tbuckley/cabot-search huggingface dataset:
Abstract 3089: Heterogenous high level HER-2 amplification in a small subset of colorectal cancers
Authors: Andreas Holger Marx, Ronald Simon, Guido Sauter
Journal: Cancer Research (2010)

Abstract HER-2 is the molecular target for antibody-based treatment of breast cancer (trastuzumab). The potential benefit of anti-HER-2 therapy is currently investigated in several other HER-2 amplified cancers. For example, trastuzumab was recently shown to be effective in HER-2 positive gastric cancer. To address the potential applicability of anti-HER-2 therapy in CRC, tissue microarray (TMA) sections and colorectal resection specimens of 1851 CRC were analyzed for HER-2 overexpression and amplification using FDA approved reagents for immunohistochemistry and fluorescence in situ hybridization. HER-2 amplification was seen in 2.5% and HER-2 overexpression in 2.7 % of 1439 interpretable CRC. Amplification was often high level with HER-2 copies ranging from 4 to 60 per tumor cell and was strongly related to protein overexpression. HER-2 amplification and overexpression were unrelated to histological tumor type, tumor localization, grading, pT, pN, pM or survival. As heterogeneity of drug target expression could represent a major drawback for targeted cancer therapy we next studied HER-2 heterogeneity in selected cases. Extensive evaluation of all available large sections from patients with HER-2 positive CRC revealed heterogenous findings in 3 of 4 cases. In summary, high level HER-2 amplification occurs in a small fraction of CRCs. Heterogeneity of amplification may limit the utility of anti HER-2 therapy in some of these tumors and therefore, adequate clinical trials are needed to further evaluate this approach. Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend. 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 3089.
750 SCREENING FAILURE RATE DURING HEPATOCELLULAR CARCINOMA SURVEILLANCE; A ROLE OF ALTERNATING SURVEILLANCE WITH ULTRASOUND AND COMPUTED TOMOGRAPHY
Authors: Y.W. Min, M.J. Lee, D.H. Sinn, J. Yi, M.S. Choi, Y.J. Kim, G.-Y. Gwak, Y.-H. Paik, J.H. Lee, K.C. Koh, S.W. Paik, B.C. Yoo
Journal: Journal of Hepatology (2012)
Breast Cancer Stem Cells Identified by ALDH1 Expression Were Associated with Resistance to Sequential Paclitaxel and Epirubicin-Based Chemotherapy for Human Breast Cancers.
Authors: T. Tanei
Journal: Cancer Research (2009)

Abstract Background: Breast cancer stem cells have been demonstrated to be associated with resistance to chemotherapy in vitro, but their clinical significance has yet to be examined in human breast cancers. The aim of this study was to investigate whether breast cancer stem cells were clinically associated with chemo-resistance or not.Material and Methods: The subjects recruited for this study comprised 108 primary invasive breast cancer patients treated with neoadjuvant chemotherapy (NAC) consisting of sequential paclitaxel and epirubicin-based chemotherapy. Cancer stem cells were identified by immunohistochemical staining of CD44/CD24 or ALDH1 in tumor tissues obtained before and after NAC.Results: The pathological complete response (pCR) was achieved in 30 patients (27.8%) of the 108 patients treated with NAC. ALDH1 positive tumors were significantly associated with a low pCR rate (9.5% vs. 32.2%; P = 0.037), but there was no significant association between CD44+/CD24- tumor cell proportions and pCR rates. Changes in the proportion of CD44+/CD24- tumor cells or ALDH1 positive tumor cells before and after NAC were examined in 78 patients who did not achieve pCR. The proportion of ALDH1 positive tumor cells significantly increased (p&amp;lt;0.001) after NAC, but no significant change was observed in the proportion of CD44+/CD24- tumor cells before and after NAC. In addition, we were able to show, by multivariate analysis, that tumors with negative ER, high Ki67, and negative ALDH1 were significantly more likely to achieve pCR.Discussion: Our findings suggest that breast cancer stem cells identified as ALDH1 positive, but not CD44+/CD24-, play a significant role in resistance to chemotherapy. ALDH1 positive tumor cells are likely to serve as a better marker for breast cancer stem cells than CD44+/CD24- tumor cells for the prediction of resistance to chemotherapy. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 1084.
THE ASSOCIATION OF THE AMERICAN HEART ASSOCIATION'S LIFE'S SIMPLE 7 WITH INCIDENT CANCER IN THE SOUTHERN COMMUNITY COHORT STUDY
Authors: Jai Singh, Deepak Gupta, Shi Huang, Javid Moslehi, Thomas Wang, Frank Harrell, William J. Blot, Loren Lipworth
Journal: Journal of the American College of Cardiology (2016)
1277 SECRET MISSION OF MORPHOGENS IN ADULT LIVER – NEW INSIGHTS IN METABOLIC CONTROL BY Wnt AND Hedgehog SIGNALING
Authors: J. Böttger, M. Matz-Soja, S. Aleithe, E. Marbach, C. Thiel, K. Arnold, U. Hofmann, S. Sales, A. Shevchenko, R. Gebhardt
Journal: Journal of Hepatology (2013)
Snare-over-scope technique for retrieval of a proximally migrated biliary stent
Authors: Ahmed Abdelgelil, Vivek Kumbhari, Alan Tieu, Payal Saxena, Sepideh Besharati, Saowanee Ngamruengphong, Mohamed El-Zein, Gerard Aguila, Vikesh Singh, Anne Lennon, Mouen Khashab
Journal: Endoscopy (2014)

There is no consensus on the optimal technique for retrieval of proximally migrated biliary stents. A biliary sphincterotomy or sphincteroplasty, together with the use of accessories such as stent-grasping forceps, Soehendra stent retrieval device, and stone extraction balloon, have been reported [1] [2] [3] [4]. We present the case of a proximally migrated biliary stent that was retrieved using a novel "snare-over-scope" (SOS) technique.
DIFFERENCES IN ATHEROSCLEROTIC BURDEN BETWEEN SOUTH ASIANS AND CAUCASIANS WITH TYPE 2 DIABETES MELLITUS AND COMPARABLE 10 YEAR PREDICTED CARDIOVASCULAR RISK
Authors: Sanjay Nandkoemar Gobardhan, Aukelien C. Dimitriu-Leen, Alexander R. van Rosendael, Erik W. van Zwet, Martin Schalij, Arthur Scholte
Journal: Journal of the American College of Cardiology (2016)
Abstract 794: RNA-Seq and whole transcriptome analyses in ependymomas.
Authors: Fabricio F. Costa, Jared M. Bischof, Chris Hamm, Elio F. Vanin, Maria F. Bonaldo, Stephen Iannaccone, Veena Rajaram, Tadanori Tomita, Stewart Goldman, Marcelo B. Soares
Journal: Cancer Research (2013)

Abstract Ependymoma is a common pediatric central nervous system (CNS) tumor that is believed to originate from ependymal cells located in the lining of ventricular surfaces in the brain. This type of pediatric tumor presents great challenges in treatment despite the advances in neurosurgical techniques and adjuvant therapy. In order to identify possible molecular markers that could improve clinical management and better treatment, we have used RNA-Seq to profile the transcriptome of ependymoma samples with different outcomes. In this study, the ABI SOLiD WT (Whole Transcriptome) technology was utilized to sequence three different ependymoma tumor samples and one normal control brain tissue (enriched for ependymal cells). Whole Transcriptome sequencing produced approximately 10-30 million reads per sample and an average of 30-40% were mapped to the human reference sequence (NCBI Build 36.1) using Novoalign software. After obtaining these mapped locations, Perl scripts were written to overlap these intervals with other annotations and Genespring was used to visualize the reads. Different protein-coding, non-coding and microRNA gene databases were searched for known genes and to calculate the RPKM (Reads Per Kilobase of transcript per Million mapped reads) for each clustered gene. Multiple gene lists were generated corresponding to different RPKM-based comparisons between tumor and control tissues, ultimately enabling the identification of protein-coding genes, non-coding RNAs and microRNAs that are differentially expressed in ependymomas. Protein interaction networks were then built with these genes using the software GeneGo (Thomson Reuters). Thirty genes that are present in these networks are being selected for validation of differential expression in a larger cohort by Real-Time PCR TaqMan customized arrays. In conclusion, we have been able to identify genes differentially expressed in ependymomas, some of which of potential clinical importance. Financial Support: Ann &amp; Robert H Lurie Children's Hospital of Chicago, The Falk Brain Tumor Foundation and The Maeve McNicholas Memorial Foundation. [FF Costa, JM Bischof, and C Hamm contributed equally to this work.] Citation Format: Fabricio F. Costa, Jared M. Bischof, Chris Hamm, Elio F. Vanin, Maria F. Bonaldo, Stephen Iannaccone, Veena Rajaram, Tadanori Tomita, Stewart Goldman, Marcelo B. Soares. RNA-Seq and whole transcriptome analyses in ependymomas. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 794. doi:10.1158/1538-7445.AM2013-794
EXPLORACION DEL COLON ASCENDENTE POR RETROVISION EN CIEGO: POSIBILIDAD TECNICA Y RENTABILIDAD DIAGNOSTICA
Authors: A Vargas, M Alburquerque, M Figa, E Cirera, E González, C Yeste, M Girones, F Jose, F Gonzalez-Huix
Journal: Endoscopy (2014)

Las lesiones polipoides en colon derecho no visualizadas son causa de cáncer de intervalo. La exploración de la cara proximal de los pliegues de colon ascendente mediante retrovisión cecal reduciría la posibilidad de perder estas lesiones. Los colonoscopios de menor diámetro pueden facilitar la retrovisión en ciego sin riesgo de complicaciones.
AB0483 Causes of hospitalisation in behcet’s syndrome over a ten-year period
Authors: Y. Ozguler, A. S. Pala, V. Hamuryudan, G. Hatemi, S. Yurdakul, H. Yazici
Journal: Annals of the Rheumatic Diseases (2013)

<h3>Objectives</h3> We are unaware of previous studies on hospitalisation in Behçet's syndrome (BS). We surveyed the causes and outcome of hospitalisations among BS patients in a dedicated center. <h3>Methods</h3> We surveyed the records of all hospitalisations in our clinic between 2002-2011 to identify patients with a diagnosis of BS. We reviewed both the inpatient and outpatient charts of all BS patients who were hospitalised to identify the demographic and clinical features, causes of hospitalisation and outcome. We tried to contact the patients to determine their current condition. <h3>Results</h3> 178 BS patients (74% men, mean age 42.9±11.3) had been hospitalized for a total of 211 times during the last ten years. We were able to contact 104(58%) of them. The reasons for hospitalisation were directly related to BS organ involvement in 118(56%) and to complications in 93(44%). The most common BS related reasons were vascular involvement in 74/118(63%) (including 21 patients with pulmonary artery aneurysms, 10 with peripheral artery aneurysms and 11 with serious venous thrombosis such as vena cava superior and Budd-Chiari syndrome), neurologic involvement in 14/118(12%), gastrointestinal involvement in 6/118(5%) and eye involvement in 6/118(5%). Hospitalisations caused by complications of BS were infections in 39/93(42%), and other drug related adverse events in 15/93(16%). Neoplasias were diagnosed in 5 patients. Among the 178 patients, 16(9%) had died. Most common causes of death were vascular involvement (n=5), infections (n=4) and malignancies (n=4). <h3>Conclusions</h3> Vascular involvement is the leading cause of hospitalisation among BS patients, followed by infections related to therapy. Adverse events related to immunosuppressives are problematic. The predominance of men among hospitalized patients underlines the more severe course of BS in this sex. The relatively low frequency of gastrointestinal involvement among hospitalisations is in line with our previous observation that this type of involvement is rare in our BS patients. <h3>Disclosure of Interest</h3> None Declared
Ga-67 Scintigraphy in Lupus Nephritis
Authors: W Y Lin, K Y Cheng, S J Wang
Journal: Clinical Nuclear Medicine (1998)

Lupus nephritis is a disease characterized by flareups and remissions. Evaluation of disease activity is important for therapeutic decisions and prognosis. In this study, 46 patients with lupus nephritis were evaluated by Ga-67 scintigraphy. Delayed 48-hour Ga-67 images were performed to evaluate kidney uptake. A patient with a 24-hour urinary protein excretion of 3 g or more or a serum creatinine level greater than 1.5 mg/dl was considered to have active lupus nephritis. Renal disease was active in 22 patients and inactive in 24 patients. Of the 22 patients with active renal disease, 18 (81.8%) showed positive Ga-67 results, whereas only 12.5% (3 of 24) of patients with inactive renal disease showed a positive Ga-67 study. The difference between the two groups was significant. Patients with positive Ga-67 scans had a significantly higher serum creatinine level and 24-hour urine protein value than patients with negative Ga-67 scans. In addition, all of the patients (100%) with a 24-hour urine protein greater than 4 g/day had a positive Ga-67 scan. It appears that Ga-67 scintigraphy is useful for the evaluation of disease activity in lupus nephritis.
PMO-003 Effect of MRI and variable stiffness colonoscopes on caecal intubation rates by experienced endoscopists
Authors: A Terlevich, J Maltby, J Linehan
Journal: Gut (2012)

<h3>Introduction</h3> Magnetic endoscopic imager (MEI) and variable stiffness colonoscopes (VSC) have been shown to improve caecal intubation rates in trainees. Many trained endoscopists in our department prefer to perform colonoscopies with them rather than without. The aim of this study was to assess colonoscopic performance data in experienced endoscopists, with and without the use of MEI and VSC, in our endoscopy department. <h3>Methods</h3> Our endoscopy department uses Olympus VSC with MEI in two theatres and standard Pentax colonoscopes with no variation in stiffness or 3D imaging, in our two other theatres. All equipment was purchased in 2009. Experienced endoscopists use both Olympus and Pentax equipment. We have conducted a retrospective case note analysis to assess caecal intubation rates, terminal Ileum intubation rates, polyp detection rates and sedation used, by individual endoscopists. <h3>Results</h3> We reviewed 3984 procedures, performed by 16 experienced endoscopists between September 2009 and November 2011. 2598 colonoscopies used Olympus VSC with MEI and 1386 with Pentax equipment. Caecal intubation rate (CIR) was higher in 13/16 endoscopists when using MEI and VSC than without. The total CIR for all colonoscopies was greater using VSC with MEI than without (89.9% vs 87.1%, p=0.0153). There was no significant difference in TI intubation rate, polyp detection rate or sedation used. <h3>Conclusion</h3> Although most endoscopists prefer to use MEI and VSC when performing colonoscopy, our data suggests that the difference in caecal intubation rates with experienced endoscopists is small. However, our observed difference in CIR of 2.8% would equate to about 168 colonoscopies in our unit completed, per year that would be otherwise incomplete. <h3>Competing interests</h3> None declared.
Abstract 2225: Differential RNA splicing in high-risk neuroblastoma detected by affymetrix exon array and next-generation sequencing
Authors: Xiang Guo, Young Song, James Badgett, Qing-Rong Chen, Jun Wei, Javed Khan
Journal: Cancer Research (2010)

Abstract RNA splicing is an important regulatory mechanism of gene expression providing various functions for specific cells including cancers. In this study, we investigated global alternative splicing pattern in neuroblastoma using Affymetrix exon array (HuEx) and deep sequencing approach (RNA-Seq). Exon array profiling was performed on 47 neuroblastoma samples in stage 1 and stage 4 with normal or amplified MYCN copy number (stage 1-, 4- and 4+). Principal component analysis demonstrated distinct splicing pattern in three groups of samples. In stage 4- compared with stage 1- tumors, differentially spliced candidate genes (n=355) had little overlap with genes showing whole gene expression changes (n=158), and most of them were involved in different biological processes. In contrast, a larger number of genes exhibited either exon-level splicing, gene-level expression, or both changes in stage 4+ versus stage 1- tumors. To validate exon array results, we performed transcriptome sequencing of selected samples with stage 1-, 4-, or 4+ neuroblastomas. The concept of splicing index was adapted to measure RNA splicing by short sequence reads. Both exon array and deep sequencing data demonstrated differential splicing of microtubule-associated genes, which may play an important role in enhanced genomic instabilities and tumor development. In conclusion, our results demonstrated a significant contribution of alternative or aberrant splicing to neuroblastoma development. The identification of differentially spliced genes and pathways in high risk neuroblastomas may be essential to the understanding of cancer biology and the discovery of diagnostic biomarkers or therapeutic targets in neuroblastoma. 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 2225.
OP0190-PC Prevalence and incidence of gout in italy. Analysis of a primary care database
Authors: L. Cavagna, G. Trifirò, R. Caporali, P. Morabito, C. Ferrajolo, S. Pecchioli, M. Simonetti, G. Medea, C. Cricelli, A. Caputi, G. Mazzaglia, C. Montecucco
Journal: Annals of the Rheumatic Diseases (2013)

<h3>Background</h3> Data from national surveys and general practitioner databases has shown an increasing prevalence of gout in several countries. However there is no data regarding the epidemiology of gout in Italy in the last decade. <h3>Objectives</h3> To assess both prevalence and incidence of gout in Italy between 2005 and 2009. <h3>Methods</h3> Data was obtained from the Italian primary care database (Health Search/Longitudinal Patient Database) which comprises about one million adults (&gt;18 years) from all around the Country. Rates together with 95% Confidence Interval (CI) have been measured overall and stratified by age, gender and calendar year. Characteristics of patients with newly diagnosed gout and hyperuricemia have been explored <h3>Results</h3> Calculated prevalence of symptomatic gout increased from 6.7 per 1,000 adults in 2005 to 9.1 in 2009, whilst incidence remained stable (0.93 per 1,000 Person Years (PYs) in 2005 and 0.95 in 2009). Prevalence increases with age and is 4 times higher in males. A similar trend was observed for hyperuricemia whose prevalence is about ten times higher than that of symptomatic gout (66.3 per 1,000 adults in 2005 and 92.1 in 2009) in our population. Therefore during the study period, the prevalence of gout and hyperuricemia appears to be always slightly higher in the Northern Italy than in the Central and Southern Italy (e.g. year 2009: gout=9.3 vs. 8.6 vs. 9.0 per 1,000 inhabitants; hyperuricemia=95.3 vs. 92.7 vs. 88.0 per 1,000 inhabitants. Recurrent gout attacks were observed in 19.1% cases within one year following the first attack and in 23.1% cases within five years. <h3>Conclusions</h3> This is the first study regarding the epidemiology of gout in Italy. The overall prevalence of both gout and hyperuricemia is remarkably lower than that reported in similar population-based investigations carried out in other western countries, namely the US, UK and Germany. This difference might in part be related to country specific diet; in fact the typical Italian diet (i.e. Mediterranean diet) is associated with low levels of serum urate. Interestingly, the prevalence of gout and, to a lesser extent, of hyperuricemia is quite different across Italian geographic areas, with the higher figures observed in the Northern Italy. This finding is likely to be attributed to different dietary habits as the adherence to Mediterranean diet is higher in Central and Southern than Northern Italy High recurrence of attacks was observed during the first year following the first episode. <h3>References</h3> Roddy E, Doherty M. Arthritis Res Ther 2010;12:R223 Cea Soriano L, et al. Arthritis Res Ther 2011;13:R39 Zhu Y, et al. Arthritis Rheum 2011;63:3136-41 Annemans L, et al. Ann Rheum Dis 2008;67:960-6 <h3>Disclosure of Interest</h3> None Declared
Bcr-Abl Kinase Domain Mutations and Other Mutations on the Response to Nilotinib in Bcr Abl –Positive Chronic Myeloid Leukemia - a Study from Eastern India
Authors: S. Banerjee, C.K. Bose, S. Mondal, P. Mitra, F.H. Gharami, A. Mukhopadhyay
Journal: Annals of Oncology (2014)
COMPARACIÓN DE PINZA DE BIOPSIA PEDIÁTRICA VS SPYBITE EN EL DIAGNOSTICO DE LAS ESTENOSIS BILIARES: ESTUDIO PROSPECTIVO ALEATORIZADO
Authors: F González-Huix, R Louvriex, M Figa, M Alburquerque, A Vargas
Journal: Endoscopy (2014)

Introducción: La precisión del diagnóstico anatomopatolológico (AP) en estenosis biliares es bajo y aumenta usando dos técnicas de obtención de muestra (cepillado, biopsias, punción). Se desconoce la efectividad de la pinza Spybite.
Antifolate resistance in a HeLa cell line associated with impaired transport independent of the reduced folate carrier
Authors: Rongbao Zhao, Shrikanta Chattopadhyay, Marie Hanscom, I. David Goldman
Journal: Cancer Research (2005)

3301  Prior studies from this laboratory documented the prevalence of methotrexate (MTX) transport activity with a low-pH optimum in a variety of human solid tumor cell lines (Clinical Cancer Research, 2004, 10: 718). In HeLa cells, derived from human cervical cancer, this low pH activity has high affinity (Kt=45 nM) for pemetrexed (PMX) and is RFC-independent, since it is not diminished in an RFC-null subline (R5) (Clinical Cancer Research, 2004, 10: 6256). R5 cells also have residual transport activity, with high specificity for PMX, at neutral pH (Cancer Research, 2004, 64: 3313). The current study addresses whether this low pH folate transport activity can be down-regulated under antifolate pressure and the consequence of this down-regulation on the activity of antifolates. An R5 subline, R1, was selected under MTX selective pressure in a medium with a modestly reduced pH (pH 6.9). In R1 cells influx of MTX, PMX and folic acid at pH 5.5 was markedly and equally decreased as compared to R5 cells. PMX influx at pH 7.4 in R1 cells was also markedly reduced while MTX influx at this pH was decreased to a lesser extent. When MTX was removed from the growth medium there was a slow return of transport activity in R1 cells, and when MTX was added back, there was loss of transport at both pHs within eight weeks. PMX influx in R5 cells at both acidic and neutral pH was increased by preloading cells with 5-formyltetrahydrofolate (trans-stimulation), consistent with a process mediated by a facilitative carrier. In R1 cells there was marked decrease in accumulation of PMX, MTX, and folic acid at both pHs as compared to R5 cells. At both pHs R1 cells were more resistant than R5 cells to antifolates, which require a facilitative process to gain entry into cells, although the extent of resistance was different for different antifolates (PMX>MTX>tomudex). These data demonstrate that (i) RFC-independent transport in HeLa cells at low and neutral pH contribute to antifolate activity, in particular, to PMX activity, and can be diminished by antifolate selective pressure and, (ii) the loss of these activities results in marked resistance to PMX, an agent for which there is little or no loss of activity when transport mediated by RFC is abolished. These observations suggest that transport activity in RFC-null HeLa R5 cells at neutral and low pH may reflect the same carrier-mediated process. This study was supported by a grant from the National Institutes of Health, CA-82621, along with a grant from the Eli Lilly Company.