tbuckley/cabot-search huggingface dataset:
Abstract 4310: Gene expression analysis of axial and appendicular osteosarcoma in the canine model
Authors: Nikolaos Dervisis, Shawna L. Klahn
Journal: Cancer Research (2011)

Abstract Spontaneously occurring canine osteosarcoma (OSA) is considered an excellent model of the human disease. Canine axial and appendicular osteosarcoma appear histopathologically identical. The clinical course of the two forms, however, seems to diverge. Following surgery, the axial form may be associated with a lower metastatic rate and longer survival than the appendicular form. Identifying gene expression profiles associated with decreased metastatic potential may be crucial for the development of targeted therapies for the human disease. We hypothesized that there are distinct gene expression patterns for canine axial and appendicular OSA. Six axial osteosarcoma tumor samples and six age, breed, and weight matched appendicular osteosarcoma clinical tumor samples were selected from the Center for Comparative Oncology, Michigan State University tissue bank. RNA extraction, amplification and labeling were performed using standard techniques. Raw gene expression values were obtained using the Affymetrix GeneChip Canine Genome 2.0 Array. Background correction, normalization, PM correction, summarization, and expression analysis were performed using the R software with the affy/limma/sva packages. Gene set enrichment analysis was performed using GSEA software. All RNA samples passed quality control and were included in the data set. The expression analysis took into account RNA degradation, which was similar in all tumor samples. A total of 184 genes were differentially expressed by &amp;gt;16-fold, between the two groups. Surrogate variable analysis did not result in any statistically significant differences in gene expression. Gene set enrichment analysis resulted in 9 gene sets enriched in axial, and 4 gene sets enriched in appendicular osteosarcoma samples at FDR &amp;lt; 25%. Gene ranking was similar between the two methods of analysis, with MMP1, ATP6AP1, SLC6A8, and dysadherin expression increased in axial tumor samples, while ICAM2 expression increased in appendicular samples. Expression analysis indicates no statistically significant differences in gene expression between the axial and appendicular OSA. Gene set enrichment analysis indicates potential differences in gene set enrichment between the two types of osteosarcoma. Further quantitative RT-PCR analysis is required to confirm our results. These data will guide hypothesis-driven translational studies, which may have direct clinical implications on the treatment of osteosarcoma. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4310. doi:10.1158/1538-7445.AM2011-4310
Detection of Herpesvirus-Like DNA Sequences in Kaposi's Sarcoma in Patients with and Those without HIV Infection
Authors: Patrick S. Moore, Yuan Chang
Journal: New England Journal of Medicine (1995)

Herpesvirus-like DNA sequences have recently been found in lesions from patients with Kaposi's sarcoma and the acquired immunodeficiency syndrome (AIDS). It is not known whether these sequences are also present in classic Kaposi's sarcoma or in the Kaposi's sarcoma that occurs in homosexual men who are seronegative for the human immunodeficiency virus (HIV).
HOW TO OPTIMIZE DRUG-ELUTING BALLOON ANGIOPLASTY FOR IN-STENT RESTENOSIS: HOST-ISR DEB REGISTRY
Authors: Kihyun Jeon, Sang Hyun Kim, Joo Myung Lee, Hack-Lyoung Kim, Jung-kyu Han, Jae-Bin Seo, Han-Mo Yang, Kyung Woo Park, Hyun-Jae Kang, Woo-Young Chung, Bon Kwon Koo, Myung-A Kim, Young-Bae Park, Hyo-Soo Kim
Journal: Journal of the American College of Cardiology (2015)
Management of Primary Hyperlipidemia
Authors: Richard J. Havel, Elliot Rapaport
Journal: New England Journal of Medicine (1995)

Epidemiologic, clinical, genetic, experimental, and pathological studies have clearly established the primary role of lipoproteins in atherogenesis.1,2 Lowering plasma cholesterol concentrations reduces the availability of atherogenic lipoproteins and also, presumably, the accumulation of cholesterol in the intima of arteries. Measures to lower plasma cholesterol have become fundamental to the practice of preventive cardiology, and their use in both patients who already have coronary disease and healthy people has materially contributed to the 50 percent reduction in mortality from coronary heart disease in the United States in the past two decades.3,4 Lowering the plasma cholesterol concentration by a variety . . .
NI-74 * DYNAMIC CONTRAST ENHANCED (DCE) T1 MRI PERFUSION DIFFERENTIATES PSEUDOPROGRESSION FROM RECURRENT GLIOBLASTOMA
Authors: A. Thomas, J. A. Perez, K. Peck, T. Schneider, J. Lyo, R. Young, T. Kaley
Journal: Neuro-Oncology (2014)

PURPOSE: Pseudoprogression may present as transient new or increasing enhancing lesion(s) that mimics recurrent tumor in patients treated for glioblastoma. The purpose of this study was to examine the utility of DCE-MRI in differentiating between pseudoprogression (PsP) and tumor progression (POD). METHODS: We retrospectively examined consecutive patients with glioblastoma, who developed new and/or increasing enhancing lesion(s) after chemoradiation. Axial contrast T1-weighted images and DCE MRI data were analyzed using Nordic Ice (NordicNeuroLabs, Milwaukee, WI) in a blinded fashion. After semiautomated arterial input function selection, plasma volume (Vp) and time-dependent leakage constant (Ktrans) maps were calculated. A volume of interest was drawn around the enhancing lesion on the contrast T1-weighted images and transferred onto the Vp and Ktrans maps. The measurements were binned, and histogram analysis was performed. Pseudoprogression was defined as stable disease not requiring new treatment for a minimum of 3 months, or by surgical pathology if available. Wilcoxon rank-sum tests were performed on normalized ratios and p set to 0.05. RESULTS: Fifty patients with newly diagnosed glioblastoma treated with standard chemoradiation were included. The mean age was 64 years (66 PsP, 64 POD), and median KPS was 82 (90 PsP, 80 POD). Patients with PsP (n = 13, 26%) had Vp(mean) = 2.64, Vp(75%tile) = 2.80; and Ktrans(mean) = 3.29 and Ktrans(75%tile) = 3.40. Patients with POD (n = 37, 74%) had Vp(mean) = 6.47, Vp(75%tile) = 6.79; and Ktrans(mean) = 7.77 and Ktrans(75%tile) = 8.55. PsP demonstrated significantly lower Vp (p <0.0005), as well as significantly lower Ktrans (p <0.005). MGMT promoter hypermethylation was present in 7 of 12 patients with PsP (58.3%). Median overall survival was 13.8 months (PsP 17.7 months, 11 patients alive; POD 12.6 months, 13 alive). CONCLUSION: DCE MRI shows lower perfusion in pseudoprogression than in tumor progression. This suggests that DCE MRI has a role in triaging glioblastoma patients with indeterminate enhancing lesions following treatment to help make better informed therapeutic decisions.
MEDICAL MANAGEMENT OF NON-OBSTRUCTIVE CORONARY ARTERY DISEASE ON CORONARY CT ANGIOGRAPHY: INSIGHT FROM A MODERN EMERGENCY DEPARTMENT CLINICAL REGISTRY
Authors: Nandini Meyersohn, Sumbal Janjua, Pedro Staziaki, Daniel Bittner, Richard Takx, Rory Weiner, Jason Wasfy, Udo Hoffmann, Brian Ghoshhajra
Journal: Journal of the American College of Cardiology (2016)
A comprehensive analysis of nine prognostic signatures reveals the high classification instability in breast cancer.
Authors: F Reyal, MH Vliet, HH Horlings, N Armstrong, KE de Visser, M Kok, AE Teschendorff, S Mook, L Van't Veer, C Caldas, RJ Salmon, MJ Van de Vijver, LF Wessels
Journal: Cancer Research (2009)

Abstract Abstract #2026 To determine the prognosis of breast cancer patients, clinical and pathological factors are currently employed. Gene expression micro-arrays offer new opportunities to determine individual prognosis. Publications have raised concerns about micro-arrays studies who have the potential to preclude their use in clinical routine. To improve the understanding of gene-expression classifiers we addressed the following issues: 1) Is the performance similar between independent classifiers? 2) Is proliferation a common biological theme that represents various signatures? 3) Are there other enriched pathways among signatures with prognostic ability?&amp;#x2028; Methods:&amp;#x2028; On 6 public datasets we applied the 76-gene signature; the Molecular subtypes; the Chromosomal Instability Signature; the Wound Signature; the Invasiveness Gene Signature; the Molecular Prognosis Index; and the Genomic Grade Index. Survival, predictive accuracy and overlap analyses were performed. We created enlarged signatures by including all probes with significant correlation to at least one of the genes in the original signatures. We gathered a collection of gene sets from four databases (GO, KEGG, Reactome, MSDB). For each signature, we evaluated whether specific gene sets (modules) are overrepresented. We tested the prognosis ability of each of them.&amp;#x2028; Results:&amp;#x2028; The survival and predictive accuracy analyses gave similar results for each of the 9 signatures. They all added significant information to a multivariate model including standard pathological and clinical criteria. Nevertheless, we showed that none of these signatures were able to identify good and poor prognosis patients when applied to samples with intrinsically poor prognosis features (Positive Lymph Node, Negative Estrogen Receptor, High Grade). Conversely they identified good and poor prognosis patients when applied to samples with intrinsically good prognosis features (Negative LN, Positive ER Low Grade). The overlap analysis showed a low agreement between the signatures. 50% of the samples had almost one discordant classification result out of the 9 classifiers tested. The intersection of the signatures revealed a set of proliferation genes. The signatures were build on 10 different gene ontology modules with prognostic ability.&amp;#x2028; Conclusion:&amp;#x2028; This study underlines the need of large prospective validation studies of gene expression signatures. Further computational intelligence and system biology studies would be held to determine the best way to use these classifiers in clinical routine. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 2026.
Abstract 5250: Optimization of an orthotopic mouse model for <i>in vivo</i> fluorescent uPA imaging in breast cancer
Authors: Johan Ides, An Wouters, Jonas Messagie, Christel Vangestel, Bea Pauwels, Jurgen Joossens, Pieter Van der Veken, Koen Augustyns, Marc Peeters, Filip Lardon
Journal: Cancer Research (2012)

Abstract The urokinase plasminogen activator (uPA) system is one of the serine protease systems involved in extracellular matrix degradation, which will facilitate tumor cell invasion and intravasation. Recently, the Medicinal Chemistry group of the University of Antwerp (UAMC) developed some very selective covalently binding uPA inhibitors. Besides its function as possible therapeutic target, uPA and its endogenous inhibitor PAI-1 are described as prognostic biomarkers for breast cancer with the highest level of evidence. Commercial ELISA and PCR kits are available for the screening of uPA in breast tumors. These ex vivo assays measure or predict the total uPA content (active and inactive). We present here a more advanced technique, which will be able to monitor the actual enzymatic uPA activity in a non-invasive manner. The technology is based on the modification of the UAMC inhibitors towards activity based probes containing a fluorescent label. Currently, we are evaluating these probes as imaging tools for uPA monitoring. The developed imaging probes will be profoundly tested in an orthotopic model of human MDA-MB-231 and MCF7 breast cancer cells since these cell lines show a high and low uPA expression respectively. We will use these models to study the potential beneficial characteristics of activity based probes in the field of bio-imaging applications targeted to uPA as a validated biomarker. The current protocol, which is still under evaluation, can be described as followed: Cell suspensions (2.106 cells/100μl) of each cell line were implanted in the mammary fat pads at both flanks of 7 mice, alternatively with and without Matrigel. Tumor size was monitored using bioluminescent imaging (BLI) and caliper measurements. When the tumor volume reached 200 - 400mm3, the rhodamine labeled uPA-inhibitor (uPA-probe) was administered (0.3 mg / kg i.v.). Fluorescent images were taken at 1, 2, 4, 6, 8, 12, 24 and 48 hours after injection. At 48 hours, the mice were sacrificed and the tumor, liver and lung were excised for ex vivo bioluminescent or fluorescent imaging and stored for histological examination. In this presentation, we describe the evaluation of the model and the first promising results. Considering the role of uPA in migration and invasion, the uPA-probe will also be tested in the future for the detection of micrometastases. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5250. doi:1538-7445.AM2012-5250
Hybrid laparoscopic colectomy with transluminal colonoscopic specimen extraction - a step toward natural orifice surgery
Authors: S. Saad, D. Schmischke, C. Martin, T. Schieren
Journal: Endoscopy (2010)

Minimally invasive surgery is the method of choice when colon polyps cannot be removed endoscopically. However, laparoscopic colon resections require a 5 – 6-cm minilaparotomy to retrieve the specimen. This laparotomy can cause pain, wound infection, and hernia formation [1] [2]. We describe a new technique to avoid a minilaparotomy by using a flexible colonoscope for transluminal specimen extraction.
Non-physician performance of lower and upper endoscopy: a systematic review and meta-analysis
Authors: Lukejohn Day, Derrick Siao, John Inadomi, Ma Somsouk
Journal: Endoscopy (2014)

<b>Background and study aims:</b> Demand for endoscopic procedures worldwide has increased while the number of physicians trained to perform endoscopy has remained relatively constant. The objective of this study was to characterize non-physician performance of lower and upper endoscopic procedures. <b>Patients and methods:</b> Bibliographical searches were conducted in Medline, EMBASE, and Cochrane Library databases. Studies were included where patients underwent flexible sigmoidoscopy, colonoscopy, or upper endoscopy done by a non-physician (nurse, nurse practitioner, physician assistant) and outcome measures were reported (detection of polyps, adenomas, cancer, and/or adverse events). Pooled rates were calculated for specific outcomes and rate ratios were determined for selected comparison groups. <b>Results:</b> Most studies involved nurses performing flexible sigmoidoscopies for colorectal cancer screening. Nurses and nurse-practitioners/physician assistants performing flexible sigmoidoscopies showed pooled polyp detection rates of 9.9 % and 23.7 %, adenoma detection rates of 2.9 % and 7.2 %, colorectal cancer detection rates of 1.3 % and 1.2 %, and adverse event rates of 0.3 and 0 per 1000 sigmoidoscopies, respectively. There was no significant difference between polyp and adenoma detection rates in sigmoidoscopy performance studies comparing nurses or nurse-practitioners/physician assistants with physicians. For the 3 studies of non-physician performance of colonoscopy, pooled adenoma detection rate was 26.4 %, cecal intubation rate was 93.5 %, and adverse event rate was 2.2 /1000 colonoscopies. In the few studies examining upper endoscopies, 99.4 % of upper endoscopy procedures performed by nurses were successful with no reported adverse events. <b>Conclusion:</b> Available studies suggest that when non-physicians perform endoscopic procedures, especially lower endoscopies, outcomes and adverse events are in line with those of physicians.
Abstract 4387: Diversity Outbred: a new, highly diverse mouse stock for toxicology and cancer
Authors: Karen S. Fancher, Karen L. Svenson, Elissa J. Chesler, Gary A. Churchill
Journal: Cancer Research (2011)

Abstract The Diversity Outbred (J:DO) stock is a new heterogeneous, highly diverse mouse resource designed for complex trait analysis and toxicology studies as well as to facilitate rapid mapping with single gene resolution. This stock was derived from crossing partially-inbred Collaborative Cross strains, which are a mixture of eight genetically well-defined JAX® Mice inbred strains, including three wild-derived. Subsequent maintenance follows a randomized outcross non-sibling mating scheme to retain maximum genetic diversity. Each Diversity Outbred mouse is genetically unique, representing a novel combination of alleles present in the founder strains. To determine the extent to which this genetic variation leads to phenotypic variation, over 50 metabolic measurements including plasma glucose, insulin, triglycerides, cholesterol, and body composition were collected, under both standard chow and high fat diet conditions. The Diversity Outbred animals displayed a wide spectrum of metabolic phenotypes, home cage nesting behavior and aggressiveness. Mouse-to-mouse variation is demonstrated by fold-differences in plasma triglycerides and creatine kinase levels, both as high as 11-12. Plasma glucose, free fatty acids, thyroxine, and percentage of fat all showed differences of 3-fold or greater. These fold-changes are comparable to the variation among unique inbred mouse strains, and mimic the diversity within human populations. The J:DO stock represents a new powerful tool for rapid gene mapping, toxicology/pharmacogenomic screens and compound evaluation for a wide variety of human diseases, including cancer and metabolic diseases. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 4387. doi:10.1158/1538-7445.AM2011-4387
Papules on the Eyelids, Lips, and Tongue
Authors: Mohammad Reza Mohajeri Tehrani, Maryam Aalaa
Journal: New England Journal of Medicine (2011)

A 16-year-old boy presented with multiple flesh-colored papules and dermal nodules on his eyelids, lips, and tongue (Panels A, B, and C, respectively). Six years earlier, his mother had received a diagnosis of metastatic medullary thyroid cancer, at the age of 38 years. At that time, both of her sons were found to have markedly elevated serum calcitonin levels but no biochemical evidence of pheochromocytoma. Both boys subsequently underwent total thyroidectomy. On pathological examination, a medullary thyroid tumor measuring 0.5 cm by 0.5 cm had been discovered in the thyroid gland of this patient. This clinical history is suggestive of . . .
Oxidative Hemolysis, or “What Made the Red Cell Break”?
Authors: Ernst R. Jaffé
Journal: New England Journal of Medicine (1972)

Oxidative hemolysis is the name frequently given to the accelerated destruction of circulating human erythrocytes exposed to "oxidant stress." This designation is a misnomer because the process is most often associated with drugs and chemicals that are really reducing agents, not oxidizing compounds. The contradiction is partly resolved when the mechanisms thought to be responsible are considered. Currently, the following sequence of events has been formulated into a reasonable and popular hypothesis.1 The potentially hemolytic agent is converted into an active metabolite, which interacts with the oxygen of oxyhemoglobin to generate hydrogen peroxide (H2O2), peroxyhemoglobin, or . . .
DURABILITY OF QUALITY OF LIFE BENEFITS OF TRANSCATHETER AORTIC VALVE REPLACEMENT IN PATIENTS WITH AORTIC STENOSIS AT EXTREME SURGICAL RISK: LONG-TERM RESULTS FROM THE COREVALVE US EXTREME RISK STUDY
Authors: Suzanne Baron, Suzanne Arnold, Matthew Reynolds, Kaijun Wang, G. Michael Deeb, Michael Reardon, James Hermiller, Steven Yakubov, David Adams, Jeffrey Popma, David Cohen
Journal: Journal of the American College of Cardiology (2016)
Abstract 4214: Stem cell antigen-1 (Sca1) modulates PI3K/PTEN signaling and mammary tumor cell survival
Authors: Geeta Upadhyay, Claire Pollock, Yuzhi Yin, Hongyan Yuan, Levi Kopelovich, Robert I. Glazer
Journal: Cancer Research (2010)

Abstract Stem cell antigen-1 (Sca-1, Ly6A/E) represents two allelic forms of a GPI-anchored membrane protein that was first identified as a murine marker of bone marrow stem cells. Although Sca-1 is widely used to enrich for stem cells in many normal tissues, little is known about its function and associated signaling pathways in tumorigenesis. To explore this further, mammary carcinogenesis was induced in Sca-1+/EGFP mice that are heterozygous for Sca-1 and express GFP under the control of the Sca-1 locus. Induction of mammary tumorigenesis by progestin/DMBA treatment resulted in a marked increase of Sca-1 in the mammary gland at the initiation of tumorigenesis, as well as in the resulting tumors. To further investigate the function of Sca1, tumor cell line 34T was established from a primary adenocarcinoma, and sorted into Sca-1hi and Sca-1lo populations. These results revealed that Sca-1 expression related inversely with proliferation, as well as PTEN, PDK1, pT308Akt and pERK1/2 expression. Furthermore, reduction of Sca-1 in 34T cells by lentivirus-mediated RNAi reversed the proliferative, PTEN and kinase phenotype, and resulted in loss of their ability to proliferate as spheroid clusters in cell culture. Isografts of 34T/Sca-1hi and 34T/Sca-1lo cells in syngeneic mice indicated that Sca-1 was essential for tumorigenicity. These results provide evidence that Sca-1 confers a proliferative and survival advantage to mammary tumor cells, and demonstrates for the first time that Sca1 is associated with modulation of the PTEN/PDK1/Akt axis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4214.