This article systematically reviews the research design and methodological characteristics of single-case experimental design (SCED) research published in peer-reviewed journals between 2000 and 2010. SCEDs provide researchers with a flexible and viable alternative to group designs with large sample sizes. However, methodological challenges have precluded widespread implementation and acceptance of the SCED as a viable complementary methodology to the predominant group design. This article includes a description of the research design, measurement, and analysis domains distinctive to the SCED; a discussion of the results within the framework of contemporary standards and guidelines in the field; and a presentation of updated benchmarks for key characteristics (e.g., baseline sampling, method of analysis), and overall, it provides researchers and reviewers with a resource for conducting and evaluating SCED research. The results of the systematic review of 409 studies suggest that recently published SCED research is largely in accordance with contemporary criteria for experimental quality. Analytic method emerged as an area of discord. Comparison of the findings of this review with historical estimates of the use of statistical analysis indicates an upward trend, but visual analysis remains the most common analytic method and also garners the most support amongst those entities providing SCED standards. Although consensus exists along key dimensions of single-case research design and researchers appear to be practicing within these parameters, there remains a need for further evaluation of assessment and sampling techniques and data analytic methods.

BackgroundGenome-scale CRISPR interference (CRISPRi) has been used in human cell lines; however, the features of effective guide RNAs (gRNAs) in different organisms have not been well characterized. Here, we define rules that determine gRNA effectiveness for transcriptional repression in Saccharomyces cerevisiae.ResultsWe create an inducible single plasmid CRISPRi system for gene repression in yeast, and use it to analyze fitness effects of gRNAs under 18 small molecule treatments. Our approach correctly identifies previously described chemical-genetic interactions, as well as a new mechanism of suppressing fluconazole toxicity by repression of the ERG25 gene. Assessment of multiple target loci across treatments using gRNA libraries allows us to determine generalizable features associated with gRNA efficacy. Guides that target regions with low nucleosome occupancy and high chromatin accessibility are clearly more effective. We also find that the best region to target gRNAs is between the transcription start site (TSS) and 200 bp upstream of the TSS. Finally, unlike nuclease-proficient Cas9 in human cells, the specificity of truncated gRNAs (18 nt of complementarity to the target) is not clearly superior to full-length gRNAs (20 nt of complementarity), as truncated gRNAs are generally less potent against both mismatched and perfectly matched targets.ConclusionsOur results establish a powerful functional and chemical genomics screening method and provide guidelines for designing effective gRNAs, which consider chromatin state and position relative to the target gene TSS. These findings will enable effective library design and genome-wide programmable gene repression in many genetic backgrounds.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-0900-9) contains supplementary material, which is available to authorized users.

Background Numerous models, frameworks, and theories exist for specific aspects of implementation research, including for determinants, strategies, and outcomes. However, implementation research projects often fail to provide a coherent rationale or justification for how these aspects are selected and tested in relation to one another. Despite this need to better specify the conceptual linkages between the core elements involved in projects, few tools or methods have been developed to aid in this task. The Implementation Research Logic Model (IRLM) was created for this purpose and to enhance the rigor and transparency of describing the often-complex processes of improving the adoption of evidence-based interventions in healthcare delivery systems. Methods The IRLM structure and guiding principles were developed through a series of preliminary activities with multiple investigators representing diverse implementation research projects in terms of contexts, research designs, and implementation strategies being evaluated. The utility of the IRLM was evaluated in the course of a 2-day training to over 130 implementation researchers and healthcare delivery system partners. Results Preliminary work with the IRLM produced a core structure and multiple variations for common implementation research designs and situations, as well as guiding principles and suggestions for use. Results of the survey indicated a high utility of the IRLM for multiple purposes, such as improving rigor and reproducibility of projects; serving as a “roadmap” for how the project is to be carried out; clearly reporting and specifying how the project is to be conducted; and understanding the connections between determinants, strategies, mechanisms, and outcomes for their project. Conclusions The IRLM is a semi-structured, principle-guided tool designed to improve the specification, rigor, reproducibility, and testable causal pathways involved in implementation research projects. The IRLM can also aid implementation researchers and implementation partners in the planning and execution of practice change initiatives. Adaptation and refinement of the IRLM are ongoing, as is the development of resources for use and applications to diverse projects, to address the challenges of this complex scientific field.

Highlights d CRISPEY-a method for highly efficient, parallel precise genome editing d Applied to measure fitness effects of thousands of natural genetic variants in yeast d Variants affecting fitness are enriched in promoters and TF binding sites d Nearby variants mostly favor the same strain's alleles, indicating natural selection

Childhood obesity has become a global pandemic in developed countries, leading to a host of medical conditions that contribute to increased morbidity and premature death. The causes of obesity in childhood and adolescence are complex and multifaceted, presenting researchers and clinicians with myriad challenges in preventing and managing the problem. This article reviews the state of the science for understanding the etiology of childhood obesity, the preventive interventions and treatment options for overweight and obesity, and the medical complications and co-occurring psychological conditions that result from excess adiposity, such as hypertension, nonalcoholic fatty liver disease, and depression. Interventions across the developmental span, varying risk levels, and service contexts (e.g.,community, school, home, health care systems) are reviewed. Future directions for research are offered with an emphasis on translational issues for taking evidence-based interventions to scale in a manner that will reduce the public health burden of the childhood obesity pandemic.

Our understanding of how genotype controls phenotype is limited by the scale at which we can precisely alter the genome and assess phenotypic consequences of each perturbation. Here we describe a CRISPR/Cas9-based method for multiplexed accurate genome editing with short, trackable, integrated cellular barcodes (MAGESTIC) in S. cerevisiae. MAGESTIC uses array-synthesized guide-donor oligos for plasmid-based high-throughput editing and features genomic barcode integration to prevent plasmid barcode loss and to enable robust phenotyping. We demonstrate that editing efficiency can be increased >5-fold by recruiting donor DNA to the site of breaks using the LexA-Fkh1p fusion protein. We performed saturation editing of the essential gene SEC14 and identified amino acids critical for chemical inhibition of lipid signaling. We also constructed thousands of natural genetic variants, characterized guide mismatch tolerance at the genome-scale, and ascertained that cryptic Pol III termination elements substantially reduce guide efficacy. MAGESTIC will be broadly useful to uncover the genetic basis of phenotypes in yeast.

The emergence and persistence of conduct problems during early childhood is a robust predictor of behavior problems in school and future maladaptation. In this study we examined the reciprocal influences between observed coercive interactions between children and caregivers, oppositional and aggressive behavior, and growth in parent report of early childhood (ages 2–5) and school-age conduct problems (age 7.5 and 8.5). Participants were drawn from the Early Steps multisite randomized prevention trial that includes an ethnically diverse sample of male and female children and their families (N = 731). A parallel process growth model combining latent trajectory and cross-lagged approaches revealed the amplifying effect of observed coercive caregiver–child interactions on children's noncompliance, whereas child oppositional and aggressive behaviors did not consistently predict increased coercion. The slope and initial levels of child oppositional and aggressive behaviors and the stability of caregiver–child coercion were predictive of teacher-reported oppositional behavior at school age. Families assigned to the Family Check-Up condition had significantly steeper declines in child oppositional and aggressive behavior and moderate reductions in oppositional behavior in school and in coercion at age 3. Results were not moderated by child gender, race/ethnicity, or assignment to the intervention condition. The implications of these findings are discussed with respect to understanding the early development of conduct problems and to designing optimal strategies for reducing problem behavior in early childhood with families most in need.

BackgroundTranscriptional reprogramming is a fundamental process of living cells in order to adapt to environmental and endogenous cues. In order to allow flexible and timely control over gene expression without the interference of native gene expression machinery, a large number of studies have focused on developing synthetic biology tools for orthogonal control of transcription. Most recently, the nuclease-deficient Cas9 (dCas9) has emerged as a flexible tool for controlling activation and repression of target genes, by the simple RNA-guided positioning of dCas9 in the vicinity of the target gene transcription start site.ResultsIn this study we compared two different systems of dCas9-mediated transcriptional reprogramming, and applied them to genes controlling two biosynthetic pathways for biobased production of isoprenoids and triacylglycerols (TAGs) in baker’s yeast Saccharomyces cerevisiae. By testing 101 guide-RNA (gRNA) structures on a total of 14 different yeast promoters, we identified the best-performing combinations based on reporter assays. Though a larger number of gRNA-promoter combinations do not perturb gene expression, some gRNAs support expression perturbations up to ~threefold. The best-performing gRNAs were used for single and multiplex reprogramming strategies for redirecting flux related to isoprenoid production and optimization of TAG profiles. From these studies, we identified both constitutive and inducible multiplex reprogramming strategies enabling significant changes in isoprenoid production and increases in TAG.ConclusionTaken together, we show similar performance for a constitutive and an inducible dCas9 approach, and identify multiplex gRNA designs that can significantly perturb isoprenoid production and TAG profiles in yeast without editing the genomic context of the target genes. We also identify a large number of gRNA positions in 14 native yeast target pomoters that do not affect expression, suggesting the need for further optimization of gRNA design tools and dCas9 engineering.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-017-0664-2) contains supplementary material, which is available to authorized users.