Toward the prediction of class I and II mouse major histocompatibility complex-peptide-binding affinity:in silico bioinformatic step-by-step guide using quantitative structure-activity relationships

Quantitative structure-activity relationship (QSAR) analysis is a cornerstone of modern informatics. Predictive computational models of peptide-major histocompatibility complex (MHC)-binding affinity based on QSAR technology have now become important components of modern computational immunovaccinology. Historically, such approaches have been built around semiqualitative, classification methods, but these are now giving way to quantitative regression methods. We review three methods--a 2D-QSAR additive-partial least squares (PLS) and a 3D-QSAR comparative molecular similarity index analysis (CoMSIA) method--which can identify the sequence dependence of peptide-binding specificity for various class I MHC alleles from the reported binding affinities (IC50) of peptide sets. The third method is an iterative self-consistent (ISC) PLS-based additive method, which is a recently developed extension to the additive method for the affinity prediction of class II peptides. The QSAR methods presented here have established themselves as immunoinformatic techniques complementary to existing methodology, useful in the quantitative prediction of binding affinity: current methods for the in silico identification of T-cell epitopes (which form the basis of many vaccines, diagnostics, and reagents) rely on the accurate computational prediction of peptide-MHC affinity. We have reviewed various human and mouse class I and class II allele models. Studied alleles comprise HLA-A*0101, HLA-A*0201, HLA-A*0202, HLA-A*0203, HLA-A*0206, HLA-A*0301, HLA-A*1101, HLA-A*3101, HLA-A*6801, HLA-A*6802, HLA-B*3501, H2-K(k), H2-K(b), H2-D(b) HLA-DRB1*0101, HLA-DRB1*0401, HLA-DRB1*0701, I-A(b), I-A(d), I-A(k), I-A(S), I-E(d), and I-E(k). In this chapter we show a step-by-step guide into predicting the reliability and the resulting models to represent an advance on existing methods. The peptides used in this study are available from the AntiJen database (http://www.jenner.ac.uk/AntiJen). The PLS method is available commercially in the SYBYL molecular modeling software package. The resulting models, which can be used for accurate T-cell epitope prediction, will be made are freely available online at the URL http://www.jenner.ac.uk/MHCPred.

The effects of cross -age peer tutoring on writing and reading comprehension skills and attitudes and self -perceptions as writers of third and fourth grade students

The purpose of this study was to investigate the effects of cross-age peer writing response groups on the writing and reading achievement of third and fourth grade students. Students' attitudes about writing and their perceptions of themselves as writers were also measured at the end of the study. ^ One hundred and twenty-two third and fourth grade students enrolled in a public school in a middle-class, multi-cultural neighborhood participated in the study. Four existing classes of students were randomly assigned to either the experimental condition (EC) or the control condition (CC). Both groups were pretested and posttested for writing and reading achievement. The intervention, cross-age peer writing groups, met for eleven weeks. ^ Three hypotheses were examined in this study: (a) writing improvement score, (b) reading comprehension improvement score, and (c) students' attitudes toward writing and their perception of themselves as writers based on the five scales measured on the Writer Self-Perception Scale. ^ ANOVAs were done on the pretests and posttests for writing and the Stanford Achievement Test reading comprehension subtest scores for the year of the study and the previous year. ANOVAs were also done for the five areas of the Writer Self-Perception Scale. Cross-tabulations were also used to compare improvement level verses treatment group, and grade level. ^ Analysis of the data revealed that there was no evidence that the tutoring (EC) groups made more progress than the non-tutoring (CC) groups in writing and reading. There was evidence of growth in writing, especially by the fourth graders. Most importantly, the fourth grade tutors, the experimental group, had the most positive feelings about writing and themselves as writers. ^

Comparison of Linear Functions in Middle Grades Textbooks from Singapore and the United States

Many U.S. students do not perform well on mathematics assessments with respect to algebra topics such as linear functions, a building-block for other functions. Poor achievement of U.S. middle school students in this topic is a problem. U.S. eighth graders have had average mathematics scores on international comparison tests such as Third International Mathematics Science Study, later known as Trends in Mathematics and Science Study, (TIMSS)-1995, -99, -03, while Singapore students have had highest average scores. U.S. eighth grade average mathematics scores improved on TIMMS-2007 and held steady onTIMMS-2011. Results from national assessments, PISA 2009 and 2012 and National Assessment of Educational Progress of 2007, 2009, and 2013, showed a lack of proficiency in algebra. Results of curriculum studies involving nations in TIMSS suggest that elementary textbooks in high-scoring countries were different than elementary textbooks and middle grades texts were different with respect to general features in the U.S. The purpose of this study was to compare treatments of linear functions in Singapore and U.S. middle grades mathematics textbooks. Results revealed features currently in textbooks. Findings should be valuable to constituencies who wish to improve U.S. mathematics achievement. Portions of eight Singapore and nine U.S. middle school student texts pertaining to linear functions were compared with respect to 22 features in three categories: (a) background features, (b) general features of problems, and (c) specific characterizations of problem practices, problem-solving competency types, and transfer of representation. Features were coded using a codebook developed by the researcher. Tallies and percentages were reported. Welch's t-tests and chi-square tests were used, respectively, to determine whether texts differed significantly for the features and if codes were independent of country. U.S. and Singapore textbooks differed in page appearance and number of pages, problems, and images. Texts were similar in problem appearance. Differences in problems related to assessment of conceptual learning. U.S. texts contained more problems requiring (a) use of definitions, (b) single computation, (c) interpreting, and (d) multiple responses. These differences may stem from cultural differences seen in attitudes toward education. Future studies should focus on density of page, spiral approach, and multiple response problems.

Class Placement and Academic and Behavioral Variables as Predictors of Graduation for Students with Disabilities

Dropout rates impacting students with high-incidence disabilities in American schools remain staggering (Bost, 2006; Hehir, 2005). Of this group, students with Emotional Behavioral Disorders (EBD) are at greatest risk. Despite the mandated national propagation of inclusion, students with EBD remain the least included and the least successful when included (Bost). Accordingly, this study investigated the potential significance of inclusive settings and other school-related variables within the context of promoting the graduation potential of students with Specific Learning Disabilities (SLD) or EBD. This mixed-methods study investigated specified school-related variables as likely dropout predictors, as well as the existence of first-order interactions among some of the variables. In addition, it portrayed the perspectives of students with SLD or EBD on the school-related variables that promote graduation. Accordingly, the sample was limited to students with SLD or EBD who had graduated or were close to graduation. For the quantitative component the numerical data were analyzed using linear and logistic regressions. For the qualitative component guided student interviews were conducted. Both strands were subsequently analyzed using Ridenour and Newman’s (2008) model where the quantitative hypotheses are tested and are later built-upon by the related qualitative meta-themes. Results indicated that a successful academic history, or obtaining passing grades was the only significant predictor of graduation potential when statistically controlling all the other variables. While at a marginal significance, results also yielded that students with SLD or EBD in inclusive settings experienced better academic results and behavioral outcomes than those in self-contained settings. Specifically, students with SLD or EBD in inclusive settings were found to be more likely to obtain passing grades and less likely to be suspended from school. Generally, the meta-themes yielded during the student interviews corroborated these findings as well as provided extensive insights on how students with disabilities view school within the context of promoting graduation. Based on the results yielded, provided the necessary academic accommodations and adaptations are in place, along with an effective behavioral program, inclusive settings can be utilized as drop-out prevention tools in special education.

Pollen profile and age determination for sediment core M72/5_619-1 (22-GC3)

Sediments from the Black Sea, a region historically dominated by forests and steppe landscapes, are a valuable source of detailed information on the changes in regional terrestrial and aquatic environments at decadal to millennial scales. Here we present multi-proxy environmental records (pollen, dinoflagellate cysts, Ca, Ti and oxygen isotope data) from the uppermost 305 cm of the core 22-GC3 (42°13.53' N, 36°29.55' E) collected from a water depth of 838 m in the southern part of the Black Sea in 2007. The records span the last ~ 18 kyr (all ages are given in cal kyr BP). The pollen data reveal the dominance of the Artemisia-steppe in the region, suggesting rather dry/cold environments ~ 18-14.5 kyr BP. Warming/humidity increase during melt-water pulses (~ 16.1-14.5 kyr BP), indicated by d18O records from the 22-GC3 core sediment and from the Sofular Cave stalagmite, is expressed in more negative d13C values from the Sofular Cave, usually interpreted as the spreading of C3 plants. The records representing the interstadial complex (~ 14.5-12.9 kyr BP) show an increase in temperature and moisture, indicated by forest development, increased primary productivity and reduced surface run-off, whereas the switch from primary terrigenous to primary authigenic Ca origin occurs ~ 500 yr later. The Younger Dryas cooling is clearly demonstrated by more negative d13C values from the Sofular Cave and a reduction of pines. The early Holocene (11.7-8.5 kyr BP) interval reveals relatively dry conditions compared to the mostly moist and warm middle Holocene (8.5-5 kyr BP), which is characterized by the establishment of the species-rich warm mixed and temperate deciduous forests in the low elevation belt, temperate deciduous beech-hornbeam forests in the middle and cool conifer forest in upper mountain belt. The border between the early and middle Holocene in the vegetation records coincides with the opening of the Mediterranean corridor at ~ 8.3 kyr BP, as indicated by a marked change in the dinocyst assemblages and in the sediment lithology. Changes in the pollen assemblages indicate a reduction in forest cover after ~ 5 kyr BP, which was likely caused by increased anthropogenic pressure on the regional vegetation.

We Are the Ones We Have Been Waiting for: Pan-African Consciousness Raising and Organizing in the United States and Venezuela

We Are the Ones We Have Been Waiting for: Pan-African Consciousness Raising and Organizing in the United States and Venezuela, draws on fifteen months of field research accompanying organizers, participating in protests, planning/strategy meetings, state-run programs, academic conferences and everyday life in these two countries. Through comparative examination of the processes by which African Diaspora youth become radically politicized, this work deconstructs tendencies to deify political s/heroes of eras past by historicizing their ascent to political acclaim and centering the narratives of present youth leading movements for Black/African liberation across the Diaspora. I employ Manuel Callahan’s description of “encuentros”, “the disruption of despotic democracy and related white middle-class hegemony through the reconstruction of the collective subject”; “dialogue, insurgent learning, and convivial research that allows for a collective analysis and vision to emerge while affirming local struggles” to theorize the moments of encounter, specifically, the moments (in which) Black/African youth find themselves becoming politically radicalized and by what. I examine the ways in which Black/African youth organizing differs when responding to their perpetual victimization by neoliberal, genocidal state-politics in the US, and a Venezuelan state that has charged itself with the responsibility of radically improving the quality of life of all its citizens. Through comparative analysis, I suggest the vertical structures of “representative democracy” dominating the U.S. political climate remain unyielding to critical analyses of social stratification based on race, gender, and class as articulated by Black youth. Conversely, I contend that present Venezuelan attempts to construct and fortify more horizontal structures of “popular democracy” under what Hugo Chavez termed 21st Century Socialism, have resulted in social fissures, allowing for a more dynamic and hopeful negation between Afro-Venezuelan youth and the state.

"Serve Canada with Men Like These": Masculinity, "Peacekeeping," and National Identity in Cold War Canada, 1956-1959

This paper explores the ways in which the construction of militarized masculinities in Cold War Canadian media reflected the hegemonic masculinities and broader social trends of the period. This paper focuses specifically on the recruiting materials produced for and by the Canadian Army between 1956 and 1959, the time of the Suez Canal Crisis and the beginnings of “Canadian peacekeeping.” Through the mobilization of modern and anti-modern masculine identities attached to hegemonic and idealized Cold War Canadian masculinities, the Army created the image of the “Modern Warrior” to portray itself as an occupation and culture for “real Canadian men.” This identity simultaneously corresponded with Canada’s new “peacekeeping” identity. By presenting certain images of Canadian manhood as the “ideal” Canadian identity and by associating this “ideal” masculinity with military service, the Army’s recruitment advertisements conflated Cold War rhetoric of service, defence, national citizenship, cultural belonging, and “ideal” ethnicity with a Canadian identity available only to a specific (and often exclusive) segment of society. Because military service has long been considered the crux of citizenship, these advertisements (re)entrenched patterns of middle-class, heterosexual, Anglo- Saxon masculine power and dominance in a time of social uncertainty and cultural anxiety through the reaffirmation of this group’s “privilege” to serve the nation.

Marginalised Mothers: Exploring Working Class Experiences

Successive moral panics have cast poor or socially excluded mothers - associated with social problems as diverse as crime, underachievement, unemployment and mental illness - as bad mothers. Their mothering practices are held up as the antithesis of good parenting and are associated with poor outcomes for children. Marginalised Mothers provides a detailed and much-needed insight into the lived experience of mothers who are frequently the focus of public concern and intervention, yet all too often have their voices and experiences overlooked. The book explores how they make sense of their lives with their children and families, position themselves within a context of inequality and vulnerability, and resist, subvert and survive material and social marginalisation. This controversial text uses qualitative data from a selection of working class mothers to highlight the opportunities and choices they face and to expose the middle class assumptions that ground much contemporary family policy. It will be of interest to students and researchers in sociology, social work and social policy, as well as social workers and policymakers.

Occupied childhoods: discourses and politics of childhood and their place in Palestinian and Pan-­Arab screen content for children

This thesis explores changing discourses of childhood and the ways in which power relations intersect with socio-cultural norms to shape screen-based media for Palestinian children. Situated within the interdisciplinary study of childhood, the research is an institutional and textual analysis that includes discursive and micro-level analysis of the socio-political circumstances within which children consume media in present-day Palestine. The thesis takes a social constructionist view, arguing that ‘childhood’ is not a fixed universal concept and that discourses of childhood are produced at specific historical moments as an effect of power. The study has a three-part research agenda. The first section uses secondary literature to explore theories and philosophies relating to definitions of childhood in Arab societies. The second employs participant observation and semi-structured interviews to understand the history and politics of children’s media in the West Bank. The final part of the research activity focuses on the impact that definitions of childhood and the politics of children’s media have on broadcasting outcomes through an analysis of (a) discourses on children’s media that circulate in Palestinian society, and (b) local and pan-Arab cultural texts consumed by Palestinian children. The analysis demonstrates that complex ideological and political factors are at play, which has led to the marginalisation, politicisation and internationalisation of local production for children. Due to the lack of alternatives, local producers often rely on international funding, and are hence forced to negotiate competing definitions of childhood, which while fitting with an international agenda of normalising the Israeli occupation, conflict culturally and politically with local conceptions of childhood and hopes for the Palestinian nation. While the Palestinian community appreciates the positive potential of local production, discourses and strategies around children’s media show that Palestinian children are constructed as vulnerable, incomplete and in constant need of guidance. Pan-Arab content presents a slightly less didactic approach and in certain cases presents childhood as a dynamic space of empowerment. However, by constructing children as ‘consumercitizens’, it alienates Arab (and Palestinian) children from disadvantaged backgrounds,as the preferred audience is middle-class children living in oil-rich countries of the Gulf.

Shakespeare and the Colonial Encounter in India in the Eighteenth and Nineteenth Centuries

Thesis (Ph.D.)--University of Washington, 2016-03

Transformative Political Spaces? Asambleas Populares, Identity, Alliances and Belonging in Buenos Aires

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

Negotiating Community and Nation in Chợ Lớn: Nation-building, Community-building and Transnationalism in Everyday Life during the Republic of Việt Nam, 1955-1975

Thesis (Ph.D.)--University of Washington, 2016-06

Micro-Foundations of Financialization. Status Anxiety and the Market for Consumer Credit in Chile

This project investigates why people in Chile acquired so much consumer debt in contexts of material prosperity, and asks what the role of inequality and commodification is in this process. The case raises an important challenge to the literature. Insofar as existing accounts assume that the financialization of consumption occurs in contexts marked by wage stagnation and a general deterioration of the middle classes, they engender two contradictory explanations: while political economists argue that people use credit in order to smooth their consumption in the face of market volatility, economists maintain that concentration of wealth at the top pushes middle income consumers to emulate the expenditures of the rich and consume beyond their means. These explanations do not necessarily fit the reality of developing countries. Triangulating in-depth interviews with middle class families, multivariate statistical analysis and secondary literature, the project shows that consumers in Chile use credit to finance “ordinary” forms of consumption that do not aim either at coping with market instability or emulating and signaling status to others. Rather, Chileans use department store credit cards in order to acquire a standard package of “inconspicuous” goods that they feel entitled to have. From this point of view, the systematic indebtedness of consumers originates in a major concern with “rank”, “achievement” and "security" that – following De Botton -- I call “status anxiety”. Status anxiety does not stem from the desire to emulate rich consumers, but from the impossibility of complying with normative expectations about what a middle class family should be (and have) that outweigh wage improvements. The project thus investigates the way in which “status anxiety” is systematically reproduced by means of two broad mechanisms that prompt people to acquire consumer debt. The first mechanism generating debt stems from an increase of real wages and high levels of inequality. It is explained by a general sociological principle known as relative deprivation, which points to the fact that general satisfaction with one´s income, possessions or status, is assessed not in absolute terms such as total income, but in relation with reference groups. In this sense, I explore the mechanisms that operate as catalyzers of relative deprivation, by making explicit social inequalities and distorting the perception of others´ wealth. Despite upward mobility and economic improvement, Chileans share the perception of “falling behind,” which materializes in an “imaginary middle class” against which people compare their status, possessions and economic independence. Finally, I show that the commodification of education, health and pension funds does not directly prompt people to acquire consumer debt, but operate as “income draining” mechanisms that demand higher shares of middle class families’ “discretionary income.” In combination with “relative deprivation,” these “income draining” mechanisms leave families with few options to perform their desired class identities, other than learning how to bring resources from the future into the present with the help of department store credit cards.

Crime and Punishment.

The study of Victorian crime and punishment is a rich area of research that has attracted the interest not only of literary scholars but also of social historians, legal historians, and criminologists. Related scholarship therefore often situates itself at the intersection of traditional disciplinary boundaries, facilitating interdisciplinary conversation. Crime and punishment was a pressing issue for the Victorians and provoked a wealth of responses from contemporaneous commentators in literature, culture, and science. As a new phase of industrialization brought immense wealth for some and abject poverty for others, Victorian urban centers in particular were afflicted by crime. Without an effective system of social welfare in place, social inequality and deprivation drove women, men, and children into petty crime and more serious offenses, resulting in severe punishment ranging from incarceration via penal transportation to hanging. Public executions, not abolished until 1868, attracted huge crowds of spectators, including authors such as Charles Dickens and William Thackeray, who wrote about these experiences. A forerunner of the popular press, street literature conveyed and illustrated these events for a broad audience. Execution broadsides of famous cases, printing the alleged last lamentations of convicts on the scaffold in verse, are estimated to have sold by the million. As the legal system was undergoing reform (comprising changes in legal evidence procedure, divorce law, women’s property rights, and punishment for sexual offenses, for example), sensational trials caused furor and stimulated commentary in literature and the media. Crime and punishment was discussed in a range of literary and popular genres, poetry, and reformist writing. The “Newgate School” of fiction was accused of glamorizing crime, and the popular penny dreadfuls were feared to corrupt public morals. Sensational fiction in the 1860s, which often drew on real-life criminal cases and newspaper reports, depicted the supposedly respectable middle-class family home as a center of transgression. Similarly, detective fiction typically focused on crime in the world of the middle classes. For the student new to the subject of crime and punishment, this area’s interdisciplinary nature can pose an initial challenge.

Arquitetura da (in)segurança: estudando relações entre configuração espacial, artifícios de segurança e violência urbana no bairro Manaíra, João Pessoa, Paraíba

João Pessoa, the capital city of the state of Paraíba (Northeast Brazil), is reputed throughout the country as a quiet place, although it has been acquiring, over the past years, an urban character with social implications similar to those of major metropolitan Brazilian areas. The new situation is evident by the social inequalities, with the creation of confined spaces, which segregate and cause enclosure of the inhabitants, leading to death the public space. This study correlates accessibility in spatial structure with two types of crime data, burglary and robbery, recorded in 2008 and 2009, by the Secretaria de Segurança da Paraíba (The government agency public in charge of safety), in the district of Manaíra, an upper middle class neighborhood, which has, in recent times, been considered one of the most violent areas in João Pessoa. Sought to understand connections between these events and morpho-social aspects of the built environment, where examined the spatial properties, such as accessibility of the urban net, the presence of control measures, the safety of buildings and their uses. Spatial properties were also validated by the observation of pedestrian flows at strategic points of the study area. It was concluded that the presence of intense flows helps to attract potential thieves, physical security and control offers little protection