Predicting class II MHC-Peptide binding:a kernel based approach using similarity scores

Background - Modelling the interaction between potentially antigenic peptides and Major Histocompatibility Complex (MHC) molecules is a key step in identifying potential T-cell epitopes. For Class II MHC alleles, the binding groove is open at both ends, causing ambiguity in the positional alignment between the groove and peptide, as well as creating uncertainty as to what parts of the peptide interact with the MHC. Moreover, the antigenic peptides have variable lengths, making naive modelling methods difficult to apply. This paper introduces a kernel method that can handle variable length peptides effectively by quantifying similarities between peptide sequences and integrating these into the kernel. Results - The kernel approach presented here shows increased prediction accuracy with a significantly higher number of true positives and negatives on multiple MHC class II alleles, when testing data sets from MHCPEP [1], MCHBN [2], and MHCBench [3]. Evaluation by cross validation, when segregating binders and non-binders, produced an average of 0.824 AROC for the MHCBench data sets (up from 0.756), and an average of 0.96 AROC for multiple alleles of the MHCPEP database. Conclusion - The method improves performance over existing state-of-the-art methods of MHC class II peptide binding predictions by using a custom, knowledge-based representation of peptides. Similarity scores, in contrast to a fixed-length, pocket-specific representation of amino acids, provide a flexible and powerful way of modelling MHC binding, and can easily be applied to other dynamic sequence problems.

The effect of the use of computer assisted instruction (CAI) on attitudes and computational scores of developmental mathematics students at two inner city schools with predominantly Black enrollment

This study examined the effects of computer assisted instruction (CAI) 1 hour per week for 18 weeks on changes in computational scores and attitudes of developmental mathematics students at schools with predominantly Black enrollment. Comparisons were made between students using CAI with differing software--PLATO, CSR or both together--and students using traditional instruction (TI) only.^ This study was conducted in the Dade County Public School System from February through June 1991, at two senior high schools. The dependent variables, the State Student Assessment Test (SSAT), and the School Subjects Attitude Scales (SSAS), measured students' computational scores and attitudes toward mathematics in 3 categories: interest, usefulness, and difficulty, respectively.^ Univariate analyses of variance were performed on the least squares mean differences from pretest to posttest for testing main effects and interactions. A t-test measured significant main effects and interactions. Results were interpreted at the.01 level of significance.^ Null hypotheses 1, 2, and 3 compared versions of CAI with the control group, for changes in mathematical computation scores measured with the SSAT. It could not be concluded that changes in standardized mathematics test scores of students using CAI with differing software 1 hour per week for 18 class hours combined with TI were significantly higher than changes in test scores for students receiving TI only.^ Null hypotheses 4, 5, and 6 tested the effects of CAI for attitudes toward mathematics for experimental groups against control groups measured with the SSAS. Changes in attitudes toward mathematics of students using CAI with differing software 1 hour per week for 18 class hours combined with TI were not significantly higher than attitude changes for students receiving TI only.^ Teacher effect on students' computational scores was a more influential variable than CAI. No interaction was found between gender and learning method on standardized mathematics test scores (null hypothesis 7). ^

An Examination of the Validity of English Language Achievement Test Scores in a LEP Student Population

Approximately 1,700 limited English proficient (LEP) and recently exited LEP students in grades 4 and 10 were tested using both an English and a comparable Spanish language achievement test. Many LEP and former LEP students performed better in math taking the test in Spanish compared to taking it in English.

The Effect of Parent Volunteers on Reading Scores and Attitudes

The purpose of this study is to investigate the relationship between student reading achievement and family involvement in urban schools. In this action research project, family members will be invited to participate as reading mentors during class time. In this study, the mentors will have the chance to impact the students by reading aloud to them in small groups. It is hypothesized that this will increase the student's reading scores and motivate students to read for enjoyment.

“I’m Trying To Bring the Scores of My School Up, Man!" Standardized Testing, Stereotypes, and High-Performing African American Elementary School Students

This qualitative study investigated factors that produced or perpetuated standardized test-based stereotype threat effects for a group of African American children. Findings revealed 4 themes: a perception of education as strictly test preparation, test-based stress and anxiety, racial salience, and stereotypes. Implications for practice and policy are discussed.

Categorical Differences in Scores of Students with Disabilities on the Florida Comprehensive Assessment Test

Students with disabilities participate in statewide assessments as required by federal law, and the success of schools is contingent on this group making Adequate Yearly Progress. This report on research includes the findings of differences between disability categories scoring proficient on the FCAT from the years 2005 through 2010.

Healthy Eating Index scores associated with symptoms of depression in Cuban-Americans with and without type 2 diabetes: a cross sectional study

Background Low diet quality and depression symptoms are independently associated with poor glycemic control in subjects with type 2 diabetes (T2D); however, the relationship between them is unclear. The aim of this study was to determine the association between diet quality and symptoms of depression among Cuban-Americans with and without T2D living in South Florida. Methods Subjects (n = 356) were recruited from randomly selected mailing list. Diet quality was determined using the Healthy Eating Index-2005 (HEI-05) score. Symptoms of depression were assessed using the Beck Depression Inventory (BDI). Both linear and logistic regression analyses were run to determine whether or not these two variables were related. Symptoms of depression was the dependent variable and independent variables included HEI-05, gender, age, marital status, BMI, education level, A1C, employment status, depression medication, duration of diabetes, and diabetes status. Analysis of covariance was used to test for interactions among variables. Results An interaction between diabetes status, gender and HEI-05 was found (P = 0.011). Among males with a HEI-05 score ≤ 55.6, those with T2D had a higher mean BDI score than those without T2D (11.6 vs. 6.6 respectively, P = 0.028). Among males and females with a HEI-05 score ≤ 55.6, females without T2D had a higher mean BDI score compared to males without T2D (11.0 vs. 6.6 respectively, P = 0.012) Conclusions Differences in symptoms of depression according to diabetes status and gender are found in Cuban-Americans with low diet quality.

Norm-based comparison of SF -12 physical and mental health scale scores for a sample of employees of Broward County

In the new health paradigm, the connotation of health has extended beyond the measures of morbidity and mortality to include wellness and quality of life. Comprehensive assessments of health go beyond traditional biological indicators to include measures of physical and mental health status, social role-functioning, and general health perceptions. To meet these challenges, tools for assessment and outcome evaluation are being designed to collect information about functioning and well-being from the individual's point of view.^ The purpose of this study was to profile the physical and mental health status of a sample of county government employees against U.S. population norms. A second purpose of the study was to determine if significant relationships existed between respondent characteristics and personal health practices, lifestyle and other health how the tools and methods used in this investigation can be used to guide program development and facilitate monitoring of health promotion initiatives.^ The SF-12 Health Survey (Ware, Kosinski, & Keller, 1995), a validated measure of health status, was administered to a convenience sample of 450 employees attending one of nine health fairs at an urban worksite. The instrument has been utilized nationally which enabled a comparative analysis of findings of this study with national results.^ Results from this study demonstrated that several respondent characteristics and personal health practices were associated with a greater percentage of physical and/or mental scale scores that were significantly "worse" or significantly "better" than the general population. Respondent characteristics that were significantly related to the SF-12 physical and/or mental health scale scores were gender, age, education, ethnicity, and income status. Personal health practices that were significantly related to SF-12 physical and/or mental scale scores were frequency of vigorous exercise, presence of chronic illness, being at one's prescribed height and weight, eating breakfast, smoking and drinking status. This study provides an illustration of the methods used to analyze and interpret SF-12 Health Survey data, using norm-based interpretation guidelines which are useful for purposes of program development and collecting information on health at the community level. ^

Factors affecting the alignment of *grades and reading scores for third-grade students on the Florida Comprehensive Assessment Test

The purpose of this study was to aid in understanding the relationship between current Reading report card grading practices and standards-based state standardized testing results in Reading and factors associated with the alignment of this relationship. Report card and Florida Comprehensive Assessment Test (FLAT) data for 2004 were collected for 1064 third grade students in nine schools of one feeder pattern in Florida's Miami-Dade County Public Schools. A Third Grade Teacher Questionnaire was administered to 48 Reading teachers. The questionnaire contained items relating to teachers' education, teaching experience, grading practices, and beliefs about the FCAT, instructional Reading activities, methods, and materials. ^ Findings of this study support a strong relationship between report card grades and FCAT Reading achievement levels. However, individual school correlational analysis showed significant differences among schools' alignment measures. Higher teacher alignment between grades and FCAT levels was associated with teachers spending more time on individualized methods of Reading instruction and to teachers feeling there was not enough time to teach and help individual students. Lower teacher alignment of grades and achievement levels was associated with teachers taking homework into account in the final Reading grade. Teacher alignment of grades and achievement levels was not associated with teacher beliefs concerning the FCAT, instructional activities in Reading and Language Arts, the Reading program used, the model of delivery of the Reading program, instruction or type of instructional planning done by the teachers. ^ This study highlights the need for further investigations related to determining additional teacher factors that may affect the alignment relationship between report card grades and standards-based state standardized testing results. ^

Examining the validity of the GRE General Test scores and undergraduate GPA for predicting success in graduate school at a large racially and ethnically diverse public university in Southeast Florida

The purpose of the study was to determine the degree of relationships among GRE scores, undergraduate GPA (UGPA), and success in graduate school, as measured by first year graduate GPA (FGPA), cumulative graduate GPA, and degree attainment status. A second aim of the study was to determine whether the relationships between the composite predictor (GRE scores and UGPA) and the three success measures differed by race/ethnicity and sex. A total of 7,367 graduate student records (masters, 5,990; doctoral: 1,377) from 2000 to 2010 were used to evaluate the relationships among GRE scores, UGPA and the three success measures. Pearson's correlation, multiple linear and logistic regression, and hierarchical multiple linear and logistic regression analyses were performed to answer the research questions. The results of the correlational analyses differed by degree level. For master's students, the ETS proposed prediction that GRE scores are valid predictors of first year graduate GPA was supported by the findings from the present study; however, for doctoral students, the proposed prediction was only partially supported. Regression and correlational analyses indicated that UGPA was the variable that consistently predicted all three success measures for both degree levels. The hierarchical multiple linear and logistic regression analyses indicated that at master's degree level, White students with higher GRE Quantitative Reasoning Test scores were more likely to attain a degree than Asian Americans, while International students with higher UGPA were more likely to attain a degree than White students. The relationships between the three predictors and the three success measures were not significantly different between men and women for either degree level. Findings have implications both for practice and research. They will provide graduate school administrators with institution-specific validity data for UGPA and the GRE scores, which can be referenced in making admission decisions, while they will provide empirical and professionally defensible evidence to support the current practice of using UGPA and GRE scores for admission considerations. In addition, new evidence relating to differential predictions will be useful as a resource reference for future GRE validation researchers.

A relationship between the Florida Comprehensive Assessment Test 2.0 mathematics scores and racial and ethnic concentration when considering socio-economic status, ESOL student population, and school climate

From the moment children are born, they begin a lifetime journey of learning about themselves and their surroundings. With the establishment of the No Child Left Behind Act of 2001, it mandates that all children receive a high-quality education in a positive school climate. Regardless of the school the child attends or the neighborhood in which the child lives, proper and quality education and resources must be provided and made available in order for the child to be academically successful. The purpose of this ex post facto study was to investigate the relationship between the FCAT 2.0 mathematics scores of public middle school students in Miami-Dade County, Florida and the concentrations of a school's racial and ethnic make-up (Whites, Blacks, and Hispanics), English for Speakers of other Languages (ESOL) population, socio-economic status (SES), and school climate. The research question of this study was: Is there a significant relationship between the FCAT 2.0 Mathematics scores and racial and ethnic concentration of public middle school students in Miami-Dade County when controlling SES, ESOL student population, and school climate for the 2010-2011 school year? The instruments used to collect the data were the FCAT 2.0 and Miami-Dade County Public Schools (M-DCPS) School Climate Survey. The study found that Economically Disadvantaged (SES) students socio-economic status had the strongest correlation with the FCAT 2.0 mathematics scores (r = -.830). The next strongest correlation was with the number of students who agreed that their school climate was positive and helped them learn (r = .741) and the third strongest correlation was a school percentage of White students (r = .668). The study concluded that the FCAT 2.0 mathematics scores of M-DCPS middle school students have a significant relationship with socio-economic status, school climate, and racial concentration.

The relationship between selected standardized test scores and performance in advanced placement math and science exams: Analyzing the differential effectiveness of scores for course identification and placement

There is a national need to increase the STEM-related workforce. Among factors leading towards STEM careers include the number of advanced high school mathematics and science courses students complete. Florida's enrollment patterns in STEM-related Advanced Placement (AP) courses, however, reveal that only a small percentage of students enroll into these classes. Therefore, screening tools are needed to find more students for these courses, who are academically ready, yet have not been identified. The purpose of this study was to investigate the extent to which scores from a national standardized test, Preliminary Scholastic Assessment Test/ National Merit Qualifying Test (PSAT/NMSQT), in conjunction with and compared to a state-mandated standardized test, Florida Comprehensive Assessment Test (FCAT), are related to selected AP exam performance in Seminole County Public Schools. An ex post facto correlational study was conducted using 6,189 student records from the 2010 - 2012 academic years. Multiple regression analyses using simultaneous Full Model testing showed differential moderate to strong relationships between scores in eight of the nine AP courses (i.e., Biology, Environmental Science, Chemistry, Physics B, Physics C Electrical, Physics C Mechanical, Statistics, Calculus AB and BC) examined. For example, the significant unique contribution to overall variance in AP scores was a linear combination of PSAT Math (M), Critical Reading (CR) and FCAT Reading (R) for Biology and Environmental Science. Moderate relationships for Chemistry included a linear combination of PSAT M, W (Writing) and FCAT M; a combination of FCAT M and PSAT M was most significantly associated with Calculus AB performance. These findings have implications for both research and practice. FCAT scores, in conjunction with PSAT scores, can potentially be used for specific STEM-related AP courses, as part of a systematic approach towards AP course identification and placement. For courses with moderate to strong relationships, validation studies and development of expectancy tables, which estimate the probability of successful performance on these AP exams, are recommended. Also, findings established a need to examine other related research issues including, but not limited to, extensive longitudinal studies and analyses of other available or prospective standardized test scores.

English Language Learners: A Correlational Study of the Relationship Between A Proficiency Level Assessment and End of Course Test Scores at one Georgia High School

Understanding the language of one’s cultural environment is important for effective communication and function. As such, students entering U.S. schools from foreign countries are given access to English to Speakers of Other Languages (ESOL) programs and they are referred to as English Language Learner (ELL) students. This dissertation examined the correlation of ELL ACCESS Composite Performance Level (CPL) score to the End of Course tests (EOCTs) and the Georgia High School Graduation Tests (GHSGTs) in the four content courses (language arts, mathematics, science, and social studies). A premise of this study was that English language proficiency is critical in meeting or exceeding state and county assessment standards. A quantitative descriptive research design was conducted using Cross-sectional archival data from a secondary source. There were 148 participants from school years 2011-2012 to 2013- 2014 from Grades 9-12. A Pearson product moment correlation was run to assess the relationship between the ACCESS CPL (independent variable) and the EOCT scores and the GHSGT scores (dependent variables). The findings showed that there was a positive correlation between ACCESS CPL scores and the EOCT scores where language arts showed a strong positive correlation and mathematics showed a positive weak correlation. Also, there was a positive correlation between ACCESS CPL scores and GHSGT scores where language arts showed a weak positive correlation. The results of this study indicated that that there is a relationship between the stated variables, ACCESS CPL, EOCT and GHSGT. Also, the results of this study showed that there were positive correlations at varying degrees for each grade levels. While the null hypothesis for Research Question 1 and Research Question 2 were rejected, there was a slight relationship between the variables.

Nasalance scores for typical Irish English-speaking adults

The aim was to establish normative nasalance values for Irish English-speaking adults. Thirty men and 30 women with normal resonance read aloud 16 sentences from the Irish nasality assessment protocol, the Zoo passage, and the Rainbow passage. The speech samples were recorded using the Nasometer II 6400. Results of a mixed between–within subjects ANOVA indicated no significant gender effect on nasalance scores. The speakers showed significantly higher nasalance scores for high-pressure consonant sentences than low-pressure consonant sentences, and for the Rainbow passage than total test sentences. There was no significant difference between high-pressure consonant sentences and the Zoo passage. Compared to previous studies, the Irish young adults had lower nasalance scores than Irish children and than young adults with North American dialects.