Publications by authors named "Kevin J Thompson"

28 Publications

  • Page 1 of 1

Characteristics and spatially-defined immune (micro)landscapes of early-stage PD-L1-positive triple-negative breast cancer.

Clin Cancer Res 2021 Jun 9. Epub 2021 Jun 9.

Division of Medical Oncology, Mayo Clinic.

Purpose: PD-(L)1-targeted therapies have shown modest survival benefit in triple-negative breast cancer (TNBC). PD-L1+ microenvironments in TNBC are not well-characterized and may inform combinatorial immune therapies. Herein, we characterized clinicopathologic features, RNA-based immune signatures and spatially-defined protein-based immune microenvironments (TIME) in early-stage PD-L1+ and PD-L1- TNBC.

Experimental Design: From a large cohort of chemotherapy-naïve TNBC, clinicopathologic features, deconvoluted RNA immune signatures, and intraepithelial and stromal TIME (Nanostring GeoMX) were identified in subsets of PD-L1+ and PD-L1- TNBC, as defined by FDA-approved PD-L1 companion assays.

Results: 228/499 (46%) TNBC were PD-L1+ (SP142: {greater than or equal to}1% immune cells-positive). Using PD-L1 22C3, 46% had combined positive score (CPS) {greater than or equal to} 1 and 16% had CPS {greater than or equal to}10. PD-L1+ TNBC were higher grade with higher TILs (p <0.05). PD-L1 was not associated with improved survival following adjustment for TILs and other variables. RNA profiles of PD-L1+ TNBC had increased dendritic cell, macrophages and T/B cell subset features; and decreased myeloid-derived suppressor cells. PD-L1+ stromal and intraepithelial TIME were highly enriched in IDO-1, HLA-DR, CD40 and CD163 compared to PD-L1- TIME, with spatially-specific alterations in CTLA-4, STING, and fibronectin. Macrophage and antigen presentation-related proteins correlated most strongly with PD-L1 protein.

Conclusions: In this early-stage TNBC cohort, nearly 50% were PD-L1+ (SP142 companion assay) while 16% were PD-L1+ with the 22C3 companion assay. PD-L1+ TNBC had specific myeloid-derived and lymphoid features. Spatially-defined PD-L1+TIME were enriched in several clinically-actionable immune proteins. These data may inform future studies on combinatorial immunotherapies for patients with PD-L1+ TNBC.
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http://dx.doi.org/10.1158/1078-0432.CCR-21-0343DOI Listing
June 2021

Frequency of MicroRNA Response Elements Identifies Pathologically Relevant Signaling Pathways in Triple-Negative Breast Cancer.

iScience 2020 Jun 6;23(6):101249. Epub 2020 Jun 6.

Department of Surgery, University of Minnesota, 420 Delaware St SE, Minneapolis, MN 55455, USA; Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA; Center for Immunology, University of Minnesota, Minneapolis, MN 55455, USA. Electronic address:

Complex interactions between mRNAs and microRNAs influence cellular functions. The mRNA-microRNA interactions also determine the post-transcriptional availability of mRNAs and unbound microRNAs. MicroRNAs binds to one or more microRNA response elements (MREs) located on the 3'UTR of mRNAs. In this study, we leveraged MREs and their frequencies in cancer and matched normal tissues to obtain insights into disease-specific interactions between mRNAs and microRNAs. We developed a bioinformatics method "ReMIx" that utilizes RNA sequencing (RNA-Seq) data to quantify MRE frequencies across the transcriptome. We applied ReMIx to triple-negative (TN) breast cancer tumor-normal adjacent pairs and identified MREs specific to TN tumors. ReMIx identified candidate mRNAs and microRNAs in the MAPK signaling cascade. Further analysis of MAPK gene regulatory networks revealed microRNA partners that influence and modulate MAPK signaling. In conclusion, we demonstrate a novel method of using MREs in the identification of functionally relevant mRNA-microRNA interactions in TN breast cancer.
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http://dx.doi.org/10.1016/j.isci.2020.101249DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7322352PMC
June 2020

How to Stop the Bleed: First Care Provider Model for Developing Public Trauma Response Beyond Basic Hemorrhage Control.

West J Emerg Med 2020 Feb 25;21(2):365-373. Epub 2020 Feb 25.

Washington University in St. Louis, Department of Surgery, St. Louis, Missouri.

Introduction: Since 2013, the First Care Provider (FCP) model has successfully educated the non-medical population on how to recognize life-threatening injuries and perform interventions recommended by the Committee for Tactical Emergency Casualty Care (C-TECC) and the Hartford Consensus in the disaster setting. Recent programs, such as the federal "Stop The Bleed" campaign, have placed the emphasis of public training on hemorrhage control. However, recent attacks demonstrate that access to wounded, recognition of injury, and rapid evacuation are equally as important as hemorrhage control in minimizing mortality. To date, no training programs have produced a validated study with regard to training a community population in these necessary principles of disaster response.

Methods: In our study, we created a reproducible community training model for implementation into prehospital systems. Two matched demographic groups were chosen and divided into "trained" and "untrained" groups. The trained group was taught the FCP curriculum, which the Department of Homeland Security recognizes as a Stop the Bleed program, while the untrained group received no instruction. Both groups then participated in a simulated mass casualty event, which required evaluation of multiple victims with varying degree of injury, particularly a patient with an arterial bleed and a patient with an airway obstruction.

Results: The objective measures in comparing the two groups were the time elapse until their first action was taken (T1A) and time to their solution of the simulation (TtS). We compared their times using one-sided t-test to demonstrate their responses were not due to chance alone. At the arterial bleed simulation, the T1A for the trained and untrained groups, respectively, were 34.75 seconds and 111 seconds (p-value = .1064), while the TtS were 3 minutes and 33 seconds in the trained group and eight minutes in the untrained groups (physiologic cutoff) (p-value = .0014). At the airway obstruction simulation, the T1A for the trained and untrained groups, respectively, were 20.5 seconds and 43 seconds (p-value = .1064), while the TtS were 32.6 seconds in the trained group and 7 minutes and 3 seconds in the untrained group (p-value = .0087). Simulation values for recently graduated nursing students and a local fire department engine company (emergency medical services [EMS]) were also given for reference. The trained group's results mirrored times of EMS.

Conclusion: This study demonstrates an effective training model to civilian trauma response, while adhering to established recommendations. We offer our model as a potential solution for accomplishing the Stop The Bleed mission while advancing the potential of public disaster response.
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http://dx.doi.org/10.5811/westjem.2019.11.44887DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7081854PMC
February 2020

Small intestinal microbial dysbiosis underlies symptoms associated with functional gastrointestinal disorders.

Nat Commun 2019 05 1;10(1):2012. Epub 2019 May 1.

Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, 55902, USA.

Small intestinal bacterial overgrowth (SIBO) has been implicated in symptoms associated with functional gastrointestinal disorders (FGIDs), though mechanisms remain poorly defined and treatment involves non-specific antibiotics. Here we show that SIBO based on duodenal aspirate culture reflects an overgrowth of anaerobes, does not correspond with patient symptoms, and may be a result of dietary preferences. Small intestinal microbial composition, on the other hand, is significantly altered in symptomatic patients and does not correspond with aspirate culture results. In a pilot interventional study we found that switching from a high fiber diet to a low fiber, high simple sugar diet triggered FGID-related symptoms and decreased small intestinal microbial diversity while increasing small intestinal permeability. Our findings demonstrate that characterizing small intestinal microbiomes in patients with gastrointestinal symptoms may allow a more targeted antibacterial or a diet-based approach to treatment.
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http://dx.doi.org/10.1038/s41467-019-09964-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6494866PMC
May 2019

PANOPLY: Omics-Guided Drug Prioritization Method Tailored to an Individual Patient.

JCO Clin Cancer Inform 2018 12;2:1-11

All authors: Mayo Clinic, Rochester, MN.

Purpose: The majority of patients with cancer receive treatments that are minimally informed by omics data. We propose a precision medicine computational framework, PANOPLY (Precision Cancer Genomic Report: Single Sample Inventory), to identify and prioritize drug targets and cancer therapy regimens.

Materials And Methods: The PANOPLY approach integrates clinical data with germline and somatic features obtained from multiomics platforms and applies machine learning and network analysis approaches in the context of the individual patient and matched controls. The PANOPLY workflow uses the following four steps: selection of matched controls to the patient of interest; identification of patient-specific genomic events; identification of suitable drugs using the driver-gene network and random forest analyses; and provision of an integrated multiomics case report of the patient with prioritization of anticancer drugs.

Results: The PANOPLY workflow can be executed on a stand-alone virtual machine and is also available for download as an R package. We applied the method to an institutional breast cancer neoadjuvant chemotherapy study that collected clinical and genomic data as well as patient-derived xenografts to investigate the prioritization offered by PANOPLY. In a chemotherapy-resistant patient-derived xenograft model, we found that that the prioritized drug, olaparib, was more effective than placebo in treating the tumor ( P < .05). We also applied PANOPLY to in-house and publicly accessible multiomics tumor data sets with therapeutic response or survival data available.

Conclusion: PANOPLY shows promise as a means to prioritize drugs on the basis of clinical and multiomics data for an individual patient with cancer. Additional studies are needed to confirm this approach.
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http://dx.doi.org/10.1200/CCI.18.00012DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7010444PMC
December 2018

Discovery of a Glucocorticoid Receptor (GR) Activity Signature Using Selective GR Antagonism in ER-Negative Breast Cancer.

Clin Cancer Res 2018 07 10;24(14):3433-3446. Epub 2018 Apr 10.

Department of Medicine, The University of Chicago, Chicago, Illinois.

Although high glucocorticoid receptor (GR) expression in early-stage estrogen receptor (ER)-negative breast cancer is associated with shortened relapse-free survival (RFS), how associated GR transcriptional activity contributes to aggressive breast cancer behavior is not well understood. Using potent GR antagonists and primary tumor gene expression data, we sought to identify a tumor-relevant gene signature based on GR activity that would be more predictive than GR expression alone. Global gene expression and GR ChIP-sequencing were performed to identify GR-regulated genes inhibited by two chemically distinct GR antagonists, mifepristone and CORT108297. Differentially expressed genes from MDA-MB-231 cells were cross-evaluated with significantly expressed genes in GR-high versus GR-low ER-negative primary breast cancers. The resulting subset of GR-targeted genes was analyzed in two independent ER-negative breast cancer cohorts to derive and then validate the GR activity signature (GRsig). Gene expression pathway analysis of glucocorticoid-regulated genes (inhibited by GR antagonism) revealed cell survival and invasion functions. GR ChIP-seq analysis demonstrated that GR antagonists decreased GR chromatin association for a subset of genes. A GRsig that comprised = 74 GR activation-associated genes (also reversed by GR antagonists) was derived from an adjuvant chemotherapy-treated Discovery cohort and found to predict probability of relapse in a separate Validation cohort (HR = 1.9; = 0.012). The GRsig discovered herein identifies high-risk ER-negative/GR-positive breast cancers most likely to relapse despite administration of adjuvant chemotherapy. Because GR antagonism can reverse expression of these genes, we propose that addition of a GR antagonist to chemotherapy may improve outcome for these high-risk patients. .
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http://dx.doi.org/10.1158/1078-0432.CCR-17-2793DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6530562PMC
July 2018

Differential Effects of Alzheimer's Disease Aβ40 and 42 on Endocytosis and Intraneuronal Trafficking.

Neuroscience 2018 03 11;373:159-168. Epub 2018 Jan 11.

Department of Pharmaceutics and Brain Barriers Research Center, College of Pharmacy, University of Minnesota, Minneapolis, MN, United States. Electronic address:

Anomalous neuronal accumulation of Aβ peptides was shown to affect synaptic transmission and contribute to neurodegeneration in Alzheimer's disease (AD) brain. Neuronal cells internalize amyloid beta (Aβ) peptides from the brain extracellular space even under normal physiological conditions, and these endocytotic pathways go awry during AD progression. We hypothesized that exposure to toxic Aβ species accumulating in AD brain contributes to perturbations in neuronal endocytosis. We have shown substantial down-regulation of KEGG endocytotic pathway genes in AD patient brain regions that accumulate Aβ compared to those in non-demented individuals. While both Aβ40 and Aβ42 perturbed endocytosis and intracellular trafficking in neuronal cells, Aβ40 had a greater effect than Aβ42. Moreover, Aβ40 decreased the neuronal uptake and lysosomal accumulation of Aβ42, which tends to oligomerize at low lysosomal pH. Hence, Aβ40 may reduce the prevalence of stable Aβ42 oligomers that are closely associated with neurodegeneration and are intercellularly propagated across the vulnerable brain regions to eventually nucleate as amyloid plaques. In conclusion, elevated brain Aβ levels and Aβ42:40 ratio apparent in the early stages of AD could perturb intraneuronal trafficking, augment the anomalous accumulation of amyloid peptides in AD brain, and drive AD pathogenesis.
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http://dx.doi.org/10.1016/j.neuroscience.2018.01.003DOI Listing
March 2018

Establishing and characterizing patient-derived xenografts using pre-chemotherapy percutaneous biopsy and post-chemotherapy surgical samples from a prospective neoadjuvant breast cancer study.

Breast Cancer Res 2017 Dec 6;19(1):130. Epub 2017 Dec 6.

Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.

Background: Patient-derived xenografts (PDXs) are increasingly used in cancer research as a tool to inform cancer biology and drug response. Most available breast cancer PDXs have been generated in the metastatic setting. However, in the setting of operable breast cancer, PDX models both sensitive and resistant to chemotherapy are needed for drug development and prospective data are lacking regarding the clinical and molecular characteristics associated with PDX take rate in this setting.

Methods: The Breast Cancer Genome Guided Therapy Study (BEAUTY) is a prospective neoadjuvant chemotherapy (NAC) trial of stage I-III breast cancer patients treated with neoadjuvant weekly taxane+/-trastuzumab followed by anthracycline-based chemotherapy. Using percutaneous tumor biopsies (PTB), we established and characterized PDXs from both primary (untreated) and residual (treated) tumors. Tumor take rate was defined as percent of patients with the development of at least one stably transplantable (passed at least for four generations) xenograft that was pathologically confirmed as breast cancer.

Results: Baseline PTB samples from 113 women were implanted with an overall take rate of 27.4% (31/113). By clinical subtype, the take rate was 51.3% (20/39) in triple negative (TN) breast cancer, 26.5% (9/34) in HER2+, 5.0% (2/40) in luminal B and 0% (0/3) in luminal A. The take rate for those with pCR did not differ from those with residual disease in TN (p = 0.999) and HER2+ (p = 0.2401) tumors. The xenografts from 28 of these 31 patients were such that at least one of the xenografts generated had the same molecular subtype as the patient. Among the 35 patients with residual tumor after NAC adequate for implantation, the take rate was 17.1%. PDX response to paclitaxel mirrored the patients' clinical response in all eight PDX tested.

Conclusions: The generation of PDX models both sensitive and resistant to standard NAC is feasible and these models exhibit similar biological and drug response characteristics as the patients' primary tumors. Taken together, these models may be useful for biomarker discovery and future drug development.
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http://dx.doi.org/10.1186/s13058-017-0920-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5719923PMC
December 2017

A comprehensive analysis of breast cancer microbiota and host gene expression.

PLoS One 2017 30;12(11):e0188873. Epub 2017 Nov 30.

Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, United States of America.

The inflammatory tumoral-immune response alters the physiology of the tumor microenvironment, which may attenuate genomic instability. In addition to inducing inflammatory immune responses, several pathogenic bacteria produce genotoxins. However the extent of microbial contribution to the tumor microenvironment biology remains unknown. We utilized The Cancer Genome Atlas, (TCGA) breast cancer data to perform a novel experiment utilizing unmapped and mapped RNA sequencing read evidence to minimize laboratory costs and effort. Our objective was to characterize the microbiota and associate the microbiota with the tumor expression profiles, for 668 breast tumor tissues and 72 non-cancerous adjacent tissues. The prominent presence of Proteobacteria was increased in the tumor tissues and conversely Actinobacteria abundance increase in non-cancerous adjacent tissues. Further, geneset enrichment suggests Listeria spp to be associated with the expression profiles of genes involved with epithelial to mesenchymal transitions. Moreover, evidence suggests H. influenza may reside in the surrounding stromal material and was significantly associated with the proliferative pathways: G2M checkpoint, E2F transcription factors, and mitotic spindle assembly. In summary, further unraveling this complicated interplay should enable us to better diagnose and treat breast cancer patients.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0188873PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5708741PMC
December 2017

Tumor Sequencing and Patient-Derived Xenografts in the Neoadjuvant Treatment of Breast Cancer.

J Natl Cancer Inst 2017 07;109(7)

Department of Surgery, Mayo Clinic, Rochester, MN, USA.

Background: Breast cancer patients with residual disease after neoadjuvant chemotherapy (NAC) have increased recurrence risk. Molecular characterization, knowledge of NAC response, and simultaneous generation of patient-derived xenografts (PDXs) may accelerate drug development. However, the feasibility of this approach is unknown.

Methods: We conducted a prospective study of 140 breast cancer patients treated with NAC and performed tumor and germline sequencing and generated patient-derived xenografts (PDXs) using core needle biopsies. Chemotherapy response was assessed at surgery.

Results: Recurrent "targetable" alterations were not enriched in patients without pathologic complete response (pCR); however, upregulation of steroid receptor signaling and lower pCR rates (16.7%, 1/6) were observed in triple-negative breast cancer (TNBC) patients with luminal androgen receptor (LAR) vs basal subtypes (60.0%, 21/35). Within TNBC, TP53 mutation frequency (75.6%, 31/41) did not differ comparing basal (74.3%, 26/35) and LAR (83.3%, 5/6); however, TP53 stop-gain mutations were more common in basal (22.9%, 8/35) vs LAR (0.0%, 0/6), which was confirmed in The Cancer Genome Atlas and British Columbia data sets. In luminal B tumors, Ki-67 responses were observed in tumors that harbored mutations conferring endocrine resistance ( p53, AKT, and IKBKE ). PDX take rate (27.4%, 31/113) varied according to tumor subtype, and in a patient with progression on NAC, sequencing data informed drug selection (olaparib) with in vivo antitumor activity observed in the primary and resistant (postchemotherapy) PDXs.

Conclusions: In this study, we demonstrate the feasibility of tumor sequencing and PDX generation in the NAC setting. "Targetable" alterations were not enriched in chemotherapy-resistant tumors; however, prioritization of drug testing based on sequence data may accelerate drug development.
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http://dx.doi.org/10.1093/jnci/djw306DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5408989PMC
July 2017

Circular RNAs and their associations with breast cancer subtypes.

Oncotarget 2016 Dec;7(49):80967-80979

Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA.

Circular RNAs (circRNAs) are highly stable forms of non-coding RNAs with diverse biological functions. They are implicated in modulation of gene expression thus affecting various cellular and disease processes. Based on existing bioinformatics approaches, we developed a comprehensive workflow called Circ-Seq to identify and report expressed circRNAs. Circ-Seq also provides informative genomic annotation along circRNA fused junctions thus allowing prioritization of circRNA candidates. We applied Circ-Seq first to RNA-sequence data from breast cancer cell lines and validated one of the large circRNAs identified. Circ-Seq was then applied to a larger cohort of breast cancer samples (n = 885) provided by The Cancer Genome Atlas (TCGA), including tumors and normal-adjacent tissue samples. Notably, circRNA results reveal that normal-adjacent tissues in estrogen receptor positive (ER+) subtype have relatively higher numbers of circRNAs than tumor samples in TCGA. Similar phenomenon of high circRNA numbers were observed in normal breast-mammary tissues from the Genotype-Tissue Expression (GTEx) project. Finally, we observed that number of circRNAs in normal-adjacent samples of ER+ subtype is inversely correlated to the risk-of-relapse proliferation (ROR-P) score for proliferating genes, suggesting that circRNA frequency may be a marker for cell proliferation in breast cancer. The Circ-Seq workflow will function for both single and multi-threaded compute environments. We believe that Circ-Seq will be a valuable tool to identify circRNAs useful in the diagnosis and treatment of other cancers and complex diseases.
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http://dx.doi.org/10.18632/oncotarget.13134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5348369PMC
December 2016

BBBomics-Human Blood Brain Barrier Transcriptomics Hub.

Front Neurosci 2016 1;10:71. Epub 2016 Mar 1.

Department of Pharmaceutics and Brain Barriers Research Center, University of Minnesota Minneapolis, MN, USA.

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http://dx.doi.org/10.3389/fnins.2016.00071DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4771746PMC
March 2016

Exome sequencing reveals frequent deleterious germline variants in cancer susceptibility genes in women with invasive breast cancer undergoing neoadjuvant chemotherapy.

Breast Cancer Res Treat 2015 Sep 22;153(2):435-43. Epub 2015 Aug 22.

Center for Individualized Medicine, Mayo Clinic, 200 First Street SW, Rochester, MN, 55905, USA.

When sequencing blood and tumor samples to identify targetable somatic variants for cancer therapy, clinically relevant germline variants may be uncovered. We evaluated the prevalence of deleterious germline variants in cancer susceptibility genes in women with breast cancer referred for neoadjuvant chemotherapy and returned clinically actionable results to patients. Exome sequencing was performed on blood samples from women with invasive breast cancer referred for neoadjuvant chemotherapy. Germline variants within 142 hereditary cancer susceptibility genes were filtered and reviewed for pathogenicity. Return of results was offered to patients with deleterious variants in actionable genes if they were not aware of their result through clinical testing. 124 patients were enrolled (median age 51) with the following subtypes: triple negative (n = 43, 34.7%), HER2+ (n = 37, 29.8%), luminal B (n = 31, 25%), and luminal A (n = 13, 10.5%). Twenty-eight deleterious variants were identified in 26/124 (21.0%) patients in the following genes: ATM (n = 3), BLM (n = 1), BRCA1 (n = 4), BRCA2 (n = 8), CHEK2 (n = 2), FANCA (n = 1), FANCI (n = 1), FANCL (n = 1), FANCM (n = 1), FH (n = 1), MLH3 (n = 1), MUTYH (n = 2), PALB2 (n = 1), and WRN (n = 1). 121/124 (97.6%) patients consented to return of research results. Thirteen (10.5%) had actionable variants, including four that were returned to patients and led to changes in medical management. Deleterious variants in cancer susceptibility genes are highly prevalent in patients with invasive breast cancer referred for neoadjuvant chemotherapy undergoing exome sequencing. Detection of these variants impacts medical management.
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http://dx.doi.org/10.1007/s10549-015-3545-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4559569PMC
September 2015

The Effect of Arthroscopic Rotator Interval Closure on Glenohumeral Volume.

Am J Orthop (Belle Mead NJ) 2015 Jun;44(6):E190-4

Division of Orthopaedic Surgery, University of Alabama at Birmingham Medical Center, Birmingham, AL.

The role of rotator interval in shoulder pathology and the effect of its closure are not well understood. In addition, the effect of rotator interval closure on intra-articular glenohumeral volume (GHV) remains unknown. We conducted a study to quantify the GHV reduction obtained with an arthroscopic rotator interval closure and to determine whether medial and lateral interval closures resulted in different degrees of volume reduction. We dissected 8 fresh-frozen cadaveric shoulders (mean age, 64.4 years) to the level of the rotator cuff. Volumetric measurements were taken before and after medial and lateral rotator interval closure incorporating the superior glenohumeral ligament and the upper portion of the subscapularis. Arthroscopic closure of the rotator interval with 2 sutures reduced GHV by a mean of 45%. More volume reduction resulted with use of a single lateral interval closure stitch than with use of a single medial stitch (35% vs 24%; P < .02). Arthroscopic rotator interval closure with 2 plication stitches is a powerful tool in reducing intracapsular volume of the shoulder and may be a useful adjunct in restoring glenohumeral stability. If a single plication stitch is preferred, a lateral stitch (vs a medial stitch) can be used for a significantly larger reduction in shoulder volume.
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June 2015

The eSNV-detect: a computational system to identify expressed single nucleotide variants from transcriptome sequencing data.

Nucleic Acids Res 2014 Dec 28;42(22):e172. Epub 2014 Oct 28.

Division of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, MN 55905, USA

Rapid development of next generation sequencing technology has enabled the identification of genomic alterations from short sequencing reads. There are a number of software pipelines available for calling single nucleotide variants from genomic DNA but, no comprehensive pipelines to identify, annotate and prioritize expressed SNVs (eSNVs) from non-directional paired-end RNA-Seq data. We have developed the eSNV-Detect, a novel computational system, which utilizes data from multiple aligners to call, even at low read depths, and rank variants from RNA-Seq. Multi-platform comparisons with the eSNV-Detect variant candidates were performed. The method was first applied to RNA-Seq from a lymphoblastoid cell-line, achieving 99.7% precision and 91.0% sensitivity in the expressed SNPs for the matching HumanOmni2.5 BeadChip data. Comparison of RNA-Seq eSNV candidates from 25 ER+ breast tumors from The Cancer Genome Atlas (TCGA) project with whole exome coding data showed 90.6-96.8% precision and 91.6-95.7% sensitivity. Contrasting single-cell mRNA-Seq variants with matching traditional multicellular RNA-Seq data for the MD-MB231 breast cancer cell-line delineated variant heterogeneity among the single-cells. Further, Sanger sequencing validation was performed for an ER+ breast tumor with paired normal adjacent tissue validating 29 out of 31 candidate eSNVs. The source code and user manuals of the eSNV-Detect pipeline for Sun Grid Engine and virtual machine are available at http://bioinformaticstools.mayo.edu/research/esnv-detect/.
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http://dx.doi.org/10.1093/nar/gku1005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4267611PMC
December 2014

Gene expression, single nucleotide variant and fusion transcript discovery in archival material from breast tumors.

PLoS One 2013 22;8(11):e81925. Epub 2013 Nov 22.

Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America.

Advantages of RNA-Seq over array based platforms are quantitative gene expression and discovery of expressed single nucleotide variants (eSNVs) and fusion transcripts from a single platform, but the sensitivity for each of these characteristics is unknown. We measured gene expression in a set of manually degraded RNAs, nine pairs of matched fresh-frozen, and FFPE RNA isolated from breast tumor with the hybridization based, NanoString nCounter (226 gene panel) and with whole transcriptome RNA-Seq using RiboZeroGold ScriptSeq V2 library preparation kits. We performed correlation analyses of gene expression between samples and across platforms. We then specifically assessed whole transcriptome expression of lincRNA and discovery of eSNVs and fusion transcripts in the FFPE RNA-Seq data. For gene expression in the manually degraded samples, we observed Pearson correlations of >0.94 and >0.80 with NanoString and ScriptSeq protocols, respectively. Gene expression data for matched fresh-frozen and FFPE samples yielded mean Pearson correlations of 0.874 and 0.783 for NanoString (226 genes) and ScriptSeq whole transcriptome protocols respectively, p<2x10(-16). Specifically for lincRNAs, we observed superb Pearson correlation (0.988) between matched fresh-frozen and FFPE pairs. FFPE samples across NanoString and RNA-Seq platforms gave a mean Pearson correlation of 0.838. In FFPE libraries, we detected 53.4% of high confidence SNVs and 24% of high confidence fusion transcripts. Sensitivity of fusion transcript detection was not overcome by an increase in depth of sequencing up to 3-fold (increase from ~56 to ~159 million reads). Both NanoString and ScriptSeq RNA-Seq technologies yield reliable gene expression data for degraded and FFPE material. The high degree of correlation between NanoString and RNA-Seq platforms suggests discovery based whole transcriptome studies from FFPE material will produce reliable expression data. The RiboZeroGold ScriptSeq protocol performed particularly well for lincRNA expression from FFPE libraries, but detection of eSNV and fusion transcripts was less sensitive.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0081925PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3838386PMC
August 2014

AT-101 downregulates BCL2 and MCL1 and potentiates the cytotoxic effects of lenalidomide and dexamethasone in preclinical models of multiple myeloma and Waldenström macroglobulinaemia.

Br J Haematol 2014 Feb 17;164(3):352-365. Epub 2013 Nov 17.

Department of Hematology and Oncology, Mayo Clinic, Jacksonville, FL, USA.

Multiple myeloma, the second most common haematological malignancy in the U.S., is currently incurable. Disruption of the intrinsic apoptotic pathway by BCL2 and MCL1 upregulation is observed in >80% of myeloma cases and is associated with an aggressive clinical course. Remarkably, there is no approved drug with the ability to target BCL2 or MCL1. Thus, we investigated the anti-tumour effects of a pan-BCL2 inhibitor, AT-101, which has high binding specificity for BCL2 and MCL1 in preclinical models of plasma cell cancers (Multiple myeloma and Waldenström macroglobulinaemia). Gene expression and immunoblot analysis of six plasma cell cancer models showed upregulation of BCL2 family members. AT-101 was able to downregulate BCL2 and MCL1 in all plasma cell cancer models and induced apoptotic cell death in a caspase-dependent manner by altering mitochondrial membrane permeability. This cytotoxic effect and BCL2 downregulation were further potentiated when AT-101 was combined with lenalidomide/dexamethasone (LDA). NanoString nCounter mRNA quantification and Ingenuity Pathways Analysis revealed differential changes in the CCNA2, FRZB, FYN, IRF1, PTPN11 genes in LDA-treated cells. In summary, we describe for the first time the cellular and molecular events associated with the use of AT-101 in combination with lenalidomide/dexamethasone in preclinical models of plasma cell malignancy.
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http://dx.doi.org/10.1111/bjh.12633DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4406280PMC
February 2014

An integrated model of the transcriptome of HER2-positive breast cancer.

PLoS One 2013 1;8(11):e79298. Epub 2013 Nov 1.

Department of Cancer Biology, Mayo Clinic, Jacksonville, Florida, United States of America ; Department of Biomedical Statistics and Informatics, Mayo Clinic, Rochester, Minnesota, United States of America.

Our goal in these analyses was to use genomic features from a test set of primary breast tumors to build an integrated transcriptome landscape model that makes relevant hypothetical predictions about the biological and/or clinical behavior of HER2-positive breast cancer. We interrogated RNA-Seq data from benign breast lesions, ER+, triple negative, and HER2-positive tumors to identify 685 differentially expressed genes, 102 alternatively spliced genes, and 303 genes that expressed single nucleotide sequence variants (eSNVs) that were associated with the HER2-positive tumors in our survey panel. These features were integrated into a transcriptome landscape model that identified 12 highly interconnected genomic modules, each of which represents a cellular processes pathway that appears to define the genomic architecture of the HER2-positive tumors in our test set. The generality of the model was confirmed by the observation that several key pathways were enriched in HER2-positive TCGA breast tumors. The ability of this model to make relevant predictions about the biology of breast cancer cells was established by the observation that integrin signaling was linked to lapatinib sensitivity in vitro and strongly associated with risk of relapse in the NCCTG N9831 adjuvant trastuzumab clinical trial dataset. Additional modules from the HER2 transcriptome model, including ubiquitin-mediated proteolysis, TGF-beta signaling, RHO-family GTPase signaling, and M-phase progression, were linked to response to lapatinib and paclitaxel in vitro and/or risk of relapse in the N9831 dataset. These data indicate that an integrated transcriptome landscape model derived from a test set of HER2-positive breast tumors has potential for predicting outcome and for identifying novel potential therapeutic strategies for this breast cancer subtype.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0079298PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3815156PMC
August 2014

The role of medial comminution and calcar restoration in varus collapse of proximal humeral fractures treated with locking plates.

J Bone Joint Surg Am 2013 Aug;95(16):e113(1-7)

Division of Orthopaedic Surgery, University of Alabama at Birmingham, Birmingham, AL 35205, USA.

Background: Proximal humeral fractures that are treated with locked plate constructs remain susceptible to collapse into a varus position. The objectives of the present study were to examine how medial comminution affects fracture stability and to determine the effect of calcar fixation on osteosynthesis stability.

Methods: Eleven matched pairs of cadaveric humeri were osteotomized to create standard three-part fractures involving the surgical neck and the greater tuberosity. Five matched pairs were randomly assigned to have the medial calcar region remain intact. Six matched pairs had removal of a 10-mm medially based wedge of bone to simulate medial comminution. All fractures were stabilized in a uniform fashion with a proximal humeral locking plate. The constructs were secured, and the superior portion of the humeral head was subjected to compressive loading to induce varus collapse. Load-to-failure and energy-to-failure values along with stiffness and displacement at the time of failure were determined.

Results: Medial comminution decreased the mean load to failure by 48% (523 N) (p = 0.015) and the mean energy to failure by 44% (2009 Nmm) (p = 0.013). The use of calcar screw fixation increased the mean load to failure by 31% (219 N) (p = 0.002) and the mean energy to failure by 44% (1279 Nmm) (p = 0.006).

Conclusions: Medial comminution significantly decreased the stability of proximal humeral fracture fixation constructs. Calcar restoration with screw fixation significantly improved the stability of repaired fractures in cadaveric specimens.

Clinical Relevance: The data suggest that medial comminution is a predictor of poor stability of proximal humeral fractures and that stability may be improved through calcar restoration.
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http://dx.doi.org/10.2106/JBJS.K.00202DOI Listing
August 2013

Re-evaluation of pectoralis major height as an anatomic reference for humeral height in fracture hemiarthroplasty.

J Shoulder Elbow Surg 2013 Nov 22;22(11):1567-72. Epub 2013 Apr 22.

Department of Surgery, Division of Orthopaedics, University of Alabama at Birmingham, Birmingham, AL, USA. Electronic address:

Background: Shoulder replacement may be indicated for complex proximal humeral fractures. The primary reason for disappointing results is the nonanatomic position of the prosthesis because the normal anatomic landmarks are disrupted when fractured. An anatomic reference outside of the zone of injury may facilitate proper positioning of fracture arthroplasty reconstructions. It is unknown whether the measurement from the top of the pectoralis major tendon (PMT) to the top of the humeral head is related to patient height.

Materials And Methods: PMT measurements were performed on 21 pairs of cadaveric shoulders. A second group of PMT measurements was performed on 107 patients receiving a shoulder magnetic resonance imaging scan. A third PMT comparison group was included using historical measurements from 20 pairs of cadaveric shoulders. All heights, sexes, and ages were known. Statistical analysis used mixed-effects linear regression models.

Results: A consistent association between patient height and PMT was found, with a mean distance from the top of the PMT to the top of the humeral head of 58.9 mm in men and 55.2 mm in women. For every 10-mm increase in patient height over 1.7 m, there is a 1.7-mm increase in PMT (P = .01). Age was not associated with PMT distance (P > .5).

Conclusions: A predictable measurement from the upper portion of the PMT to the top of the humeral head exists to guide implant height in fracture hemiarthroplasty and may be approximated by use of patient height and sex.
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http://dx.doi.org/10.1016/j.jse.2013.01.039DOI Listing
November 2013

The LO-BaFL method and ALS microarray expression analysis.

BMC Bioinformatics 2012 Sep 24;13:244. Epub 2012 Sep 24.

Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.

Background: Sporadic Amyotrophic Lateral Sclerosis (sALS) is a devastating, complex disease of unknown etiology. We studied this disease with microarray technology to capture as much biological complexity as possible. The Affymetrix-focused BaFL pipeline takes into account problems with probes that arise from physical and biological properties, so we adapted it to handle the long-oligonucleotide probes on our arrays (hence LO-BaFL). The revised method was tested against a validated array experiment and then used in a meta-analysis of peripheral white blood cells from healthy control samples in two experiments. We predicted differentially expressed (DE) genes in our sALS data, combining the results obtained using the TM4 suite of tools with those from the LO-BaFL method. Those predictions were tested using qRT-PCR assays.

Results: LO-BaFL filtering and DE testing accurately predicted previously validated DE genes in a published experiment on coronary artery disease (CAD). Filtering healthy control data from the sALS and CAD studies with LO-BaFL resulted in highly correlated expression levels across many genes. After bioinformatics analysis, twelve genes from the sALS DE gene list were selected for independent testing using qRT-PCR assays. High-quality RNA from six healthy Control and six sALS samples yielded the predicted differential expression for 7 genes: TARDBP, SKIV2L2, C12orf35, DYNLT1, ACTG1, B2M, and ILKAP. Four of the seven have been previously described in sALS studies, while ACTG1, B2M and ILKAP appear in the context of this disease for the first time. Supplementary material can be accessed at: http://webpages.uncc.edu/~cbaciu/LO-BaFL/supplementary_data.html.

Conclusion: LO-BaFL predicts DE results that are broadly similar to those of other methods. The small healthy control cohort in the sALS study is a reasonable foundation for predicting DE genes. Modifying the BaFL pipeline allowed us to remove noise and systematic errors, improving the power of this study, which had a small sample size. Each bioinformatics approach revealed DE genes not predicted by the other; subsequent PCR assays confirmed seven of twelve candidates, a relatively high success rate.
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http://dx.doi.org/10.1186/1471-2105-13-244DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3526454PMC
September 2012

ArrayInitiative - a tool that simplifies creating custom Affymetrix CDFs.

BMC Bioinformatics 2011 May 6;12:136. Epub 2011 May 6.

Department of Bioinformatics and Genomics, University of North Carolina - Charlotte, Charlotte, NC 28223-0001, USA.

Background: Probes on a microarray represent a frozen view of a genome and are quickly outdated when new sequencing studies extend our knowledge, resulting in significant measurement error when analyzing any microarray experiment. There are several bioinformatics approaches to improve probe assignments, but without in-house programming expertise, standardizing these custom array specifications as a usable file (e.g. as Affymetrix CDFs) is difficult, owing mostly to the complexity of the specification file format. However, without correctly standardized files there is a significant barrier for testing competing analysis approaches since this file is one of the required inputs for many commonly used algorithms. The need to test combinations of probe assignments and analysis algorithms led us to develop ArrayInitiative, a tool for creating and managing custom array specifications.

Results: ArrayInitiative is a standalone, cross-platform, rich client desktop application for creating correctly formatted, custom versions of manufacturer-provided (default) array specifications, requiring only minimal knowledge of the array specification rules and file formats. Users can import default array specifications, import probe sequences for a default array specification, design and import a custom array specification, export any array specification to multiple output formats, export the probe sequences for any array specification and browse high-level information about the microarray, such as version and number of probes. The initial release of ArrayInitiative supports the Affymetrix 3' IVT expression arrays we currently analyze, but as an open source application, we hope that others will contribute modules for other platforms.

Conclusions: ArrayInitiative allows researchers to create new array specifications, in a standard format, based upon their own requirements. This makes it easier to test competing design and analysis strategies that depend on probe definitions. Since the custom array specifications are easily exported to the manufacturer's standard format, researchers can analyze these customized microarray experiments using established software tools, such as those available in Bioconductor.
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http://dx.doi.org/10.1186/1471-2105-12-136DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3113937PMC
May 2011

Sequential volume reduction with capsular plications: relationship between cumulative size of plications and volumetric reduction for multidirectional instability of the shoulder.

Am J Sports Med 2011 Mar 2;39(3):526-31. Epub 2011 Feb 2.

Division of Orthopaedics, The University of Alabama at Birmingham, 1313 13th Street South, Birmingham, AL 35205, USA.

Purpose: To quantify the relationship between the amount of shoulder capsule imbricated with a simple stitch and the degree of glenohumeral volume reduction in a multidirectional instability model. Secondary purposes were to identify the number of arthroscopic plication stitches required to reduce the shoulder volume equal to that of an open lateral-based inferior capsular shift and to compare volume reductions between suture anchor and suture-only capsular plication stitches.

Study Design: Controlled laboratory study.

Methods: Twelve fresh-frozen cadaveric shoulders (mean age, 64.4 years) were dissected to the level of the rotator cuff. A viscous liquid was injected into each joint, and measurements were taken before and after six 1-cm arthroscopic capsular plication stitches were performed. The sizes of the capsular plications were measured to quantify the amount of capsule imbricated with each simple stitch. A repeated random-intercept regression model was fitted for each outcome, with significance set at P = .05.

Results: There was a near-linear relationship, with each 1 cm of total plication equaling 10% volume reduction up to 4.0 cm. After this, each additional 1-cm plication stitch resulted in 2% to 6% more reduction (mean, 4%). Five simple plication stitches reduced the volume by 52% in the suture anchor group and 49% in the suture-only group. The suture anchor achieved 3% greater volumetric reduction than the suture-only plication stitches, but this effect was not statistically significant (P = .06). Conclusion/

Clinical Relevance: A 1-cm capsular plication stitch results in a roughly 10% volume reduction of the glenohumeral joint. Five simple capsular plication stitches result in a volume reduction equivalent to an open lateral-based capsular shift.
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http://dx.doi.org/10.1177/0363546510391634DOI Listing
March 2011

A white-box approach to microarray probe response characterization: the BaFL pipeline.

BMC Bioinformatics 2009 Dec 29;10:449. Epub 2009 Dec 29.

Computer Science Dept, University of North Carolina at Charlotte, Charlotte, NC 28223, USA.

Background: Microarrays depend on appropriate probe design to deliver the promise of accurate genome-wide measurement. Probe design, ideally, produces a unique probe-target match with homogeneous duplex stability over the complete set of probes. Much of microarray pre-processing is concerned with adjusting for non-ideal probes that do not report target concentration accurately. Cross-hybridizing probes (non-unique), probe composition and structure, as well as platform effects such as instrument limitations, have been shown to affect the interpretation of signal. Data cleansing pipelines seldom filter specifically for these constraints, relying instead on general statistical tests to remove the most variable probes from the samples in a study. This adjusts probes contributing to ProbeSet (gene) values in a study-specific manner. We refer to the complete set of factors as biologically applied filter levels (BaFL) and have assembled an analysis pipeline for managing them consistently. The pipeline and associated experiments reported here examine the outcome of comprehensively excluding probes affected by known factors on inter-experiment target behavior consistency.

Results: We present here a 'white box' probe filtering and intensity transformation protocol that incorporates currently understood factors affecting probe and target interactions; the method has been tested on data from the Affymetrix human GeneChip HG-U95Av2, using two independent datasets from studies of a complex lung adenocarcinoma phenotype. The protocol incorporates probe-specific effects from SNPs, cross-hybridization and low heteroduplex affinity, as well as effects from scanner sensitivity, sample batches, and includes simple statistical tests for identifying unresolved biological factors leading to sample variability. Subsequent to filtering for these factors, the consistency and reliability of the remaining measurements is shown to be markedly improved.

Conclusions: The data cleansing protocol yields reproducible estimates of a given probe or ProbeSet's (gene's) relative expression that translates across datasets, allowing for credible cross-experiment comparisons. We provide supporting evidence for the validity of removing several large classes of probes, and for our approaches for removing outlying samples. The resulting expression profiles demonstrate consistency across the two independent datasets. Finally, we demonstrate that, given an appropriate sampling pool, the method enhances the t-test's statistical power to discriminate significantly different means over sample classes.
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http://dx.doi.org/10.1186/1471-2105-10-449DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2804686PMC
December 2009

MMPI and headache: a special focus on differential diagnosis, prediction of treatment outcome, and patient-treatment matching.

Pain 1986 Feb;24(2):143-158

UAB Pain Center, Department of Anesthesiology, School of Medicine, and Departments of Psychology and Psychiatry, University of Alabama in Birmingham, Birmingham, ALU.S.A.

The relation between personality characteristics and the psychological functioning of headache patients has long been a topic of interest. Early investigations focused on clinical and anecdotal reports while recent research has moved toward a more objective evaluation of headache groups by using the MMPI. However, the findings from diverse studies have not been integrated, nor has a rationale for the use of these data in the clinical management of headache been formally presented. The focus of this review is to present a concise, integrated analysis of previous group MMPI headache studies and apply these findings to differential diagnosis, prediction of treatment outcome, and client-treatment matching. Five selected clinical case studies indicating various degrees of psychopathology in migraine headache patients are presented to highlight treatment issues in support of an idiographic utilization of the MMPI for the clinical treatment of headache patients.
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http://dx.doi.org/10.1016/0304-3959(86)90037-0DOI Listing
February 1986

Re: A brief comment on 'the headache scale: a new approach to the assessment of headache pain based on pain descriptions'.

Pain 1984 Sep;20(1):107-108

Dept. of Psychology, Univ. of Alabama, Birmingham, AL 35294 U.S.A.

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http://dx.doi.org/10.1016/0304-3959(84)90816-9DOI Listing
September 1984

Psychophysiological characteristics of headache patients.

Pain 1984 Jan;18(1):41-52

Department of Psychiatry, University of Alabama at Birmingham, School of Medicine, Birmingham, Ala. 35294,USA Department of Psychology, University of Georgia, Athens, Ga.U.S.A.

Migraine, muscle-contraction headache patients, and non-headache controls were physiologically assessed during self-selected 'stressful' and 'relaxing' imagery in headache and non-headache states. Musculoskeletal (frontalis, bilateral temporalis), vascular (heart rate, bilateral temporal artery pulse volume), and autonomic (skin conductance response) measures failed to differentiate the groups on resting response levels--in both headache and non-headache states. 'Stressful' imagery elicited greater reactivity than 'relaxing' imagery in all three response systems, regardless of headache type. However, a group by condition interaction eventuated only for the electromyographic measures, indicating that the muscle-contraction patients were significantly more reactive during stressful imagery than migrainers and controls.
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http://dx.doi.org/10.1016/0304-3959(84)90125-8DOI Listing
January 1984