Trials without tribulations: Minimizing the burden of pragmatic research on healthcare systems.

Pragmatic clinical trials are increasingly common because they have the potential to yield findings that are directly translatable to real-world healthcare settings. Pragmatic clinical trials need to integrate research into clinical workflow without placing an undue burden on the delivery system. This requires a research partnership between investigators and healthcare system representatives. This paper, organized as a series of case studies drawn from our experience in the NIH Health Care Systems Research Collaboratory, presents guidance from informational interviews of physician-scientists, health services researchers, and delivery system leaders who recently launched pragmatic clinical trials.

Genome-wide Purification of Extrachromosomal Circular DNA from Eukaryotic Cells.

Extrachromosomal circular DNAs (eccDNAs) are common genetic elements in Saccharomyces cerevisiae and are reported in other eukaryotes as well. EccDNAs contribute to genetic variation among somatic cells in multicellular organisms and to evolution of unicellular eukaryotes. Sensitive methods for detecting eccDNA are needed to clarify how these elements affect genome stability and how environmental and biological factors induce their formation in eukaryotic cells. This video presents a sensitive eccDNA-purification method called Circle-Seq. The method encompasses column purification of circular DNA, removal of remaining linear chromosomal DNA, rolling-circle amplification of eccDNA, deep sequencing, and mapping. Extensive exonuclease treatment was required for sufficient linear chromosomal DNA degradation. The rolling-circle amplification step by φ29 polymerase enriched for circular DNA over linear DNA. Validation of the Circle-Seq method on three S. cerevisiae CEN.PK populations of 10(10) cells detected hundreds of eccDNA profiles in sizes larger than 1 kilobase. Repeated findings of ASP3-1, COS111, CUP1, RSC30, HXT6, HXT7 genes on circular DNA in both S288c and CEN.PK suggests that DNA circularization is conserved between strains at these loci. In sum, the Circle-Seq method has broad applicability for genome-scale screening for eccDNA in eukaryotes as well as for detecting specific eccDNA types.

Online cognitive behavioral therapy for depressed primary care patients: a pilot feasibility project.

CONTEXT: Cognitive behavioral therapy (CBT) is a goal-oriented treatment that guides patients to healthy thoughts and behaviors. Internet-delivered CBT with supportive coaching can be as effective as in-person psychotherapy treatment of depression. OBJECTIVE: To test the feasibility of engaging depressed primary care patients not currently receiving psychotherapy and to measure the outcomes of Internet-delivered CBT with supportive coaching. DESIGN: Pilot feasibility project. MAIN OUTCOME MEASURES: 1) Uptake rate. 2) Reduction in depressive symptoms (average score on 20-item Hopkins Symptom Checklist) from baseline to 4-month follow-up. METHODS: Medical records data were queried to identify patients experiencing a new episode of depression. Eligible patients were invited via secure messaging (patient and clinician communication using a secure Web site linked to the medical record) to participate in the Internet-delivered CBT program (also known as Thrive), which was algorithm-driven and delivered through didactic segments, interactive tools, and assessments. Patients completed a self-administered online follow-up survey four months after enrollment. RESULTS: Of 196 eligible patients who were sent an invitation, 39 (20%) enrolled in the Internet-delivered CBT program. At follow-up, enrolled patients experienced a clinically significant decrease (average = 46%) in depressive symptoms. Suicidal thoughts also decreased both overall and by severity. CONCLUSIONS: Seamless, scalable integration of Internet-delivered CBT into health care systems is feasible. The 20% uptake rate suggests that future work should focus on strategies to increase the initial response rate. One promising direction is the addition of "human touch" to the secure message invitation. Depression outcomes suggest promise for systemwide implementation of Internet-delivered CBT programs.

Multiple pathways are co-regulated by the protein kinase Snf1 and the transcription factors Adr1 and Cat8.

ADR1 and CAT8 encode carbon source-responsive transcriptional regulators that cooperatively control expression of genes involved in ethanol utilization. These transcription factors are active only after the diauxic transition, when glucose is depleted and energy-generating metabolism has shifted to the aerobic oxidation of non-fermentable carbon sources. The Snf1 protein kinase complex is required for activation of their downstream target genes described previously. Using DNA microarrays, we determined the extent to which these three factors collaborate in regulating the expression of the yeast genome after glucose depletion. The expression of 108 genes is significantly decreased in the absence of ADR1. The importance of ADR1 during the diauxic transition is illustrated by the observation that expression of almost one-half of the 40 most highly glucose-repressed genes is ADR1-dependent. ADR1-dependent genes fall into a variety of functional classes with carbon metabolism containing the largest number of members. Most of the genes in this class are involved in the oxidation of different non-fermentable carbon sources. These microarray data show that ADR1 coordinates the biochemical pathways that generate acetyl-CoA and NADH from non-fermentable substrates. Only a small number of ADR1-dependent genes are also CAT8-dependent. However, nearly one-half of the ADR1-dependent genes are also dependent on the Snf1 protein kinase for derepression. Many more genes are SNF1-dependent than are either ADR1- or CAT8-dependent suggesting that SNF1 plays a broader role in gene expression than either ADR1 or CAT8. The largest class of SNF1-dependent genes encodes regulatory proteins that could extend SNF1 dependence to additional pathways.