MBAT: A scalable informatics system for unifying digital atlasing workflows

Abstract Background Digital atlases provide a common semantic and spatial coordinate system that can be leveraged to compare, contrast, and correlate data from disparate sources. As the quality and amount of biological data continues to advance and grow, searching, referencing, and comparing this data with a researcher's own data is essential. However, the integration process is cumbersome and time-consuming due to misaligned data, implicitly defined associations, and incompatible data sources. This work addressing these challenges by providing a unified and adaptable environment to accelerate the workflow to gather, align, and analyze the data. Results The MouseBIRN Atlasing Toolkit (MBAT) project was developed as a cross-platform, free open-source application that unifies and accelerates the digital atlas workflow. A tiered, plug-in architecture was designed for the neuroinformatics and genomics goals of the project to provide a modular and extensible design. MBAT provides the ability to use a single query to search and retrieve data from multiple data sources, align image data using the user's preferred registration method, composite data from multiple sources in a common space, and link relevant informatics information to the current view of the data or atlas. The workspaces leverage tool plug-ins to extend and allow future extensions of the basic workspace functionality. A wide variety of tool plug-ins were developed that integrate pre-existing as well as newly created technology into each workspace. Novel atlasing features were also developed, such as supporting multiple label sets, dynamic selection and grouping of labels, and synchronized, context-driven display of ontological data. Conclusions MBAT empowers researchers to discover correlations among disparate data by providing a unified environment for bringing together distributed reference resources, a user's image data, and biological atlases into the same spatial or semantic context. Through its extensible tiered plug-in architecture, MBAT allows researchers to customize all platform components to quickly achieve personalized workflows

Transforming Primary Care for Lesbian, Gay, Bisexual, and Transgender People: A Collaborative Quality Improvement Initiative

PURPOSE: Lesbian, gay, bisexual, and transgender (LGBT) people experience multiple disparities in access to care and health outcomes. We developed a quality improvement initiative, Transforming Primary Care for LGBT People, to enhance the capacity of federally qualified health centers (FQHCs) to provide culturally affirming care for this population. METHODS: The 1-year intervention blended the models of Practice Improvement Collaboratives and Project ECHO (Extension for Community Health Outcomes) to facilitate learning and translate knowledge into action. FQHC teams received coaching in creating LGBT-inclusive environments, collecting sexual orientation and gender identity (SOGI) data, taking risk-based sexual histories, and screening LGBT people for syphilis, chlamydia and gonorrhea, and HIV. We used a preintervention-postintervention evaluation design. RESULTS: We selected 10 FQHCs serving 441,387 patients in 123 clinical sites in 9 states. The intervention spread from 10 clinicians in 10 clinical sites to 431 clinicians in 79 clinical sites. FQHCs reported increases in culturally affirming practices, including collecting patient pronoun information (42.9% increase) and identifying LGBT patient liaisons (300.0% increase). Postintervention, among 9 FQHCs reporting SOGI data from electronic health records, SOGI documentation increased from 13.5% to 50.8% of patients (276.3% increase). Among 8 FQHCs reporting number of LGBT patients, screening of LGBT patients increased from 22.3% (95% CI, 4.9%-40.0%) to 34.6% (95% CI, 19.4%-48.6%) for syphilis (86.5% increase); from 25.3% (95% CI, 7.6%-43.1%) to 44.1% (95% CI, 30.2%-58.1%) for chlamydia and gonorrhea (109.0% increase); and from 14.8% (95% CI, 3.2%-26.5%) to 30.5% (95% CI, 26.7%-34.3%) for HIV (132.4% increase). CONCLUSIONS: FQHCs participating in this initiative reported improved capacity to provide culturally affirming care and targeted screening for LGBT patients

A quasi-experiment assessing the six-months effects of a nurse care coordination program on patient care experiences and clinician teamwork in community health centers

Background Recognition that coordination among healthcare providers is associated with better quality of care and lower costs has increased interest in interventions designed to improve care coordination. One intervention is to add care coordination to nurses’ role in a formal way. Little is known about effects of this approach, which tends to be pursued by small organizations and those in lower-resource settings. We assessed effects of this approach on care experiences of high-risk patients (those most in need of care coordination) and clinician teamwork during the first 6 months of use. Methods We conducted a quasi-experimental study using a clustered, controlled pre-post design. Changes in staff and patient experiences at six community health center practice locations that introduced the added-role approach for high-risk patients were compared to changes in six locations without the program in the same health system. In the pre-period (6 months before intervention training) and post-period (about 6 months after intervention launch, following 3 months of training), we surveyed clinical staff (N = 171) and program-qualifying patients (3007 pre-period; 2101 post-period, including 113 who were enrolled during the program’s first 6 months). Difference-in-differences models examined study outcomes: patient reports about care experiences and clinician-reported teamwork. We assessed frequency of patient office visits to validate access and implementation, and contextual factors (training, resources, and compatibility with other work) that might explain results. Results Patient care experiences across all high-risk patients did not improve significantly (p > 0.05). They improved somewhat for program enrollees, 5% above baseline reports (p = 0.07). Staff-perceived teamwork did not change significantly (p = 0.12). Office visits increased significantly for enrolled patients (p < 0.001), affirming program implementation (greater accessing of care). Contextual factors were not reported as problematic, except that 41% of nurses reported incompatibility between care coordination and other job demands. Over 75% of nurses reported adequate training and resources. Conclusions There were some positive effects of adding care coordination to nurses’ role within 6 months of implementation, suggesting value in this improvement strategy. Addressing compatibility between coordination and other job demands is important when implementing this approach to coordination

Adding Value to Crop Production Systems by Integrating Forage Cover Crop Grazing

In addition to their value as cereal grains, wheat (Triticum aestivum L.) and triticale (× Triticosecale Wittmack) are important cool-season annual forages and cover crops. Yearling steer (Bos taurus) performance was compared in the spring following autumn establishment as for age cover crops after soybean [Glycine max (L.) Merr.] grain harvest. Replicated pastures (0.4 ha) were no-till seeded in three consecutive years into soybean stubble in autumn, fertilized, and grazed the following spring near Ithaca, Nebraska, USA. Each pasture (n = 3) was continuously stocked in spring with four yearling steers (380 ± 38 kg) for 17, 32, and 28 d in 2005, 2006, and 2007, respectively. In 2005, average daily gain (ADG) for steers grazing triticale exceeded the ADG for wheat by 0.31 kghd−1d−1. In 2006, wheat ADG exceeded that for triticale by 0.12 kghd−1d−1. In 2007, steers grazing wheat lost weight, while steers grazing triticale gained 0.20 kghd−1d−1. Based on the 3-year average animal gains valued at $1.32 kg−1, mean net return ($ ha−1yr−1) was $62.15 for triticale and$22.55 for wheat. Since these grazed cover crops provide ecosystem services in addition to forage, grazing could be viewed as a mechanism for recovering costs and adds additional value to the system. Based on this 3-year grazing trial, triticale was superior to wheat and likely will provide the most stable beef yearling performance across years with variable weather for the western Cornbelt USA

Variation and Change Over Time in PROMIS-29 Survey Results Among Primary Care Patients With Type 2 Diabetes

Purpose: We sought to describe results of patient-reported outcome measures implemented among primary care patients with diabetes and explore factors associated with changes in scores over time. Methods: Two organizations serving diverse patient populations collected the PROMIS-29 survey at baseline and 3-month follow-up for patients with type 2 diabetes. Bayesian regression analysis was used to examine the relationship between patient characteristics and changes in PROMIS-29 scores. Exploratory analyses assessed relationships between goal-setting and changes in scores. Results: The study population reported substantially more problems with physical functioning (mean: 42.5 at Site 1 and 38.9 at Site 2) and pain interference (mean: 58.0 at Site 1 and 61.1 at Site 2) compared to the general population (mean: 50; standard deviation: 10). At least 33% of patients had a clinically meaningful change (ie, at least half the standard deviation, or 5 points) in each PROMIS domain. For pain interference, 55% had no change, 22% improved by 5 or more points, and 23% worsened by 5 or more points. Bayesian regression analyses suggest that chronic conditions, insurance status, and Hispanic ethnicity are likely associated with decreased functioning over time. Exploratory analyses found that setting a mental health goal did not appear to be associated with improvement for anxiety or depression. Conclusions: Use of patient-reported outcome measures in routine clinical care identified areas of functional limitations among people with diabetes. However, changes in participants’ PROMIS-29 scores over time were minimal. Research is needed to understand patterns of change in global and domain-specific functioning, particularly among racial/ethnic minorities