Growth Curve Models for the Analysis of Phenotype Arrays for a Systems Biology Overview of Yersinia pestis

The Phenotype MicroArray technology of Biolog, Inc. (Hayward, CA) measures the respiration of cells as a function of time in thousands of microwells simultaneously, and thus provides a high-throughput means of studying cellular phenotypes. The microwells contain compounds involved in a number of biochemical pathways, as well as chemicals that test the sensitivity of cells against antibiotics and stress. While the PM experimental workflow is completely automated, statistical methods to analyze and interpret the data are lagging behind. To take full advantage of the technology, it is essential to develop efficient analytical methods to quantify the information in the complex datasets resulting from PM experiments. We propose the use of statistical growth-curve models to rigorously quantify observed differences in PM experiments, in the context of the growth and metabolism of Yersinia pestis cells grown under different physiological conditions. The information from PM experiments complement genomic and proteomic results and can be used to identify gene function and in drug development. Successful coupling of phenomics results with genomics and proteomics will lead to an unprecedented ability to characterize bacterial function at a systems biology level

The First Phylogenetic Analysis of Palpigradi (Arachnida)—The Most Enigmatic Arthropod Order

Palpigradi are a poorly understood group of delicate arachnids, often found in caves or other subterranean habitats. Concomitantly, they have been neglected from a phylogenetic point of view. Here we present the first molecular phylogeny of palpigrades based on specimens collected in different subterranean habitats, both endogean (soil) and hypogean (caves), from Australia, Africa, Europe, South America and North America. Analyses of two nuclear ribosomal genes and COI under an array of methods and homology schemes found monophyly of Palpigradi, Eukoeneniidae, and a division of Eukoeneniidae into four main clades, three of which include samples from multiple continents. This supports either ancient vicariance or long-range dispersal, two alternatives we cannot distinguish with the data at hand. In addition, we show that our results are robust to homology scheme and analytical method, encouraging further use of the markers employed in this study to continue drawing a broader picture of palpigrade relationships.Organismic and Evolutionary Biolog

High school boys' and girls' writing conceptions and writing self-efficacy beliefs : what is their role in writing performance?

ABSTRACT: This study investigated the conceptions about writing and writing self-efficacy beliefs held by high school students in relation to the students’ gender as well as their associations with writing achievement. The results show that female students have more sophisticated writing conceptions than their male counterparts but no gender differences were found in writing self-efficacy beliefs. In addition, results reveal that writing self-efficacy beliefs and gender play an important role in predicting writing performance and that writing performance is moderated by students’ writing conceptions. Educational implications and further research are discussed

The Effect of Keyboard-Based Word Processing on Students With Different Working Memory Capacity During the Process of Academic Writing

This study addresses the current debate about the beneficial effects of text processing software on students with different working memory (WM) during the process of academic writing, especially with regard to the ability to display higher-level conceptual thinking. A total of 54 graduate students (15 male, 39 female) wrote one essay by hand and one by keyboard. Our results show a beneficial effect of text processing software, in terms of both the qualitative and quantitative writing output. A hierarchical cluster analysis was used to detect distinct performance groups in the sample. These performance groups mapped onto three differing working memory profiles. The groups with higher mean WM scores manifested superior writing complexity using a keyboard, in contrast to the cluster with the lowest mean WM. The results also point out that more revision during the writing process itself does not inevitably reduce the quality of the final output

Inner Speech during Silent Reading Reflects the Reader's Regional Accent

While reading silently, we often have the subjective experience of inner speech. However, there is currently little evidence regarding whether this inner voice resembles our own voice while we are speaking out loud. To investigate this issue, we compared reading behaviour of Northern and Southern English participants who have differing pronunciations for words like ‘glass’, in which the vowel duration is short in a Northern accent and long in a Southern accent. Participants' eye movements were monitored while they silently read limericks in which the end words of the first two lines (e.g., glass/class) would be pronounced differently by Northern and Southern participants. The final word of the limerick (e.g., mass/sparse) then either did or did not rhyme, depending on the reader's accent. Results showed disruption to eye movement behaviour when the final word did not rhyme, determined by the reader's accent, suggesting that inner speech resembles our own voice

An Arthroscopic Device to Assess Articular Cartilage Defects and Treatment with a Hydrogel

The hydraulic resistance R across osteochondral tissue, especially articular cartilage, decreases with degeneration and erosion. Clinically useful measures to quantify and diagnose the extent of cartilage degeneration and efficacy of repair strategies, especially with regard to pressure maintenance, are still developing. The hypothesis of this study was that hydraulic resistance provides a quantitative measure of osteochondral tissue that could be used to evaluate the state of cartilage damage and repair. The aims were to (1) develop a device to measure R in an arthroscopic setting, (2) determine whether the device could detect differences in R for cartilage, an osteochondral defect, and cartilage treated using a hydrogel ex vivo, and (3) determine how quickly such differences could be discerned. The apparent hydraulic resistance of defect samples was ~35% less than intact cartilage controls, while the resistance of hydrogel-filled groups was not statistically different than controls, suggesting some restoration of fluid pressurization in the defect region by the hydrogel. Differences in hydraulic resistance between control and defect groups were apparent after 4 s. The results indicate that the measurement of R is feasible for rapid and quantitative functional assessment of the extent of osteochondral defects and repair. The arthroscopic compatibility of the device demonstrates the potential for this measurement to be made in a clinical setting

How portuguese and american teachers plan for literacy instruction

This study explored American and Portuguese elementary teachers' preferences in planning for literacy instruction using the Language Arts Activity Grid (LAAG; Cunningham, Zibulsky, Stanovich, & Stanovich, 2009), on which teachers described their preferred instructional activities for a hypothetical 2-h language arts block. Portuguese teachers (N = 186) completed Portuguese versions of a background questionnaire and LAAG electronically, in Survey Monkey; American teachers (N = 102) completed identical English measures using paper and pencil. Results showed that teachers in both groups usually addressed comprehension and reading fluency on their LAAGs and that they also allocated the most time to these two areas. However, American teachers were more likely to include teacher-directed fluency activities, whereas Portuguese teachers were more likely to include fluency activities that were not teacher directed. Significantly more American than Portuguese teachers addressed phonics in their planning, whereas significantly more Portuguese than American teachers addressed writing processes such as revision. Both groups of educators demonstrated large variability in planning, with many teachers omitting important components of literacy identified by researchers, for writing as well as reading. The study highlights the importance of providing teachers with comprehensive, research-based core literacy curricula as well as professional development on key components of literacy. Study findings also suggest significant relationships between orthographic transparency and teachers' instructional planning.This research was supported by a 2-year grant from the Foundation Francisco Manuel dos Santos in Portugal as well as by a Connecticut State University research grant in the U.S.A. We would like to express our sincere gratitude to these funding agencies as well as to the teachers and school districts who participated in the study and sent messages of interest about our research. In addition, warm thanks to our research assistants for their help with data collection, coding, and analysis, and to Anne Cunningham for providing us with inspiration as well as guidance in this work.info:eu-repo/semantics/publishedVersio

Cognitive predictors of shallow-orthography spelling speed and accuracy in 6th grade children

Spelling accuracy and time course was investigated in a sample of 100 Norwegian 6th grade students completing a standardized spelling-to-dictation task. Students responded by keyboard with accurate recordings of response-onset latency (RT) and inter-keypress interval (IKI). We determined effects of a number of child-level cognitive ability factors, and of word-level factors—particularly the location within the word of a spelling challenge (e.g., letter doubling), if present. Spelling accuracy was predicted by word reading (word split) performance, non-word spelling accuracy, keyboard key-finding speed and short-term memory span. Word reading performance predicted accuracy just for words with spelling challenges. For correctly spelled words, RT was predicted by non-word spelling response time and by speed on a key-finding task, and mean IKI by non-verbal cognitive ability, word reading, non-word spelling response time, and key-finding speed. Compared to words with no challenge, mean IKI was shorter for words with an initial challenge and longer for words with a mid-word challenge. These findings suggest that spelling is not fully planned when typing commences, a hypothesis that is confirmed by the fact that IKI immediately before within word challenges were reliably longer than elsewhere within the same word. Taken together our findings imply that routine classroom spelling tests better capture student competence if they focus not only on accuracy but also on production time course