Migration and Residence Patterns of Salmonids in Puget Sound, Washington

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

Analysis of Molecular Dynamics Simulations of Protein Folding

Microsecond long Molecular Dynamics (MD) trajectories of biomolecular processes are now possible due to advances in computer technology. Soon, trajectories long enough to probe dynamics over many milliseconds will become available. Since these timescales match the physiological timescales over which many small proteins fold, all atom MD simulations of protein folding are now becoming popular. To distill features of such large folding trajectories, we must develop methods that can both compress trajectory data to enable visualization, and that can yield themselves to further analysis, such as the finding of collective coordinates and reduction of the dynamics. Conventionally, clustering has been the most popular MD trajectory analysis technique, followed by principal component analysis (PCA). Simple clustering used in MD trajectory analysis suffers from various serious drawbacks, namely, (i) it is not data driven, (ii) it is unstable to noise and change in cutoff parameters, and (iii) since it does not take into account interrelationships amongst data points, the separation of data into clusters can often be artificial. Usually, partitions generated by clustering techniques are validated visually, but such validation is not possible for MD trajectories of protein folding, as the underlying structural transitions are not well understood. Rigorous cluster validation techniques may be adapted, but it is more crucial to reduce the dimensions in which MD trajectories reside, while still preserving their salient features. PCA has often been used for dimension reduction and while it is computationally inexpensive, being a linear method, it does not achieve good data compression. In this thesis, I propose a different method, a nonmetric multidimensional scaling (nMDS) technique, which achieves superior data compression by virtue of being nonlinear, and also provides a clear insight into the structural processes underlying MD trajectories. I illustrate the capabilities of nMDS by analyzing three complete villin headpiece folding and six norleucine mutant (NLE) folding trajectories simulated by Freddolino and Schulten [1]. Using these trajectories, I make comparisons between nMDS, PCA and clustering to demonstrate the superiority of nMDS. The three villin headpiece trajectories showed great structural heterogeneity. Apart from a few trivial features like early formation of secondary structure, no commonalities between trajectories were found. There were no units of residues or atoms found moving in concert across the trajectories. A flipping transition, corresponding to the flipping of helix 1 relative to the plane formed by helices 2 and 3 was observed towards the end of the folding process in all trajectories, when nearly all native contacts had been formed. However, the transition occurred through a different series of steps in all trajectories, indicating that it may not be a common transition in villin folding. The trajectories showed competition between local structure formation/hydrophobic collapse and global structure formation in all trajectories. Our analysis on the NLE trajectories confirms the notion that a tight hydrophobic core inhibits correct 3-D rearrangement. Only one of the six NLE trajectories folded, and it showed no flipping transition. All the other trajectories get trapped in hydrophobically collapsed states. The NLE residues were found to be buried deeply into the core, compared to the corresponding lysines in the villin headpiece, thereby making the core tighter and harder to undo for 3-D rearrangement. Our results suggest that the NLE may not be a fast folder as experiments suggest. The tightness of the hydrophobic core may be a very important factor in the folding of larger proteins. It is likely that chaperones like GroEL act to undo the tight hydrophobic core of proteins, after most secondary structure elements have been formed, so that global rearrangement is easier. I conclude by presenting facts about chaperone-protein complexes and propose further directions for the study of protein folding.

Cuerpos censurados: construcci?n de identidad de g?nero en el tr?nsito femenino a masculino en hombres transexuales de la ciudad de Santiago de Cali y la incidencia de este proceso en sus relaciones familiares [recurso electr?nico]

El presente informe contiene los resultados del proceso de investigaci?n cualitativa realizado por una estudiante como requisito para optar al t?tulo profesional de Trabajadora Social. Con el fin de evidenciar el proceso de construcci?n de identidad de g?nero en hombres transexuales1 de Santiago de Cali y la incidencia de este proceso en las relaciones familiares; el documento se ha estructurado en cuatro (4) cap?tulos. En el primer cap?tulo encontrar?n el problema de investigaci?n, el cual incluye los antecedentes, la justificaci?n, la pregunta de investigaci?n, los objetivos generales y espec?ficos, la estrategia metodol?gica empleada y una reflexi?n en t?rminos de aciertos y desaciertos vividos durante la investigaci?n. Posteriormente, se le da entrada al marco contextual con el segundo cap?tulo, realizando descripciones hist?ricas, demogr?ficas, geogr?ficas y sociales del contexto donde se llev? a cabo la indagaci?n. Mientras que en el tercer cap?tulo se exponen los referentes conceptuales en los que se enmarca el presente informe final. Finalmente, en el cuarto cap?tulo por medio de cuatro subcap?tulos: 1) ?Cuerpos censurados?, 2) ?Siempre me han gustado ellas?, 3) ??D?nde encajo yo??, 4) ?Mi familia es una fortuna?, se presenta el an?lisis y hallazgos del proceso de investigaci?n sobre construcci?n de identidad de g?nero vivido por dos hombres transexuales de Santiago Cali. Seguidamente aparecen las conclusiones, las recomendaciones para y desde Trabajo Social, la bibliograf?a, la webgrafia consultadas y los anexos que contienen dos ?relatos literarios? con las historias de vida de los respectivos protagonistas de esta investigaci?n

Professional exposure to fungal pathogens: an update to exposure conditions and exposure measurement

In many occupational settings an exposure to fungi occurs. Fungal exposure may occur for instance in the form of dermatocytes, yeasts or mold. Associated to the fungi themselves an exposure to cell wall components like ß(1 ? 3)-D-glucans, to mycotoxins or to microbial volatile compounds can occur. Health hazards may differ across species because fungi may produce different allergens and mycotoxins, and some species can infect humans. Occupational settings are often characterized by special exposure conditions with respect to duration, frequency and especially to the level of exposure resulting at least sometimes to high or very high fungal exposure. Because of these special conditions occupational settings are suitable for epidemiologic studies. However, the knowledge about occupational exposure to fungi and associated compounds like mycotoxins is still fragmentary and not well disseminated. An indication for a high fungal exposure is for instance the handling of dry natural products like grain, hay or herbal plants with a high specific surface and the tendency to release dust during handling. The fungal components often form the determinative part of such dusts and might be a vehicle to respiratory airways. The authors will present results of exposure measurements of occupational settings and exposure conditions which are only rarely investigated.

Intrastromal corneal ring segments: how successful is the surgical treatment of keratoconus?

This review evaluates the outcomes of intrastromal corneal ring segment (ICRS) implantation for the treatment of keratoconus considering a new grading system based on the preoperative visual impairment of the patient. Additionally, a five-year follow-up analysis of patients with stable and progressive keratoconus is performed in order to assess the long term stability of the surgical procedure. Corrected distance visual acuity decreased statistically significantly in patients with mild keratoconus (P < 0.01) but statistically significantly increased in all other grades (P < 0.05). The improvement in visual acuity and the decrease of keratometric and aberrometric values were stable throughout a long period of time in patients with stable keratoconus. In patients with progressive form keratoconus, a significant improvement was found immediately after the procedure, however clinically relevant regression greater than 3 D was observed at the end of the follow up period.

Valoração do efluente da indústria processadora de pescado por incorporação de nutrientes em aphanothece microscopica nägeli

Nesta tese procurou-se demonstrar a valoração do efluente do processamento de pescado por incorporação dos nutrientes em Aphanothece microscopica Nägeli a diferentes temperaturas. Para tanto o trabalho é composto de cinco artigos que objetivaram avaliar sob o ponto de vista do tratamento do efluente pela cianobactéria Aphanothece e a separação e avaliação da biomassa gerada. O primeiro artigo intitula-se “Influência da temperatura na remoção de nutrientes do efluente da indústria de pescado por Aphanothece microscopica Nägeli”, e teve por objetivo avaliar a influência da temperatura (10, 20 e 30ºC) em um sistema de tratamento pela cianobactéria Aphanothece na remoção de matéria orgânica, nitrogênio e fósforo do efluente oriundo do processamento de pescado. A análise dos resultados mostrou que a temperatura influenciou significativamente na remoção de DQO, NTK, N-NH4 + e P-PO4 -3 . Para os experimentos a 20 e 30ºC todos os limites estabelecidos para os parâmetros avaliados foram atingidos. O segundo artigo intitulado “Efeito de coagulantes no efluente da indústria da pesca visando à separação de biomassa quando tratado por cianobactéria” avaliou o efeito da concentração e pH de dois tipos de coagulantes, cloreto férrico (FeCl3) e sulfato de alumínio (Al2(SO4)3), na separação da biomassa da cianobactéria Aphanothece microscopica Nägeli cultivada em efluente da indústria da pesca, assim como a remoção de matéria orgânica e nutrientes do efluente. Os resultados indicaram que o coagulante FeCl3 foi mais eficaz na remoção de todos os parâmetros testados. No que concerne à separação da biomassa, com um número de seis lavagens foi removido cerca de 97,6% da concentração de FeCl3 adicionado inicialmente. O terceiro artigo com o título “Caracterização da biomassa de Aphanothece microscopica Nägeli gerada no efluente da indústria da pesca em diferentes temperaturas de cultivo” avaliou a composição química da biomassa da cianobactéria Aphanothece microscopica Nägeli quando desenvolvida em meio de cultivo padrão BG11 e no efluente do processamento de pescado. O quarto artigo teve como título “Influência do meio de cultivo e temperatura em compostos nitrogenados na cianobactéria Aphanothece microscopica Nägeli” objetivou avaliar o teor de compostos nitrogenados presentes na biomassa da cianobactéria Aphanothece microscopica Nägeli quando cultivada em meio padrão e no efluente da indústria da pesca nas diferentes fases de crescimento. Para o estudo da composição química e nitrogenados no efluente foram realizados experimentos nas temperaturas de 10, 20 e 30ºC. As concentrações de proteína, cinzas e pigmentos aumentaram com o aumento da temperatura. Por outro lado, foi observada uma redução do teor de lipídios e carboidratos com o aumento da temperatura. O íon amônio juntamente com os ácidos nucléicos representa uma importante fração do nitrogênio não protéico presente na biomassa da cianobactéria Aphanothece. Ficou demonstrada a influência do meio de cultivo na concentração de nitrogênio, bem como a determinação de proteína pelo método de Kjeldahl superestima a concentração protéica em cianobactérias. O quinto artigo intitulado “Produção de proteína unicelular a partir do efluente do processamento do pescado: modelagem preditiva e simulação” avaliou a produção de proteína unicelular através do cultivo da cianobactéria Aphanothece microscopica Nägeli no efluente da indústria da pesca. Os dados cinéticos de crescimento celular foram ajustados a quatro modelos matemáticos (Logístico, Gompertz, Gompertz Modificado e Baranyi). Os resultados demonstraram que o modelo Logístico foi considerado o mais adequado para descrever a formação de biomassa. A análise preditiva mostrou a possibilidade da obtenção de 1,66, 18,96 e 57,36 kg.m-3.d-1 de biomassa por volume do reator em 1000 h de processo contínuo, para as temperaturas de 10, 20 e 30ºC, respectivamente.

Y como frenar la drogadicción

Fondo Margaritainés Restrepo

Effects of incomplete combustion on atmospheric chemistry: Black carbon climate forcing and global carbon monoxide emissions

This thesis is actually the composition of two separate studies aimed at further understanding the role of incomplete combustion products on atmospheric chemistry. The first explores the sensitivity of black carbon (BC) forcing to aerosol vertical location since BC has an increased forcing per unit mass when it is located above reflective clouds. We used a column radiative transfer model to produce globally-averaged values of normalized direct radiative forcing (NDRF) for BC over and under different types of clouds. We developed a simple column-weighting scheme based on the mass fractions of BC that are over and under clouds in measured vertical profiles. The resulting NDRF is in good agreement with global 3-D model estimates, supporting the column-weighted model as a tool for exploring uncertainties due to diversity in vertical distribution. BC above low clouds accounts for about 20% of the global burden but 50% of the forcing. We estimate maximum-minimum spread in NDRF due to modeled profiles as about 40% and uncertainty as about 25%. Models overestimate BC in the upper troposphere compared with measurements; modeled NDRF might need to be reduced by about 15%. Redistributing BC within the lowest 4 km of the atmosphere affects modeled NDRF by only about 5% and cannot account for very high forcing estimates. The second study estimated global year 2000 carbon monoxide (CO) emissions using a traditional bottom-up inventory. We applied literature-derived emission factors to a variety of fuel and technology combinations. Combining these with regional fuel use and production data we produced CO emissions estimates that were separable by sector, fuel type, technology, and region. We estimated year 2000 stationary source emissions of 685.9 Tg/yr and 885 Tg/yr if we included adopted mobile sources from EDGAR v3.2FT2000. Open/biomass burning contributed most significantly to global CO burden, while the residential sector, primarily in Asia and Africa, were the largest contributors with respect to contained combustion sources. Industry production in Asia, including brick, cement, iron and steel-making, also contributed significantly to CO emissions. Our estimates of biofuel emissions are lower than most previously published bottom-up estimates while our other fuel emissions are generally in good agreement. Our values are also universally lower than recently estimated CO emissions from models using top-down methods.

Eleuterio envuelve el mundo con sus venas : Vida por montones II

Fondo Margaritainés Restrepo

Se acabó la familia : En casa I

Fondo Margaritainés Restrepo

A numerical model for prediction of oil, trajectory due to extraction activity in the north coasts of the Persian Gulf

This thesis considers a three- dimensional numerical model based on 3-D Navier— Stokes and continuity equations involving various wind speeds (North west), water surface levels, horizontal shier stresses, eddy viscosity, densities of oil and gas condensate- water mixture flows. The model is used to simulate the prediction of the surface movement of oil and gas condensate slicks from spill accident in the north coasts of Persian Gulf.

Foot of Columbus Avenue, Sandusky, Ohio

The foot of Columbus Avenue in Sandusky, Ohio was the location of Lake Erie steamer service during the years from 1870 to 1930. As this picture shows hundreds of men and women have arrived and parked their automobiles and are preparing to board steamers for Lakeside, Kelleys Island, Cedar Point, and South Bass Island.

La Plazuela de San Ignacio : un espacio para mirones apasionados

Fondo Margaritainés Restrepo

Seismic waveform inversion for core-mantle boundary topography

International audience

Advanced parametrical modelling of 24 GHz radar sensor IC packaging components

This paper deals with the development of an advanced parametrical modelling concept for packaging components of a 24 GHz radar sensor IC used in automotive driver assistance systems. For fast and efficient design of packages for system-in-package modules (SiP), a simplified model for the description of parasitic electromagnetic effects within the package is desirable, as 3-D field computation becomes inefficient due to the high density of conductive elements of the various signal paths in the package. By using lumped element models for the characterization of the conductive components, a fast indication of the design's signal-quality can be gained, but so far does not offer enough flexibility to cover the whole range of geometric arrangements of signal paths in a contemporary package. This work pursues to meet the challenge of developing a flexible and fast package modelling concept by defining parametric lumped-element models for all basic signal path components, e.g. bond wires, vias, strip lines, bumps and balls. © Author(s) 2011. CC Attribution 3.0 License.