tbuckley/cabot-search huggingface dataset:
Abstract SY23-01: Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues
Authors: Yoshiyuki Shibata, Pankaj Kumar, Ryan Layer, Smaranda Willcox, Jeffrey R. Gagan, Jack D. Griffith, Anindya Dutta
Journal: Cancer Research (2012)

Abstract DNA in normal mammalian somatic cells is either in long chromosomes or in mitochondria. Furthermore, other than in specialized tissues like B and T cells, the genomic DNA in normal tissues is usually considered to be an exact copy of germ-line DNA. We hypothesized that errors in DNA replication may lead to the production of extra-chromosomal DNA and/or changes in copy number of segments of the DNA in normal somatic tissue. We have identified tens of thousands of short double-stranded and single-stranded extrachromosomal circular DNA (microDNA) that are derived from unique, non-repetitive sequences of chromosomes in normal mouse brain, heart and liver as well as mouse and human cell lines. MicroDNAs are 200-400 bases long and high in GC content. Short direct repeats are often present at the start and end of the corresponding chromosomal sequence suggesting that microDNAs are produced by replication slippage, homologous recombination or microhomology mediated repair. Several of the microDNAs overlap with nucleosome-occupied DNA, explaining how such short double-stranded DNA can be bent into a circle. The genomic sources of the microDNAs are enriched in the 5′ region of genes, exons and CpG islands. Ultrahighthroughput sequencing of adult brain DNA targeted to chromosomal loci that are enriched sources of microDNA, reveals a small fraction of genomic DNA molecules with micro-deletions that may be generated by the excision of microDNAs. We have thus identified a new DNA entity in somatic cells and provide evidence that deletions may occur in different genomic loci in somatic tissues, leading to genetic variability between normal somatic cells. 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 SY23-01. doi:1538-7445.AM2012-SY23-01
Cancer Rates in Florida Spark Strong Competition
Authors: L. Fintor
Journal: JNCI Journal of the National Cancer Institute (1991)

Journal Article Cancer Rates in Florida Spark Strong Competition Get access Lou Fintor Lou Fintor Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 83, Issue 23, 4 December 1991, Pages 1704–1706, https://doi.org/10.1093/jnci/83.23.1704 Published: 04 December 1991
Palmoplantar Keratoderma Associated with Esophageal Cancer
Authors: Zone-En Lee, Alexandra Modiri
Journal: New England Journal of Medicine (2012)

A 55-year-old black man presented with a 1-year history of dysphagia. He also reported a 6.8-kg (15-lb) weight loss, anorexia, and progressive hoarseness over the previous 6 months.
Abstract 4155: The small leucine-rich proteoglycan biglycan localizes to the nucleus of neoplastic cells in glioblastoma biopsies and tumor xenografts
Authors: Ana C. deCarvalho, Artem Berezovsky, Nancy Lemke, Tom Mikkelsen, Steven N. Kalkanis
Journal: Cancer Research (2010)

Abstract Global molecular profiling efforts are leading to the identification of prognostic gene expression signatures for gliobastoma. Recently, several extracellular matrix (ECM) components typically expressed in mesenchymal tissues, have been shown to be overexpressed in a subgroup of high grade gliomas from poor prognosis patients, including the highly related small leucine-rich repeat proteoglycans (SLRPs) biglycan and decorin. These proteins were originally isolated from cartilage and are widely expressed in differentiated mesenchymal tissues, but their involvement in glioblastoma pathology is not understood. Biglycan expression in glioblastoma surgical specimens, cancer stem cells, and xenografts was assessed by RNA microarray, real-time PCR, Western blot and immunohistochemistry, and compared to decorin. Over 80% of the glioblastoma surgical specimens expressed both proteoglycans in the pericellular location of endothelial cells. In neoplastic cells, while decorin was observed in the pericellular location of discrete regions of about 40% of the samples, biglycan localized to the nucleus in most tumors analyzed. It has been previously reported that biglycan possess a nuclear localization signal, but in vivo nuclear localization in a glial tumor has not been shown. The unglycosylated core biglycan protein was ubiquitous, while the glycosylated form was less uniformly distributed among the tumor samples. Glioblastoma cancer stem cell enriched neurosphere cultures derived from the tumor specimens did not express biglycan or decorin in vitro. However, biglycan was re-expressed upon tumor formation, as nuclear staining was observed in the orthotopic tumor xenograft initiated by the neurospheres. Using the Rembrandt data base (http://caintegrator-info.nci.nih.gov/rembrandt) we observed a robust inverse correlation of biglycan expression in GBMs with survival. The nuclear localization in GBMs suggests an unconventional role for this proteoglycan in the pathology of this malignancy. 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 4155.
Abstract 5212: Akt signaling enhances carcinoid cell secretion, migration, and invasion
Authors: Scott R. Silva, Jing Li, Kanika A. Bowen, Courtney M. Townsend, B. M. Evers
Journal: Cancer Research (2010)

Abstract Carcinoid tumors are slow growing neuroendocrine tumors characterized by the secretion of peptides and biogenic amines such as serotonin (5-HT) and TGF-β. Although relatively indolent, carcinoid tumors of the GI tract can metastasize to the liver and release secretory products into the systemic circulation resulting in the carcinoid syndrome. PI3K/Akt signaling is increased in carcinoid tumors and is hypothesized to promote carcinoid progression. The purpose of our current study was to delineate the role of Akt signaling in carcinoid cell secretion, migration, and invasion using the BON cell line, derived from a human pancreatic carcinoid tumor. Methods. i.) BON cells were transfected with either non-targeting control shRNA (BON shControl) or shRNA to PTEN (BON shPTEN), the natural inhibitor of Akt activation. Conditioned media was collected from BON shControl and shPTEN cells and assessed for 5-HT and TGF-β by ELISA. Western blots were performed to assess changes in the expression of 5-HT and TGF-β. ii.) Scratch and Boyden chamber assays were performed to compare the migration and invasion, respectively, of BON shControl and shPTEN cells. The protein levels of the epithelial-to-mesenchymal transition (EMT) markers E-cadherin, a cell adhesion protein, and snail were assessed in both cell groups with western blot. Cells were injected into the pancreas of athymic nude mice and liver metastases were assessed via immunofluorescence. Results. i.) Knockdown of PTEN increased the secretion of 5-HT and TGF-β from BON cells. Compared to control, lysates from BON shPTEN cells displayed increased expression of tryptophan hydroxylase, the rate limiting enzyme of 5-HT biosynthesis, and TGF-β. ii.) Compared to BON shControl cells, BON shPTEN cells exhibited a 3.2- and a 1.6-fold increase in migration at 24 h and 48 h, respectively. At 24 h BON shPTEN cells displayed an 8-fold increase in invasion, while at 48 h a 2.6-fold increase in invasion was noted compared to BON shControl cells. Knockdown of PTEN in BON cells significantly decreased E-cadherin expression, whereas snail expression was increased. BON shPTEN and BON shControl cells formed liver metastases in 60% and 10% of mice, respectively. Conclusions. The Akt pathway enhances carcinoid cell secretion and metastatic potential by increasing expression and synthesis of secretory products and by altering expression of EMT markers, respectively. In addition to promoting metastasis, Akt signaling may also contribute to carcinoid syndrome. These results suggest that targeting Akt signaling may provide a dual strategy to decrease peptide secretion and inhibit carcinoid cell invasion. 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 5212.
OP0121-PARE Youtube Videoguides for People with Rheumatic Diseases
Authors: J. Grygielska, P. Samel-Kowalik, J. Komolka, F. Raciborski
Journal: Annals of the Rheumatic Diseases (2014)

<h3>Background</h3> Rheumatic diseases are chronic and progressing conditions to disability. Prevention of disability is the most important task for health system and for people living with those diseases. Adaptation of environment for needs and abilities of rheumatic patients is very important to minimalize impact of the disease on quality of life. <h3>Objectives</h3> The aim of the project was to provide people with rheumatic disease and their relatives simple tips and advices for an easier life with the disease. The basic assumption was to use modern communication tools (YouTube) in order to increase the number of recipients. <h3>Methods</h3> In order to achieve the objectives the Institute of Rheumatology has created a series of video-guides for people with rheumatic diseases and their relatives. Each film presented only one simple issue. According to the assumptions the message should be simple and short to make it easier to understand and remember. Short message is also useful for maintain the viewer9s attention. The average duration of the film is between 100 and 150 seconds. <h3>Results</h3> The first series consisted of five films: <i>Kitchen of rheumatic person</i>, <i>Bathroom for rheumatic person</i>, <i>Rheumatic person on shopping</i>, <i>Rheumatic person on stairs</i> and <i>Rheumatic person in the car</i>. There are plans to prepare next series – the first movie will be <i>Rheumatic person in public transport</i>. Video-Guides were put on YouTube and published in the World Arthritis Day 2013 on the website of Institute of Rheumatology and additional website: www.dzienreumatyzmu.pl under WAD slogan “Living better, ageing well”. <h3>Conclusions</h3> Video-guides published on YouTube is an easy and useful tool for health promotion. It is good way to communicate with people with rheumatic disease and help them cope with the problems of everyday lives. The main difficulty, except technical aspect, it9s getting to the interested persons with information about the video-guides. Good collaboration with associations of people with rheumatic diseases is crucial to solve this problem. <h3>Disclosure of Interest</h3> None declared <h3>DOI</h3> 10.1136/annrheumdis-2014-eular.2005
Abstract 4116: Predictive biomarkers for the PI3 kinase inhibitor GDC-0941 in NSCLC
Authors: Jill Spoerke, Carol O'Brien, Zach Boyd, Sankar Mohan, Ajay Pandita, Leanne Berry, Jane Fridlyand, Lori Friedman, Garret Hampton, Lukas Amler, Mark Lackner
Journal: Cancer Research (2011)

Abstract The class I phosphatidylinositol 3’ kinase (PI3K) plays a major role in proliferation and survival in a wide variety of human cancers. A key factor in successful development of drugs targeting the PI3K pathway is likely to be the identification of responsive patient populations with predictive diagnostic biomarkers. GDC-0941 is a pan-inhibitor of all 4 isoforms of class 1 PI3K that is currently undergoing testing in the clinic. We were interested in the predictive value of candidate biomarkers in NSCLC to help inform clinical trial biomarker strategies in this indication. We assembled a focused panel of cell lines with key alterations in the PI3K pathway isolated from other genetic events to the extent possible. The approach involved pharmacogenomic and proteomic profiling. We found that models harboring key pathway alterations were exquisitely sensitive to GDC-0941. In particular, cell lines with EGFR mutations, PIK3CA mutations or amplification were the most sensitive. Inhibition of PI3K in mechanism of action studies showed effects consistent with induction of apoptosis, cell cycle arrest, and impairment of translation in models with these key alterations. In addition, gene expression changes of genes downstream of PI3K were seen upon treatment with GDC-0941 in sensitive cell lines but not those that were resistant. We extended these studies to NSCLC tumor samples and evaluated the prevalence of important pathway alterations, including PTEN loss, PIK3CA amplification, LKB1 loss in tumors representing distinct histopathological subtypes. We find that certain candidate biomarkers show subtype specific associations, and will discuss the implications for the development of PI3K-targeting agents in NSCLC. 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 4116. doi:10.1158/1538-7445.AM2011-4116
P11.04 * MALT CNS LYMPHOMAS: A MONOCENTRIC EXPERIENCE
Authors: D. Larrieu, S. Choquet, K. Hoang-Xuan, K. Mokhtari, S. Navarro, N. Martin-Duverneuil, V. Leblond, F. Charlotte, C. Houillier
Journal: Neuro-Oncology (2014)

INTRODUCTION: MALT (mucosae associated lymphoid tissue) lymphomas represent a low grade, rare and poorly known subtype (approximately 5%) of central nervous system (CNS) lymphoma. Their management is not standardized and their long-term prognosis remains unknown. The main objective of this study is to better define the clinical and radiological patterns of these tumors as well as their evolution and prognosis after treatment. METHODS: The cases of MALT CNS lymphomas treated since 2000 in our institution have been identified through the neuro-oncology department database. All biological, clinical and radiological data were collected retrospectively from medical records. RESULTS: Ten out of 422 CNS lymphomas listed were diagnosed as MALT lymphomas. Four of them were primary CNS lymphomas while 6 were associated with systemic involvement. Median age at diagnosis was 57,9 years (48,4-77,8) and sex ratio (F/M) was 9:1. Seven out of 10 patients showed dural location, 2/10 both dural and parenchymatous location and 1/10 exclusive parenchymatous location. Four out of 10 cases were located/unique forms while 6/10 were diffuse/multiple forms. Only 2/10 cases had a lymphomatous meningitis. Five out of 10 patients received chemotherapy (CT) alone, 4/10 surgery and chemotherapy and 1/10 chemotherapy and radiotherapy (RT). Chemotherapy consisted in rituximab-fludarabine-based CT in 4/10 cases, R-CHOP-based CT in 2/10 cases and high-dose methotrexate-based CT in 4/10 cases. Median duration of follow-up was 49 months, without neurotoxicity reported. Six out of 10 patients achieved complete response (CR) after initial therapy, 3/10 achieved partial response (PR) and 1/10 was stable. Median progression free survival was 43 months (95% CI, 17-68) and 4 years overall survival was 86%. DISCUSSION AND CONCLUSION: We report the largest chemotherapy-treated cohort of MALT CNS lymphomas. As previously described, most of them had dural location and looked like meningioma, but they were more often diffuse/multiple forms (only 1/3 of the cases in the literature). All our cases received CT while the great majority of the 79 MALT CNS lymphomas reported in the literature underwent surgery and/or RT with about 70% of CR. Adjuvant CT was associated in only about 1/3 of the cases. Response duration and long-term neurotoxicity were rarely reported because of a short follow-up period (≤3 years in about 2/3 of the cases). In our series, similar results were obtained with CT on disease control without neurotoxicity reported. Accordingly, chemotherapy should be discussed in multidisciplinary national meeting as a valid treatment option for MALT CNS lymphoma.
AB0743 A hand positioning frame improves joint recognition on hand radiographs
Authors: O. Schenk, J. A. Kauffman, C. H. Slump, H. J. Bernelot Moens
Journal: Annals of the Rheumatic Diseases (2013)

<h3>Background</h3> Current clinical scoring methods for hand radiographs in RA are time consuming and subject to intra and inter-reader variance. Several methods for partially automatic radiographic assessment of hand radiographs were proposed [1]. These methods depend on detection (segmentation) of bones and joints. Their success rate is unpublished. We developed a semi-automated pattern recognition method [2]. To model bone shape variation independent from hand positions, this method used connected submodels and an iterative search to find the bones of the hand. These models were combined into a single model of the entire hand. The wide variation in the position of hands on subsequent radiographs was an obstacle in joint recognition and measurement of joint space width. We have therefore developed a positioning frame with 7 pins to reduce positioning error. <h3>Objectives</h3> Compare the success rate of joint recognition on hand radiographs made without and with a positioning aid. <h3>Methods</h3> The positioning frame was introduced in 2011 for hand radiographs of RA patients. A random selection of 91 images made before, and 87 made after introduction of the frame was analyzed using the previous described model [2]. Radiographs made with the frame were analyzed with the same model, with the addition to check for correct detection of hands relative to the pins. Processed images are intended for measurements of joint damage and have bone outlines surrounded by boxes. For 14 joints per hand (MCP, PIP, DIP) segmentation was judged by a rheumatologist and considered correct when at least part of the joint space was included in the overlapping boxes around the adjoining bones. <h3>Results</h3> <h3>Conclusions</h3> The use of a hand positioning frame improves the performance of previously developed segmentation software for analysis of hand radiographs. This brings us closer to a fully automated system that measures joint damage. Training of the model using a wider range of hands may further improve segmentation. <h3>References</h3> J.T.Sharp et al, <i>Computer based methods for measurement of joints space width: update of an ongoing OMERACT project</i>, <i>Journal of Rheumatology,</i> 34(4):874-883,2007 J.A.Kauffman et al, <i>Segmentation of hand radiographs by using multi-level connected active appearance models</i>, <i>Proceedings of Medical Imaging2005: Image Processing,</i> 5747:1571-1581,2005 <h3>Disclosure of Interest</h3> None Declared
764 INPATIENT MORTALITY AND RESOURCE UTILIZATION ASSOCIATED WITH HEPATOCELLUAR CARCINOMA (HCC) IN THE UNITED STATES (U.S.) FROM 2005 TO 2009
Authors: Z.M. Younossi, M. Otgonsuren, C. Venkatesan, M. Afendy, M. Erario, A. Mishra
Journal: Journal of Hepatology (2012)
Tc-99m MDP and Ga-67 Scintigraphy in Gangrenous Muscle
Authors: Y. HAN LOH, JOHN S. MAGNUSSEN, KEVIN C. ALLMAN, HANS VAN DER WALL
Journal: Clinical Nuclear Medicine (1996)

A 64-year-old man recently underwent a right above-knee amputation for a gangrenous limb. Although the patient was given broad-spectrum antibiotics, he continued to have high fevers. A bone scan was initially performed to investigate the possible site of infection. An unexpected increase in soft-tissue uptake was seen in the proximal left calf. A striking distal-photon-deficient area was also noted. The results of a subsequent Ga-67 scan showed an increase in soft-tissue uptake in the proximal left calf with a distal area of decreased tracer accumulation. At surgery, the gastrocnemius-soleus complex was found to be gangrenous with a large distal area of nonviable tissue.
FRI0285 Prognostic factors associated with mortality in pediatric systemic lupus erythematosus (SLE).
Authors: L. M. Suárez-Larios, E. Faugier-Fuentes, R. Maldonado-Velázquez, M. U. Martinez Martinez
Journal: Annals of the Rheumatic Diseases (2013)

<h3>Background</h3> Systemic lupus erythematosus (SLE) is an autoimmune disease with significant morbidity and mortality. Recent studies suggest that childhood-onset SLE is more frequent and severe in nonwhite populations, especially Hispanics. <h3>Objectives</h3> To assess the factors associated with mortality in pediatric patients with SLE. <h3>Methods</h3> Retrospective cohort. Children and adolescents with SLE admitted to the intensive care unit (ICU) of a single pediatric center in Mexico City from January 1999 to December 2008 were included. We reviewed the medical records of these patients, including age, sex, disease evolution, diagnostic criteria, disease activity (MEX-SLEDAI), neurological and kidney disease, nephropathy (histological classification), treatment at admission, reason for ICU admission, days in pediatric ICU, requirement of catecholamines, invasive procedures, complications, reason of death and PRISM score. Statistical analysis: Categorical variables were analyzed with X² test or Fisher`s exact test. Continuous variables were analyzed with Student t-test. <h3>Results</h3> Fifty-six patients were included: thirty-two died and 24 survived. Forty-four were women (78.6%) and 12 men (21.4%). Table 1 shows the main clinical characteristics evaluated in our cohort. <h3>Conclusions</h3> Mortality in pediatric SLE patients admitted to ICU is the same of that reported in patients admitted with other diagnoses. Factors associated with mortality were the high SLEDAI score, high PRISM score, necessity of catecholamines, glucocorticoids, mechanical ventilation and infections. The main cause of death in our patients was infections. <b>Disclosure of Interest</b>: None Declared
Growth and Biochemical Response of Preterm Infants Fed Human Milk or Modified Infant Formula
Authors: Steven J. Gross
Journal: New England Journal of Medicine (1983)

My colleagues and I compared the biochemical status and rates of growth of three groups of preterm infants: one group was fed milk obtained early from mothers of preterm infants; one group received milk produced during the mature stage of lactation by mothers of term infants; and one group received a whey-based infant formula. Sixty healthy preterm infants with birth weights of 1600 g or less were randomly assigned to one of the three feeding groups. The 20 infants in each group were followed until they reached a weight of 1800 g. The mean (±S.E.M.) number of days required to regain birth weight was similar for infants receiving the formula (10.3±0.8) and those receiving milk from mothers of preterm infants (11.4±0.8); both were significantly less than the number (18.8±1.7) for infants receiving milk from mothers of term infants (P<0.001). Subsequent rates of weight gain were greater for the groups receiving formula (27.0±0.8 g per day) and milk from mothers of preterm infants (23.7±1.1) than for the group receiving milk from mothers of term infants (15.8±0.8) (P<0.001). Similarly, the average increments in crown-to-heel length and in the head circumference were significantly greater for the groups given formula and milk from mothers of preterm infants (P<0.005 and P<0.001, respectively). These data indicate that feeding with either milk from mothers of preterm infants or a whey-based infant formula results in more appropriate growth in preterm infants than feeding with milk from mothers of term infants. (N Engl J Med. 1983; 308:237–41.)