Trauma-Informed Pediatric Primary Care: Facilitators and Challenges to the Implementation Process

This article describes the process of integrating trauma-informed behavioral health practices into a pediatric primary care clinic serving low-income and minority families while facing barriers of financial, staffing, and time limitations common to many community healthcare clinics. By using an iterative approach to evaluate each step of the implementation process, the goal was to establish a feasible system in which primary care providers take the lead in addressing traumatic stress. This article describes (1) the process of implementing trauma-informed care into a pediatric primary care clinic, (2) the facilitators and challenges of implementation, and (3) the impact of this implementation process at patient, provider, and community levels. Given the importance of trauma-informed care, especially for families who lack access to quality care, the authors conceptualize this paper as a guide for others attempting to integrate best behavioral health practices into pediatric clinics while working with limited resources

Decoding the massive genome of loblolly pine using haploid DNA and novel assembly strategies

BACKGROUND: The size and complexity of conifer genomes has, until now, prevented full genome sequencing and assembly. The large research community and economic importance of loblolly pine, Pinus taeda L., made it an early candidate for reference sequence determination. RESULTS: We develop a novel strategy to sequence the genome of loblolly pine that combines unique aspects of pine reproductive biology and genome assembly methodology. We use a whole genome shotgun approach relying primarily on next generation sequence generated from a single haploid seed megagametophyte from a loblolly pine tree, 20-1010, that has been used in industrial forest tree breeding. The resulting sequence and assembly was used to generate a draft genome spanning 23.2 Gbp and containing 20.1 Gbp with an N50 scaffold size of 66.9 kbp, making it a significant improvement over available conifer genomes. The long scaffold lengths allow the annotation of 50,172 gene models with intron lengths averaging over 2.7 kbp and sometimes exceeding 100 kbp in length. Analysis of orthologous gene sets identifies gene families that may be unique to conifers. We further characterize and expand the existing repeat library based on the de novo analysis of the repetitive content, estimated to encompass 82% of the genome. CONCLUSIONS: In addition to its value as a resource for researchers and breeders, the loblolly pine genome sequence and assembly reported here demonstrates a novel approach to sequencing the large and complex genomes of this important group of plants that can now be widely applied

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

The Impact of Negative Reinforcement Contingent on Revision on Students\u27 Writing: Can Writing Less Lead to Writing More?

This dissertation examined the impact of negative reinforcement contingent on revision added to an instructional package consisting of positive reinforcement (programmed reinforcement) and prompting (i.e., a list of self-guided questions for revision) on the writing production and writing accuracy of high school students. A multiple-baseline across participants consisting of two cohorts of three participants each was used to evaluate the effectiveness of the independent variable. Prior to baseline, participants were assessed for proficiency in revision skills, and programmed reinforcers were validated. During baseline, participants were instructed to revise a previously written composition using a document that prompted them to make revisions and then to write a short story. Upon completion of both tasks, students were provided access to a preferred activity according to a fixed-ratio schedule. After stable baselines were achieved for each participant, negative reinforcement contingencies for revising one’s writing were introduced. Students were instructed that they could escape having to write a story contingent upon making a set criterion number of revisions to their writing. Conditions were implemented with a high degree of integrity, and results demonstrated that negative reinforcement was effective for increasing the number of revisions that students attempted, the number of correct revisions that students made, and the number of unique revisions that students made. However, results suggested differential responding patterns among participants for increasing writing accuracy (i.e., increasing the percentage of correct writing sequences). Results are discussed in terms of performance deficits in revising behavior, individual differences in students’ writing skills, implications for intervention in revision, and additional contingencies of reinforcement in the classroom. Discussion also focuses on the need for future research on intervention components to increase students’ revising behavior

A Helping Hand Out of the River: Refugee Perspectives for Provider Engagement

Purpose: A growing number of refugee groups are seeking care within the U.S. health care system for medical, psychological, and social needs. Research is limited in understanding refugee-specific conceptualizations of helping relationships and provider characteristics that improve interactions in health systems. This study aimed to identify provider characteristics that facilitate engagement and helpfulness in a refugee-specific population from refugee participant voices to inform future practices of health care clinics. Methods: Semi-structured interviews with refugee participants were conducted to assess 1) experiences moving on from difficult experiences, 2) engagement with the health system, and 3) provider characteristics that facilitated engagement and healing. Qualitative data were analyzed using a grounded theory approach. Results: An emergent theory was revealed on refugee-defined provider characteristics that facilitated healing and engagement in the health system. Providers who support an individual’s story to be told, show awareness of barriers to accessing resources and prioritization of addressing barriers, maintain cultural humility, and demonstrate compassion, empathy, warmth, and openness toward patient engagement were the primary characteristics that facilitated engagement and healing. Conclusions: Utilization of engagement strategies by providers at the onset of treatment is critical to providing culturally sensitive health care. Nonspecific but essential provider characteristics are thought to improve relational dynamics, trust-building, and overall engagement in the U.S. health care system from the perspective of refugee participants

Insights into the loblolly pine genome: characterization of BAC and fosmid sequences.

Despite their prevalence and importance, the genome sequences of loblolly pine, Norway spruce, and white spruce, three ecologically and economically important conifer species, are just becoming available to the research community. Following the completion of these large assemblies, annotation efforts will be undertaken to characterize the reference sequences. Accurate annotation of these ancient genomes would be aided by a comprehensive repeat library; however, few studies have generated enough sequence to fully evaluate and catalog their non-genic content. In this paper, two sets of loblolly pine genomic sequence, 103 previously assembled BACs and 90,954 newly sequenced and assembled fosmid scaffolds, were analyzed. Together, this sequence represents 280 Mbp (roughly 1% of the loblolly pine genome) and one of the most comprehensive studies of repetitive elements and genes in a gymnosperm species. A combination of homology and de novo methodologies were applied to identify both conserved and novel repeats. Similarity analysis estimated a repetitive content of 27% that included both full and partial elements. When combined with the de novo investigation, the estimate increased to almost 86%. Over 60% of the repetitive sequence consists of full or partial LTR (long terminal repeat) retrotransposons. Through de novo approaches, 6,270 novel, full-length transposable element families and 9,415 sub-families were identified. Among those 6,270 families, 82% were annotated as single-copy. Several of the novel, high-copy families are described here, with the largest, PtPiedmont, comprising 133 full-length copies. In addition to repeats, analysis of the coding region reported 23 full-length eukaryotic orthologous proteins (KOGS) and another 29 novel or orthologous genes. These discoveries, along with other genomic resources, will be used to annotate conifer genomes and address long-standing questions about gymnosperm evolution

Sequencing and Assembly of the 22-Gb Loblolly Pine Genome

Conifers are the predominant gymnosperm. The size and complexity of their genomes has presented formidable technical challenges for whole-genome shotgun sequencing and assembly. We employed novel strategies that allowed us to determine the loblolly pine (Pinus taeda) reference genome sequence, the largest genome assembled to date. Most of the sequence data were derived from whole-genome shotgun sequencing of a single megagametophyte, the haploid tissue of a single pine seed. Although that constrained the quantity of available DNA, the resulting haploid sequence data were well-suited for assembly. The haploid sequence was augmented with multiple linking long-fragment mate pair libraries from the parental diploid DNA. For the longest fragments, we used novel fosmid DiTag libraries. Sequences from the linking libraries that did not match the megagametophyte were identified and removed. Assembly of the sequence data were aided by condensing the enormous number of paired-end reads into a much smaller set of longer “super-reads,” rendering subsequent assembly with an overlap-based assembly algorithm computationally feasible. To further improve the contiguity and biological utility of the genome sequence, additional scaffolding methods utilizing independent genome and transcriptome assemblies were implemented. The combination of these strategies resulted in a draft genome sequence of 20.15 billion bases, with an N50 scaffold size of 66.9 kbp

Sequence of the Sugar Pine Megagenome

Until very recently, complete characterization of the megagenomes of conifers has remained elusive. The diploid genome of sugar pine (Pinus lambertiana Dougl.) has a highly repetitive, 31 billion bp genome. It is the largest genome sequenced and assembled to date, and the first from the subgenus Strobus, or white pines, a group that is notable for having the largest genomes among the pines. The genome represents a unique opportunity to investigate genome “obesity” in conifers and white pines. Comparative analysis of P. lambertiana and P. taeda L. reveals new insights on the conservation, age, and diversity of the highly abundant transposable elements, the primary factor determining genome size. Like most North American white pines, the principal pathogen of P. lambertiana is white pine blister rust (Cronartium ribicola J.C. Fischer ex Raben.). Identification of candidate genes for resistance to this pathogen is of great ecological importance. The genome sequence afforded us the opportunity to make substantial progress on locating the major dominant gene for simple resistance hypersensitive response, Cr1. We describe new markers and gene annotation that are both tightly linked to Cr1 in a mapping population, and associated with Cr1 in unrelated sugar pine individuals sampled throughout the species’ range, creating a solid foundation for future mapping. This genomic variation and annotated candidate genes characterized in our study of the Cr1 region are resources for future marker-assisted breeding efforts as well as for investigations of fundamental mechanisms of invasive disease and evolutionary response

Sequence of the Sugar Pine Megagenome.

Until very recently, complete characterization of the megagenomes of conifers has remained elusive. The diploid genome of sugar pine (Pinus lambertiana Dougl.) has a highly repetitive, 31 billion bp genome. It is the largest genome sequenced and assembled to date, and the first from the subgenus Strobus, or white pines, a group that is notable for having the largest genomes among the pines. The genome represents a unique opportunity to investigate genome "obesity" in conifers and white pines. Comparative analysis of P. lambertiana and P. taeda L. reveals new insights on the conservation, age, and diversity of the highly abundant transposable elements, the primary factor determining genome size. Like most North American white pines, the principal pathogen of P. lambertiana is white pine blister rust (Cronartium ribicola J.C. Fischer ex Raben.). Identification of candidate genes for resistance to this pathogen is of great ecological importance. The genome sequence afforded us the opportunity to make substantial progress on locating the major dominant gene for simple resistance hypersensitive response, Cr1 We describe new markers and gene annotation that are both tightly linked to Cr1 in a mapping population, and associated with Cr1 in unrelated sugar pine individuals sampled throughout the species' range, creating a solid foundation for future mapping. This genomic variation and annotated candidate genes characterized in our study of the Cr1 region are resources for future marker-assisted breeding efforts as well as for investigations of fundamental mechanisms of invasive disease and evolutionary response