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BAF250a Protein Regulates Nucleosome Occupancy and Histone Modifications in Priming Embryonic Stem Cell Differentiation. - The Journal of biological chemistry
The unique chromatin signature of ES cells is fundamental to the pluripotency and differentiation of ES cells. One key feature is the poised chromatin state of master developmental genes that are transcriptionally repressed in ES cells but ready to be activated in response to differentiation signals. Poised chromatin in ES cells contains both H3 Lys-4 trimethylation (H3K4me3) and H3 Lys-27 trimethylation (H3K27me3) methylation, indicating activating and repressing potential. However, the contribution of non-covalent chromatin structure to the poised state is not well understood. To address whether remodeling of nucleosomes is important to the poised state, we characterized the function of BAF250a, a key regulatory subunit of the ES cell ATP-dependent Brahma-associated factor (BAF) chromatin remodeling complex (esBAF). Acute deletion of BAF250a disrupted the differentiation potential of ES cells by altering the expression timing of key developmental genes and pluripotent genes. Our genome-wide nucleosome and histone modification analyses indicated that the disruption of gene expression timing was largely due to changes of chromatin structures at poised genes, particularly those key developmental genes mediated by BAF250a. Specifically, BAF250a deletion caused a nucleosome occupancy increase at H3K4me3- and/or H3K27me3-associated promoters. Moreover, H3K27me3 levels and the number of bivalent promoter genes were reduced in BAF250a KO ES cells. We revealed that BAF250a ablation led to elevated Brg1 but reduced Suz12 recruitment at nucleosome occupancy-increased regions, indicating an unexpected and complicated role of BAF250a in regulating esBAF and Polycomb repressive complex (PRC) activities. Together, our studies identified that BAF250a mediates esBAF and PRC functions to establish the poised chromatin configuration in ES cells, which is essential for the proper differentiation of ES cells.Â© 2015 by The American Society for Biochemistry and Molecular Biology, Inc.
Purification of specific chromatin regions using oligonucleotides: capture hybridization analysis of RNA targets (CHART). - Methods in molecular biology (Clifton, N.J.)
Identification of genomic binding sites and proteins associated with noncoding RNAs will lead to more complete mechanistic characterization of the regulatory activities of noncoding RNAs. Capture hybridization analysis of RNA targets (CHART) is a powerful technique wherein specific RNA molecules are isolated from cross-linked nuclear extracts using complementary, biotinylated capture oligonucleotides, allowing subsequent identification of genomic DNA and proteins cross-linked to the RNA of interest. Here, we describe the procedure for CHART and list strategies to optimize nuclear extract preparation, capture oligonucleotide design, and isolation of nucleic acids and proteins enriched through CHART.
Nucleosomal occupancy changes locally over key regulatory regions during cell differentiation and reprogramming. - Nature communications
Chromatin structure determines DNA accessibility. We compare nucleosome occupancy in mouse and human embryonic stem cells (ESCs), induced-pluripotent stem cells (iPSCs) and differentiated cell types using MNase-seq. To address variability inherent in this technique, we developed a bioinformatic approach to identify regions of difference (RoD) in nucleosome occupancy between pluripotent and somatic cells. Surprisingly, most chromatin remains unchanged; a majority of rearrangements appear to affect a single nucleosome. RoDs are enriched at genes and regulatory elements, including enhancers associated with pluripotency and differentiation. RoDs co-localize with binding sites of key developmental regulators, including the reprogramming factors Klf4, Oct4/Sox2 and c-Myc. Nucleosomal landscapes in ESC enhancers are extensively altered, exhibiting lower nucleosome occupancy in pluripotent cells than in somatic cells. Most changes are reset during reprogramming. We conclude that changes in nucleosome occupancy are a hallmark of cell differentiation and reprogramming and likely identify regulatory regions essential for these processes.
The long noncoding RNAs NEAT1 and MALAT1 bind active chromatin sites. - Molecular cell
Mechanistic roles for many lncRNAs are poorly understood, in part because their direct interactions with genomic loci and proteins are difficult to assess. Using a method to purify endogenous RNAs and their associated factors, we mapped the genomic binding sites for two highly expressed human lncRNAs, NEAT1 and MALAT1. We show that NEAT1 and MALAT1 localize to hundreds of genomic sites in human cells, primarily over active genes. NEAT1 and MALAT1 exhibit colocalization to many of these loci, but display distinct gene body binding patterns at these sites, suggesting independent but complementary functions for these RNAs. We also identified numerous proteins enriched by both lncRNAs, supporting complementary binding and function, in addition to unique associated proteins. Transcriptional inhibition or stimulation alters localization of NEAT1 on active chromatin sites, implying that underlying DNA sequence does not target NEAT1 to chromatin, and that localization responds to cues involved in the transcription process.Copyright Â© 2014 Elsevier Inc. All rights reserved.
The association between headache and elevated blood pressure among patients presenting to an ED. - The American journal of emergency medicine
Elevated blood pressure (BP) and headache have long been linked in the medical literature, although data on association are conflicting. We used previously collected data to address these related aims: (1) using the National Hospital Ambulatory Medical Care Survey (NHAMCS), we determined whether elevated BP is more likely in patients who present to an emergency department (ED) with headache than in patients who present with other complaints; (2) using data collected in 3 ED-based migraine clinical trials, we determined the association between improvement in headache pain and improvement in BP among patients who present to an ED with migraine and elevated BP; (3) using the data from the migraine clinical trials, we also determined if an elevated baseline BP identifies a group of patients less likely to respond to standard migraine treatment.We analyzed 2 distinct data sets. The first, NHAMCS, is a national probability sample of all US ED visits. The second is a compilation of data gathered during 3 ED-based migraine randomized controlled trials. We defined elevated BP as follows: moderate elevation-systolic BP (SBP) â‰¥150 mm Hg or diastolic BP (DBP) â‰¥95 mm Hg; marked elevation-SBP â‰¥165 mm Hg or DBP â‰¥100 mm Hg; and severe elevation-SBP â‰¥180 mm Hg or DBP â‰¥110 mm Hg. We report the association between headache and elevated BP in NHAMCS using odds ratios (ORs) with 95% confidence intervals (CI). We report the correlation coefficient and r(2) for the association between improvement in BP and improvement in headache pain in our clinical trials data set. Finally, using our clinical trials database, we determined the influence of elevated BP at baseline on response to migraine medication by constructing a linear regression model in which the dependent variable was improvement in 0 to 10 pain score between baseline and 1 hour, and the primary predictor variable was presence or absence of elevated BP at baseline.Headache was the primary complaint in 3.7% (95% CI, 3.4-4.0%) of all US ED visits, corresponding to 4.8 million (95% CI, 4.2-5.4 million) patient visits. Among US ED patients, those with headache were more likely than patients with other chief complaints to have markedly (OR, 1.37; 95% CI, 1.16-1.61) or severely elevated BP (OR, 1.49; 95% CI, 1.17-1.90). In our clinical trials data set of patients with migraine with moderately elevated BP, there was no correlation between improvement in pain score and improvement in SBP (r = -0.07, r(2) = 0, P = .465) or DBP (r = -0.03, r(2) = 0, P = .75). Similarly, there was no correlation between improvement in headache and improvement in BP among patients with migraine with markedly elevated BP (for SBP, r = -0.19, r(2) = 0.04, P = .89; for DBP, r = -0.02, r(2) = 0, P = .87), nor among patients with severely elevated BP (for SBP, r = 0.06, r(2) = 0, P = .81; for DBP, r = 0.03, r(2) = 0, P = .90). Patients with moderately elevated BP had slightly less improvement in their 0 to 10 pain score than patients with BPs below this cutoff (-0.6; 95% CI, -1.2 to -0.1; P = .03). This was more pronounced among patients with markedly elevated BP (-0.9; 95% CI, -1.7 to -0.2).Although there is an association between elevated BP and headache among patients presenting to an ED, improvement in headache is not associated with improvement in BP.Copyright Â© 2014 Elsevier Inc. All rights reserved.
Current management of migraine in US emergency departments: an analysis of the National Hospital Ambulatory Medical Care Survey. - Cephalalgia : an international journal of headache
Published data from 1998 revealed that most patients treated for migraine in an emergency department received opioids. Over the intervening years, a large body of evidence has emerged demonstrating the efficacy and safety of non-opioid alternatives. Expert opinion during these years has cautioned against use of opioids for migraine. Our objectives were to compare current frequency of use of various medications for acute migraine in US emergency departments with use of these same medications in 1998 and to identify factors independently associated with opioid use.We analyzed National Hospital Ambulatory Medical Care Survey data from 2010, the most current dataset available. The National Hospital Ambulatory Medical Care Survey is a public dataset collected and distributed by the Centers for Disease Control and Prevention. It is a multi-stage probability sample from randomly selected emergency departments across the country, designed to be representative of all US emergency department visits. We included in our analysis all patients with the ICD9 emergency department discharge diagnosis of migraine. We tabulated frequency of use of specific medications in 2010 and compared these results with the 1998 data. Using a logistic regression model, into which all of the following variables were entered, we explored the independent association between any opioid use in 2010 and sex, age, race/ethnicity, geographic region, type of hospital, triage pain score and history of emergency department use within the previous 12 months.In 2010, there were 1.2 (95% confidence interval 0.9, 1.4) million migraine visits to US emergency departments. Including opioid-containing oral analgesic combinations, opioids were administered in 59% of visits (95% confidence interval 51, 67). The most commonly used parenteral agent, hydromorphone, was used in 25% (95% confidence interval 19, 33) of visits in 2010 versus less than 1% (95% confidence interval 0, 3) in 1998. Conversely, use of meperidine had decreased markedly over the same timeframe. In 2010, it was used in just 7% (95% confidence interval 4, 12) of visits compared to 37% (95% confidence interval 29, 45) in 1998. Metoclopramide, the most commonly used anti-dopaminergic, was administered in 17% (95% confidence interval 12, 23) of visits in 2010 and 3% (95% confidence interval 1, 6) of visits in 1998. Use of any triptan was relatively uncommon in 2010 (7% (95% confidence interval 4, 11) of visits) and in 1998 (10% (95% confidence interval 6, 15) of visits). Of the predictor variables listed above, only emergency department use within the previous 12 months was associated with opioid administration (adjusted odds ratio: 2.87 (95% confidence interval 1.03, 7.97)).In spite of recommendations to the contrary, opioids are still used in more than half of all emergency department visits for migraine. Though use of meperidine has decreased markedly between 1998 and 2010, it has largely been replaced by hydromorphone. Opioid use in migraine visits is independently associated with prior visits to the same emergency department in the previous 12 months.Â© International Headache Society 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.
Co-benefits of Global Greenhouse Gas Mitigation for Future Air Quality and Human Health. - Nature climate change
Actions to reduce greenhouse gas (GHG) emissions often reduce co-emitted air pollutants, bringing co-benefits for air quality and human health. Past studies(1-6) typically evaluated near-term and local co-benefits, neglecting the long-range transport of air pollutants(7-9), long-term demographic changes, and the influence of climate change on air quality(10-12). Here we simulate the co-benefits of global GHG reductions on air quality and human health using a global atmospheric model and consistent future scenarios, via two mechanisms: a) reducing co-emitted air pollutants, and b) slowing climate change and its effect on air quality. We use new relationships between chronic mortality and exposure to fine particulate matter(13) and ozone(14), global modeling methods(15), and new future scenarios(16). Relative to a reference scenario, global GHG mitigation avoids 0.5Â±0.2, 1.3Â±0.5, and 2.2Â±0.8 million premature deaths in 2030, 2050, and 2100. Global average marginal co-benefits of avoided mortality are $50-380 (ton CO2)(-1), which exceed previous estimates, exceed marginal abatement costs in 2030 and 2050, and are within the low range of costs in 2100. East Asian co-benefits are 10-70 times the marginal cost in 2030. Air quality and health co-benefits, especially as they are mainly local and near-term, provide strong additional motivation for transitioning to a low-carbon future.
Chiropractic management of a patient with persistent headache. - Journal of chiropractic medicine
The purpose of this case report is to describe chiropractic care of a patient with persistent headache treated using chiropractic manipulative therapy and adjunct treatments.A 54-year-old multiparous woman had chronic debilitating headaches for 11 months. Previous care from a variety of specialties had brought no appreciable relief.The patient was managed with chiropractic manipulative therapy, injections, and electromagnetic therapy. Five treatments over 6 weeks brought resolution of the headaches.This patient with persistent headache responded favorably to a course of chiropractic and adjunctive care.
The effect of grid resolution on estimates of the burden of ozone and fine particulate matter on premature mortality in the United States. - Air quality, atmosphere, & health
Assessments of human health impacts associated with outdoor air pollution often use air quality models to represent exposure, but involve uncertainties due to coarse model resolution. Here we quantify how estimates of mortality in the United States attributable to ozone (O3) and fine particulate matter (PM2.5) at coarse resolution differ from those at finer resolution. Using the finest modeled concentrations (12 km), we estimate that 66,000 (95% CI, 39,300 - 84,500) all-cause and 21,400 (5,600 - 34,200) respiratory deaths per year are attributable to PM2.5 and O3 concentrations above low-concentration thresholds, respectively. Using model results at 36 km resolution gives mortality burdens that are 11% higher for PM2.5 and 12% higher for O3 than the 12 km estimates, suggesting a modest positive bias. We also scale modeled concentrations at 12 km to coarser resolutions by simple averaging, and repeat the mortality assessment at multiple resolutions from 24 to 408 km, including the resolutions of global models; in doing so, we account for the effect of resolution on population exposure. Coarse grid resolutions produce mortality estimates that are substantially biased low for PM2.5 (30-40% lower than the 12 km estimate at >250 km resolution), but less than 6% higher for O3 at any resolution. Mortality estimates for primary PM2.5 species show greater bias at coarse resolution than secondary species. These results suggest that coarse resolution global models (>100 km) are likely biased low for PM2.5 health effects. For ozone, biases due to coarse resolution may be much smaller, and the effect on modeled chemistry likely dominates.
Surgery for constipation in patients with prior spinal cord injury: the Department of Veterans Affairs experience. - The journal of spinal cord medicine
Patients with spinal cord injury (SCI) typically have difficulty with constipation. Some undergo surgery for bowel management. We predicted that SCI patients would have higher mortality and/or morbidity rates following such surgery than neurally intact patients receiving the same procedures. We sought to evaluate this using a large population-based data set.Patients receiving care at Department of Veterans Affairs Medical Centers (DVAMCs) with computer codes for SCI and constipation who later underwent colectomy, colostomy, or ileostomy during fiscal years 1993-2002 were identified. Charts were requested from the VAMCs where the surgery had been performed and a retrospective chart review of these charts was done. We collected data on patient demographics, six specific pre-operative co-morbidities, surgical complications, and post-operative mortality. Comparisons were made to current literature evaluating a population receiving total abdominal colectomy and ileorectal anastomosis for constipation but not selected for SCI.Of 299 patients identified by computer search, 43 (14%) had codes for SCI and 10 of 43 (24%) met our inclusion criteria. All were symptomatic and had received appropriate medical management. Co-morbid conditions were present in 9 of 10 patients (90%). There were no deaths within 30 days. The complication rate was zero. The mean post-operative length of stay was 17 days.Patients with SCI comprise about 14% of the population who receive surgery for severe constipation in the Department of Veterans Affairs system. The mortality and morbidity rates in these patients are similar to those reported in other constipated patients who have surgery for intractable constipation. Our data suggest that stoma formation Â± bowel resection in patients with SCI is a safe and effective treatment for chronic constipation.
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