Discriminating antigen and non-antigen using proteome dissimilarity II:viral and fungal antigens

Immunogenicity arises via many synergistic mechanisms, yet the overall dissimilarity of pathogenic proteins versus the host proteome has been proposed as a key arbiter. We have previously explored this concept in relation to Bacterial antigens; here we extend our analysis to antigens of viral and fungal origin. Sets of known viral and fungal antigenic and non-antigenic protein sequences were compared to human and mouse proteomes. Both antigenic and non-antigenic sequences lacked human or mouse homologues. Observed distributions were compared using the non-parametric Mann-Whitney test. The statistical null hypothesis was accepted, indicating that antigen and non-antigens did not differ significantly. Likewise, we could not determine a threshold able meaningfully to separate non-antigen from antigen. We conclude that viral and fungal antigens cannot be predicted from pathogen genomes based solely on their dissimilarity to mammalian genomes.

Long memory and multifractality:a joint test

The properties of statistical tests for hypotheses concerning the parameters of the multifractal model of asset returns (MMAR) are investigated, using Monte Carlo techniques. We show that, in the presence of multifractality, conventional tests of long memory tend to over-reject the null hypothesis of no long memory. Our test addresses this issue by jointly estimating long memory and multifractality. The estimation and test procedures are applied to exchange rate data for 12 currencies. Among the nested model specifications that are investigated, in 11 out of 12 cases, daily returns are most appropriately characterized by a variant of the MMAR that applies a multifractal time-deformation process to NIID returns. There is no evidence of long memory.

The effects of coloured light filter overlays on reading rates in age-related macular degeneration

Purpose: To determine the effect of coloured light filter overlays on reading rates for people with age-related macular degeneration (AMD). Method: Using a prospective clinical trial design, we examined the null hypothesis that coloured light filter overlays do not improve reading rates in AMD when compared to a clear filter. Reading rates for 12 subjects with non-exudative AMD, associated with a relative scotoma and central fixation (mean age 81 years, SD 5.07 years) were determined using the Rate of Reading Test® (printed, nonsense, lower case sans serif, stationary text) with 10 different, coloured light filter overlays (Intuitive Overlays®; figures in brackets are percentage transmission values); rose (78%), pink (78%), purple (67%), aqua (81%), blue (74%), lime-green (86%), mint-green (85%), yellow (93%), orange (83%) and grey (71%). A clear overlay (Roscolene # 00) (360 cdm-2) with 100% transmittance was used as a control. Results: ANOVA indicated that there was no statistically significant difference in reading rates with the coloured light filter overlays compared to the clear filter. Furthermore, chi-squared analysis indicated that the rose, purple and blue filters had a significantly poorer overall ranking in terms of reading rates compared to the other coloured and clear light filters. Conclusion: Coloured light filter overlays are unlikely to provide a clinically significant improvement in reading rates for people with non-exudative AMD associated with a relative scotoma and central fixation. Copyright © Acta Ophthalmol Scand 2004.

When to use the Bonferroni correction

PURPOSE: The Bonferroni correction adjusts probability (p) values because of the increased risk of a type I error when making multiple statistical tests. The routine use of this test has been criticised as deleterious to sound statistical judgment, testing the wrong hypothesis, and reducing the chance of a type I error but at the expense of a type II error; yet it remains popular in ophthalmic research. The purpose of this article was to survey the use of the Bonferroni correction in research articles published in three optometric journals, viz. Ophthalmic & Physiological Optics, Optometry & Vision Science, and Clinical & Experimental Optometry, and to provide advice to authors contemplating multiple testing. RECENT FINDINGS: Some authors ignored the problem of multiple testing while others used the method uncritically with no rationale or discussion. A variety of methods of correcting p values were employed, the Bonferroni method being the single most popular. Bonferroni was used in a variety of circumstances, most commonly to correct the experiment-wise error rate when using multiple 't' tests or as a post-hoc procedure to correct the family-wise error rate following analysis of variance (anova). Some studies quoted adjusted p values incorrectly or gave an erroneous rationale. SUMMARY: Whether or not to use the Bonferroni correction depends on the circumstances of the study. It should not be used routinely and should be considered if: (1) a single test of the 'universal null hypothesis' (Ho ) that all tests are not significant is required, (2) it is imperative to avoid a type I error, and (3) a large number of tests are carried out without preplanned hypotheses.

Are European equity markets efficient? New evidence from fractal analysis

We report an empirical analysis of long-range dependence in the returns of eight stock market indices, using the Rescaled Range Analysis (RRA) to estimate the Hurst exponent. Monte Carlo and bootstrap simulations are used to construct critical values for the null hypothesis of no long-range dependence. The issue of disentangling short-range and long-range dependence is examined. Pre-filtering by fitting a (short-range) autoregressive model eliminates part of the long-range dependence when the latter is present, while failure to pre-filter leaves open the possibility of conflating short-range and long-range dependence. There is a strong evidence of long-range dependence for the small central European Czech stock market index PX-glob, and a weaker evidence for two smaller western European stock market indices, MSE (Spain) and SWX (Switzerland). There is little or no evidence of long-range dependence for the other five indices, including those with the largest capitalizations among those considered, DJIA (US) and FTSE350 (UK). These results are generally consistent with prior expectations concerning the relative efficiency of the stock markets examined. © 2011 Elsevier Inc.

Conditional Confidence Interval for the Scale Parameter of a Weibull Distribution

2000 Mathematics Subject Classification: 62F25, 62F03.

A Bimodality Test in High Dimensions

We present a test for identifying clusters in high dimensional data based on the k-means algorithm when the null hypothesis is spherical normal. We show that projection techniques used for evaluating validity of clusters may be misleading for such data. In particular, we demonstrate that increasingly well-separated clusters are identified as the dimensionality increases, when no such clusters exist. Furthermore, in a case of true bimodality, increasing the dimensionality makes identifying the correct clusters more difficult. In addition to the original conservative test, we propose a practical test with the same asymptotic behavior that performs well for a moderate number of points and moderate dimensionality. ACM Computing Classification System (1998): I.5.3.

Long memory and multifractality:a joint test

The properties of statistical tests for hypotheses concerning the parameters of the multifractal model of asset returns (MMAR) are investigated, using Monte Carlo techniques. We show that, in the presence of multifractality, conventional tests of long memory tend to over-reject the null hypothesis of no long memory. Our test addresses this issue by jointly estimating long memory and multifractality. The estimation and test procedures are applied to exchange rate data for 12 currencies. In 11 cases, the exchange rate returns are accurately described by compounding a NIID series with a multifractal time-deformation process. There is no evidence of long memory.

Első- és másodfajú etikai kudarcok (Type I and type II ethical errors)

A cikkben a szerző a piac és a kormányzat kudarcaiból kiindulva azonosítja a közjó elérését célzó harmadik rendszer, az etikai felelősség kudarcait. Statisztikai analógiát használva elsőfajú kudarcként azonosítja, mikor az etikát nem veszik figyelembe, pedig szükség van rá. Ugyanakkor másodfajú kudarcként kezeli az etika profitnövelést célzó használatát, mely megtéveszti az érintetteteket, így még szélesebb utat enged az opportunista üzleti tevékenységnek. Meglátása szerint a három rendszer egymást nemcsak kiegészíti, de kölcsönösen korrigálja is. Ez az elsőfajú kudarc esetében általánosabb, a másodfajú kudarc megoldásához azonban a gazdasági élet alapvetéseinek átfogalmazására, az önérdek és az egydimenziós teljesítményértékelés helyett egy új, holisztikusabb szemléletű közgazdaságra van szükség. _______ In the article the author identifies the errors of ethical responsibility. That is the third system to attain common good, but have similar failures like the other two: the hands of the market and the government. Using statistical analogy the author identifies Type I error when ethics are not considered but it should be (null hypothesis is rejected however it’s true). She treats the usage of ethics to extend profit as Type II error. This misleads the stakeholders and makes room for opportunistic behaviour in business (null hypothesis is accepted in turn it’s false). In her opinion the three systems: the hand of the market, the government and the ethical management not only amend but interdependently correct each other. In the case of Type I error it is more general. Nevertheless to solve the Type II error we have to redefine the core principles of business. We need a more holistic approach in economics instead of self-interest and one-dimensional interpretation of value.

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). ^

The effects of sex of teacher, sex of scenario principal, and leadership style on the performance ratings of scenario principals by teachers

This study was designed to address questions regarding the effects of sex and leadership style on teacher perceptions of principal effectiveness. On a researcher-designed instrument, middle school teachers rated the effectiveness of a scenario principal's response in several situations. The responses reflected varying levels of Task and Relationship Behavior.^ The design incorporated two between subjects factors (Teacher Sex and Principal Sex) and one within subjects factor (Leadership Style) which was treated as a repeated measure. An analysis of variance revealed no significant effects except for Leadership Style. Overall, High Task/High Relationship behavior rated significantly higher and Low Task/Low Relationship rated significantly lower than the others. The null hypothesis concerning differences could not be rejected and the stated research hypotheses were not supported.^ Additional analyses of variance were conducted substituting subject demographic variables for Teacher Sex in the research design. No significant interactions or main effects other than Leadership Style were noted when either Age or Ethnicity were substituted.^ A significant two-way interaction was noted for Teacher Experience and Leadership Style (p =.0316). Less experienced teachers rated principal's performance lower when exhibiting High Task/Low Relationship style than did more experienced teachers. A significant three-way interaction was noted for Administrative Aspiration x Principal Sex x Leadership Style (p =.0294). Teachers who indicated an intent to enter administration differed more on their ratings between male and female principals exhibiting mixed styles of High Task/Low Relationship and Low Task/High Relationship than did teachers who indicated no or undecided.^ Sex of the teacher appears less important than sex of the principal on performance ratings. Results suggest further study of the effects of teacher experience and teacher administrative aspiration on perceptions of principal effectiveness. ^

Genomic variation of HIV-1 and its effects on drug resistance and molecular epidemiology analyses

In the first part of this study human immunodeficiency virus type 1 (HIV-1) proviral DNA sequences derived from 201 clones of the C2-V3 env region and the first exon of the tat gene were obtained from six MV-1 infected heterosexual couples. These molecular data were used to confirm the epidemiological relationships. The ability of the molecular data to draw such conclusions was also tested with multiple phylogenetic analyses. The tat region was much more useful in establishing epidemiological relationships than the commonly used C2-V3.^ Subsequently, using nucleotide sequences from the first exon of the Tat gene, we tested the hypothesis that a Florida dentist (a common source) infected five of his patients in the course of dental procedures, against the null hypothesis that the dentist and each individual of the dental group independently acquired the virus within the local community. Multiple phylogenetic analyses demonstrated that the sequences of the five patients were significantly more related to each other than to sequences of the controls. Our results using Tat sequences, combined with envelope sequence data, strongly support a common phylogenetic epidemiological relationship among these five patients.^ A third study is presented, which deals with the effects of genomic variations in drug resistance. HIV-1 reverse transcriptase (RT) mutations were detected in DNA from peripheral blood mononuclear cells from 11 of 12 HIV-infected children after 11-20 months of zidovudine monotherapy. The codon 41/215 mutant combination was associated with general decline in health status. Patients developing the codon 70 mutation tended to have a better health status. ^

Implementing aspects of Blueprint 2000: Investigating readiness expectations in selected elementary schools in Broward County, Florida

The purpose of this research study was to investigate if the determination of school readiness as it was evaluated by Broward County kindergarten teachers on the Florida's Expectations of School Readiness checklist can be attributed to the effects of gender, chronological age on school entry, racial or ethnic background, attending public preschool, native language other than English, or socioeconomic status.^ This is a descriptive study in which the number of expectations passed or failed for each of the identifier categories was compared. The Chi-squared distribution was used to evaluate the null hypothesis that "chronological age at entry to school, gender, race or ethnicity, native language other than English, public preschool experience, and socioeconomic status have no effect on the determination of readiness for school". Results were confirmed using t-tests, ANOVA, and linear regression models. The cohort of 1555 Broward County students in the study were evaluated using the Florida's Expectations for School Readiness checklist and were determined not ready for school during the initial data collection year 1996-1997.^ The determination of school readiness was significantly dependent on the gender, and racial or ethnic background of the students in the cohort. The socioeconomic status and native language other than English designations were significant for students only in the areas of preacademic, academic and literacy development. Chronological age on entry to school or attendance in public preschool prior to entry in kindergarten for the cohort was not significant in the determination of readiness for school.^ Given the fact that this study followed only students that were determined not ready for school, it is recommended that a second cohort of both "ready" and "not ready" students be studied. ^

The winds of change? Exploring political effects of Hurricane Andrew

Before dawn on August 24, 1992, Hurricane Andrew smashed into south Florida, particularly southern Dade County, and soon become the costliest natural disaster in U.S. history. Andrew's impacts quickly overwhelmed local and state emergency response capabilities and eventually required major federal assistance, including regular military units. While the social and economic impacts of Hurricane Andrew are relatively well researched, much less attention has been given to its possible political effects. ^ Focusing on incumbent officeholders at three levels (municipal, state legislative, and statewide) who stood for reelection after Hurricane Andrew, this study seeks to determine whether they experienced any political effects from Andrew. That is, this study explores the possible interaction between the famous “incumbency advantage” and an “extreme event,” in this case a natural disaster. The specific foci were (1) campaigns and campaigning (a research process that included 43 personal interviews), and (2) election results before and after the event. ^ Given well-documented response problems, the working hypothesis was that incumbents experienced largely negative political fallout from the disaster. The null hypothesis was that incumbents saw no net political effects, but the reverse hypothesis was also considered: incumbents benefited politically from the event. ^ In the end, this study found that although the election process was physically disrupted, especially in south Dade County, the disaster largely reinforced the incumbency advantage. More specifically, the aftermath of Hurricane Andrew allowed most incumbent officeholders to (1) enhance constituency service, (2) associate themselves with the flow of external assistance, (3) achieve major personal visibility and media coverage, and yet (4) appear non-political or at least above normal politics. Overall, this combination allowed incumbents to very effectively “campaign without campaigning,” a point borne out by post-Andrew election results. ^

An examination of Lotka's law in the field of Library and Information Studies

The purpose of this study was to test Lotka’s law of scientific publication productivity using the methodology outlined by Pao (1985), in the field of Library and Information Studies (LIS). Lotka’s law has been sporadically tested in the field over the past 30+ years, but the results of these studies are inconclusive due to the varying methods employed by the researchers. ^ A data set of 1,856 citations that were found using the ISI Web of Knowledge databases were studied. The values of n and c were calculated to be 2.1 and 0.6418 (64.18%) respectively. The Kolmogorov-Smirnov (K-S) one sample goodness-of-fit test was conducted at the 0.10 level of significance. The Dmax value is 0.022758 and the calculated critical value is 0.026562. It was determined that the null hypothesis stating that there is no difference in the observed distribution of publications and the distribution obtained using Lotka’s and Pao’s procedure could not be rejected. ^ This study finds that literature in the field of Library and Information Studies does conform to Lotka’s law with reliable results. As result, Lotka’s law can be used in LIS as a standardized means of measuring author publication productivity which will lead to findings that are comparable on many levels (e.g., department, institution, national). Lotka’s law can be employed as an empirically proven analytical tool to establish publication productivity benchmarks for faculty and faculty librarians. Recommendations for further study include (a) exploring the characteristics of the high and low producers; (b) finding a way to successfully account for collaborative contributions in the formula; and, (c) a detailed study of institutional policies concerning publication productivity and its impact on the appointment, tenure and promotion process of academic librarians. ^