Citations

AbstractObjectiveTo determine whether disparities in access to invasive cardiac procedures still exist for Medicaid patients, given how old earlier studies are and given changes in the interim in appropriateness guidelines.Patients and MethodsA total of 5,022 Medicaid and private insurance patients in New York from January 1, 2008 through December 31, 2009 under age 65 with ST‐elevation myocardial infarction (STEMI) were compared with regard to their access to percutaneous coronary interventions (PCI) before and after controlling for numerous patient characteristics and other important factors.ResultsMedicaid patients were significantly less likely to be admitted initially to a hospital certified to perform PCI (90.4% vs. 94.3%, P < 0.001). Also, Medicaid patients were found to be significantly less likely to undergo PCI than other patients (adjusted odds ratio [AOR] = 0.81, 95% CI 0.66, 0.98, P = 0.03). When the probability of each hospital performing PCI for STEMI patients was controlled for, Medicaid patients were still less likely to undergo PCI after controlling for other risk factors (AOR = 0.80, 95% CI 0.65, 0.99, P = 0.04).ConclusionsMedicaid STEMI patients are significantly less likely to undergo PCI within the same day of admission as private pay patients even after adjusting for patient characteristics related to receiving PCI, and the strength of this relationship is not diminished when controlling for whether the admitting hospital has approval to perform PCI or controlling for the tendency of the admitting hospital to treat STEMI with PCI. (J Interven Cardiol 2013;26:470‐481)

Abstract Background: Given the high technical reproducibility and orders of magnitude greater resolution than microarrays, next-generation sequencing of mRNA (RNA-Seq) is quickly becoming the de facto standard for measuring levels of gene expression in biological experiments. Two important questions must be taken into consideration when designing a particular experiment, namely, 1) how deep does one need to sequence? and, 2) how many biological replicates are necessary to observe a significant change in expression? Results: Based on the gene expression distributions from 127 RNA-Seq experiments, we find evidence that 91% ± 4% of all annotated genes are sequenced at a frequency of 0.1 times per million bases mapped, regardless of sample source. Based on this observation, and combining this information with other parameters such as biological variation and technical variation that we empirically estimate from our large datasets, we developed a model to estimate the statistical power needed to identify differentially expressed genes from RNA-Seq experiments. Conclusions: Our results provide a needed reference for ensuring RNA-Seq gene expression studies are conducted with the optimally sample size, power, and sequencing depth. We also make available both R code and an Excel worksheet for investigators to calculate for their own experiments.

Disease overviewChronic myelomonocytic leukemia (CMML) is a clonal hematopoietic stem cell disorder that is classified as a myelodysplastic/myeloproliferative neoplasm by the 2008 World Health Organization classification of hematopoietic tumors. It is characterized by absolute monocytosis (>1 × 109/L) in the peripheral blood that persists for at least 3 months.DiagnosisThe diagnosis of CMML rests on a combination of morphologic, histopathologic and chromosomal abnormalities in the bone marrow. It is important to exclude other myeloproliferative neoplasms and infectious/autoimmune conditions that can cause monocytosis.Risk stratificationSeveral CMML‐specific prognostic models incorporating novel mutations have been recently reported. The Mayo prognostic model classified CMML patients into three risk groups based on: increased absolute monocyte count, presence of circulating blasts, hemoglobin <10 gm/dL and platelets <100 × 109/L. The median survival was 32 months, 18.5 months and 10 months in the low, intermediate, and high‐risk groups, respectively. The Groupe Francophone des (GFM) score segregated CMML patients into three risk groups based on: age >65 years, WBC >15 × 109/L, anemia, platelets <100 × 109/L, and ASXL1 mutation status. After a median follow‐up of 2.5 years, survival ranged from not reached in the low‐risk group to 14.4 months in the high‐risk group.Risk‐adapted therapyThe Food and Drug Administration has approved azacitidine and decitabine for the treatment of patients with CMML. An allogeneic stem cell transplant can potentially offer a curative option to a subset of CMML patients. It is hoped that with the discovery of several novel mutations, targeted therapies will become available in the near future. Am. J. Heamtol. 88:968–974, 2013. © 2013 Wiley Periodicals, Inc.

ABSTRACTIntroduction: The utility of F‐waves in assessing radiculopathies is debated. The aim of this study is to determine the frequency of abnormal minimum tibial F‐wave latencies compared to an F‐estimate and an absolute reference value in patients with electromyography (EMG) confirmed S1 radiculopathies. Methods: A retrospective review of F‐waves in patients with an EMG‐confirmed isolated S1 radiculopathy was performed. The minimum and mean latencies of 8 tibial F‐waves were compared with the calculated F‐estimate and to an absolute reference value, and the frequencies of abnormal responses were determined. Results: Of the 50 patients with an S1 radiculopathy, 4% had prolongation of the minimum reproducible F‐wave latency, and 8% had prolongation of the mean latency relative to the calculated F‐estimate. Conclusions: The minimum and mean F‐wave latencies are infrequently abnormal when compared with an estimated F‐wave latency in S1 radiculopathies and are insensitive in the assessment of S1 nerve root injury. Muscle Nerve 49: 809–813, 2014

Abstract Hypoxia-inducible factor 1 (HIF-1) is a master transcription factor that controls cellular homeostasis. Although its activation benefits normal tissue, HIF-1 activation in tumors is a major risk factor for angiogenesis, therapeutic resistance, and poor prognosis. HIF-1 activity is usually suppressed under normoxic conditions because of rapid oxygen-dependent degradation of HIF-1α. Here, we show that, under normoxic conditions, HIF-1α is upregulated in tumor cells in response to doxorubicin, a chemotherapeutic agent used to treat many cancers. In addition, doxorubicin enhanced VEGF secretion by normoxic tumor cells and stimulated tumor angiogenesis. Doxorubicin-induced accumulation of HIF-1α in normoxic cells was caused by increased expression and activation of STAT1, the activation of which stimulated expression of iNOS and its synthesis of nitric oxide (NO) in tumor cells. Mechanistic investigations established that blocking NO synthesis or STAT1 activation was sufficient to attenuate the HIF-1α accumulation induced by doxorubicin in normoxic cancer cells. To our knowledge, this is the first report that a chemotherapeutic drug can induce HIF-1α accumulation in normoxic cells, an efficacy-limiting activity. Our results argue that HIF-1α-targeting strategies may enhance doxorubicin efficacy. More generally, they suggest a broader perspective on the design of combination chemotherapy approaches with immediate clinical impact. Cancer Res; 73(20); 6230–42. ©2013 AACR.

Abstract Motivation: Batch effects are due to probe-specific systematic variation between groups of samples (batches) resulting from experimental features that are not of biological interest. Principal component analysis (PCA) is commonly used as a visual tool to determine whether batch effects exist after applying a global normalization method. However, PCA yields linear combinations of the variables that contribute maximum variance and thus will not necessarily detect batch effects if they are not the largest source of variability in the data. Results: We present an extension of PCA to quantify the existence of batch effects, called guided PCA (gPCA). We describe a test statistic that uses gPCA to test whether a batch effect exists. We apply our proposed test statistic derived using gPCA to simulated data and to two copy number variation case studies: the first study consisted of 614 samples from a breast cancer family study using Illumina Human 660 bead-chip arrays, whereas the second case study consisted of 703 samples from a family blood pressure study that used Affymetrix SNP Array 6.0. We demonstrate that our statistic has good statistical properties and is able to identify significant batch effects in two copy number variation case studies. Conclusion: We developed a new statistic that uses gPCA to identify whether batch effects exist in high-throughput genomic data. Although our examples pertain to copy number data, gPCA is general and can be used on other data types as well. Availability and implementation: The gPCA R package (Available via CRAN) provides functionality and data to perform the methods in this article. Contact: reesese@vcu.edu or eckel@mayo.edu Supplementary information: Supplementary data are available at Bioinformatics online.