Investigating the effect of prophylactic claw trimming on the interval between calving and first observed elevated locomotion score in pasture-based dairy cows

AIMS

To evaluate, in a pasture-based dairy herd, the response to a three-time point hoof trimming regime on lameness incidence and time from calving to observation of an elevated locomotion score (LS).

METHODS

This study was conducted on a 940-cow spring-calving herd in New Zealand's North Island between May 2018 and May 2019. Cows (n = 250) were randomly allocated to the hoof trimming group, with the remainder assigned to the non-trim cohort. One trained professional hoof trimmer used the five-step Dutch method to trim the hind feet of the trimming group. Throughout the subsequent production season, the whole herd was locomotion-scored fortnightly using the 4-point (0-3) Dairy NZ lameness score. Kaplan-Meier survival curves were used to assess the univariable effect of trimming on the interval between calving and first LS of ≥ 2 and first LS ≥ 1. A multivariable Cox proportional hazards regression was used to further evaluate the effect of trimming on time to elevated LS.

RESULTS

Mean lameness (LS ≥ 2) prevalence was 2.6%, with 30% of cows having ≥ 4 observations during the study period when at least one LS was ≥ 2. For LS ≥ 1, mean prevalence was 40%, with 98.6% of cows having ≥ 4 observations during the study period when at least one LS was ≥ 1 during lactation. Hoof trimming had no apparent effect on the incidence of clinical lameness (LS ≥ 2) (trimmed vs. non-trimmed: 33.2% vs. 28.8%, respectively), but for LS ≥ 1, there was a small decrease in the incidence of LS ≥ 1 (trimmed vs. non-trimmed: 96.9% vs. 99.3%, respectively). The hazard of a cow having a first observed LS ≥ 2 in the control group was 0.87 (95% CI = 0.66-1.14) times that of the trimmed group; however, the hazard of a cow having a first LS ≥ 1 was 1.60 (95% CI = 1.37-1.88) times higher in the control than in the trimmed group.

CONCLUSION AND CLINICAL RELEVANCE

On this farm, prophylactic hoof trimming had no clinically relevant impact on the incidence of clinical lameness and was not associated with clinically beneficial reductions in time to first observed LS ≥ 2. This may be because claw horn imbalance was not pronounced on this farm, with 53% of cows needing no trim on either hind limb on the first trimming occasion. Further research on the response to prophylactic trimming in pasture-based dairy cattle is required.

The Long-Term Care Data Cooperative: The Next Generation of Data Integration

Despite important advances in the linkage of residents' Medicare claims and Minimum Data Set (MDS) information, the data infrastructure for long-term care remains inadequate for public health surveillance and clinical research. It is widely known that the evidence base supporting treatment decisions for older nursing home residents is scant as residents are systematically excluded from clinical trials. Electronic health records (EHRs) hold the promise to improve this population's representation in clinical research, especially with the more timely and detailed clinical information available in EHRs that are lacking in claims and MDS. The COVID-19 pandemic shined a spotlight on the data gap in nursing homes. To address this need, the National Institute on Aging funded the Long-Term Care (LTC) Data Cooperative, a collaboration among providers and stakeholders in academia, government, and the private sector. The LTC Data Cooperative assembles residents' EHRs from major specialty vendors and facilitates linkage of these data with Medicare claims to create a comprehensive, longitudinal patient record. These data serve 4 key purposes: (1) health care operations and population health analytics; (2) public health surveillance; (3) observational, comparative effectiveness research; and (4) clinical research studies, including provider and patient recruitment into Phase 3 and Phase 4 randomized trials. Federally funded researchers wanting to conduct pragmatic trials can now enroll their partnering sites in this Cooperative to more easily access the clinical data needed to close the evidence gaps in LTC. Linkage to Medicare data facilitates tracking patients' long-term outcomes after being discharged back to the community. As of August 2022, nearly 1000 nursing homes have joined, feedback reports to facilities are being piloted, algorithms for identifying infections are being tested, and proposals for use of the data have been reviewed and approved. This emerging EHR system is a substantial innovation in the richness and timeliness of the data infrastructure of the nursing home population.

Ranking reprogramming factors for cell differentiation

Transcription factor over-expression is a proven method for reprogramming cells to a desired cell type for regenerative medicine and therapeutic discovery. However, a general method for the identification of reprogramming factors to create an arbitrary cell type is an open problem. Here we examine the success rate of methods and data for differentiation by testing the ability of nine computational methods (CellNet, GarNet, EBseq, AME, DREME, HOMER, KMAC, diffTF and DeepAccess) to discover and rank candidate factors for eight target cell types with known reprogramming solutions. We compare methods that use gene expression, biological networks and chromatin accessibility data, and comprehensively test parameter and preprocessing of input data to optimize performance. We find the best factor identification methods can identify an average of 50-60% of reprogramming factors within the top ten candidates, and methods that use chromatin accessibility perform the best. Among the chromatin accessibility methods, complex methods DeepAccess and diffTF have higher correlation with the ranked significance of transcription factor candidates within reprogramming protocols for differentiation. We provide evidence that AME and diffTF are optimal methods for transcription factor recovery that will allow for systematic prioritization of transcription factor candidates to aid in the design of new reprogramming protocols.

Advancing clinical trials in nursing homes: A proposed roadmap to success

An effective clinical research effort in nursing homes to address prevention and treatment of COVID-19 faced overwhelming challenges. Under the Health Care Systems Research Network-Older Americans Independence Centers AGING Initiative, a multidisciplinary Stakeholder Advisory Panel was convened to develop recommendations to improve the capability of the clinical research enterprise in US nursing homes. The Panel considered the nursing home as a setting for clinical trials, reviewed the current state of clinical trials in nursing homes, and ultimately developed recommendations for the establishment of a nursing home clinical trials research network that would be centrally supported and administered. This report summarizes the Panel's recommendations, which were developed in alignment with the following core principles: build on available research infrastructure where appropriate; leverage existing productive partnerships of researchers with groups of nursing homes and nursing home corporations; encompass both efficacy and effectiveness clinical trials; be responsive to a broad range of stakeholders including nursing home residents and their care partners; be relevant to an expansive range of clinical and health care delivery research questions; be able to pivot as necessary to changing research priorities and circumstances; create a pathway for industry-sponsored research as appropriate; invest in strategies to increase diversity in study populations and the research workforce; and foster the development of the next generation of nursing home researchers.

Pragmatic Trials in Long-Term Care: Implementation and Dissemination Challenges and Opportunities

Randomized controlled trials are considered the most rigorous research design in efficacy and effectiveness research; however, such trials present numerous challenges that limit their applicability in real-world settings. As a consequence, pragmatic trials are increasingly viewed as a research design that overcomes some of these barriers with the potential to produce findings that are more reproducible. Although pragmatic methodology in long-term care is receiving increasing attention as an approach to improve successful dissemination and implementation, pragmatic trials present complexities of their own. To address these complexities and related issues, experts with experience conducting pragmatic trials, developing nursing home policy, participating in advocacy efforts, and providing clinical care in long-term care settings participated in a virtual consensus conference funded by the National Institute on Aging in Spring 2021. Participants identified 4 cross-cutting principles key to dissemination and implementation of pragmatic trial interventions: (1) stakeholder engagement, (2) diversity and inclusion, (3) organizational strain and readiness, and (4) learn from adaptations. Participants emphasized that implementation processes must be grounded in the perspectives of the people who will ultimately be responsible for implementing the intervention once it is proven to be effective. In addition, messaging must speak to long-term care staff and all others who have a stake in its outcomes. Although our understanding of dissemination and implementation strategies remains underdeveloped, this article is designed to guide long-term care researchers and community providers who are increasingly aware of the need for pragmatism in disseminating and implementing evidence-based care interventions.

Advancing Clinical Trials in Nursing Homes: A Proposed Roadmap to Success

An effective clinical research effort in nursing homes to address prevention and treatment of COVID-19 faced overwhelming challenges. Under the Health Care Systems Research Network-Older Americans Independence Centers AGING Initiative, a multidisciplinary Stakeholder Advisory Panel was convened to develop recommendations to improve the capability of the clinical research enterprise in US nursing homes. The Panel considered the nursing home as a setting for clinical trials, reviewed the current state of clinical trials in nursing homes, and ultimately developed recommendations for the establishment of a nursing home clinical trials research network that would be centrally supported and administered. This report summarizes the Panel's recommendations, which were developed in alignment with the following core principles: build on available research infrastructure where appropriate; leverage existing productive partnerships of researchers with groups of nursing homes and nursing home corporations; encompass both efficacy and effectiveness clinical trials; be responsive to a broad range of stakeholders including nursing home residents and their care partners; be relevant to an expansive range of clinical and health care delivery research questions; be able to pivot as necessary to changing research priorities and circumstances; create a pathway for industry-sponsored research as appropriate; invest in strategies to increase diversity in study populations and the research workforce; and foster the development of the next generation of nursing home researchers.

Evaluating the Findings of the IMPACT-C Randomized Clinical Trial to Improve COVID-19 Vaccine Coverage in Skilled Nursing Facilities

IMPORTANCE

Identifying successful strategies to increase COVID-19 vaccination among skilled nursing facility (SNF) residents and staff is integral to preventing future outbreaks in a continually overwhelmed system.

OBJECTIVE

To determine whether a multicomponent vaccine campaign would increase vaccine rates among SNF residents and staff.

DESIGN, SETTING, AND PARTICIPANTS

This was a cluster randomized trial with a rapid timeline (December 2020-March 2021) coinciding with the Pharmacy Partnership Program (PPP). It included 133 SNFs in 4 health care systems across 16 states: 63 and 70 facilities in the intervention and control arms, respectively, and participants included 7496 long-stay residents (>100 days) and 17 963 staff.

INTERVENTIONS

Multicomponent interventions were introduced at the facility level that included: (1) educational material and electronic messaging for staff; (2) town hall meetings with frontline staff (nurses, nurse aides, dietary, housekeeping); (3) messaging from community leaders; (4) gifts (eg, T-shirts) with socially concerned messaging; (5) use of a specialist to facilitate consent with residents' proxies; and (6) funds for additional COVID-19 testing of staff/residents.

MAIN OUTCOMES AND MEASURES

The primary outcomes of this study were the proportion of residents (from electronic medical records) and staff (from facility logs) who received a COVID-19 vaccine (any), examined as 2 separate outcomes. Mixed-effects generalized linear models with a binomial distribution were used to compare outcomes between arms, using intent-to-treat approach. Race was examined as an effect modifier in the resident outcome model.

RESULTS

Most facilities were for-profit (95; 71.4%), and 1973 (26.3%) of residents were Black. Among residents, 82.5% (95% CI, 81.2%-83.7%) were vaccinated in the intervention arm, compared with 79.8% (95% CI, 78.5%-81.0%) in the usual care arm (marginal difference 0.8%; 95% CI, -1.9% to 3.7%). Among staff, 49.5% (95% CI, 48.4%-50.6%) were vaccinated in the intervention arm, compared with 47.9% (95% CI, 46.9%-48.9%) in usual care arm (marginal difference: -0.4%; 95% CI, -4.2% to 3.1%). There was no association of race with the outcome among residents.

CONCLUSIONS AND RELEVANCE

A multicomponent vaccine campaign did not have a significant effect on vaccination rates among SNF residents or staff. Among residents, vaccination rates were high. However, half the staff remained unvaccinated despite these efforts. Vaccination campaigns to target SNF staff will likely need to use additional approaches.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier: NCT04732819.

Advancing Clinical Trials in Nursing Homes: A Proposed Roadmap to Success

An effective clinical research effort in nursing homes to address prevention and treatment of COVID-19 faced overwhelming challenges. Under the Health Care Systems Research Network-Older Americans Independence Centers AGING Initiative, a multidisciplinary Stakeholder Advisory Panel was convened to develop recommendations to improve the capability of the clinical research enterprise in US nursing homes. The Panel considered the nursing home as a setting for clinical trials, reviewed the current state of clinical trials in nursing homes, and ultimately developed recommendations for the establishment of a nursing home clinical trials research network that would be centrally supported and administered. This report summarizes the Panel’s recommendations, which were developed in alignment with the following core principles: build on available research infrastructure where appropriate; leverage existing productive partnerships of researchers with groups of nursing homes and nursing home corporations; encompass both efficacy and effectiveness clinical trials; be responsive to a broad range of stakeholders including nursing home residents and their care partners; be relevant to an expansive range of clinical and health care delivery research questions; be able to pivot as necessary to changing research priorities and circumstances; create a pathway for industry-sponsored research as appropriate; invest in strategies to increase diversity in study populations and the research workforce; and foster the development of the next generation of nursing home researchers.

88. Review of nursing home antibiotic stewardship citation deficiencies to identify opportunities to improve antibiotic stewardship implementation, 2018-2019

Background

Centers for Medicare & Medicaid Services (CMS) set standards for nursing homes (NH) and conduct inspections to assess adherence to regulatory requirements, including antibiotic stewardship implementation. NHs not meeting requirements are issued a citation. We reviewed text summaries for citations related to antibiotic stewardship to assess implementation in NHs.

Methods

We obtained publicly available antibiotic stewardship deficiency citations issued to NHs from 9/2018—7/2019 and NH characteristics data from CMS Nursing Home Compare. We used the χ2 test to compare characteristics of NHs with and without citations.

We did a qualitative review of a randomly selected subset (318/635) of antibiotic stewardship citations and classified citations into one or more of four categories based on Centers for Disease Control and Prevention’s Core Elements of Antibiotic Stewardship: 1) Leadership & Accountability, 2) Action, 3) Tracking & Reporting, 4) Education (Fig 1). We developed subcategories based on our iterative review process to further describe the citations. Each citation was reviewed by two reviewers and yielded 95% agreement in categorization. Discordant citations were reviewed by a third reviewer, and core element categories with agreement by ≥2/3 reviewers were assigned, resulting in 99% agreement.

Antibiotic Stewardship Citation Deficiency Category Common Themes and Examples from Citation Text from Qualitative Review of Antibiotic Stewardship Citation Deficiencies.

Results

There were 635 NH stewardship citation deficiencies across 44 states from 9/2018—7/2019. NHs with a citation were more likely to have < 100 beds (60% vs. 50%) and for-profit ownership (75% vs. 70%) (Table 1).

Of the 318 reviewed citations, Action was cited in 67% of NHs; 115/213 had missing or incomplete criteria documented for antibiotic initiation. Tracking & Reporting was cited in 40% of NHs; 117/126 had missing or incomplete antibiotic or infection tracking logs. Leadership & Accountability was cited in 23% of NHs; 41/72 NHs had no stewardship policy available. Education was cited in 13% of NHs (Fig 2).

Table 1. Characteristics of US Nursing Homes With and Without an Antibiotic Stewardship Citation Deficiency from 9/2018-7/2019.

Conclusion

The most common opportunities for improvement fell under appropriate assessment and documentation of criteria for antibiotic initiation at the resident and facility-level. Training NH staff to use available resources for antibiotic stewardship activities may improve implementation. Further evaluation to identify barriers to implementation is needed.

Disclosures

David Gifford, MD, MPH, American Healthcare Association (Employee)

The BNT162b2 vaccine is associated with lower new COVID-19 cases in nursing home residents and staff

Background/Objectives

The effectiveness of the BNT162b2 vaccine on preventing the spread of COVID‐19 and deaths in nursing homes (NH) is unknown.

Design

We used zero‐inflated negative binomial mixed effects regressions to model the associations of time since the vaccine clinic ending the week of December 27, 2020 (cohort 1), January 3, 2021 (cohort 2), or January 10, 2021 (cohort 3) controlling for county rate of COVID‐19, bed size, urban location, racial and ethnic census, and level of registered nurses with resident cases and deaths of COVID‐19 and staff cases of COVID‐19.

Setting and Participants

All 2501 NHs who held a vaccine clinic from the first 17 states to initiate clinics as part of the Pharmacy Partnership for Long‐Term Care Program.

Main Outcome(s) and Measure(s)

Adjusted Incidence Rate Ratio (IRR) for time in 3, 4, 5, and 6 weeks after the first vaccine clinic for resident cases and deaths of COVID‐19 and staff cases of COVID‐19.

Results

Resident and staff cases trended downward in all three cohorts following the vaccine clinics. Time following the first clinic at 5 and 6 weeks was consistently associated with fewer resident cases (IRR: 0.68 [95% CI: 0.54–0.84], IRR: 0.64 [95% CI: 0.48–0.86], respectively); resident deaths (IRR: 0.59 [95% CI: 0.45–0.77], IRR: 0.45 [95% CI: 0.31–0.65], respectively); and staff cases (IRR: 0.64 [95% CI: 0.56–0.73], IRR: 0.51 [95% CI: 0.42–0.62], respectively). Other factors associated with fewer resident and staff cases included facilities with less than 50 certified beds and high nurse staffing per resident day (>0.987). Contrary to prior research, higher Hispanic non‐white resident census was associated with fewer resident cases (IRR: 0.42, 95% CI: 0.31–0.56) and deaths (IRR: 0.18, 95% CI: 0.12–0.27).

Conclusions

The BNT162b2 vaccine is associated with decreased spread of SARS‐CoV‐2 in both residents and staff as well as decreased deaths among residents.

See related editorial by Ouslander et al and related articles by Mor et al, Moore et al, and Rudolph et al. in this issue.

Lessons learned from frontline skilled nursing facility staff regarding COVID-19 vaccine hesitancy

Background

Presently a median of 37.5% of the U.S. skilled nursing facility (SNF) workforce has been vaccinated for COVID‐19. It is essential to understand vaccine hesitancy among SNF workers to inform vaccine campaigns going forward.

Objective

To describe the concerns raised among healthcare workers and staff from SNFs during town hall meetings.

Design

Sixty‐three SNFs from four corporations were invited to send Opinion Leaders, outspoken staff from nursing, nurse aid, dietary, housekeeping or recreational therapy, to attend a 1‐h virtual town hall meeting. Meetings used a similar format where the moderator solicited concerns that the attendees themselves had or had heard from others in the facility about the COVID‐19 vaccine. Physicians and moderators used personal stories to address concerns and reaffirmed positive emotions.

Setting

Twenty‐six video town hall meetings with SNF staff.

Participants

Healthcare workers and staff, with physicians serving as content experts.

Measurement

Questions and comments about the COVID‐19 vaccines noted by physicians.

Results

One hundred and ninety three staff from 50 facilities participated in 26 meetings between December 30, 2020 and January 15, 2021. Most staff reported getting information about the vaccine from friends or social media. Concerns about how rapidly the vaccines were developed and side effects, including infertility or pregnancy related concerns, were frequently raised. There were no differences in concerns raised by discipline. Questions about returning to prior activities after being vaccinated were common and offered the opportunity to build on positive emotions to reduce vaccine hesitancy.

Conclusions

Misinformation about the COVID‐19 vaccine was widespread among SNF staff. Sharing positive emotions and stories may be more effective than sharing data when attempting to reduce vaccine hesitancy in SNF staff.

"Somebody Like Me": Understanding COVID-19 Vaccine Hesitancy among Staff in Skilled Nursing Facilities

Objective

The vaccination of skilled nursing facility (SNF) staff is a critical component in the battle against COVID-19. Together, residents and staff constitute the single most vulnerable population in the pandemic. The health of these workers is completely entangled with the health of those they care for. Vaccination of SNF staff is key to increasing uptake of the vaccine, reducing health disparities, and reopening SNFs to visitors. Yet, as the vaccine rollout begins, some SNF staff are declining to be vaccinated. The purpose of this article is to describe reasons for COVID-19 vaccine hesitancy reported by staff of skilled nursing facilities and understand factors that could potentially reduce hesitancy.

Design

Five virtual focus groups were conducted with staff of SNFs as part of a larger project to improve vaccine uptake.

Setting and Participants

Focus groups with 58 staff members were conducted virtually using Zoom.

Measures

Focus groups sought to elicit concerns, perspectives, and experiences related to COVID-19 testing and vaccination.

Results

Our findings indicate that some SNF staff are hesitant to receive the COVID-19 vaccine. Reasons for this hesitancy include beliefs that the vaccine has been developed too fast and without sufficient testing; personal fears about pre-existing medical conditions, and more general distrust of the government.

Conclusions and Implications

SNF staff indicate that seeing people like themselves receive the vaccination is more important than seeing public figures. We discuss the vaccination effort as a social enterprise and the need to develop long-term care provider-academic-community partnerships in response to COVID-19 and in expectation of future pandemics.

The CoreQ: Development and Testing of a Nursing Facility Resident Satisfaction Survey

The development and testing of a nursing facility resident satisfaction survey (i.e., CoreQ) that could be used for public reporting purposes is presented here. This is important as very little satisfaction with care information is publicly available for nursing facility consumers. Validity testing is reported detailing the development of the CoreQ: Short Stay Discharge questionnaire and a measure that was calculated from the items in the questionnaire. This questionnaire resulted in four items whose combined score gives a measure representing participants' overall satisfaction with the nursing facility. The measure parsimoniously reports this satisfaction as a score (ranging from 0 to 100) and was recently endorsed by the National Quality Forum (NQF). The measure may have significance for report cards and payment metrics, as it incorporates the consumers' opinion.

Maximizing Overall Diversity for Improved Uncertainty Estimates in Deep Ensembles

The inaccuracy of neural network models on inputs that do not stem from the distribution underlying the training data is problematic and at times unrecognized. Uncertainty estimates of model predictions are often based on the variation in predictions produced by a diverse ensemble of models applied to the same input. Here we describe Maximize Overall Diversity (MOD), an approach to improve ensemble-based uncertainty estimates by encouraging larger overall diversity in ensemble predictions across all possible inputs. We apply MOD to regression tasks including 38 Protein-DNA binding datasets, 9 UCI datasets, and the IMDB-Wiki image dataset. We also explore variants that utilize adversarial training techniques and data density estimation. For out-of-distribution test examples, MOD significantly improves predictive performance and uncertainty calibration without sacrificing performance on test data drawn from same distribution as the training data. We also find that in Bayesian optimization tasks, the performance of UCB acquisition is improved via MOD uncertainty estimates.

USING A UNIVERSAL SATISFACTION SCORE IN LONG-TERM CARE SETTINGS

The CoreQ (not an acronym) consists of a limited number of satisfaction items (3-4 items, depending on setting) that are used to create an overall satisfaction score for long-term care facilities. This measure has been used in assisted living (AL) and skilled nursing facilities (SNFs) and has been endorsed by the National Quality Forum (NQF). Briefly, the development and psychometric testing of the CoreQ will be described, including the rationale for producing an overall satisfaction score and correlation with important quality indicators like Five-Star. Using data collected over the past 3 years, comprising more than 100,000 respondents, the use of the CoreQ measure will be described. For example, the CoreQ scores are used in MA to allow providers to benchmark their performance. The use of the scores in this way will be discussed including how providers have used the scores for quality improvement. Some states have elected to use CoreQ in pay for performance and other state initiatives. A case study of how New Jersey uses CoreQ with SNFs will be presented, including distribution of scores and addressing data collection challenges. CoreQ can be utilized as a short customer satisfaction measure to allow providers to benchmark their performance, residents and families in decision-making, and states and others to use for accountability.

Modeling Persistent Trends in Distributions

We present a nonparametric framework to model a short sequence of probability distributions that vary both due to underlying effects of sequential progression and confounding noise. To distinguish between these two types of variation and estimate the sequential-progression effects, our approach leverages an assumption that these effects follow a persistent trend. This work is motivated by the recent rise of single-cell RNA-sequencing experiments over a brief time course, which aim to identify genes relevant to the progression of a particular biological process across diverse cell populations. While classical statistical tools focus on scalar-response regression or order-agnostic differences between distributions, it is desirable in this setting to consider both the full distributions as well as the structure imposed by their ordering. We introduce a new regression model for ordinal covariates where responses are univariate distributions and the underlying relationship reflects consistent changes in the distributions over increasing levels of the covariate. This concept is formalized as a trend in distributions, which we define as an evolution that is linear under the Wasserstein metric. Implemented via a fast alternating projections algorithm, our method exhibits numerous strengths in simulations and analyses of single-cell gene expression data.

Working toward precision medicine: Predicting phenotypes from exomes in the Critical Assessment of Genome Interpretation (CAGI) challenges

Precision medicine aims to predict a patient's disease risk and best therapeutic options by using that individual's genetic sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of genotype-phenotype prediction challenges; participants build models, undergo assessment, and share key findings. For CAGI 4, three challenges involved using exome-sequencing data: Crohn's disease, bipolar disorder, and warfarin dosing. Previous CAGI challenges included prior versions of the Crohn's disease challenge. Here, we discuss the range of techniques used for phenotype prediction as well as the methods used for assessing predictive models. Additionally, we outline some of the difficulties associated with making predictions and evaluating them. The lessons learned from the exome challenges can be applied to both research and clinical efforts to improve phenotype prediction from genotype. In addition, these challenges serve as a vehicle for sharing clinical and research exome data in a secure manner with scientists who have a broad range of expertise, contributing to a collaborative effort to advance our understanding of genotype-phenotype relationships.

Long-term persistence and development of induced pancreatic beta cells generated by lineage conversion of acinar cells

Direct lineage conversion is a promising approach to generate therapeutically important cell types for disease modeling and tissue repair. However, the survival and function of lineage-reprogrammed cells in vivo over the long term has not been examined. Here, using an improved method for in vivo conversion of adult mouse pancreatic acinar cells toward beta cells, we show that induced beta cells persist for up to 13 months (the length of the experiment), form pancreatic islet-like structures and support normoglycemia in diabetic mice. Detailed molecular analyses of induced beta cells over 7 months reveal that global DNA methylation changes occur within 10 d, whereas the transcriptional network evolves over 2 months to resemble that of endogenous beta cells and remains stable thereafter. Progressive gain of beta-cell function occurs over 7 months, as measured by glucose-regulated insulin release and suppression of hyperglycemia. These studies demonstrate that lineage-reprogrammed cells persist for >1 year and undergo epigenetic, transcriptional, anatomical and functional development toward a beta-cell phenotype.

Lineage-based identification of cellular states and expression programs

We present a method, LineageProgram, that uses the developmental lineage relationship of observed gene expression measurements to improve the learning of developmentally relevant cellular states and expression programs. We find that incorporating lineage information allows us to significantly improve both the predictive power and interpretability of expression programs that are derived from expression measurements from in vitro differentiation experiments. The lineage tree of a differentiation experiment is a tree graph whose nodes describe all of the unique expression states in the input expression measurements, and edges describe the experimental perturbations applied to cells. Our method, LineageProgram, is based on a log-linear model with parameters that reflect changes along the lineage tree. Regularization with L(1) that based methods controls the parameters in three distinct ways: the number of genes change between two cellular states, the number of unique cellular states, and the number of underlying factors responsible for changes in cell state. The model is estimated with proximal operators to quickly discover a small number of key cell states and gene sets. Comparisons with existing factorization, techniques, such as singular value decomposition and non-negative matrix factorization show that our method provides higher predictive power in held, out tests while inducing sparse and biologically relevant gene sets.

Stochastic motion planning and applications to traffic

This paper presents a stochastic motion planning algorithm and its application to traffic navigation. The algorithm copes with the uncertainty of road traffic conditions by stochastic modeling of travel delay on road networks. The algorithm determines paths between two points that optimize a cost function of the delay data probability distribution. It can be used to find paths that maximize the probability of reaching a destination within a particular travel deadline. For such problems, standard shortest-path algorithms do not work because the optimal substructure property does not hold. We evaluate our algorithm using both simulations and real-world drives, using delay data gathered from a set of taxis equipped with global positioning system sensors and a wireless network. Our algorithm can be integrated into on-board navigation systems as well as route-finding websites, providing drivers with good paths that meet their desired goals.

Low-fat, low-glycemic load diet and gene expression in human prostate epithelium: a feasibility study of using cDNA microarrays to assess the response to dietary intervention in target tissues

PURPOSE

We examined the feasibility of using gene expression changes in human prostate epithelium as a measure of response to a dietary intervention.

MATERIALS AND METHODS

Eight men with newly diagnosed prostate cancer were randomized to a low-fat/low-glycemic load intervention arm (<20% energy from fat and total daily glycemic load <100) or a "standard American" control arm (approximately 35% energy from fat and total daily glycemic load >200). Prostate tissue was collected before randomization and approximately 6 weeks later, at the time of radical prostatectomy. Epithelium was acquired by laser capture microdissection, and transcript abundance levels were measured by cDNA microarray hybridization and confirmed by quantitative reverse transcription-PCR.

RESULTS

Men in the intervention arm consumed 39% less total energy (P = 0.004) and the difference in weight change between intervention and control arms was -6.1 kg (P = 0.02). In the intervention arm, 23 (0.46%) of 5,711 cDNAs with measurable expression were significantly altered (P < 0.05; false discovery rate, <or=10%). In the control arm, there were no significant changes in transcript expression, even when using a false discovery rate as high as 50%.

CONCLUSIONS

A 6-week, low-fat/low-glycemic load diet was associated with significant gene expression changes in human prostate epithelium. These results show the feasibility of using prostate tissues collected at diagnosis and at surgery to study the effects of dietary manipulation on prostate tissue, which may give insight into the molecular mechanisms underlying the associations of diet and obesity with the development or progression of prostate cancer.

GSE: a comprehensive database system for the representation, retrieval, and analysis of microarray data

We present GSE, the Genomic Spatial Event database, a system to store, retrieve, and analyze all types of high-throughput microarray data. GSE handles expression datasets, ChIP-chip data, genomic annotations, functional annotations, the results of our previously published Joint Binding Deconvolution algorithm for ChIP-chip, and precomputed scans for binding events. GSE can manage data associated with multiple species; it can also simultaneously handle data associated with multiple 'builds' of the genome from a single species. The GSE system is built upon a middle software layer for representing streams of biological data; we outline this layer, called GSEBricks, and show how it is used to build an interactive visualization application for ChIP-chip data. The visualizer software is written in Java and communicates with the GSE database system over the network. We also present a system to formulate and record binding hypotheses--simple descriptions of the relationships that may hold between different ChIP-chip experiments. We provide a reference software implementation for the GSE system.

Collaborative Clinical Quality Improvement for Pressure Ulcers in Nursing Homes

The National Nursing Home Improvement Collaborative aimed to reduce pressure ulcer (PU) incidence and prevalence. Guided by subject matter and process experts, 29 quality improvement organizations and six multistate long-term care corporations recruited 52 nursing homes in 39 states to implement recommended practices using quality improvement methods. Facilities monitored monthly PU incidence and prevalence, healing, and adoption of key care processes. In residents at 35 regularly reporting facilities, the total number of new nosocomial Stage III to IV PUs declined 69%. The facility median incidence of Stage III to IV lesions declined from 0.3 per 100 occupied beds per month to 0.0 (P<.001) and the incidence of Stage II to IV lesions declined from 3.2 to 2.3 per 100 occupied beds per month (P=.03). Prevalence of Stage III to IV lesions trended down (from 1.3 to 1.1 residents affected per 100 occupied beds (P=.12). The incidence and prevalence of Stage II lesions and the healing time of Stage II to IV lesions remained unchanged. Improvement teams reported that Stage II lesions usually healed quickly and that new PUs corresponded with hospital transfer, admission, scars, obesity, and immobility and with noncompliant, younger, or newly declining residents. The publicly reported quality measure, prevalence of Stage I to IV lesions, did not improve. Participants documented disseminating methods and tools to more than 5,359 contacts in other facilities. Results suggest that facilities can reduce incidence of Stage III to IV lesions, that the incidence of Stage II lesions may not correlate with the incidence of Stage III to IV lesions, and that the publicly reported quality measure is insensitive to substantial improvement. The project demonstrated multiple opportunities in collaborative quality improvement, including improving the measurement of quality and identifying research priorities, as well as improving care.

A molecular correlate to the Gleason grading system for prostate adenocarcinoma

Adenocarcinomas of the prostate can be categorized into tumor grades based on the extent to which the cancers histologically resemble normal prostate glands. Because grades are surrogates of intrinsic tumor behavior, characterizing the molecular phenotype of grade is of potential clinical importance. To identify molecular alterations underlying prostate cancer grades, we used microdissection to obtain specific cohorts of cancer cells corresponding to the most common Gleason patterns (patterns 3, 4, and 5) from 29 radical prostatectomy samples. We paired each cancer sample with matched benign lumenal prostate epithelial cells and profiled transcript abundance levels by microarray analysis. We identified an 86-gene model capable of distinguishing low-grade (pattern 3) from high-grade (patterns 4 and 5) cancers. This model performed with 76% accuracy when applied to an independent set of 30 primary prostate carcinomas. Using tissue microarrays comprising >800 prostate samples, we confirmed a significant association between high levels of monoamine oxidase A expression and poorly differentiated cancers by immunohistochemistry. We also confirmed grade-associated levels of defender against death (DAD1) protein and HSD17 beta4 transcripts by immunohistochemistry and quantitative RT-PCR, respectively. The altered expression of these genes provides functional insights into grade-associated features of therapy resistance and tissue invasion. Furthermore, in identifying a profile of 86 genes that distinguish high- from low-grade carcinomas, we have generated a set of potential targets for modulating the development and progression of the lethal prostate cancer phenotype.

Influence of surgical manipulation on prostate gene expression: implications for molecular correlates of treatment effects and disease prognosis

PURPOSE

Measurements of tissue gene expression are increasingly used for disease stratification, clinical trial eligibility, and assessment of neoadjuvant therapy response. However, the method of tissue acquisition alone could significantly influence the expression of specific transcripts or proteins. This study examines whether there are transcript alterations associated with surgical resection of the prostate gland by radical retropubic prostatectomy.

MATERIALS AND METHODS

Twelve patients with clinically localized prostate cancer underwent immediate in situ prostate biopsy after induction of anesthesia for radical prostatectomy. Ex vivo prostate biopsies were performed immediately after surgical removal. Prostate epithelium was acquired by laser-capture microdissection, and transcript abundance levels were quantitated by cDNA microarray hybridization and confirmed by quantitative polymerase chain reaction. Data were analyzed by paired, two-sample t test using Statistical Analysis of Microarray algorithms, and linear models were fit as a function of clinical characteristics.

RESULTS

Of 5,753 cDNAs with measurable expression in prostate epithelium, 88 (1.5%) were altered as a result of surgery (false-discovery rate < or = 10%), representing 62 unique genes. These included transcripts encoding acute phase response proteins, IER2 and JUNB, and regulators of cell proliferation, p21Cip1 and KLF6. Of the clinical characteristics examined, including patient age, prostate volume, serum prostate-specific antigen, blood loss, and operative time, only gland volume was significantly and negatively associated with the magnitude of gene expression difference between pre- and postsurgical specimens.

CONCLUSION

Surgical manipulation results in significant gene expression changes. Molecular analyses of surgical samples should recognize that transcript alterations occur rapidly, and these results are important when designing and analyzing molecular correlates of clinical studies.

The Employment of Nurse Practitioners and Physician Assistants in U.S. Nursing Homes

PURPOSE

Nursing facilities with nurse practitioners or physician assistants (NPs or PAs) have been reported to provide better care to residents. Assuming that freestanding nursing homes in urban areas that employ these professionals are making an investment in medical infrastructure, we test the hypotheses that facilities in states with higher Medicaid rates, and those in more competitive markets and markets with higher managed care penetration, are more likely to employ NPs or PAs.

DESIGN AND METHODS

The Online Survey Certification and Reporting System (OSCAR) database, Area Resource File, and information from surveys of state policies from 1993 to 2002 are used to study the employment of NPs or PAs, using a cross-sectional time-series generalized estimating equation model with surveys nested within facilities, testing several market and state-policy effects while controlling for facility and market characteristics.

RESULTS

Throughout the 1990s the proportion of nursing facilities with NPs or PAs doubled, from less than 10% to over 20%. Facilities in states in the upper quartile of Medicaid reimbursement rates were 10% more likely to employ NPs or PAs. Facilities in more competitive markets, and in markets with higher managed care penetration, were more likely to employ NPs or PAs (adjusted odds ratio = 1.27, 1.20 respectively).

IMPLICATIONS

More generous state Medicaid nursing home reimbursement and higher competition may advance the investment in medical infrastructure, which in turn may positively affect the quality of care provided to nursing home residents.

Microbubble production in an in vitro cardiopulmonary bypass circuit ventilated with xenon

Xenon, as an anaesthetic gas, has the potential to be used in an increasing range of applications. However, its use in cardiopulmonary bypass (CPB) has not yet progressed from the rat model due to concerns that its relative insolubility may cause microbubble formation and/or expansion in the micro-vasculature of the patient. An in vitro CPB circuit was designed to create and measure gaseous microbubbles over a range of temperature gradients, pressure drop and gas tensions. We were able to demonstrate that our test circuit did not produce any significant microbubbles and that, under normal physiological blood pressures, a fixed gas bubble in connection with the circuit did not grow in the presence of Xe.

Detection of delirium in the intensive care unit: comparison of confusion assessment method for the intensive care unit with confusion assessment method ratings

OBJECTIVES

To compare the Confusion Assessment Method (CAM) and CAM for the Intensive Care Unit (CAM-ICU) methods for detecting delirium in alert, nonintubated older ICU patients.

DESIGN

Comparison study.

SETTING

Fourteen-bed medical ICU of an 800-bed university teaching hospital.

PARTICIPANTS

Twenty-two patients aged 65 and older admitted to the ICU.

MEASUREMENTS

Two blinded, trained clinician-researchers who had undergone interrater reliability testing interviewed patients separately, usually within 10 minutes of each other (up to 120 minutes). Each researcher examined patients for the four key CAM criteria: acuteness, inattention, disorganized thinking, and altered level of consciousness. One researcher used the CAM method with the Mini-Mental State Examination and Digit Span; the other researcher used the CAM-ICU method with nonverbal cognitive and attention tasks.

RESULTS

Rates of delirium were 68% according to CAM and 50% according CAM-ICU. Comparing the two methods, agreement was 82%, with a kappa of 0.64. Using the CAM as the reference standard, the CAM-ICU had a sensitivity of 73% (95% confidence interval (CI)=60-86) and specificity of 100% (95% CI=56-100). There were four false-negative ratings using the CAM-ICU. Reasons for disparate results were that the CAM used more-detailed cognitive testing that detected more deficits (3 patients) and the time elapsed (90 minutes) between ratings in one patient with markedly fluctuating symptoms.

CONCLUSION

CAM and CAM-ICU agreement was moderately high. Although the CAM-ICU is recommended for ICU patients because of its brevity and ease of use, the standard CAM method may detect more subtle cases of delirium in nonintubated, verbal ICU patients.

Loss of stearoyl-CoA desaturase expression is a frequent event in prostate carcinoma

Prostate carcinogenesis is influenced by genetic alterations resulting in a biochemical condition that favors cell proliferation and survival. Studies of prostate carcinoma using comparative genomic hybridization and cDNA microarray analysis indicate that numerous biochemical processes may be affected during cellular transformation and progression to an invasive phenotype. Among the consistently observed tumor-associated changes are alterations in fatty acid metabolism that influence diverse cellular activities such as signaling, energy utilization, and membrane fluidity. Increases in fatty acid synthase (FAS) levels have been shown to be one of the earliest and most frequent molecular alterations in prostate carcinogenesis. We sought to identify tumor-associated changes in the expression of genes with functional roles associated with lipid metabolism. Defined populations of normal and neoplastic prostate epithelium were acquired by laser capture microdissection and transcript levels were measured by cDNA microarray hybridization. We determined that stearoyl-CoA desaturase (SCD) transcripts were downregulated in cancer relative to normal epithelium. These results were confirmed by quantitative PCR. Further analysis by immunohistochemical evaluation of radical prostatectomy samples employed a quantitative scoring system with a range of 0-300. The median SCD expression levels were 150, 45 and 10 for normal, PIN and carcinoma samples, respectively. Statistically significant differential SCD expression between normal and cancerous epithelium was determined at the p=0.001 level, and between PIN and prostate carcinoma at the p=0.03 level. Of these cases, 92% overexpressed fatty acid synthase (FAS) in cancerous cells and 84.7% exhibited the signature of FAS overexpression and SCD loss in prostate carcinoma as compared to normal prostate epithelium. These results indicate that loss of SCD expression is a frequent event in prostate adenocarcinoma, and further supports a role for altered lipid metabolism as a factor in the process of carcinogenesis.

Approaches to quality improvement in nursing homes: lessons learned from the six-state pilot of CMS's Nursing Home Quality Initiative

BACKGROUND

In November 2002, the Centers for Medicare & Medicaid Services (CMS) launched a Nursing Home Quality Initiative that included publicly reporting a set of Quality Measures for all nursing homes in the country, and providing quality improvement assistance to nursing homes nationwide. A pilot of this initiative occurred in six states for six months prior to the launch.

METHODS

Review and analysis of the lessons learned from the six Quality Improvement Organizations (QIOs) that led quality improvement efforts in nursing homes from the six pilot states.

RESULTS

QIOs in the six pilot states found several key outcomes of the Nursing Home Quality Initiative that help to maximize the potential of public reporting to leverage effective improvement in nursing home quality of care. First, public reporting focuses the attention of all stakeholders in the nursing home industry on achieving good quality outcomes on a defined set of measures, and creates an incentive for partnership formation. Second, publicly reported quality measures motivate nursing home providers to improve in certain key clinical areas, and in particular to seek out new ways of changing processes of care, such as engaging physicians and the medical director more directly. Third, the lessons learned by QIOs in the pilot of this Initiative indicate that certain approaches to providing quality improvement assistance are key to guiding nursing home providers' desire and enthusiasm to improve towards a using a systematic approach to quality improvement.

CONCLUSION

The Nursing Home Quality Initiative has already demonstrated the potential of public reporting to foster collaboration and coordination among nursing home stakeholders and to heighten interest of nursing homes in quality improvement techniques. The lessons learned from this pilot project have implications for any organizations or individuals planning quality improvement projects in the nursing home setting.

The quality of quality measurement in U.S. nursing homes

PURPOSE

This article examines various technical challenges inherent in the design, implementation, and dissemination of health care quality performance measures.

DESIGN AND METHODS

Using national and state-specific Minimum Data Set data from 1999, we examined sample size, measure stability, creation of ordinal ranks, and risk adjustment as applied to aggregated facility quality indicators.

RESULTS

Nursing home Quality Indicators now in use are multidimensional and quarterly estimates of incidence-based measures can be relatively unstable, suggesting the need for some averaging of measures over time.

IMPLICATIONS

Current public reports benchmarking nursing homes' performances may require additional technical modifications to avoid compromising the fairness of comparisons.

Reporting quality of nursing home care to consumers: the Maryland experience

OBJECTIVE

To design and implement a reporting system for quality of long-term care to empower consumers and to create incentives for quality improvement. To identify a model to approach this technically and politically difficult task.

APPROACH

Establishment of a credible and transparent decision process using a public forum. Development of the system based on: (1) review of the literature and existing systems, and discussions with stakeholders about strengths and weaknesses; (2) focus on consumer preferences in the design; and (3) responsiveness to industry concerns in the implementation.

LESSONS LEARNED

None of the existing systems appeared to be a suitable model. We decided to develop an entirely new system based on three key design principles that allowed us to tailor the system to consumer needs: (1) designing a decision tool rather than a database; (2) summarizing rather than simplifying information; and (3) accounting for the target audience in the creative execution. Industry concerns focused on the burden of the system, the potential for errors, and the possible communication of a negative impression of the industry. As methodological and data limitations prevented us from resolving those concerns, we addressed them by using cautionary language in the presentation and by making a commitment to incorporate improvements in the future. All stakeholders regarded the final design as an acceptable compromise.

CONCLUSIONS

Despite its potentially controversial nature and many methodological challenges, the system has been well received by both the public and the industry. We attribute this success to two key factors: a collaborative decision process, in which all critical design and execution choices were laid out explicitly and debated with stakeholders in a public forum, and realism and honesty regarding the limitations of the system.

Benchmarking and quality in residential and nursing homes: lessons from the US

BACKGROUND

Performance measurement and benchmarking are common concerns in the delivery of long term care. It is common to measure the performance of providers and to publicly report these data. This paper examines selected technical challenges facing those who design, implement and disseminate health care quality performance measures.

METHOD

Review of the application of measures of performance in the US nursing home sector.

RESULTS

Using examples drawn from the skilled nursing home arena, problems ranging from data reliability and validity, the multi-dimensional nature of quality measures and selection bias as well as differential measurement abilities are discussed.

CONCLUSIONS

Benchmarking of performance is an inherently complex issue. However, to ensure that such comparisons are both fair and valid requires measures to be more technically sophisticated and sensitive to real changes attributable to changes in care.

Bayesian network approach to cell signaling pathway modeling

The modeling of cellular signaling pathways is an emerging field. Sachs et al. illustrate the application of Bayesian networks to an example cellular pathway involving the activation of focal adhesion kinase (FAK) and extracellular signal-regulated kinase (ERK) in response to fibronectin binding to an integrin. They describe how to use the analysis to select from among proposed models, formulate hypotheses regarding component interactions, and uncover potential dynamic changes in the interactions between these components. Although the data sets currently available for this example problem are too small to definitively point to a particular model, the approach and results provide a glimpse into the power that these methods will achieve once the technology for obtaining the necessary data becomes readily available.

Access to postacute nursing home care before and after the BBA. Balanced Budget Act

Anecdotal reports in the wake of the Balanced Budget Act (BBA) of 1997 raised concerns about restricted access to postacute nursing facility care for Medicare beneficiaries requiring costly, medically complex services. Using all Medicare Part A hospital and nursing facility claims for providers in the state of Ohio and a refined method of identifying hospitalized beneficiaries who were the most at risk, we observed only a small decrease in the proportion of the costliest patients discharged to nursing facilities in 1999 compared with pre-BBA years. Average hospital length-of-stay increased only slightly in 1999, and there were no changes in rehospitalization rates for the costliest patient types. However, reduced rates of admission were concentrated in specific types of nursing facilities, suggesting a need to closely monitor the effects of ongoing post-BBA policy updates.

External threats and nursing home administrator turnover

External threats and volatility in the long-term-care sector in recent decades have posed serious challenges for nursing home administrators. Greater job complexity and administrative responsibilities resulting from public policies and more specialization and competitiveness in nursing home markets have made turnover a significant issue. This article examines administrator turnover from 1970 through 1997 in New York State and describes how turnover increased markedly in the late 1980s and early 1990s.