Cooperativity and Stability in a Langevin Model of Protein Folding

We present two simplified models of protein dynamics based on Langevin's equation of motion in a viscous medium. We explore the effect of the potential energy function's symmetry on the kinetics and thermodynamics of simulated folding. We find that an isotropic potential energy function produces, at best, a modest degree of cooperativity. In contrast, a suitable anisotropic potential energy function delivers strong cooperativity.Comment: 45 pages, 16 figures, 2 tables. LaTeX. Submitted to the Journal of Chemical Physic

Improving the performance of the iterative signature algorithm for the identification of relevant patterns

The iterative signature algorithm (ISA) has become very attractive to detect co-regulated genes from microarray data matrices and can be a useful tool for the identification of similar patterns in many other kinds of numerical data matrices. Nevertheless, its algorithmic strategy exhibits some limitations since it is based on statistical behavior of the average and considers averages weighted by scores not necessarily positive. Hence, we propose to take the median instead of the average and to use absolutes scores in ISA's structure. Furthermore, a generalized function is also introduced in the algorithm in order to improve its algorithmic strategy for detecting high value or low value biclusters. The effects of these simple modifications on the performance of the biclustering algorithm are evaluated through an experimental comparative study involving synthetic data sets and real data from the organism Saccharomyces cerevisiae. The experimental results show that the proposed variations of ISA outperform the original version in many situations. Absolute scores in ISA are shown to be essential for the correct interpretation of the biclusters found by the algorithm. The median instead of the average turns the biclustering algorithm more resilient to outliers in the data sets. Copyright © 2011 Wiley Periodicals, Inc

Introduction to Art as Voice: Creating Access for Emergent Bilingual Learners

In this introductory chapter, we begin by introducing ourselves, so that you immediately know our positionalities—who we are and the lens we see the world through—and in the hope to provide you with knowledge of why this special issue is so close to our hearts. We then share current demographic information regarding emergent bilingual learners to further explain the importance of this work today. In the current political context, the topic of displaced populations, immigration policies (such as The Deferred Action for Childhood Arrivals [DACA]), refugees, as well as those who are undocumented is very alive in classrooms and relevant to our students’ lives. Case studies within this issue address the needs of displaced groups in a way that is inclusive and validates their lived experiences, providing a sense of belonging through the arts. After contextualizing these realities, we touch upon theories that drive this work, specifically relating to the arts, literacies, and language acquisition, and demonstrate how we have put these theories into practice by providing rich examples of using the arts as voice with emergent bilingual students, families, and communities. Finally, we conclude with an invitation to read onwards, to review the final chapter that includes multiple resources for those working with EB learners, and to develop and share your own bank of resources

Diverse Experiences and Complex Identities: A Resource Archive of Artists’ and Educators’ Works

This concluding article builds on the ideas developed throughout this special issue by providing a wide range of resources to enrich arts-based work within the field of literacy development with families and communities of emergent bilinguals. We include a bank of resources that may serve as the beginning of an archive. Coming from three different fields, with varying professional experiences, the sources we find helpful intersect and diverge. To honor this range of possibilities, we have taken an expansive approach that includes poets, visual and performing artists, arts and cultural organizations, literary associations, language learning standards and anti-bias and critical pedagogy sources. While expansive in content, this list is limited, based on sources that have inspired and shaped our work. We invite you to explore it, edit it, add to it, develop your own and share it

Annotation concept synthesis and enrichment analysis: a logic-based approach to the interpretation of high-throughput experiments

Motivation: Annotation Enrichment Analysis (AEA) is a widely used analytical approach to process data generated by high-throughput genomic and proteomic experiments such as gene expression microarrays. The analysis uncovers and summarizes discriminating background information (e.g. GO annotations) for sets of genes identified by experiments (e.g. a set of differentially expressed genes, a cluster). The discovered information is utilized by human experts to find biological interpretations of the experiments

Genome-wide functional analysis of human 5' untranslated region introns

Genes with short 5'UTR introns have higher expression than genes with no or long 5'UTR introns. Complex evolutionary forces act on these introns

The Synergizer service for translating gene, protein and other biological identifiers

Summary: The Synergizer is a database and web service that provides translations of biological database identifiers. It is accessible both programmatically and interactively