tbuckley/cabot-search huggingface dataset:
Abstract 3235: Characterization of tumor explant models using next-generation sequencing.
Authors: Zhongwu Lai, James Bradford, Qi Zhang, Sara Dempster, Brian Dougherty, Celina D'Cruz, Jonathan Dry
Journal: Cancer Research (2013)

Abstract Tumor explant models (human tumor tissue directly transplanted into mice) are believed to conserve original tumor characteristics, including molecular heterogeneity and tumor architecture. Thus, they better represent patient population and can provide more relevant predictive insight into clinical outcome. They potentially offer a clinically relevant model in which to compare drug response to genomic and molecular profiles. So called next generation sequencing (NGS) technologies (Exome sequencing and RNA-seq) are becoming the standard choices for genetic profiling due to the rich information they can provide. The sequence based nature of these technologies offers the potential to differentiate results by species and remove mouse derived stromal ‘contamination’ when assessing tumor cells directly. This also presents a unique opportunity to differentiate and assess molecular interaction between the tumor and the stromal tissue. To this aim, we have developed algorithms to differentiate NGS sequences between human and mouse. Using mixtures of human and mouse derived cell lines we demonstrated that the algorithm achieved high sensitivity (99.8%) and specificity (99.5%). More than 90% of sequence reads mapped to both human and mouse can be effectively differentiated. We applied the approach to differentiate human and mouse sequences for several explant models derived from both exome sequencing and RNA-seq. We demonstrated that the process resulted in more accurate expression quantification, and reduction of false positives in variance calling. In addition, we compared the variance calling between paired exome and RNA-seq and found that the two methods are complimentary to each other where genes were expressed. We also highlighted a number of interesting features and anomalies between RNAseq and exome data. In summary, we demonstrated the feasibility of using exome and RNA-seq to effectively differentiate human and mouse sequences in tumor explants models. We highlight the value of this approach to rationally guide their application in drug discovery. Citation Format: Zhongwu Lai, James Bradford, Qi Zhang, Sara Dempster, Brian Dougherty, Celina D'Cruz, Jonathan Dry. Characterization of tumor explant models using next-generation sequencing. [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 3235. doi:10.1158/1538-7445.AM2013-3235
Incidental Appendix Carcinoid
Authors: STEFAN HOEGERLE, EGBERT U. NITZSCHE, ALEXANDER STUMPF, GERHARD H. SIMON, ANDREAS OTTE, GEORG SCHWARZKOPF, ERNST MOSER
Journal: Clinical Nuclear Medicine (1997)

Purpose: Somatostain receptor scintigraphy is used to diagnose carcinoid of the gastrointestinal tract. Its sensitivity ranges from approximately 75%-100%. Therefore, it was hypothesized that it can be used in the postsurgical follow-up to detect residual carcinoid, recurrence, and metastatic disease. Results: This article is concerned with the findings of somatostatin receptor imaging performed on a 12-year-old girl 8 weeks after appendectomy. Histologic examination showed an incidental appendix carcinoid. Somatostatin receptor scintigraphy performed for detection of lymph node metastatic spread of the carcinoid showed focal tracer accumulation at the former operative site; subsequently, a right hemicolectomy was performed. However, histologic examination of the surgical tissue showed no evidence for carcinoid. Conclusion: It is concluded that there are some potential pitfalls for somatostatin receptor imaging at least soon after surgery. Therefore, it should not be used to aid in reoperation.
AB0435 Cross-cultural adaptation and psychometric properties of the “eular sjögren’s syndrome patient report index” for portuguese language
Authors: M. Paganotti, V. Valim, E. V. Serrano, S. T. Miyamoto, R. Altoé, M. C. S. Santos
Journal: Annals of the Rheumatic Diseases (2013)

<h3>Background</h3> The “EULAR Sjögren’s Syndrome Patient Report Index - ESSPRI” is a patient-administered questionnaire to assess patient symptoms. There is not any instrument to evaluate symptoms in Sjögren’s Syndrome (SSp) in Portuguese. <h3>Objectives</h3> To perform cultural adaptation and to study psychometric properties of the ESSPRI to Portuguese Language. <h3>Methods</h3> Cross-sectional observational study with patients with pSS according to the European-American Consensus 2002. In the adaptation process, there were six steps: conceptual equivalence, item, semantic, operational, measurement and functional. Semantic equivalence included translation, back translation, evaluation of semantics between the original and back translations, discussion with experts for final adjustments and pre-test of consensual version in twenty patients. In measurement equivalence, the psychometric properties of intra-observer reproducibility (interval of 02 days) and construct validity were assessed in 62 subjects. The ESSPRI was compared to Patient’s Global Assessment (PaGA), Profile of Fatigue and Discomfort (PROFAD), Sicca Symptoms Inventory (SSI) and Functional Assessment of Chronic Illness Therapy (FACIT-fatigue) to construct validity. Statistical tests used wereCronbach’s alpha for internal consistency; intraclass correlation coefficient (ICC) and Bland-Altman plot for intraobserver reproducibility; Spearman correlation. It was considered significant p &lt;0.05 <h3>Results</h3> There were no differences in the versions in both languages and the Brazilian consensual version was obtained. The individuals of the sample were women, 49.4 ± 11.6 years old, onset of symptoms was 7.2 ± 5.4 years and the time of diagnosis was 3.0 ± 3.3 years. The mean ESSPRI was 6.87 ± 1.97. The intraobserver reproducibility was high and significant (ICC = 0.895) there was no systematic bias in measures of agreement between assessments in the Bland-Altman analysis. There was a moderate correlation, statistically significant to all instruments (PaGA, PROFAD, SSI and FACIT-fatigue). The correlation was positive (Table 1). <b>Conclusion:</b> The Portuguese version of ESSPRI is an adaptable, reproducible and valid instrument for Portuguese Language and it can be used in Brazilian context. <h3>Conclusions</h3> The Portuguese version of ESSPRI is an adaptable, reproducible and valid instrument for Portuguese Language and it can be used in Brazilian context. <h3>Acknowledgements</h3> Financial Support: CNPQ- Brazilian Government <h3>Disclosure of Interest</h3> None Declared
785 CONTINUED LOW UPTAKE OF TREATMENT FOR HCV IN A LARGE COMMUNITY-BASED COHORT OF INNER CITY RESIDENTS
Authors: M. Alavi, J.D. Raffa, G.D. Deans, C. Lai, M. Krajden, G.J. Dore, M.W. Tyndall, J. Grebely
Journal: Journal of Hepatology (2013)
Alternative Analytic Methods for Case-Control Studies of Estrogens and Endometrial Cancer
Authors: Ralph I. Horwitz, Alvan R. Feinstein
Journal: New England Journal of Medicine (1978)

In a case-control study of estrogens and endometrial cancer, alternative sampling methods were used to eliminate the detection bias that arises from the increased diagnostic attention received by women with uterine bleeding after estrogen exposure. In a set of cases and controls chosen by conventional procedures the odds ratio was 11.98. In an alternative set of cases and controls at the same institution, consisting of patients who had all received dilatation and curettage or hysterectomy because of uterine bleeding, the odds ratio was 1.7. A methodologic analysis demonstrates detection bias arising from the pattern of hospital referral and shows the way in which the bias is neglected or increased by conventional sampling procedures, but reduced by the alternative procedure. The magnitude of the association between estrogens and endometrial cancer has been greatly overestimated because of detection bias; when an appropriate compensation for the bias is introduced, the odds ratio approaches a value much closer to 1.
Multi-tiered quality improvement strategy to reduce maternal and neonatal death in complex delivery systems in Ghana
Authors: Rohit Ramaswamy, Brianne Kallam, Emmanuel Srofenyoh, Medge Owen
Journal: The Lancet Global Health (2016)

Background Referral hospitals see a disproportionate number of maternal and neonatal deaths in low-income settings such in Ghana. In 2013, the maternal mortality ratio in Ghana was 380 per 10 0000 livebirths: in 2015, combined data from three large referral and teaching hospitals showed a rate of 895 maternal deaths per 100 000 livebirths. For these deaths to be reduced, staff capacity needs to be developed to routinely identify problems with service delivery processes, and data-driven approaches will be required. In this study, we describe implementation of a quality improvement programme at Ridge Regional Hospital in Accra, Ghana.
Abstract 4237: Inhibition of prostate cancer associated kinases by Tillandsia recurvata: A Jamaican medicinal plant
Authors: henry Lowe, Ngeh J. Toyang, Joseph Bryant
Journal: Cancer Research (2012)

Abstract Prostate cancer is the second most common cause of death from cancer in men of all ages. The three conventional treatment options include surgery, radiation and chemotherapy. In many cases, these treatments are used in combination. Chemotherapy is however the most widely used tool in prostate cancer treatment especially where the cancer has metastasized or spread to other organs of the body. Increased resistance to current chemotherapies by prostate cancer calls for an urgent need to discover and develop new therapeutics that can slow the growth of cancer cells while having lesser side effects on the patients. The development of target therapies for the treatment of human cancers is revolutionizing the concept of cancer treatment today. This type of therapeutic approach is directed to the inhibition of molecular targets that play a pivotal role in tumor progression such as the kinases. It is only in recent years that kinases have emerged as major targets for therapeutics, particularly for cancer related therapies. Relatively few kinase inhibitors have been identified to date and efforts are being made to discover new small molecules kinase inhibitors. The Island of Jamaica is known for its rich biodiversity and abundance of medicinal plants used in folk medicines. In an effort to discover new anticancer drugs from natural products several Jamaican medicinal plants were screened for anticancer activity. The Jamaican Ball Moss (Tillandsia recurvata L.) was one such plant that exhibited potent activity against the PC-3 prostate cancer cell line in vitro (IC50 = 2.4µg/ml) and was selected for further studies. The crude extract of Ball Moss was screened for interaction with 451 kinases. The crude Ball Moss extract showed potent kinase inhibitory activity against 5 kinases (kd = 8-14 µg/ml), of which 4 are implicated in prostate cancer growth and proliferation. The four kinases are; CSNK2A2, DRAK1, GAK and MEK5. The above results validate the folk use of this medicinal plant as well as make it a good candidate for development into a prostate cancer treatment or for the discovery of the bioactive molecules in the plant. Studies are currently underway to confirm the ability of Ball Moss to halt the growth of prostate tumors in mice as well as measure the inhibitory effects of the crude extract on the 4 related kinases in vivo. The isolation and characterization of the kinase inhibitors in ball moss is also in progress. 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 4237. doi:1538-7445.AM2012-4237
TCT-537 Long-term Outcomes of Self-Expanding Nitinol Stent Implantation for Chronic Total Occlusion of the Superficial Femoral and Proximal Popliteal Artery
Authors: Yasunari Sakamoto, Keisuke Hirano, Tamon Kato, Yoshimitsu Soga, Osamu Iida, Kenji Suzuki, Daiz Kawasak, Akihiro Shintani, Nobuhiro Suematsu, Terutoshi Yamaoka, Taketsugu Tsuchiya, Yusuke Miyashita, Shinya Okazaki, Norihiko Shinozaki, Hiroki Takahashi, Toshiya Muramatsu, Reiko Tsukahara
Journal: Journal of the American College of Cardiology (2013)
Gene Promoter Hypermethylation in Tumors and Matched Affected Lymph Nodes of Breast Cancer Patients.
Authors: I. Van der Auwera, I. Renard, G. Van den Eynden, R. Limame, X. Trinh, P. van Dam, E. Van Marck, S. Van Laere, P. Vermeulen, L. Dirix
Journal: Cancer Research (2009)

Abstract Gene promoter hypermethylation plays a pivotal role in breast carcinogenesis and breast cancer progression. In this study, we investigated 6 gene promoters (RASSF1A, HIN-1, RARβ2, TWIST, CCND2 and APC) for aberrant DNA methylation by real-time methylation-specific PCR in primary tumors and matched affected lymph nodes from 30 patients with breast cancer. These data were used to explore associations between gene promoter hypermethylation and clinicopathological features, including tumor cell proliferation, angiogenesis and hypoxia marker expression.Overall, gene promoter methylation levels (ratios of DNA copy numbers for methylated and reference genes) were higher in primary tumors than in matched lymph nodes. Notably, we found significant correlations between methylation levels in primary tumors and matched lymph nodes for 5 of 6 genes (P&amp;lt;0.05). An identical gene promoter methylation status (high or low according to the median methylation level) in primary tumors and matched lymph nodes was observed in 67% to 83% of cases. No significant associations between risk factors and gene promoter hypermethylation of the 6 genes was observed, except for the degree of spreading into nearby lymph nodes, which associated with high RASSF1A methylation levels in tumors (P=0.020) and high CCDN2 methylation levels in lymph nodes, and for HER2 expression, which was most frequently observed in tumors with low HIN-1 methylation levels (P=0.039). HIN-1 methylation levels in tumors negatively correlated with the fractions of proliferating tumor and endothelial cells determined by CD34/Ki-67 immunohistochemistry in both primary tumors (r=-0.594, P=0.001 and r=-0.619, P&amp;lt;0.001) and in lymph nodes (r=-0.412, P=0.024 and r=-0.400, P=0.029). Furthermore, high HIN-1 methylation levels in primary tumors tended to associate with breast tumors lacking expression of the hypoxia marker carbonic anhydrase IX in tumor cells (P=0.063) and associated stroma (P=0.086). CCND2 methylation levels in affected lymph nodes positively correlated with the ratios of the fractions of proliferating tumor cells to the fractions of proliferating endothelial cells observed in both primary tumors (r=0.418, P=0.002) and in lymph nodes (r=0.563, P=0.002).In summary, gene promoter hypermethylation in primary breast tumors and matched lymph nodes are highly correlated. Further studies with larger numbers of samples are necessary to investigate the prognostic or predictive potential of these observations. For two genes, HIN-1 and CCDN2, we observed correlations between gene promoter methylation levels and tumor cell proliferation. HIN-1 and CCDN2 are frequently lost in breast cancer and are both involved in cell cycle regulation. The biological significance of these findings needs to be further explored. Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 1149.
THU0303 Hypovitaminosis D and the Metabolic Syndrome in Patients with Systemic Lupus Erythematosus (SLE)
Authors: C. C. Mok, P. T. Chan, L. Y. Ho, D. Birmingham
Journal: Annals of the Rheumatic Diseases (2013)

<h3>Background</h3> Low vitamin D level has been linked to cardiovascular diseases and mortality in the general population. Hypovitaminosis D is associated with certain traditional vascular risk factors in patients with SLE. <h3>Objectives</h3> To study the relationship between the metabolic syndrome (MetS) and serum 25-hydroxyvitamin D level in patients with SLE <h3>Methods</h3> Consecutive patients who fulfilled &gt;=4 ACRcriteria for SLEin a two-month period were recruited from our out-patient lupus clinics. Blood was taken in the morning for the assay of 25-hydroxyvitamin D3 (enzyme immunoassay; Immunodiagnostic Systems Inc, Fountain Hills, AZ, USA) and high sensitivity C-reactive protein (hsCRP) (solid phase chemilluminescence immunometric assay; Siemens Healthcare Diagnostics, Deerfield, Il., USA). Clinical assessments (waist circumference, fasting glucose and lipid level, blood pressure) were made for each patient who was stratified for the MetS according to the 2009 International joint consensus criteria, using the Asian criteria for abdominal obesity(ref 1). The relationship between 25-hydroxyvitamin D level and the MetS was studied by linear regression, with adjustment for other confounding covariates. <h3>Results</h3> 257 SLE patients (94% women) were studied. All were ethnic Chinese. The mean age was 39.6±13.1 years and SLE duration was 8.3±6.9 years. Vitamin D insufficiency (25-hydroxyvitamin D3 &lt;30ng/mL), deficiency (25-hydroxyvitamin D3 &lt;15ng/mL, and severe deficiency (level&lt;10ng/mL) was present in 95%, 25% and 3.5% of patients, respectively. The prevalence of the MetS was 8.3%, 11% and 22.2% in patients with vitamin D insufficiency, deficiency and severe deficiency, respectively. None of the patients with 25-hydroxyvitamin D3 levels &gt;30ng/mL fulfilled the criteria for the MetS. Linear regression analysis revealed that levels of 25(OH)vitamin D3 were independently associated with age (Beta 0.19; p=0.002), the presence of the MetS (Beta -0.14; p=0.049) and hsCRP level (Beta -0.14; p=0.04) after adjustment for gender, SLE duration, duration of sunshine in the month of venepuncture, SLE damage scores (SDI), smoking ³3 years, renal insufficiency (estimated CrCl &lt; 50ml/min), photosensitivity and ever use of glucocorticoids. <h3>Conclusions</h3> Vitamin D deficiency is prevalent in patients with SLE. Hypovitaminosis D is independently associated with the MetS and hsCRP, suggesting that it is a novel risk factor for vascular thrombosis in patients with SLE. <h3>References</h3> Alberti KG et al. Circulation 2009;120:1640–5. <h3>Disclosure of Interest</h3> None Declared
Human papillomavirus in breast carcinomas of Korean women.
Authors: J Choi, K Lee, W Kim, S Lee, H Lim, Y Choi, D Kim, J Lee, S Nam, J Yang
Journal: Cancer Research (2009)

Abstract Abstract #3086 Introduction&amp;#x2028; The association between human papillomavirus (HPV) and cervical cancer is well documented. However, it remains unclear whether there is also a correlation between HPV infection and human breast cancer. The aim of this study was to investigate the status of HPV-DNA in breast carcinoma of Korean women and to examine the possible association between HPV and breast cancer development.&amp;#x2028; Patients and Methods&amp;#x2028; We examined the HPV-DNA of 154 patients including 123 cases of breast carcinoma, 31 cases of intraductal papilloma, and 27 cases of adequate nipple from cancer patients using DNA-chip method.&amp;#x2028; Results&amp;#x2028; The HPV-DNA was detected in 8 breast carcinomas (6.5%), but in none of the intraductal papillomas. All detected HPV was high-risk groups; the HPV-18 and HPV-70 were found in each two cases and each one cases HPV-16, 31, 56/58 and 59. In one case of nipple, both low-risk (HPV-62) and high-risk (HPV-18) group HPV-DNA was obtained. The papillary carcinomas and the invasive ductal carcinomas with adjacent intraductal papillomas showed slightly increased incidence (11% vs. 3-4%), however, there was no significant difference. No correlation between the presence of HPV-DNA and specific prognostic predictors for the disease outcome was observed.&amp;#x2028; Conclusions&amp;#x2028; Our results suggest that the presence of high-risk group HPV in the breast might be related to breast carcinogenesis, especially papillary phenotype. Further studies are warranted. Citation Information: Cancer Res 2009;69(2 Suppl):Abstract nr 3086.
Echocardiographic Detection of a Renal-Cell Carcinoma
Authors: L B Croft, M E Goldman
Journal: New England Journal of Medicine (1998)

Figure 1. A 59-year-old man with hypertension presented with a three-month history of fatigue and progressive shortness of breath. Physical examination revealed mild jaundice, tachypnea, tachycardia, bibasilar rales, and mild hepatomegaly. Laboratory studies disclosed microcytic anemia and elevated concentrations of total bilirubin and alkaline phosphatase. Urinalysis revealed no evidence of hematuria or proteinuria. Transthoracic echocardiography performed to investigate heart failure demonstrated mild, concentric left ventricular hypertrophy and mild, diffuse left ventricular dysfunction. A standard subcostal view revealed a multilobar cystic mass (arrows in Panel A) in the inferior vena cava (IVC) that appeared to originate from the right kidney. At . . .
Rheumatoid Lung Disease with Cavitary Nodules, Pneumothorax and Eosinophilia
Authors: M. M. Portner, W. A. Gracie
Journal: New England Journal of Medicine (1966)

THE broadening spectrum of rheumatoid disease is presenting new diagnostic problems for the clinician. This report is based on our investigation of obscure lung disease accompanied by migratory arthritis and peripheral eosinophilia in 2 women who later acquired classic rheumatoid arthritis.Case ReportsCase 1. H.R. (U.M.M.C. 893007), a 48-year-old housewife, had the onset of pain and stiffness in the shoulders in February, 1957. During the next year migratory arthralgia, morning stiffness and painful swelling of the wrists and finger joints developed. Examination at this hospital in February, 1958, revealed symmetric swelling of the proximal finger joints and a subcutaneous . . .