A mathematical resolution to log transformations and the binning effect in applied processing of data in flow cytometry

This dissertation develops a new mathematical approach that overcomes the effect of a data processing phenomenon known as “histogram binning” inherent to flow cytometry data. A real-time procedure is introduced to prove the effectiveness and fast implementation of such an approach on real-world data. The histogram binning effect is a dilemma posed by two seemingly antagonistic developments: (1) flow cytometry data in its histogram form is extended in its dynamic range to improve its analysis and interpretation, and (2) the inevitable dynamic range extension introduces an unwelcome side effect, the binning effect, which skews the statistics of the data, undermining as a consequence the accuracy of the analysis and the eventual interpretation of the data. ^ Researchers in the field contended with such a dilemma for many years, resorting either to hardware approaches that are rather costly with inherent calibration and noise effects; or have developed software techniques based on filtering the binning effect but without successfully preserving the statistical content of the original data. ^ The mathematical approach introduced in this dissertation is so appealing that a patent application has been filed. The contribution of this dissertation is an incremental scientific innovation based on a mathematical framework that will allow researchers in the field of flow cytometry to improve the interpretation of data knowing that its statistical meaning has been faithfully preserved for its optimized analysis. Furthermore, with the same mathematical foundation, proof of the origin of such an inherent artifact is provided. ^ These results are unique in that new mathematical derivations are established to define and solve the critical problem of the binning effect faced at the experimental assessment level, providing a data platform that preserves its statistical content. ^ In addition, a novel method for accumulating the log-transformed data was developed. This new method uses the properties of the transformation of statistical distributions to accumulate the output histogram in a non-integer and multi-channel fashion. Although the mathematics of this new mapping technique seem intricate, the concise nature of the derivations allow for an implementation procedure that lends itself to a real-time implementation using lookup tables, a task that is also introduced in this dissertation. ^

Dimensions of gender relations and reproductive health inequity perceived by female undergraduate students in the Mekong Delta of Vietnam: a qualitative exploration

Introduction Increasing evidence indicates that gender equity has a significant influence on women’s health; yet few culturally specific indicators of gender relations exist which are applicable to health. This study explores dimensions of gender relations perceived by female undergraduate students in southern Vietnamese culture, and qualitatively examines how this perceived gender inequity may influence females’ sexual or reproductive health. Methods Sixty-two female undergraduate students from two universities participated in eight focus group discussions to talk about their perspectives regarding national and local gender equity issues. Results Although overall gender gaps in the Mekong Delta were perceived to have decreased in comparison to previous times, several specific dimensions of gender relations were emergent in students’ discussions. Perceived dimensions of gender relations were comparable to theoretical structures of the Theory of Gender and Power, and to findings from several reports describing the actual inferiority of women. Allocation of housework and social paid work represented salient dimensions of labor. The most salient dimension of power related to women in positions of authority. Salient dimensions of cathexis related to son preference, women’s vulnerability to blame or criticism, and double standards or expectations. Findings also suggested that gender inequity potentially influenced women’s sexual and reproductive health as regards to health information seeking, gynecological care access, contraceptive use responsibility, and child bearing. Conclusion Further investigations of the associations between gender relations and different women’s sexual and reproductive health outcomes in this region are needed. It may be important to address gender relations as a distal determinant in health interventions in order to promote gender-based equity in sexual and reproductive health.

Teacher perception of self -determination skills in the inclusive and special education classroom

It has been proposed that special education teachers, who promote self-determination and link it to educational standards, help students with a disability succeed in school. The current school reform movement has focused on accountability through mandates such as the No Child Left Behind Act, 2001, and has emphasized participation in the general curriculum through amendments to the Individuals with Disabilities Education Act (IDEA) of 1997 and 2004. This study informs educators if educational setting, students' type of disability, and subject area taught, influence teachers' opinions about the importance of teaching components leading to self-determination and self-management. ^ The research questions that drive this study are: (1) do secondary school teachers who instruct students with a disability think that self-determination components taught in the classroom will make an important difference in students' school and later postsecondary achievements? and (2) does the type of classroom setting, students' type of disability, or specific subject matter influence teachers' opinions regarding the importance of teaching components related to self-determination and self-management? The collection and interpretation of data were done using descriptive and quantitative methods employing a teacher survey. The survey was administered to secondary teachers who instruct students with disabilities. Data were analyzed using descriptive and inferential statistics. The sample consisted of 97 special education teachers currently teaching at the secondary level. ^ The results of the study indicated that teachers believe that self-determination is important for both school life and post school life. However teachers thought these skills to be more important for post school success. Teachers believe that self-determination is more important than self-management skills. Type of disability, educational environment, and subject area were not significant factors. ^

La representacion de la masculinidad y la violencia de genero en la novela Espanola de la posguerra

While it may be argued that aggression against women is part of a culture of violence deeply rooted in Spanish society, the gender-related violence that exists in today’s Spain is more specifically a legacy of Franco’s dictatorship (1939-1975). Franco’s Spain endorsed unequal gender relations, championed patriarchal dominance and power over women, and imposed models of hegemonic and authoritarian masculinities that internalized violence by rendering it a feature inseparable from manhood and virility. ^ This dissertation provides a comprehensive analysis of masculinity and gender violence in Franco’s Spain, by analyzing the novel as the primary cultural vehicle of social criticism and political dissent against the new regime during a period (1939-1962) dominated by silence and censorship. The first part of this work defines and elucidates the concepts of masculinity and gender violence and the relationship between them. It also compares the significant social and cultural achievements of Spanish women during the Second Republic (1931-1939) with the reactionary curbing of those achievements during Francoism. The second part of this research presents a multidisciplinary analysis of masculinity and gender violence in three novels: Nada (1944) by Carmen Laforet, Juegos de manos (1954) by Juan Goytisolo and Tiempo de silencio (1962) by Luis Martin Santos. ^ Through the literary representation of different models of masculinity and the psychological and social parameters that encourage and incite gender violence, these authors conceptualize and express their political ideology, as well as their symbolic interpretation of Francoist Spain.^

A mathematical resolution to log transformations and the binning effect in applied processing of data in flow cytometry

This dissertation develops a new mathematical approach that overcomes the effect of a data processing phenomenon known as "histogram binning" inherent to flow cytometry data. A real-time procedure is introduced to prove the effectiveness and fast implementation of such an approach on real-world data. The histogram binning effect is a dilemma posed by two seemingly antagonistic developments: (1) flow cytometry data in its histogram form is extended in its dynamic range to improve its analysis and interpretation, and (2) the inevitable dynamic range extension introduces an unwelcome side effect, the binning effect, which skews the statistics of the data, undermining as a consequence the accuracy of the analysis and the eventual interpretation of the data. Researchers in the field contended with such a dilemma for many years, resorting either to hardware approaches that are rather costly with inherent calibration and noise effects; or have developed software techniques based on filtering the binning effect but without successfully preserving the statistical content of the original data. The mathematical approach introduced in this dissertation is so appealing that a patent application has been filed. The contribution of this dissertation is an incremental scientific innovation based on a mathematical framework that will allow researchers in the field of flow cytometry to improve the interpretation of data knowing that its statistical meaning has been faithfully preserved for its optimized analysis. Furthermore, with the same mathematical foundation, proof of the origin of such an inherent artifact is provided. These results are unique in that new mathematical derivations are established to define and solve the critical problem of the binning effect faced at the experimental assessment level, providing a data platform that preserves its statistical content. In addition, a novel method for accumulating the log-transformed data was developed. This new method uses the properties of the transformation of statistical distributions to accumulate the output histogram in a non-integer and multi-channel fashion. Although the mathematics of this new mapping technique seem intricate, the concise nature of the derivations allow for an implementation procedure that lends itself to a real-time implementation using lookup tables, a task that is also introduced in this dissertation.

Hourly values of X, Y and Z geomagnetic components recorded at Coimbra Station (IAGA code: COI) and local geomagnetic K indices for 2007 to 2014

This study examines the performance of series of two geomagnetic indices and series synthesized from a semi-empirical model of magnetospheric currents, in explaining the geomagnetic activity observed at Northern Hemipshere's mid-latitude ground-based stations. We analyse data, for the 2007 to 2014 period, from four magnetic observatories (Coimbra, Portugal; Panagyurishte, Bulgary; Novosibirsk, Russia and Boulder, USA), at geomagnetic latitudes between 40° and 50° N. The quiet daily (QD) variation is firstly removed from the time series of the geomagnetic horizontal component (H) using natural orthogonal components (NOC) tools. We compare the resulting series with series of storm-time disturbance (Dst) and ring current (RC) indices and with H series synthesized from the Tsyganenko and Sitnov (2005, doi:10.1029/2004JA010798) (TS05) semi-empirical model of storm-time geomagnetic field. In the analysis, we separate days with low and high local K-index values. Our results show that NOC models are as efficient as standard models of QD variation in preparing raw data to be compared with proxies, but with much less complexity. For the two stations in Europe, we obtain indication that NOC models could be able to separate ionospheric and magnetospheric contributions. Dst and RC series explain the four observatory H-series successfully, with values for the mean of significant correlation coefficients, from 0.5 to 0.6 during low geomagnetic activity (K less than 4) and from 0.6 to 0.7 for geomagnetic active days (K greater than or equal to 4). With regard to the performance of TS05, our results show that the four observatories separate into two groups: Coimbra and Panagyurishte, in one group, for which the magnetospheric/ionospheric ratio in QD variation is smaller, a dominantly QD ionospheric contribution can be removed and TS05 simulations are the best proxy; Boulder and Novosibirsk,in the other group, for which the ionospheric and magnetospheric contributions in QD variation can not be differentiated and correlations with TS05 series can not be made to improve. The main contributor to magnetospheric QD signal are Birkeland currents. The relatively good success of TS05 model in explaining ground-based irregular geomagnetic activity at mid-latitudes makes it an effective tool to classify storms according to their main sources. For Coimbra and Panagyurishte in particular, where ionospheric and magnetospheric daily contributions seem easier to separate, we can aspire to use the TS05 model for ensemble generation in space weather (SW) forecasting and interpretation of past SW events.

Seismic scattering and absorption mapping of debris flows, feeding paths, and tectonic units at Mount St. Helens volcano

Acknowledgments We thank Edoardo Del Pezzo, Ludovic Margerin, Haruo Sato, Mare Yamamoto, Tatsuhiko Saito, Malcolm Hole, and Seth Moran for the valuable suggestions regarding the methodology and interpretation. Greg Waite provided the P wave velocity model of MSH. An important revision of the methods was done after two blind reviews performed before submission. The suggestions of two anonymous reviewers greatly enhanced our ability of imaging structures, interpreting our results, and testing their reliability. The facilities of the IRIS Data Management System, and specifically the IRIS Data Management Center, were used for access to waveform and metadata required in this study, and provided by the Cascades Volcano Observatory – USGS. Interaction with geologists and geographers part of the Landscape Dynamics Theme of the Scottish Alliance for Geoscience, Environment and Society (SAGES) has been important for the interpretation of the results.

Occupational exposure to asthmagens and adult onset wheeze and lung function in people who did not have childhood wheeze : A 50-year cohort study

Acknowledgements Funding: Chest, Heart and Stroke Scotland, grant ref. R13/A148. The funder had no role in study design, data collection, analysis and interpretation, writing of the manuscript, and in the decision to submit the manuscript for publication. All authors had full access to all the data in the study. The corresponding author had final responsibility for the decision to submit for publication.

Risk of fracture amongst patients with Parkinson's disease and other forms of parkinsonism

Acknowledgements We thank all the participants who took part, the research fellows (Kate Taylor, Robert Caslake, David McGhee, Angus Macleod) and nurses (Clare Harris, Joanna Gordon, Anne Hayman, Hazel Forbes) who helped assess the participants, and the study secretaries (Susan Kilpatrick, Pam Rebecca) and data management team (Katie Wilde, David Ritchie). The PINE study was funded by the BMA Doris Hillier award, Parkinson's UK, the RS McDonald Trust, NHS Grampian Endowments, SPRING and the BUPA Foundation. None of the funders had any influence in the study design, the collection, analysis and interpretation of the data, the writing of the report or the decision to submit the article for publication.

Managing chronic widespread pain in primary care : a qualitative study of patient perspectives and implications for treatment delivery

Funding The MUSICIAN trial was supported by an award from Arthritis Research UK, Chesterfield, UK. Grant number: 17292. The funding body approved the design of the study. They played no role in the collection, analysis, and interpretation of data or the writing of the manuscript.

Identifying the Structure and Fate of Wastewater Derived Organic Micropollutants by High-resolution Mass Spectrometry

Human activities represent a significant burden on the global water cycle, with large and increasing demands placed on limited water resources by manufacturing, energy production and domestic water use. In addition to changing the quantity of available water resources, human activities lead to changes in water quality by introducing a large and often poorly-characterized array of chemical pollutants, which may negatively impact biodiversity in aquatic ecosystems, leading to impairment of valuable ecosystem functions and services. Domestic and industrial wastewaters represent a significant source of pollution to the aquatic environment due to inadequate or incomplete removal of chemicals introduced into waters by human activities. Currently, incomplete chemical characterization of treated wastewaters limits comprehensive risk assessment of this ubiquitous impact to water. In particular, a significant fraction of the organic chemical composition of treated industrial and domestic wastewaters remains uncharacterized at the molecular level. Efforts aimed at reducing the impacts of water pollution on aquatic ecosystems critically require knowledge of the composition of wastewaters to develop interventions capable of protecting our precious natural water resources.

The goal of this dissertation was to develop a robust, extensible and high-throughput framework for the comprehensive characterization of organic micropollutants in wastewaters by high-resolution accurate-mass mass spectrometry. High-resolution mass spectrometry provides the most powerful analytical technique available for assessing the occurrence and fate of organic pollutants in the water cycle. However, significant limitations in data processing, analysis and interpretation have limited this technique in achieving comprehensive characterization of organic pollutants occurring in natural and built environments. My work aimed to address these challenges by development of automated workflows for the structural characterization of organic pollutants in wastewater and wastewater impacted environments by high-resolution mass spectrometry, and to apply these methods in combination with novel data handling routines to conduct detailed fate studies of wastewater-derived organic micropollutants in the aquatic environment.

In Chapter 2, chemoinformatic tools were implemented along with novel non-targeted mass spectrometric analytical methods to characterize, map, and explore an environmentally-relevant “chemical space” in municipal wastewater. This was accomplished by characterizing the molecular composition of known wastewater-derived organic pollutants and substances that are prioritized as potential wastewater contaminants, using these databases to evaluate the pollutant-likeness of structures postulated for unknown organic compounds that I detected in wastewater extracts using high-resolution mass spectrometry approaches. Results showed that application of multiple computational mass spectrometric tools to structural elucidation of unknown organic pollutants arising in wastewaters improved the efficiency and veracity of screening approaches based on high-resolution mass spectrometry. Furthermore, structural similarity searching was essential for prioritizing substances sharing structural features with known organic pollutants or industrial and consumer chemicals that could enter the environment through use or disposal.

I then applied this comprehensive methodological and computational non-targeted analysis workflow to micropollutant fate analysis in domestic wastewaters (Chapter 3), surface waters impacted by water reuse activities (Chapter 4) and effluents of wastewater treatment facilities receiving wastewater from oil and gas extraction activities (Chapter 5). In Chapter 3, I showed that application of chemometric tools aided in the prioritization of non-targeted compounds arising at various stages of conventional wastewater treatment by partitioning high dimensional data into rational chemical categories based on knowledge of organic chemical fate processes, resulting in the classification of organic micropollutants based on their occurrence and/or removal during treatment. Similarly, in Chapter 4, high-resolution sampling and broad-spectrum targeted and non-targeted chemical analysis were applied to assess the occurrence and fate of organic micropollutants in a water reuse application, wherein reclaimed wastewater was applied for irrigation of turf grass. Results showed that organic micropollutant composition of surface waters receiving runoff from wastewater irrigated areas appeared to be minimally impacted by wastewater-derived organic micropollutants. Finally, Chapter 5 presents results of the comprehensive organic chemical composition of oil and gas wastewaters treated for surface water discharge. Concurrent analysis of effluent samples by complementary, broad-spectrum analytical techniques, revealed that low-levels of hydrophobic organic contaminants, but elevated concentrations of polymeric surfactants, which may effect the fate and analysis of contaminants of concern in oil and gas wastewaters.

Taken together, my work represents significant progress in the characterization of polar organic chemical pollutants associated with wastewater-impacted environments by high-resolution mass spectrometry. Application of these comprehensive methods to examine micropollutant fate processes in wastewater treatment systems, water reuse environments, and water applications in oil/gas exploration yielded new insights into the factors that influence transport, transformation, and persistence of organic micropollutants in these systems across an unprecedented breadth of chemical space.

Modern major element concentrations and ratios measured in Atlantic surface sediments (36°N-49°S)

Numerous studies use major element concentrations measured on continental margin sediments to reconstruct terrestrial climate variations. The choice and interpretation of climate proxies however differ from site to site. Here we map the concentrations of major elements (Ca, Fe, Al, Si, Ti, K) in Atlantic surface sediments (36°N-49°S) to assess the factors influencing the geochemistry of Atlantic hemipelagic sediments and the potential of elemental ratios to reconstruct different terrestrial climate regimes. High concentrations of terrigenous elements and low Ca concentrations along the African and South American margins reflect the dominance of terrigenous input in these regions. Single element concentrations and elemental ratios including Ca (e.g., Fe/Ca) are too sensitive to dilution effects (enhanced biological productivity, carbonate dissolution) to allow reliable reconstructions of terrestrial climate. Other elemental ratios reflect the composition of terrigenous material and mirror the climatic conditions within the continental catchment areas. The Atlantic distribution of Ti/Al supports its use as a proxy for eolian versus fluvial input in regions of dust deposition that are not affected by the input of mafic rock material. The spatial distributions of Al/Si and Fe/K reflect the relative input of intensively weathered material from humid regions versus slightly weathered particles from drier areas. High biogenic opal input however influences the Al/Si ratio. Fe/K is sensitive to the input of mafic material and the topography of Andean river drainage basins. Both ratios are suitable to reconstruct African and South American climatic zones characterized by different intensities of chemical weathering in well-understood environmental settings.

(Table T1) Lithologic and ichnologic description of ODP Hole 174-1073A

When examined in their sedimentologic and stratigraphic context, ichnofabrics and component ichnofossils can help decipher paleoceanography and sea-level histories from marine deposits (Savrda, 1995, http://www.jstor.org/stable/3515095). Thus far, applications of ichnology in paleoceanographic investigations have been restricted to slowly deposited, predominantly biogenic sediments and/or strata deposited in oxygen-deficient, tectonically active basins. Moreover, ichnologic applications in sequence stratigraphic studies largely have been restricted to strata deposited in relatively shallow-water shelf or foreland basin settings. The limits of previous studies provided impetus for detailed postcruise examination of Quaternary deposits recovered at Ocean Drilling Program (ODP) Site 1073 on the New Jersey margin. These deposits provide the opportunity to assess the sedimentary and ichnofabric record of glacio-eustatic cycles in a passive continental slope setting characterized by relatively rapid accumulation of siliciclastic sediments in an area not far removed from the Laurentide ice margin. The primary purpose of this data report is to present basic sedimentologic and ichnologic observations made at the decimeter scale throughout the Quaternary sequence from Site 1073. Data analysis and interpretation in the context of climate and sea-level histories, as inferred from oxygen isotopic, palynologic, and seismic studies, are ongoing and will be presented in subsequent papers prepared for open literature (e.g., Savrda et al., in press).

Organizing and Interpreting Unstructured Qualitative Data

In the last several years there has been an increase in the amount of qualitative research using in-depth interviews and comprehensive content analyses in sport psychology. However, no explicit method has been provided to deal with the large amount of unstructured data. This article provides common guidelines for organizing and interpreting unstructured data. Two main operations are suggested and discussed: first, coding meaningful text segments, or creating tags, and second, regrouping similar text segments,or creating categories. Furthermore, software programs for the microcomputer are presented as away to facilitate the organization and interpretation of qualitative data

Peruanos y bolivianos en la sátira chilena de la Guerra del Pacífico (1879 - 1884)

A partir de los grabados publicados en las páginas de los periódicos que incluyeron humor gráfico en sus ediciones durante la Guerra del Pacífico (1879 - 1883), los caricaturistas chilenos desplegaron un discurso visual agresivo en clave patriótica y belicista, donde presentaron a sus lectores una imagen crítica y despectiva respecto de los adversarios de Chile. Recalcaron la supuesta falta de ánimo y valor combativo, ante la sola presencia de los efectivos militares chilenos tanto en el mar como en tierra. Así, la tinta y el papel, se transformaron en otra de las armas que intervinieron en el conflicto de Chile contra el Perú y Bolivia por la posesión de los ricos territorios salitreros de Tarapacá y Antofagasta. Las imágenes fueron interpretadas a partir de los postulados de la Escuela de Warburg, en especial los de Erwin Panofsky, que propone tres niveles de estudio del significado de cada obra, a saber, la “descripción preiconográfica”, luego el “estudio iconográfico” en cuanto tal y, finalmente, la “interpretación iconológica”.