The reference human genome sequence set the stage for studies of genetic variation and its association with human disease, but epigenomic studies lack a similar reference. To address this need, the NIH Roadmap Epigenomics Consortium generated the largest collection so far of human epigenomes for primary cells and tissues. Here we describe the integrative analysis of 111 reference human epigenomes generated as part of the programme, profiled for histone modification patterns, DNA accessibility, DNA methylation and RNA expression. We establish global maps of regulatory elements, define regulatory modules of coordinated activity, and their likely activators and repressors. We show that disease- and trait-associated genetic variants are enriched in tissue-specific epigenomic marks, revealing biologically relevant cell types for diverse human traits, and providing a resource for interpreting the molecular basis of human disease. Our results demonstrate the central role of epigenomic information for understanding gene regulation, cellular differentiation and human disease.

Integrative analysis of 111 reference human epigenomes

We summarize some of the most important findings from research evaluating the hypothesized causes of specific reading disability (dyslexia) over the past four decades. After outlining components of reading ability, we discuss manifest causes of reading difficulties, in terms of deficiencies in component reading skills that might lead to such difficulties. The evidence suggests that inadequate facility in word identification due, in most cases, to more basic deficits in alphabetic coding is the basic cause of difficulties in learning to read. We next discuss hypothesized deficiencies in readingrelated cognitive abilities as underlying causes of deficiencies in component reading skills. The evidence in these areas suggests that, in most cases, phonological skills deficiencies associated with phonological coding deficits are the probable causes of the disorder rather than visual, semantic, or syntactic deficits, although reading difficulties in some children may be associated with general language deficits. Hypothesized deficits in general learning abilities (e.g., attention, association learning, cross-modal transfer etc.) and low-level sensory deficits have weak validity as causal factors in specific reading disability. These inferences are, by and large, supported by research evaluating the biological foundations of dyslexia. Finally, evidence is presented in support of the idea that many poor readers are impaired because of inadequate instruction or other experiential factors. This does not mean that biological factors are not relevant, because the brain and environment interact to produce the neural networks that support reading acquisition. We conclude with a discussion of the clinical implications of the research findings, focusing on the need for enhanced instruction.

http://www.dr-hatfield.com/educ538/docs/Vellutino,+etal+2004.pdf

Specific reading disability (dyslexia): what have we learned in the past four decades?

This article presents the findings of the final phase of a 5-year longitudinal study with 168 middle- and upper middle-class children in which the complex relations among early home literacy experiences, subsequent receptive language and emergent literacy skills, and reading achievement were examined. Results showed that children's exposure to books was related to the development of vocabulary and listening comprehension skills, and that these language skills were directly related to children's reading in grade 3. In contrast, parent involvement in teaching children about reading and writing words was related to the development of early literacy skills. Early literacy skills directly predicted word reading at the end of grade 1 and indirectly predicted reading in grade 3. Word reading at the end of grade 1 predicted reading comprehension in grade 3. Thus, the various pathways that lead to fluent reading have their roots in different aspects of children's early experiences.

Parental Involvement in the Development of Children’s Reading Skill: A Five-Year Longitudinal Study

The authors propose an alternative conceptualization of the developmental dyslexias, the double-deficit hypothesis (i.e., phonological deficits and processes underlying naming-speed deficits represent 2 separable sources of reading dysfunction). Data from cross-sectional, longitudinal, and cross-linguistic studies are reviewed supporting the presence of 2 single-deficit subtypes with more limited reading impairments and 1 double-deficit subtype with more pervasive and severe impairments. Naming-speed and phonological-awareness variables contribute uniquely to different aspects of reading according to this conception, with a model of visual letter naming illustrating both the multicomponential nature of naming speed and why naming speed Should not be subsumed under phonological processes. Two hypotheses concerning relationships between naming-speed processes and reading are considered. The implications of processing speed as a second core deficit in dyslexia are described for diagnosis and intervention.

The double-deficit hypothesis for the developmental dyslexias.

http://media.journals.elsevier.com/content/files/s0742051x10001435-04221022.pdf

Teacher professional development in Teaching and Teacher Education over ten years

Home literacy (reports of children's literacy activities at home and parents' storybook title recognition) and literacy interest (children's reports of feelings about literacy activities) were identified as 2 independent sources of literacy experience among 92 kindergarten prereaders. Together, they accounted for significant variance in oral vocabulary (21%) and on a letter-name and letter-sound measure of early written language (18%). Entering phonological awareness first in hierarchical regression eliminated home literacy's unique contribution to written language but not to vocabulary, indicating that home literacy is directly related to vocabulary but that phonological awareness mediates its relationship with written language. Literacy interest was unrelated to phonological awareness and accounted for unique variance in written language only. Discussion focused on print exposure versus explicit print-sound instruction in home literacy activities.

Direct and Mediated Influences of Home Literacy and Literacy Interest on Prereaders' Oral Vocabulary and Early Written Language Skill.

The double-deficit hypothesis (Wolf, 1997; Wolf & Bowers, 1999, this issue) contends that deficits in phonological awareness and deficits in visual naming speed represent two independent causal impediments to reading acquisition for children with developmental reading disabilities (RD). One hundred and sixty-six children with severe RD from 7 to 13 years of age were classified into three deficit subgroups according to a double-deficit framework. A total of 140 children with RD, 84% of the sample, were classified; 54% demonstrated a double deficit (DD), 22% a phonological deficit only (PHON), and 24% a visual-naming speed deficit only (VNS). Diagnostic test profiles highlighted the joint contributions of the two core deficits in depressing written language acquisition. The children in the DD group were more globally impaired than those in the other subgroups, and the VNS group children were the highest achieving and most selectively impaired readers. Following 35 hours of word identification training, siza...

Remediating the Core Deficits of Developmental Reading Disability A Double-Deficit Perspective

This study investigated rapid automatized naming and effects of stimulant medication in school-age children with attention-deficit/hyperactivity disorder (ADHD) with and without concurrent reading disorder (RD). Two ADHD groups (67 ADHD only; 21 ADHD + RD) and a control group of 27 healthy age-matched peers were compared on four variables: color naming speed, letter naming speed, phonologic decoding, and arithmetic computation. Discriminant function analysis (DFA) was conducted to predict group membership. The four variables loaded onto two discriminant functions with good specificity: phonologic decoding, letter naming speed, and arithmetic defined the first function; color naming speed defined the second function. Both ADHD groups were significantly slower in color naming than controls, but did not differ from one another. DFA correctly classified 96% of the control group, 91% of ADHD + RD, and 82% of ADHD only. A subset of children in the ADHD groups participated subsequently in an acute, randomized, placebo-controlled, crossover trial with three single doses (10, 25, 20 mg) of methylphenidate. Methylphenidate selectively improved color-naming speed but had no effect on the speed of naming letters or digits. These findings challenge the tenet that naming speed deficits are specific to RD and implicate naming speed deficits associated with effortful semantic processing in ADHD, which are improved but not normalized by stimulant medication.

Naming Speed Performance and Stimulant Effects Indicate Effortful, Semantic Processing Deficits in Attention-Deficit/Hyperactivity Disorder

Within psychological and educational research, self-report methodology dominates the study of student motivation. The present review argues that the scope of motivation research can be expanded by incorporating a wider range of methodologies and measurement tools. Several authors have suggested that current study of motivation is overly reliant on self-report measures, warranting a move toward alternative approaches. This review critiques self-report methodology as a basis for examining alternative conceptualizations of motivation (e.g., phenomenological, neuropsychological/physiological, and behavioral) and related measurement tools. Future directions in motivational methodology are addressed, including attempts at integration or combination of these approaches and a preliminary functional framework for the development of novel, multidimensional approaches to the study of motivation.

Jan C. Frijters

Papers

Direct and Mediated Influences of Home Literacy and Literacy Interest on Prereaders' Oral Vocabulary and Early Written Language Skill.

Remediating the Core Deficits of Developmental Reading Disability A Double-Deficit Perspective

Naming Speed Performance and Stimulant Effects Indicate Effortful, Semantic Processing Deficits in Attention-Deficit/Hyperactivity Disorder

A Review of Self-Report and Alternative Approaches in the Measurement of Student Motivation.

Components of effective remediation for developmental reading disabilities: Combining phonological and strategy-based instruction to improve outcomes.