Motivation Sequence-based methods for phylogenetic reconstruction from (nucleic acid) sequence data are notoriously plagued by two effects: homoplasies and alignment errors. Large evolutionary distances imply a large number of homoplastic sites. As most protein-coding genes show dramatic variations in substitution rates that are not uncorrelated across the sequence, this often leads to a patchwork pattern of (i) phylogenetically informative and (ii) effectively randomized regions. In highly variable regions, furthermore, alignment errors accumulate resulting in sometimes misleading signals in phylogenetic reconstruction. Results We present here a method that, based on assessing the distribution of character states along a cyclic ordering of the taxa, allows the identification of phylogenetically uninformative homoplastic sites in a multiple sequence alignment. Removal of these sites appears to improve the performance of phylogenetic reconstruction algorithms as measured by various indices of 'tree quality'. In particular, we obtain more stable trees due to the exclusion of phylogenetically incompatible sites that most likely represent strongly randomized characters. Software The computer program noisy implements this approach. It can be employed to improving phylogenetic reconstruction capability with quite a considerable success rate whenever (1) the average bootstrap support obtained from the original alignment is low, and (2) there are sufficiently many taxa in the data set – at least, say, 12 to 15 taxa. The software can be obtained under the GNU Public License from http://www.bioinf.uni-leipzig.de/Software/noisy/.

Cyclic-di-GMP, a common bacterial second messenger, has been thought to help develop virulence and biofilms in bacteria, most specifically in Salmonella Typhimurium. By being able to dysregulate cyclic-di-GMP production, virulence may be better combatted. STM1987, an L-arginine-responsive diguanylate cyclase with a periplasmic sensory domain, dimerizes and generates the bacterial second messenger cyclic-di-GMP in response to the amino acid L-arginine in a pathway that also requires the periplasmic L-arginine-binding protein ArtI. Their biochemical responses to L-arginine and when they dimerize could help clarify this pathway, so I sought to develop a periplasmic dimerization sensor to better monitor these biochemical interactions. Similar to STM1987, the ToxR transcriptional regulator from Vibrio cholera is also activated by dimerization. By switching out the periplasmic domain of ToxR for the periplasmic regions of interest, I can better evaluate the cyclic-di-GMP response to L-arginine. This research aims to find the specific responses in this pathway to be able to use this in combatting bacterial virulence. I was able to successfully show that the STM1987 periplasmic domain dimerizes in response to L-arginine, providing an important insight into this signaling pathway.

In late 2007, a perched lava channel, built up to 45 m above the preexisting surface, developed during the ongoing eruption near Pu'u 'Ō'ō cone on Kīlauea Volcano's east rift zone. The lava channel was segmented into four pools extending over a total of 1.4 km. From late October to mid-December, a cyclic behavior, consisting of steady lava level rise terminated by vigorous spattering and an abrupt drop in lava level, was commonly observed in pool 1. We use geologic observations, video, time-lapse camera images, and seismicity to characterize and understand this cyclic behavior. Spattering episodes occurred at intervals of 40-100 min during peak activity and involved small (5-10-m-high) fountains limited to the margins of the pool. Most spattering episodes had fountains which migrated downchannel. Each spattering episode was associated with a rapid lava level drop of about 1 m, which was concurrent with a conspicuous cigar-shaped tremor burst with peak frequencies of 4-5 Hz. We interpret this cyclic behavior to be gas pistoning, and this is the first documented instance of gas pistoning in lava well away from the deeper conduit. Our observations and data indicate that the gas pistoning was driven by gas accumulation beneath the visco-elastic component of the surface crust, contrary to other studies which attribute similar behavior to the periodic rise of gas slugs. The gas piston events typically had a gas mass of about 2,500 kg (similar to the explosions at Stromboli), with gas accumulation and release rates of about 1.1 and 5.7 kg s-1, respectively. The time-averaged gas output rate of the gas pistoning events accounted for about 1-2% of the total gas output rate of the east rift zone eruption.

Geogrid reinforcement can improve the performance of pavements by stiffening the aggregate base material and decreasing pavement deformations. Understanding the effects of cyclic loading on the modulus of geogrid-reinforced base materials would help engineers better anticipate actual increases in the modulus of aggregate base materials under given traffic loads. The objective of this laboratory research was to investigate the effects of cyclic loading on the resilient modulus, the modulus to peak axial stress, the elastic modulus, and the modulus at 2 percent strain of geogrid-reinforced aggregate base materials. The scope of the research included two aggregate base materials (Wells Draw and Springville) having different particle-size distributions and particle angularity. Geogrid-reinforced and unreinforced specimens were subjected to conditioning periods consisting of cyclic loading ranging from 10 to 10,000 cycles. Immediately following cyclic loading, all specimens were tested using the quick shear portion of the American Association of State Highway and Transportation Officials T 307 (Determining the Resilient Modulus of Soils and Aggregate Materials). Specimen preparation involved material weigh-outs, compaction, and membrane applications. Specimen testing in the loading machine consisted of two testing portions, including cyclic loading and quick shear testing. The cyclic loading data were used to calculate the resilient modulus on 200-cycle intervals throughout the duration of the conditioning period. The quick shear data were used to calculate the peak axial stress, the modulus to peak axial stress, the elastic modulus and the modulus at 2 percent strain. For the Wells Draw material, the resilient modulus increases by 11 percent for the specimens with geogrid and increases by 8 percent for the specimens without geogrid as the number of load cycles increases from 1,000 to 10,000. For the Springville material, the resilient modulus increases by 2 percent for the specimens with geogrid and increases by 3 percent for the specimens without geogrid as the number of load cycles increases from 1,000 to 10,000. As with other studies, the results do not show a consistent or significant effect of geogrid reinforcement on the resilient modulus of the tested materials. The modulus at 2 percent strain has the most potential for consistently showing improvements to aggregate base materials due to both cyclic loading and geogrid reinforcement. For the Wells Draw and Springville materials, the modulus at 2 percent strain increases by 31 and 9 percent, respectively, as the number of load cycles increases from 10 to 10,000. Additionally, for the Wells Draw and Springville materials, the modulus at 2 percent strain of the specimens with geogrid is 23 and 46 percent, respectively, greater than that of the specimens without geogrid. The results show a consistent and significant positive effect of geogrid reinforcement on modulus at 2 percent strain of the tested materials. According to the modulus at 2 percent strain results, a sufficient conditioning period appears to occur at 5,000 cycles for the Wells Draw material and 10,000 cycles for the Springville material.

Abstract Acinetobacter baumannii is a prevalent nosocomial where infections are typically secondary infections to patients that already have an infection or other source of being immunocompromised. Like many other infectious bacteria, A. baumannii is increasingly considered a multi-drug resistant pathogen. This eliminates the ability to treat A. baumannii infections with traditional antibiotics, hence the need for another method of treating A. baumannii. This research study was designed to find a way to affect the survival of A. baumannii such that it can be applied to a hospital setting to prevent further infections to immunocompromised patients. One mechanism potentially used by A. baumannii to persist on hospital surfaces is through the use of the bacterial second messenger cyclic-di-GMP (c-di-GMP). This nucleotide signal is regulated in response to environmental conditions, and then activates c-di-GMP-binding proteins that induce phenotypic changes. I hypothesized that by deleting these c-di-GMP-binding proteins that it will produce measurable differences in phenotype like biofilm formation, motility, and desiccation survival. Reducing phenotypes such as these may alter A. baumannii’s ability to persist on hospital surfaces, and potentially lead to future surface eradication. A. baumannii encodes two potential c-di-GMP-binding proteins of particular interest, one that contains a sole PilZ domain and another that pairs a PilZ domain with a hydrolase domain. PilZ domains bind c-di-GMP within a conserved binding site, regulating the conformational structure of the protein, and are named for the first studied PilZ domain within the pilus-associated PilZ protein. Pili are used in pilus-mediated motility and surface attachment, and they are A. baumannii’s primary method of motility due to not having flagellum. I hypothesized that by removing these c-di-GMP-binding proteins, I would interrupt the c-di-GMP signaling that might regulate motility. I am testing two A. baumannii strains: 5075, a recent military hospital isolate and 17978, an older lab strain. A notable difference between these two strains is that 5075 demonstrates twitching motility where it utilizes type IV pili, but 17978 demonstrates swarming motility that has unknown mechanisms. Both c-di-GMP-binding proteins were tested for their role in twitching or swarming motility of the respective strains. I found that swarming motility of 17978 is regulated by both c-di-GMP-binding proteins. While I am still generating the deletion strain for the c-di-GMP-binding hydrolase enzyme, the sole PilZ domain protein is also required for twitching motility in the 5075 strain. These results suggest c-di-GMP regulates both forms of motility in A. baumannii. Future plans include determining the role of the c-di-GMP-binding hydrolase enzyme in twitching motility and identifying the role that these proteins play through binding of c-di-GMP.

>Magister Scientiae - MSc / This project focuses on the development of simple, highly sensitive, accurate, and low cost electrochemical sensors based on the modification of pencil graphite electrodes by the electrochemical reduction of graphene oxide-metal salts as nanocomposites (ERGO-MC-PGE; MC = Sb or Au nanocomposite). The electrochemical sensors ERGO-Sb-PGE and ERGO-Au-PGE were used in the determination of paracetamol (PC) in pharmaceutical formulations using adsorptive stripping differential pulse voltammetry. The GO was prepared from graphite via a modified Hummers’ method and characterized by FTIR and Raman spectroscopy to confirm the presence of oxygen functional groups in the conjugated carbon-based structure whilst, changes in crystalline structure was observed after XRD analysis of graphite and GO. / 2023-10-07

No description available.

Indiana University-Purdue University Indianapolis (IUPUI) / Additive manufacturing (AM) or 3D printing has gained significant advancement in recent years. However the potential of 3D printed metals still has not been fully explored. A main reason is the lack of accurate knowledge of the load capacity of 3D printed metals, such as fatigue behavior under cyclic load conditions, which is still poorly understood as compared with the conventional wrought counterpart. The goal of the thesis is to advance the knowledge of fatigue behavior of 15-5 PH stainless steel manufactured through laser powder bed fusion process. To achieve the goal, a combined numerical and experimental study is carried out. First, using a rotary fatigue testing experiment, the fatigue life of the 15-5 PH stainless steel is measured. The strain life curve shows that the numbers of the reversals to failure increase from 13,403 to 46,760 as the applied strain magnitudes decrease from 0.214\% from 0.132\%, respectively. The micro-structure analysis shows that predominantly brittle fracture is presented on the fractured surface. Second, a finite element model based on cyclic plasticity including the damage model is developed to predict the fatigue life. The model is calibrated with two cases: one is the fatigue life of 3D printed 17-4 stainless steel under constant amplitude strain load using the direct cyclic method, and the other one is the cyclic behavior of Alloy 617 under multi-amplitude strain loads using the static analysis method. Both validation models show a good correlation with the literature experimental data. Finally, after the validation, the finite element model is applied to the 15-5 PH stainless steel. Using the direct cyclic method, the model predicts the fatigue life of 15-5 PH stainless steel under constant amplitude strain. The extension of the prediction curve matches well with the previously measured experimental results, following the combined Coffin-Manson Basquin Law. Under multi-amplitude strain, the kinematic hardening evolution parameter is incorporated into the model. The model is capable to capture the stresses at varied strain amplitudes. Higher stresses are predicted when strain amplitudes are increased. The model presented in the work can be used to design reliable 3D printed metals under cyclic loading conditions.

No description available.

京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第21777号 / 工博第4594号 / 新制||工||1716(附属図書館) / 京都大学大学院工学研究科材料化学専攻 / (主査)教授 木村 俊作, 教授 瀧川 敏算, 教授 藤田 晃司 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DGAM