV-B were also studied on a natural sub-Arctic community in Abisko, Sweden. In addition, all plant samples were analysed by Fourier-Transform Infrared Spectroscopy (FT-IR) to obtain a ‘metabolic fingerprint’ which was used to detect chemical differences to the whole biochemical complement of the sample. The results showed that enhanced UV-B altered the competitive interaction of Lolium perenne and Lotus corniculatus in favour of Lolium perenne although ambient levels of UV-B did not elicit an effect in the sub-montane community. Only one dwarf shrub species in the sub-Arctic experiment, Vaccinium myrtillus, was negatively affected by UV-B. In most cases, elevated UV-B elicited a change in the metabolic fingerprint in the samples and in some cases an alteration in competitive stress altered the metabolome. This suggests that FT-IR can be used as a screening tool to detect for both abiotic stress and competitive biochemical alterations. In addition, this thesis proposes that the facilitative effect between the grass-legume mixture of Lolium perenne and Lotus corniculatus is not related to nitrogen fixation in the early stages of competition which has traditionally been believed.