Mining for Class-Specific Motifs in Protein Sequence Classification

Background: In protein sequence classification, identification of the sequence motifs or n-grams that can precisely discriminate between classes is a more interesting scientific question than the classification itself. A number of classification methods aim at accurate classification but fail to explain which sequence features indeed contribute to the accuracy. We hypothesize that sequences in lower denominations (n-grams) can be used to explore the sequence landscape and to identify class-specific motifs that discriminate between classes during classification. Discriminative n-grams are short peptide sequences that are highly frequent in one class but are either minimally present or absent in other classes. In this study, we present a new substitution-based scoring function for identifying discriminative n-grams that are highly specific to a class. Results: We present a scoring function based on discriminative n-grams that can effectively discriminate between classes. The scoring function, initially, harvests the entire set of 4- to 8-grams from the protein sequences of different classes in the dataset. Similar n-grams of the same size are combined to form new n-grams, where the similarity is defined by positive amino acid substitution scores in the BLOSUM62 matrix. Substitution has resulted in a large increase in the number of discriminatory n-grams harvested. Due to the unbalanced nature of the dataset, the frequencies of the n-grams are normalized using a dampening factor, which gives more weightage to the n-grams that appear in fewer classes and vice-versa. After the n-grams are normalized, the scoring function identifies discriminative 4- to 8-grams for each class that are frequent enough to be above a selection threshold. By mapping these discriminative n-grams back to the protein sequences, we obtained contiguous n-grams that represent short class-specific motifs in protein sequences. Our method fared well compared to an existing motif finding method known as Wordspy. We have validated our enriched set of class-specific motifs against the functionally important motifs obtained from the NLSdb, Prosite and ELM databases. We demonstrate that this method is very generic; thus can be widely applied to detect class-specific motifs in many protein sequence classification tasks. Conclusion: The proposed scoring function and methodology is able to identify class-specific motifs using discriminative n-grams derived from the protein sequences. The implementation of amino acid substitution scores for similarity detection, and the dampening factor to normalize the unbalanced datasets have significant effect on the performance of the scoring function. Our multipronged validation tests demonstrate that this method can detect class-specific motifs from a wide variety of protein sequence classes with a potential application to detecting proteome-specific motifs of different organisms.

The Investigation of the Ways in Which Gender Stereotypes are Perpetuated through Questioning and Assessment Strategies in Inquiry-Based Science Classroom

The purpose of this study was to investigate the questioning strategies of preservice teachers whenteaching science as inquiry. The guiding questions for this research were: In what ways do the questioning strategies of preservice teachers differ for male and female elementary students when teaching science as inquiry and how is Bloom’s Taxonomy evident within the questioning strategies of preservice teachers? Examination of the data indicated that participants asked a total of 4,158 questions to their elementary aged students. Of these questions, 974 (23%) were asked to boys, and 991 (24%) were asked to girls. The remaining questions (53%) were asked to the class as a whole, therefore no gender could be assigned to these questions. In relation to Bloom’s Taxonomy, 74% of the questions were basic knowledge, 15% were secondary comprehension, 2% were application, 4% were analysis, 1% were synthesis, and 3% were evaluation.

"Enemigos de la virilidad": Sex, Masturbation, and Celibacy in Nineteenth-Century Spain

The discourse on sexuality in nineteenth-century Spain presents a fundamental difference between the masculine ideal of that period and our current definition of masculinity. According to today’s popular stereotype, the typical man seeks out sexual contact and takes any opportunities that arise. By contrast, within the hygiene texts of the nineteenth century one detects a sense of unease associated with sexual activity and its corresponding role in the construction of hegemonic masculinity. In particular, sexual excess, masturbation, and celibacy were viewed as antagonistic to middle-class masculinity, which was instead associated with venereal moderation, marriage, and fatherhood. Men who transgressed this model risked their health as well as their masculinity. This formula reveals an element of fragility with regard to notions of manhood, in contrast to the traditional image of Spanish masculinity that originated during the Reconquest and is based on bellicose heroism, bravado, and sexual prowess.