tbuckley/cabot-search huggingface dataset:
Abstract LB-121: Serrated colorectal adenocarcinoma: Specific copy number alterations
Authors: Karoliina Tuppurainen, Yilong Li, Eevi Kaasinen, Anne Tuomisto, Lauri A. Aaltonen, Auli Karhu, Markus J. Makinen
Journal: Cancer Research (2010)

Abstract The serrated pathway in the colorectal cancer (CRC) development shows characteristic morphological and genetic differences as compared with the traditional Vogelstein's adenoma-carcinoma sequence. According to current estimations, about 15-20% of colorectal cancers originate from serrated polyps. Activating mutations of BRAF and KRAS genes and microsatellite instability are common features in serrated polyps and cancers. To identify the driver genes behind the serrated colorectal pathway we analyzed gene copy number variations (CNVs) in 19 serrated colorectal carcinomas. DNA was extracted from fresh-frozen tissues according to standard procedures. By using the Illumina HumanCNV-370 platform we analyzed the samples for somatic copy number alterations. Raw-data were normalized using the built-in Illumina BeadStudio normalization method. To segment the LRRs (tumor vs. normal logarithmic intensity ratios) we used CBS (circular binary segmentation) and BAFsegmentation (B allele frequency) and the driver genomic alterations were searched using GISTIC algorithm. To determine genetic changes specific for serrated adenocarcinomas, the recurrent genomic variations detected were compared with those previously reported in colorectal carcinomas. The recurrent genomic alterations in serrated carcinomas overlap substantially with the previously reported alterations seen in colorectal carcinomas; losses in 1p, 4p, 4q, 5q, 8p, 17p, 18p and 18q, and the gains in 7p, 7q, 8q, 13q and 20q. However, regions that are frequently altered specifically in serrated carcinomas were also found. For example, the gains of 1q, 5p, 6p and 6q are not commonly found in primary tumors in colorectal cancer, but only in liver metastases. The frequent losses specific for serrated carcinoma occur in 3p, 6q, 9p, 11q, 16p, 22q, Xp and Xq. The highest deletion peaks observed in the current sample set are those located at 9p21.3. In summary, our whole-genome screening of serrated colorectal adenocarcinomas with SNP arrays revealed several copy number alterations previously reported in colorectal cancers. Moreover, we detected several novel copy number alterations, which were specific for the serrated adenocarcinoma. The upcoming sequence analysis of genes within regions of copy number alterations may allow detection of mutations of genes linked to serrated adenocarcinoma pathogenesis. 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 LB-121.
O8.06 * ATRX AND TERT EXPRESSION IN RELAPSING LOW GRADE GLIOMA
Authors: C. Calatozzolo, M. Patane, S. Mazzetti, M. Eoli, M. Farinotti, R. Nunziata, G. Finocchiaro, B. Pollo
Journal: Neuro-Oncology (2014)

Mechanisms responsible for telomere maintenance are been recently elucidated: many cancers harbor mutations in alpha thalassemia/mental retardation syndrome X-linked (ATRX) gene resulting in a phenomenon known as alternative lengthening of telomeres (ALT) or point mutations in the promoter of the telomerase reverse transcriptase (TERT) gene leading to an increased telomerase expression. ATRX and TERT mutations have been recently identified also in brain tumors. In gliomas, a molecular stratification based on IDH and ATRX mutational status and 1p/19q codeletion has been suggested. ATRX mutations have been observed mainly in astrocytic tumors and TERT promoter mutations mainly in oligodendroglial tumors. Aim of our study was to evaluate the expression of both ATRX and TERT in WHO grade II gliomas and in their resected recurrences, related to a set of confirmed molecular markers and to clinical data. We performed an immunohistochemical analysis of ATRX and TERT expression in 30 grade II gliomas (astrocytomas, oligoastrocytomas and oligodendroglioma) and in their respective recurrences (grade III-IV). Also evaluation of IDH1 and p53 status and 1p/19q LOH were carried out. Loss of expression of ATRX protein has been associated to the mutated gene and ALT phenotype, while expression of TERT protein could be related to TERT promoter mutations. We found a loss of ATRX expression in 70% of cases; recurrences showed the same pattern of ATRX expression. In the most part of cases ATRX loss was associated to IDH1 and p53 mutation and intact 1p/19q, as previously observed. In the major part of cases with ATRX loss of expression TERT was not detected. TERT high expression was observed in about 30% of grade II gliomas at the first surgery, minor expression of TERT was found in grade III-IV recurrent tumors. In most case high expression of TERT was associated to 1p/19q deletion. We observed a statistically significant correlation between TERT high expression and a better outcome. Our study of protein expression of both ATRX and TERT in low grade gliomas and in their recurrences in relationship with established molecular markers and follow-up data, confirm the possibility of using immunohistochemistry in routine diagnostic procedures for better define this subset of neoplasm.
1344 NON-CIRRHOTIC PORTAL HYPERTENSION IN HIV INFECTION HAS A VARIED CLINICAL PHENOTYPE AND IS ASSOCIATED WITH DIDANOSINE AND THROMBOPHILIA: REVIEW OF TWENTY-ONE CASES
Authors: M. Cowan, L.J. Garvey, E.C. Thomson, M.R. Thursz, G.S. Cooke, J. Main
Journal: Journal of Hepatology (2012)
Hydrothorax in Continuous Ambulatory Peritoneal Dialysis
Authors: Pablo Contreras-Puertas, Manuel Benítez-Sánchez, Amelia Jiménez-Heffernan, Angel Rebollo-Aguirre, Sonia Cruz-Muñoz
Journal: Clinical Nuclear Medicine (2002)

CONTRERAS-PUERTAS, PABLO M.D.*; BENÍTEZ-SÁNCHEZ, MANUEL M.D.†; JIMÉNEZ-HEFFERNAN, AMELIA M.D.*; REBOLLO-AGUIRRE, ANGEL M.D.*; CRUZ-MUÑOZ, SONIA M.D.† Author Information
NOD2/CARD15 Genotype and HLA-DPB1 Matching Status Can Be Used To Predict Disease Relapse in Recipients of an Unrelated Donor Haematopoietic Stem Cell Transplant for Acute Leukaemia.
Authors: J. Alejandro Madrigal, Neema P. Mayor, Hazael Maldonado-Torres, Bronwen E. Shaw, Steven G.E. Marsh
Journal: Blood (2007)
ECHOCARDIOGRAPHIC MARKERS OF IMPLANTABLE CARDIOVERTER-DEFIBRILLATOR THERAPY
Authors: Yang Shi, Chi Cho, Lydia Garlie, Ruth Perez, Robyn Shearer, Nasir Sulemanjee, Dianne Zwicke, Thomas Hastings, Omar Cheema, Vinay Thohan
Journal: Journal of the American College of Cardiology (2015)
Predicting carcinogenicity by using batteries of dependent short-term tests.
Authors: B S Kim, B H Margolin
Journal: Environmental Health Perspectives (1994)

Among the various methods for predicting carcinogenicity from a battery of short-term tests (STTs), the carcinogenicity prediction and battery selection (CPBS) procedure is the most prominent. A major assumption of CPBS is that the STTs used in the prediction are conditionally independent. Results of recent National Toxicology Program studies of four commonly used in vitro STTs contradict this assumption, thereby necessitating modification of CPBS to accommodate dependencies. This is accomplished via log-linear modeling, which then also yields an important dividend: standard errors for the predicted probabilities of carcinogenicity.
P2-16-12: Skin Reducing Nipple Sparing Mastectomy – A Treatment Option for Patients with Significant Ptosis or Macromastia.
Authors: Young A Ott, K Alizadeh, C Hodyl, M Pronovost, T Davenport
Journal: Cancer Research (2011)

Abstract Background: With new data showing the oncologic safety of nipple sparing mastectomy with immediate reconstruction - nipple sparing mastectomies are now offered to an increasing number of mastectomy patients. Unfortunately cosmetically acceptable reconstruction of nipple sparing mastectomies is technically limited to women with perfect breast anatomy - where the skin envelope shows no or little redundancy and where the nipple areolar complex is located in the perfect location on the breast mount. Especially in countries with a high incidence of obesity and associated macromastia only a small percentage of women fall into this category. A high percentahge of patients who would otherwise be good candidates for nipple sparing procedures are excluded based on their unfavorable breast anatomy. We describe a surgical technique that reduces the redundant mastectomy skin envelope in a breast reduction pattern and places the native nipple areolar complex as a free skin graft into proper anatomical position. This technique in conjunction with implant or autologous reconstruction combines the benefits of shorter better vascularized skin flaps with the cosmetic and emotional benefits of preserving the nipple areolar complex even in the anatomically difficult cases. Methods: To investigate the safety and efficiency of this method we reviewed medical records of 40 patients who underwent 60 nipple preserving skin reducing mastectomies over the last 4 years. All procedures were performed by the senior author and follow up ranged from 4 weeks to 50 months. The charts were analyzed for the occurrence of complications such as infection, seroma, hematoma, mastectomy flap necrosis, nipple-areolar loss and loco regional recurrence. All patients were asked to rate their reconstruction on a scale of poor- good - excellent. Results: In 60 reconstructed breasts we encountered one case of seroma, four cases of limited mastectomy flap necrosis treated with local wound care and one case of partial areolar necrosis treated with local excision. No loco regional recurrences, hematomas or infections were encountered. Out of the group of 40 patients, 31 patients rated their result as excellent, 8 as good, and one as poor. Conclusion: Our results compare favorably with data published in the literature. Patient satisfaction rates are high and complication rates are low in a patient population that historically has been a challenge for the breast surgeon, as well as, the plastic surgeon. The use of a skin reducing mastectomy in conjunction with a free nipple graft enables the breast surgeon to offer nipple sparing procedures for all patients who are good oncological candidates regardless of their breast anatomy. Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P2-16-12.
Abstract 839: HER2 expression occurs early in breast cancer dissemination
Authors: Michail Ignatiadis, Virginie Durbecq, Isabelle Veys, Jose Rosari, Carmen Criscitiello, Philippe Bedard, Sandeep K. Singhal, Frédéric Buxant, Carole Chaboteaux, Rouas Ghizlane, Denis Larsimont, Fabienne Liebens, Martine Piccart, Christos Sotiriou
Journal: Cancer Research (2010)

Abstract Background: Systemic spread of disseminated tumor cells from the primary site may occur early in breast tumorigenesis. The role of HER2 in breast cancer (BC) dissemination is not well understood. We evaluated the expression of HER2 on peripheral blood Circulating Tumor Cells (CTCs) from women with various stages of breast cancer (BC). Methods: 81 women with preinvasive breast lesions (Atypical Ductal Hyperplasia, Lobular Carcinoma In Situ and Ductal Carcinoma In Situ), 101 women with early invasive BC and 35 women with metastatic BC were included. CTCs were defined as Cytokeratin 8,18,19+/CD45-/DAPI+ cells detected using the CellSearch® technology. Any staining for HER2 on CTCs using the CellSearch® HER2 profiling kit was considered positive. HER2 detection was calibrated through peripheral blood spiking experiments with MCF7 and SKBR3 cells. Results: &amp;gt; 1 CTCs/22.5mL of blood were detected in 6 of 81 (7%) women with preinvasive breast lesions (range 0-3 CTCs) and 15 of 101 (15%) women with early invasive BC (range 0-8 CTCs), whereas &amp;gt; 1 CTCs/7.5mL of blood were detected in 17 of 35 (49%) women with metastatic BC (range 0-1160 CTCs) (p&amp;lt;0.001). HER2 expression on CTCs was not associated with estrogen receptor (ER) and progesterone receptor (PR) expression or the histological grade of the primary tumor. In women with detectable CTCs, the ratio of HER2-positive CTCs/total CTCs was higher in HER2-positive than HER2-negative primary tumors (p=0.023). Despite a higher detection rate of CTCs, the ratio of HER2-positive CTCs/total CTCs was lower in metastatic BC (median 0.15, range 0-1.0) than in preinvasive (median 1.0, range 0-1.0) or early invasive BC (median 1.0, range 0.3-1.0) (p&amp;lt;0.001). Similar results were observed when only HER2-negative primary tumors were considered (p=0.004). Conclusion: This is the first report showing that HER2-positive CTCs can be detected in women with preinvasive breast lesions, further supporting the hypothesis that dissemination occurs early in breast tumorigenesis. HER2 expression on CTCs is more commonly observed in earlier stages of breast cancer, suggesting that HER2 plays an important role in early dissemination. The EORTC 90091-10093 trial will test the hypothesis that trastuzumab can eliminate HER2-positive CTCs in patients with HER2-negative early breast cancer. 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 839.
EFICACIA Y RENTABILIDAD DE LA TECNICA DE MANOS LIBRES SIN ANCLAJE PARA LA COLANGIOSCOPIA DIRECTA CON ENDOSCOPIOS ULTRAFINOS
Authors: S Rodríguez Muñoz, F Sánchez Gómez, AJ Del Pozo García, C Marin Gabriel Jose, M Pérez Carreras, G Castellano Tortajada
Journal: Endoscopy (2013)

Introducción: El acceso directo a la vía biliar con endoscopios ultrafinos puede resultar complicado y presenta unas tasas variables de éxito (50 – 95%) en las series publicadas. Objetivo: Verificar la eficacia y rentabilidad del método de “manos libres” sin fijación en el interior de la vía biliar, en la canulación del colédoco con endoscopios ultrafinos. Material y Método: Se practicó colangiografía directa en 28 pacientes con vía biliar dilatada portadores de una esfinterotomía endoscópica, en los que existía duda de la presencia de cálculos residuales, o en los que no habíamos conseguido la extracción completa del material incluido en el interior de la vía biliar (cálculos o stents). Utilizamos la técnica de “manos libre total” sin ningún sistema de anclaje a la vía biliar intrahepática, con un endoscopio ultrafino de 5.9 mm de diámetro, 4 angulaciones y 2.0 mm de canal de trabajo. Resultados: La colangioscopia directa fue posible en los 28 pacientes (100%), con inserción hasta los hepáticos en 11 pacientes (39%) y hasta el cístico en 13 (46%), no pudiendo ascender por el colédoco distal en 4 (14%). En 5 enfermos (17.9%) fue necesaria una esfinteroplastia con balón. El tiempo medio de introducción en la vía biliar fue de 10,32 ± 8.3 minutos, con tiempo total de 21.07 ± 8.7 minutos de exploración. En los 28 pacientes (100%) la exploración fue diagnóstica y en 12 (42,9%) terapéutica. En un paciente (3.5%) apareció colangitis después de la exploración, resuelta con antibióticos. Conclusiones: La técnica de manos libres sin anclaje es eficaz, segura y reproducible para el acceso a la vía biliar con endoscopios ultrafinos. Una vez en el interior de la vía biliar, la versatilidad de estos endoscopios permite una revisión de la vía biliar extrahepática en su totalidad en un 85% con toma de biopsias dirigidas, canulación selectiva y extracción de cálculos y stents retenidos.
P29 * CLINICAL MANAGEMENT AND OUTCOME IN ASTROCYTOMA WHO GRADE II: THE IMPORTANCE OF RESECTION
Authors: S. Hanif, M. Waqar, B. Haylock, A. Brodbelt, M. D. Jenkinson, C. Walker
Journal: Neuro-Oncology (2014)

INTRODUCTION: Astrocytomas WHO grade II (AII) are diffusely infiltrating tumours whose management is challenging with the role of biopsy vs. resection and the timing of oncology therapy remaining controversial. The aim of this single-institution study was to review clinical management and outcome for patients with AII diagnosed between 2006 and 2012. METHOD: Adult newly-diagnosed AII were identified from histopathology records and case notes reviewed. Data analysis used SPSS. RESULTS: 92 patients were identified: median age 42 (20-73), median follow-up of live patients 45 months and median overall survival (OS) 85 months. 91% had surgery within 6 months of referral. Seizures were the most common mode of presentation (75%) associated with increased OS and progression-free survival (PFS) Radiology diagnosis was consistent with histology in 76% with a trend for patients with radiological evidence of higher grade to receive early radiotherapy (Fisher Exact, p = 0.055). Surgical management was either resection (51%) or biopsy (49%), with 28% and 51% of patients respectively receiving radiotherapy (RT) immediately following surgery. Resection was associated with better PFS (Breslow, p = 0.027) and OS (Log-rank, p < 0.001). Early RT was more commonly used in patients with biopsy (Chi2, p = 0.012) and age >40 (Chi2, p = 0.001) associated with decreased OS (Log-rank, p = <0.001) but not PFS. Contrast enhancement (Cox Regression p = 0.004) and surgery (Cox Regression p = 0.002) were independent prognostic factors for OS. CONCLUSION: Our data for the clinical management of AII demonstrated the benefit of maximum resection where possible with early radiotherapy for patients with poor prognosis, supporting international guidelines.
Abstract 2802: <i>Salmonella typhimurium</i> A1-R inhibits brain metastasis in an orthotropic breast cancer nude-mouse model.
Authors: Yong Zhang, Nan Zhang, Robert M. Hoffman, Ming Zhao
Journal: Cancer Research (2013)

Abstract We have previously developed tumor-targeting Salmonella typhimurium A1-R (A1-R), which has shown efficacy against multiple cancer types in nude mouse models. In this study, we demonstrated that S. typhimurium A1-R can inhibit and eradicate brain metastasis in an orthotopic metastatic BALB/c mouse model of breast cancer. To establish the model, 4T1 breast cancer cells expressing RFP (5.0 × 106/100 μL) in 100 μl serum-free solution were injected slowly into the right second mammary gland. Two weeks after cells implantation, the primary tumors were removed. Approximately 30% of post-surgery nude mice were found with brain metastasis using fluorescence imaging 4-5 weeks after injection of 4T1-RFP cells. When the mice were found with brain metastasis, S. typhimurium A1-R [5×107 CFU/100 μl] was injected into the tail vein once a week for 3 weeks. Inhibition of brain metastatic growth was observed noninvasively by the Maestro fluorescence imaging system (Perkin-Elmer Inc.) compared with untreated mice. Intravenous administration of S. typhimurium A1-R improved survival 70%. This study shows the important potential of bacterial therapy of brain metastasis. Citation Format: Yong Zhang, Nan Zhang, Robert M. Hoffman, Ming Zhao. Salmonella typhimurium A1-R inhibits brain metastasis in an orthotropic breast cancer nude-mouse model. [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 2802. doi:10.1158/1538-7445.AM2013-2802
Re-Emphasis on Bone Marrow as a Medium for Administration of Fluid
Authors: Samuel Pillar
Journal: New England Journal of Medicine (1954)

NUMEROUS investigators have emphasized the value of the bone marrow as a medium for the parenteral administration of fluids. Drinker, Drinker and Lund,1 Doan,2 Benda, Orinstein and Depitre,3 Tocantins,4 Macht5 , 6 and Turkel et al.7 , 8 were among the early investigators in this field. They all demonstrated the feasibility and practicability of intramedullary infusion and the extensive capillary network within the bone marrow and its intimate connections with the general vascular system. It was clearly shown that substances infused into the bone marrow were absorbed readily and quickly into the general circulation, and had effects similar to those obtained by injection directly . . .
P31 * MEDIUM-TERM OUTCOME FOLLOWING INTERHEMISPHERIC TRANSCALLOSAL APPROACH FOR INTRAVENTRICULAR TUMOURS IN CHILDREN AND ADULTS
Authors: J. Yousaf, C. Chamilos, C. L. Mallucci, M. D. Jenkinson
Journal: Neuro-Oncology (2014)

INTRODUCTION: Intraventricular tumours are a heterogenous group that present a unique clinical and surgical challenge. Surgical resection is the preferred treatment in most cases and is associated with improved prognosis. We present our experience of interhemispheric transcallosal surgical approach for intraventricular tumours. METHOD: Retrospective case note review of all consecutive patients who underwent a transcallosal approach at the Walton Centre and Alder Hey Children's Hospital between 2008-2012. RESULTS: 35 patients (15 adults [median 35 years; range 18-64 years], 20 paediatric [median 9.5 years; range 1-18 years]) underwent surgery. The most common presenting symptoms were headaches (54%) and visual disturbance (37%). Tumour location was third ventricle (n = 18), lateral ventricle (n = 11), thalamus (n = 5) and tectal plate (n = 1). Pilocytic astrocytoma was the commonest (adults: n = 5; children: n = 8). Gross total resection (GTR) was achieved in 40% and subtotal resection in 51% of cases. GTR was achieved in 82% of lateral ventricle tumours and 27% of third ventricle tumours. Median follow-up was 3 years (range = 1-5.5 years). None of the patients who underwent GTR showed evidence of tumour recurrence during the follow-up period. The major transient morbidities included memory disturbance (37%), hormone imbalance (34%) and focal neurological deficits (29%). Persistent deficits were seen in 13% adults and 20% children. There was no surgery-related mortality. CONCLUSION: Interhemispheric transcallosal approach for intraventricular tumours has relatively low surgical morbidity. Lateral ventricle tumours are more amenable to gross total resection than third ventricle tumours.