We describe a flexible system for gene expression profiling using arrays of tens of thousands of oligonucleotides synthesized in situ by an ink-jet printing method employing standard phosphoramidite ...chemistry. We have characterized the dependence of hybridization specificity and sensitivity on parameters including oligonucleotide length, hybridization stringency, sequence identity, sample abundance, and sample preparation method. We find that 60-mer oligonucleotides reliably detect transcript ratios at one copy per cell in complex biological samples, and that ink-jet arrays are compatible with several different sample amplification and labeling techniques. Furthermore, results using only a single carefully selected oligonucleotide per gene correlate closely with those obtained using complementary DNA (cDNA) arrays. Most of the genes for which measurements differ are members of gene families that can only be distinguished by oligonucleotides. Because different oligonucleotide sequences can be specified for each array, we anticipate that ink-jet oligonucleotide array technology will be useful in a wide variety of DNA microarray applications.
Implementation of guideline-recommended depression screening in medical oncology remains challenging. Evidence suggests that multicomponent care pathways with algorithm-based referral and management ...are effective, yet implementation of sustainable programs remains limited and implementation-science guided approaches are understudied.
To evaluate the effectiveness of an implementation-strategy guided depression screening program for patients with breast cancer in a community setting.
A pragmatic cluster randomized clinical trial conducted within Kaiser Permanente Southern California (KPSC). The trial included 6 medical centers and 1436 patients diagnosed with new primary breast cancer who had a consultation with medical oncology between October 1, 2017, through September 30, 2018. Patients were followed up through study end date of May 31, 2019.
Six medical centers in Southern California participated and were randomized 1:1 to tailored implementation strategies (intervention, 3 sites, n = 744 patients) or education-only (control, 3 sites, n = 692 patients) groups. The program consisted of screening with the 9-item Patient Health Questionnaire (PHQ-9) and algorithm-based scoring and referral to behavioral health services based on low, moderate, or high score. Clinical teams at tailored intervention sites received program education, audit, and feedback of performance data and implementation facilitation, and clinical workflows were adapted to suit local context. Education-only controls sites received program education.
The primary outcome was percent of eligible patients screened and referred (based on PHQ-9 score) at intervention vs control groups measured at the patient level. Secondary outcomes included outpatient health care utilization for behavioral health, primary care, oncology, urgent care, and emergency department.
All 1436 eligible patients were randomized at the center level (mean age, 61.5 years; 99% women; 18% Asian, 17% Black, 26% Hispanic, and 37% White) and were followed up to the end of the study, insurance disenrollment, or death. Groups were similar in demographic and tumor characteristics. For the primary outcome, 7.9% (59 of 744) of patients at tailored sites were referred compared with 0.1% (1 of 692) at education-only sites (difference, 7.8%; 95% CI, 5.8%-9.8%). Referrals to a behavioral health clinician were completed by 44 of 59 patients treated at the intervention sites (75%) intervention sites vs 1 of 1 patient at the education-only sites (100%). In adjusted models patients at tailored sites had significantly fewer outpatient visits in medical oncology (rate ratio, 0.86; 95% CI, 0.86-0.89; P = .001), and no significant difference in utilization of primary care, urgent care, and emergency department visits.
Among patients with breast cancer treated in community-based oncology practices, tailored strategies for implementation of routine depression screening compared with an education-only control group resulted in a greater proportion of referrals to behavioral care. Further research is needed to understand the clinical benefit and cost-effectiveness of this program.
ClinicalTrials.gov Identifier: NCT02941614.
The majority of microbial genomic diversity remains unexplored. This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome ...sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is amplified directly from a single cell using the whole-genome amplification technique of multiple displacement amplification (MDA). However, MDA from a single chromosome copy suffers from amplification bias and a large loss of specificity from even very small amounts of DNA contamination, which makes assembling a genome difficult and completely finishing a genome impossible except in extraordinary circumstances. Gel microdrop cultivation allows culturing of a diverse microbial community and provides hundreds to thousands of genetically identical cells as input for an MDA reaction. We demonstrate the utility of this approach by comparing sequencing results of gel microdroplets and single cells following MDA. Bias is reduced in the MDA reaction and genome sequencing, and assembly is greatly improved when using gel microdroplets. We acquired multiple near-complete genomes for two bacterial species from human oral and stool microbiome samples. A significant amount of genome diversity, including single nucleotide polymorphisms and genome recombination, is discovered. Gel microdroplets offer a powerful and high-throughput technology for assembling whole genomes from complex samples and for probing the pan-genome of naturally occurring populations.
Objectives
Implementation of guideline-recommended depression screening in oncology presents numerous challenges. Implementation strategies that are responsive to local context may be critical ...elements of adoption and sustainment. We evaluated barriers and facilitators to implementation of a depression screening program for breast cancer patients in a community medical oncology setting as part of a cluster randomized controlled trial.
Methods
Guided by the Consolidated Framework for Implementation Research, we employed qualitative methods to evaluate clinician, administrator, and patient perceptions of the program using semi-structured interviews. We used a team-coding approach for the data; thematic development focused on barriers and facilitators to implementation using a grounded theory approach. The codebook was refined through open discussions of subjectivity and unintentional bias, coding, and memo applications (including emergent coding), and the hierarchical structure and relationships of themes.
Results
We conducted 20 interviews with 11 clinicians/administrators and 9 patients. Five major themes emerged: (1) gradual acceptance and support of the intervention and workflow; (2) compatibility with system and personal norms and goals; (3) reinforcement of the value of and need for adaptability; (4) self-efficacy within the nursing team; and (5) importance of identifying accountable front-line staff beyond leadership “champions.”
Conclusions
Findings suggest a high degree of acceptability and feasibility due to the selection of appropriate implementation strategies, alignment of norms and goals, and a high degree of workflow adaptability. These findings will be uniquely helpful in generating actionable, real-world knowledge to inform the design, implementation, and sustainment of guideline-recommended depression screening programs in oncology.
Trial Registration
ClinicalTrials.gov
#NCT02941614
Marsupials are born with immature lungs when compared to eutherian mammals and rely, to various extents, on cutaneous gas exchange in order to meet metabolic requirements. Indeed, the fat-tailed ...dunnart is born with lungs in the canalicular stage of development and relies almost entirely on the skin for gas exchange at birth; consequently undergoing the majority of lung development in air. Plane radiographs and computed tomography data sets were acquired using phase contrast imaging with a synchrotron radiation source for two marsupial species, the fat-tailed dunnart and the larger tammar wallaby, during the first weeks of postnatal life. Phase contrast imaging revealed that only two lung sacs contain air after the first hour of life in the fat-tailed dunnart. While the lung of the tammar wallaby was comparatively more developed, both species demonstrated massive increases in air sac number and architectural complexity during the postnatal period. In addition, both the tammar wallaby and fat-tailed dunnart had lower lung volumes and parenchymal surface areas than were expected from morphometrically determined allometric equations relating these variables to body mass during the neonatal period. However, lung volume is predicted to scale with mass as expected after the neonatal marsupial reaches a body mass of ∼1 g and no longer relies on the skin for gas exchange. Decreased lung volume in the marsupial neonate further supports the maxim that cutaneous gas exchange occurs in the marsupial neonate because the respiratory apparatus is not yet capable of meeting the gas exchange requirements of the newborn.
The genetic make-up of most bacteria is encoded in a single chromosome while about 10% have more than one chromosome. Among these, Vibrio cholerae, with two chromosomes, has served as a model system ...to study various aspects of chromosome maintenance, mainly replication, and faithful partitioning of multipartite genomes. Here, we describe the genomic characterization of strains that are an exception to the two chromosome rules: naturally occurring single-chromosome V. cholerae. Whole genome sequence analyses of NSCV1 and NSCV2 (natural single-chromosome vibrio) revealed that the Chr1 and Chr2 fusion junctions contain prophages, IS elements, and direct repeats, in addition to large-scale chromosomal rearrangements such as inversions, insertions, and long tandem repeats elsewhere in the chromosome compared to prototypical two chromosome V. cholerae genomes. Many of the known cholera virulence factors are absent. The two origins of replication and associated genes are generally intact with synonymous mutations in some genes, as are recA and mismatch repair (MMR) genes dam, mutH, and mutL; MutS function is probably impaired in NSCV2. These strains are ideal tools for studying mechanistic aspects of maintenance of chromosomes with multiple origins and other rearrangements and the biological, functional, and evolutionary significance of multipartite genome architecture in general.
Microarray technology has become a standard tool in many laboratories. Agilent Technologies manufactures a variety of catalog and custom long-oligonucleotide (60-mer) microarrays that can be used in ...multiple two-color microarray applications. Optimized methods and techniques have been developed for two such applications: gene expression profiling and comparative genomic hybridization. Methods for a third technique, location analysis, are evolving rapidly. This chapter outlines current best methods for using Agilent microarrays, provides detailed instructions for the most recently developed techniques, and discusses solutions to common problems encountered with two-color microarrays.
The genus Burkholderia encompasses both pathogenic (including Burkholderia mallei and Burkholderia pseudomallei, U.S. Centers for Disease Control and Prevention Category B listed), and nonpathogenic ...Gram-negative bacilli. Here we present full genome sequences for a panel of 59 Burkholderia strains, selected to aid in detection assay development.
In 2011, the Association of Analytical Communities (AOAC) International released a list of Bacillus strains relevant to biothreat molecular detection assays. We present the complete and annotated ...genome assemblies for the 15 strains listed on the inclusivity panel, as well as the 20 strains listed on the exclusivity panel.
Yersinia pestis, the causative agent of plague, is endemic to the Caucasus region but few reference strain genome sequences from that region are available. Here, we present the improved draft or ...finished assembled genomes from 11 strains isolated in the nation of Georgia and surrounding countries.
PDF
