Nucleic Acid Diagnostics using Isotachophoresis and Isothermal Amplification

Thesis (Ph.D.)--University of Washington, 2016-08

Mesure de sections efficaces absolues vibrationnelles pour la collision d’électrons de basse énergie (1-19 eV) avec le tétrahydrofurane (THF) condensé

Résumé: Ce mémoire de maîtrise est une étude des probabilités d’interactions (sections efficaces) des électrons de basse énergie avec une molécule d’intérêt biologique. Cette molécule est le tétrahydrofurane (THF) qui est un bon modèle de la molécule constituant la colonne vertébrale de l’ADN; le désoxyribose. Étant donné la grande quantité d’électrons secondaires libérés lors du passage des radiations à travers la matière biologique et sachant que ceux-ci déposent la majorité de l’énergie, l’étude de leurs interactions avec les molécules constituant l’ADN devient rapidement d’une grande importance. Les mesures de sections efficaces sont faites à l’aide d’un spectromètre à haute résolution de pertes d’énergie de l’électron. Les spectres de pertes d’énergie de l’électron obtenus de cet appareil permettent de calculer les valeurs de sections efficaces pour chaque vibration en fonction de l’énergie incidente de l’électron. L’article présenté dans ce mémoire traite de ces mesures et des résultats. En effet, il présente et explique en détail les conditions expérimentales, il décrit la méthode de déconvolution qui est utilisée pour obtenir les valeurs de sections efficaces et il présente et discute des 4 résonances observées dans la dépendance en énergie des sections efficaces. En effet, cette étude a permis de localiser en énergie 4 résonances et celles-ci ont toutes été confirmées par des recherches expérimentales et théoriques antérieures sur le sujet des collisions électrons lents-THF. En outre, jamais ces résonances n’avaient été observées simultanément dans une même étude et jamais la résonance trouvée à basse énergie n’avait été observée avec autant d’intensité que cette présente étude. Cette étude a donc permis de raffiner notre compréhension fondamentale des processus résonants impliqués lors de collisions d’électrons secondaires avec le THF. Les valeurs de sections efficaces sont, quant à elles, très prisées par les théoriciens et sont nécessaires pour les simulations Monte Carlo pour prédire, par exemple, le nombre d’ions formées après le passage des radiations. Ces valeurs pourront justement être utilisées dans les modèles de distribution et dépôt d’énergie au niveau nanoscopique dans les milieux biologiques et ceux-ci pourront éventuellement améliorer l’efficacité des modalités radiothérapeutiques.

BEHAVIOR OF FIBER REINFORCED POLYMER COMPOSITE PILES WITH ELLIPTICAL CROSS SECTIONS IN INTEGRAL ABUTMENT BRIDGE FOUNDATIONS

Every year in the US and other cold-climate countries considerable amount of money is spent to restore structural damages in conventional bridges resulting from (or “caused by”) salt corrosion in bridge expansion joints. Frequent usage of deicing salt in conventional bridges with expansion joints results in corrosion and other damages to the expansion joints, steel girders, stiffeners, concrete rebar, and any structural steel members in the abutments. The best way to prevent these damages is to eliminate the expansion joints at the abutment and elsewhere and make the entire bridge abutment and deck a continuous monolithic structural system. This type of bridge is called Integral Abutment Bridge which is now widely used in the US and other cold-climate countries. In order to provide lateral flexibility, the entire abutment is constructed on piles. Piles used in integral abutments should have enough capacity in the perpendicular direction to support the vertical forces. In addition, piles should be able to withstand corrosive environments near the surface of the ground and maintain their performance during the lifespan of the bridge. Fiber Reinforced Polymer (FRP) piles are a new type of pile that can not only accommodate large displacements, but can also resist corrosion significantly better than traditional steel or concrete piles. The use of FRP piles extends the life of the pile which in turn extends the life of the bridge. This dissertation studies FRP piles with elliptical shapes. The elliptical shapes can simultaneously provide flexibility and stiffness in two perpendicular axes. The elliptical shapes can be made using the filament winding method which is a less expensive method of manufacturing compared to the pultrusion or other manufacturing methods. In this dissertation a new way is introduced to construct the desired elliptical shapes with the filament winding method. Pile specifications such as dimensions, number of layers, fiber orientation angles, material, and soil stiffness are defined as parameters and the effects of each parameter on the pile stresses and pile failure have been studied. The ANSYS software has been used to model the composite materials. More than 14,000 nonlinear finite element pile models have been created, each slightly different from the others. The outputs of analyses have been used to draw curves. Optimum values of the parameters have been defined using generated curves. The best approaches to find optimum shape, angle of fibers and types of composite material have been discussed.

EFFECT OF ISOTHERMAL AGING ON SAC305 HARMONIC VIBRATION DURABILITY

The effect of isothermal aging on the harmonic vibration durability of Sn3.0Ag0.5Cu solder interconnects is examined. Printed wiring assemblies with daisy-chained leadless chip resistors (LCRs) are aged at 125°C for 0, 100, and 500 hours. These assemblies are instrumented with accelerometers and strain gages to maintain the same harmonic vibration profile in-test, and to characterize PWB behavior. The tested assemblies are excited at their first natural frequencies until LCRs show a resistance increase of 20%. Dynamic finite element models are employed to generate strain transfer functions, which relate board strain levels observed in-test to respective solder strain levels. The transfer functions are based on locally averaged values of strains in critical regions of the solder and in appropriate regions of the PWB. The vibration test data and the solder strains from FEA are used to estimate lower-bound material fatigue curves for SAC305 solder materials, as a function of isothermal pre-aging.

Sequestering of Fe and Pb ions from Wastewater by Canarium schweinfurthii after carbonization and chemical treatment: Isothermal and Kinetic Modeling

In this paper agricultural waste; Canarium schweinfurthii was explored for the sequestering of Fe and Pb ions from wastewater solution after carbonization and chemical treatment at 400oC. Optimum time of 30 and 150 min with percentage removal of 95 and 98% at optimum pH of 2 and 6 was obtained for Fe and Pb ions. Kinetics model followed pseudofirst order as sum of absolute error (EABS) between Qe and Qc greater than that of pseudo second order. Parameters evaluated from isothermal equation (Freundlich and Langmuir) showed that KL and QO for Fe > Pb and R2 for Langmuir> Freundlich. The study reveals the suitability of the adsorbent for sequestering of Fe and Pb ions from industrial wastewater.

Location analysis of city sections: socio-demographic segmentation and restaurant potentiality estimation : a case study of Lisbon

One of the objectives of this study is to perform classification of socio-demographic components for the level of city section in City of Lisbon. In order to accomplish suitable platform for the restaurant potentiality map, the socio-demographic components were selected to produce a map of spatial clusters in accordance to restaurant suitability. Consequently, the second objective is to obtain potentiality map in terms of underestimation and overestimation in number of restaurants. To the best of our knowledge there has not been found identical methodology for the estimation of restaurant potentiality. The results were achieved with combination of SOM (Self-Organized Map) which provides a segmentation map and GAM (Generalized Additive Model) with spatial component for restaurant potentiality. Final results indicate that the highest influence in restaurant potentiality is given to tourist sites, spatial autocorrelation in terms of neighboring restaurants (spatial component), and tax value, where lower importance is given to household with 1 or 2 members and employed population, respectively. In addition, an important conclusion is that the most attractive market sites have shown no change or moderate underestimation in terms of restaurants potentiality.

Measurement of the inclusive and differential t/t cross sections at 13 TeV in the all-jets boosted regime with CMS

The t/t production cross section is measured with the CMS detector in the all-jets channel in $pp$ collisions at the centre-of-mass energy of 13 TeV. The analysis is based on the study of t/t events in the boosted topology, namely events in which decay products of the quark top have a high Lorentz boost and are thus reconstructed in the detector as a single, wide jet. The data sample used in this analysis corresponds to an integrated luminosity of 2.53 fb-1. The inclusive cross section is found to be sigma(t/t) = 727 +- 46 (stat.) +115-112 (sys.) +- 20~(lumi.) pb, a value which is consistent with the theoretical predictions. The differential, detector-level cross section is measured as a function of the transverse momentum of the leading jet and compared to the QCD theoretical predictions. Finally, the differential, parton-level cross section is reported, measured as a function of the transverse momentum of the leading parton, extrapolated to the full phase space and compared to the QCD predictions.

Theoretical and experimental study on electron interactions with chlorobenzene: Shape resonances and differential cross sections

In this work, we report theoretical and experimental cross sections for elastic scattering of electrons by chlorobenzene (ClB). The theoretical integral and differential cross sections (DCSs) were obtained with the Schwinger multichannel method implemented with pseudopotentials (SMCPP) and the independent atom method with screening corrected additivity rule (IAM-SCAR). The calculations with the SMCPP method were done in the static-exchange (SE) approximation, for energies above 12 eV, and in the static-exchange plus polarization approximation, for energies up to 12 eV. The calculations with the IAM-SCAR method covered energies up to 500 eV. The experimental differential cross sections were obtained in the high resolution electron energy loss spectrometer VG-SEELS 400, in Lisbon, for electron energies from 8.0 eV to 50 eV and angular range from 7 degrees to 110 degrees. From the present theoretical integral cross section (ICS) we discuss the low-energy shape-resonances present in chlorobenzene and compare our computed resonance spectra with available electron transmission spectroscopy data present in the literature. Since there is no other work in the literature reporting differential cross sections for this molecule, we compare our theoretical and experimental DCSs with experimental data available for the parent molecule benzene. Published by AIP Publishing.

Age and growth of the smooth hammerhead shark, Sphyrna zygaena, in the Eastern Equatorial Atlantic Ocean, using vertebral sections

The smooth hammerhead shark Sphyrna zygaena (Sphyrnidae) is regularly caught as bycatch in pelagic longline fisheries, but is one of the least studied of all pelagic sharks. Recently, ICCAT (International Commission for the Conservation of Atlantic Tunas) issued recommendations underlining the need for more studies on the life history parameters of this and other pelagic shark species. To this end, the age and growth of S. zygaena were studied in the Eastern Equatorial Atlantic Ocean, in an area where growth parameters were not yet available for this species. Data from 139 specimens, caught between June and September 2009, ranging in size from 136 to 233 cm fork length (FL), were analysed. Preliminary trials were carried out to assess the most efficient growth band enhancement technique. These indicated that sectioning the vertebrae into 500 μm sections followed by staining with crystal violet produced the best results. Growth models were fitted using the traditional von Bertalanffy growth equation and a modification of this equation using a known size at birth. Growth models were compared using the Akaike information criterion (AIC). The von Bertalanffy growth equation seemed to be the most adequate model to describe growth in this species, with resulting growth parameters of L inf = 272 cm FL, k = 0.06 year for males and L inf = 285 cm FL, k = 0.07 year for females. In the first four years of life, S. zygaena grows 25 cm per year on average, but its growth slows down in later life. Future stock assessment models should incorporate these age and growth parameters for species management and conservation.

Poset associahedra as sections of graph associahedra

Poset associahedra are a family of convex polytopes recently introduced by Pavel Galashin in 2021. The associahedron An is an (n-2)-dimensional convex polytope whose facial structure encodes the ways of parenthesizing an n-letter word (among several equivalent combinatorial objects). Associahedra are deeply studied polytopes that appear naturally in many areas of mathematics: algebra, combinatorics, geometry, topology... They have many presentations and generalizations. One of their incarnations is as a compactification of the configuration space of n points on a line. Similarly, the P-associahedron of a poset P is a compactification of the configuration space of order preserving maps from P to R. Galashin presents poset associahedra as combinatorial objects and shows that they can be realized as convex polytopes. However, his proof is not constructive, in the sense that no explicit coordinates are provided. The main goal of this thesis is to provide an explicit construction of poset associahedra as sections of graph associahedra, thus solving the open problem stated in Remark 1.5 of Galashin's paper.

Analysis of fragmentation cross sections of GSI 2021 data for the FOOT experiment

Hadrontherapy is a medical treatment based on the use of charged particles beams accelerated towards deep-seated tumors on clinical patients. The reason why it is increasingly used is the favorable depth dose profile following the Bragg Peak distribution, where the release of dose is almost sharply focused near the end of the beam path. However, nuclear interactions between the beam and the human body constituents occur, generating nuclear fragments which modify the dose profile. To overcome the lack of experimental data on nuclear fragmentation reactions in the energy range of hadrontherapy interest, the FOOT (FragmentatiOn Of Target) experiment has been conceived with the main aim of measuring differential nuclear fragmentation cross sections with an uncertainty lower than 5\%. The same results are of great interest also in the radioprotection field, studying similar processes. Long-term human missions outside the Earth’s orbit are going to be planned in the next years, among which the NASA foreseen travel to Mars, and it is fundamental to protect astronauts health and electronics from radiation exposure .\\ In this thesis, a first analysis of the data taken at the GSI with a beam of $^{16}O$ at 400 $MeV/u$ impinging on a target of graphite ($C$) will be presented, showing the first preliminary results of elemental cross section and angular differential cross section. A Monte Carlo dataset was first studied to test the performance of the tracking reconstruction algorithm and to check the reliability of the full analysis chain, from hit reconstruction to cross section measurement. An high agreement was found between generated and reconstructed fragments, thus validating the adopted procedure. A preliminary experimental cross section was measured and compared with MC results, highlighting a good consistency for all the fragments.

Communication: Transient Anion States Of Phenol…(h₂o)n (n = 1, 2) Complexes: Search For Microsolvation Signatures.

We report on the shape resonance spectra of phenol-water clusters, as obtained from elastic electron scattering calculations. Our results, along with virtual orbital analysis, indicate that the well-known indirect mechanism for hydrogen elimination in the gas phase is significantly impacted on by microsolvation, due to the competition between vibronic couplings on the solute and solvent molecules. This fact suggests how relevant the solvation effects could be for the electron-driven damage of biomolecules and the biomass delignification [E. M. de Oliveira et al., Phys. Rev. A 86, 020701(R) (2012)]. We also discuss microsolvation signatures in the differential cross sections that could help to identify the solvated complexes and access the composition of gaseous admixtures of these species.

Effect Of Aloe Vera Application On The Content And Molecular Arrangement Of Glycosaminoglycans During Calcaneal Tendon Healing.

Although several treatments for tendon lesions have been proposed, successful tendon repair remains a great challenge for orthopedics, especially considering the high incidence of re-rupture of injured tendons. Our aim was to evaluate the pharmacological potential of Aloe vera on the content and arrangement of glycosaminoglycans (GAGs) during tendon healing, which was based on the effectiveness of A. vera on collagen organization previously observed by our group. In rats, a partial calcaneal tendon transection was performed with subsequent topical A. vera application at the injury site. The tendons were treated with A. vera ointment for 7 days and excised on the 7(th) , 14(th) , or 21(st) day post-surgery. Control rats received ointment without A. vera. A higher content of GAGs and a lower amount of dermatan sulfate were detected in the A. vera-treated group on the 14(th) day compared with the control. Also at 14 days post-surgery, a lower dichroic ratio in toluidine blue stained sections was observed in A. vera-treated tendons compared with the control. No differences were observed in the chondroitin-6-sulfate and TGF-β1 levels between the groups, and higher amount of non-collagenous proteins was detected in the A. vera-treated group on the 21(st) day, compared with the control group. No differences were observed in the number of fibroblasts, inflammatory cells and blood vessels between the groups. The application of A. vera during tendon healing modified the arrangement of GAGs and increased the content of GAGs and non-collagenous proteins.

Cytotoxic Granules In Distinct Subsets Of Cutaneous Lupus Erythematosus.

In cutaneous lupus erythematosus (CLE), the pathogenetic role of cytotoxic granules has been demonstrated in the subacute and discoid subtypes, which show interface dermatitis, but little is known about tumid (T)CLE, which does not show this interface dermatitis, and evolves with minimal epidermal changes. We studied cytotoxic T lymphocytes and cytotoxic granules in discoid (n = 21), subacute (n = 17), and tumid (n = 21) CLE samples. Skin sections were immunohistochemically stained for CD8, CD56, perforin, granzyme A, granzyme B, and granulysin. Inflammatory cells containing the four subtypes of cytotoxic granules were found in all the three CLE forms; however, only the TCLE group showed a positive correlation between the density of CD8+ cells and each subtype of cytotoxic granule-positive cells. In addition, only the TCLE group showed synergy between the densities of cells containing cytotoxic granule subtypes. Cytotoxic granules are important in the pathomechanism of TCLE. They may perform functions other than apoptosis, including maintenance of inflammation and dermal mucinous deposits in TCLE.