tbuckley/cabot-search huggingface dataset:
Duodenal Mycobacterium genavense infection in a patient with acquired immunodeficiency syndrome
Authors: K. Abe, T. Yamamoto, T. Ishii, Y. Kuyama, I. Koga, Y. Ota
Journal: Endoscopy (2013)

Mycobacterial infection is sometimes fatal in patients with acquired immunodeficiency syndrome (AIDS). Mycobacterium genavense, a rare pathogen identified in 1992, causes about 10 % of disseminated nontuberculous mycobacterial infections in patients with AIDS and mainly involves the small intestine [1] [2] [3]. The endoscopic findings of intestinal M. genavense infection are known to be nodules with a velvety appearance that is similar to that seen with Mycobacterium avium-intracellulare (M. avium complex [MAC]) [4].
P37 Changes in daily physical activity in COPD
Authors: AM Albarrati, NS Gale, S Enright, IC Munnery, MM Munnery, JR Cockcroft, DJ Shale
Journal: Thorax (2013)

<h3>Background</h3> COPD is associated with extrapulmonary manifestations that worsen patient’s daily physical activity (DPA)(1). However, changes in DPA over time and contributing factors in this population have not been established. We hypothesise that patients with COPD would have lower DPA after one year. <h3>Method</h3> As part of a longitudinal study in COPD (ARCADE), DPA was recorded as the number of steps using a multisensor armband (SenseWear Pro armband) in 28 patients with stable COPD for 7 days and repeated after one year for a further 7 days. Spirometry, body composition, handgrip strength (HGS), six-minute walk distance (6MWD), the COPD assessment test (CAT) were also recorded. <h3>Results</h3> Patients mean (SD) age was 69 (7) years, BMI 27.2 (4.7) Kg/m<sup>2</sup> and FEV<sub>1</sub>% predicted 52 (15). After one year, there was a reduction in the number of daily steps by 498 (218) steps and fat free mass (FFM) 1.10 (1.75) kg, with an increase in fat mass (FM) 1.06 (2.24) kg and FFM/FM 0.11 (01), all p &lt; 0.01. No changes were observed in FEV<sub>1</sub>%, BMI, HGSor 6MWD. The rate of decline in the number of steps was 12.3% per year which related to baseline FFM, r = -0.51 and HGS, r = -0.53, all p &lt; 0.01. Linear regression analysis showed that FFM and HGS can predict 23% and 26% respectively of the variability in the reduction in the number of steps. <h3>Conclusion</h3> There was a significant reduction in daily physical activity after one year, which related to baseline FFM and HGS, but was not associated with lung function and 6MWD. Despite maintaining the BMI level, there was a fat free mass turnover, which may indicate a hidden muscle catabolism. Therefore, early management to prevent muscle mass loss would improve patient’s daily physical activity and quality of health. <h3>References</h3> Watz, K et al (2008) <i>AJRCCM</i> 177(7), pp.743–751.
FRI0006 Frequency of TH17 CD4+ T cells in early rheumatoid arthritis
Authors: I. Arroyo-Villa, M.-B. Bautista-Caro, A. Balsa, P. Aguado-Acín, L. Nuño, M.-G. Bonilla-Hernán, A. Puig-Kröger, E. Martín-Mola, M.-E. Miranda-Carus
Journal: Annals of the Rheumatic Diseases (2013)

<h3>Objectives</h3> To examine the frequency and phenotype of Th17 cells in the peripheral blood of early RA (eRA) patients. <h3>Methods</h3> CD4+ T cells were isolated from the peripheral blood of 33 eRA patients and 33 healthy controls (HC), and from the synovial fluid of 20 established RA patients (RASF), by ficoll-hypaque gradient and magnetical negative selection. After polyclonal stimulation, the frequency of Th17 and Th1 cells was determined by flow cytometry and concentrations of IL-17, IFN-g, TNF-a and IL-10 were measured by ELISA in cell-free supernatants. <h3>Results</h3> When all of our eRA patients were analyzed together, a significantly lower percentage of circulating Th17 cells and a lower CD4-derived IL-17 secretion were observed in comparison with HC. However, after stratifying by anti-CCP antibody status, circulating Th17 cells were decreased in anti-CCP(+) but not in anti-CCP(–)-eRA. All Th17 cells were CD45RO+CD45RA- and CCR6+. Dual Th17/Th1 cells were also exclusively decreased in anti-CCP(+)-eRA. Circulating Th17 and Th17/Th1 cells were negatively correlated with anti-CCP titres. When anti-CCP(+)-eRA patients were retested one year after initiating treatment with oral methotrexate, their circulating Th17 frequency was no longer different from HC. Of note, the percentage of circulating Th1 cells and the secretion of CD4-derived IFN-g, TNF-a and IL-10 were not different between eRA patients and HC. In RASF, both Th17 and Th1 cells were increased when compared with blood. <h3>Conclusions</h3> Decreased circulating Th17 levels in eRA seem to be a marker of anti-CCP seropositivity, and return to levels observed in healthy controls after treatment with methotrexate. <h3>Disclosure of Interest</h3> None Declared
Abstract 1130: ING4 tumor suppressor binds to a transcription co-activator, CCAR1, and modulates estrogen-dependent cell growth and gene expression
Authors: Katherine Dempsey, Timothy G. Whitsett, Suwon Kim
Journal: Cancer Research (2010)

Abstract The tumor suppressor ING4 (Inhibitor of Growth family member 4) has been shown to play a role in diverse cancer-related cellular processes including gene regulation, apoptosis, cell migration, contact inhibition, and angiogenesis. Deletion or reduced expression of ING4 has been shown in various human malignancies including breast cancer, suggesting the tumor suppressive role of ING4. ING4 has been shown to interact with a number of proteins in different cell types, that include p53, NFkB, p300, HBO1-HAT complex, and HPH1. However, the binding partner(s) relevant to the ING4 tumor suppressor function in breast cancer have not been identified. We employed a bacterial two-hybrid screening system using the N-terminal half of the ING4 protein as bait and identified a number of candidate ING4 binding proteins (IBPs). One of the candidate IBPs was CCAR1 (Cell-Cycle and Apoptosis Regulator Protein 1). CCAR1 has recently been characterized as a transcriptional coactivator that is required for estrogen-induced gene expression and cell growth in human breast cancer cells (Kim JH, Yang CK, Heo K, Roeder RG, An W, and Stallcup MR, Mol Cell, 2008). We show the full length ING4 co-immunoprecipitated with endogenous CCAR1 in MCF7 breast cancer cells. In addition, we show that overexpression of ING4 blocked estrogen-dependent cell proliferation of MCF7 cells. These results indicated that ING4 directly binds to CCAR1 and may antagonize the CCAR1 activity required for estrogen-dependent cell growth. We conclude that ING4 may function as a tumor suppressor in breast cancer by modulating estrogen/CCAR1-dependent cell proliferation and gene transcription. 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 1130.
The application of miniature ultrasonic probes in diagnostic and follow-up with gastric varices by method of U-type reverse gastroscopy
Authors: Hong Xu, Zhuo Zhao, Jian-Guang Zhang, Shuang Wu
Journal: Endoscopy (2011)

To investigate the diagnostic value of miniature ultrasonic probes (MUPs) in digestive tract diseases by method of U-type reverse gastroscopy.
SAT0578 Patients with Rheumatoid Arthritis, Spondyloarthritis and Psoriatic Arthritis Treated with BIOLOGICS Use Similar Coping Strategies: A Study of 671 Patients:
Authors: A.-C. Rat, B. Fautrel, E. Flipon, L. Gossec, L. Marguerie, H. Nataf, B. Pallot Prades, R.M. Poilvert, V. Royant, F. Sadji, C. Sordet, C. Thevenot, C. Beauvais
Journal: Annals of the Rheumatic Diseases (2014)

<h3>Background</h3> Several coping models have been proposed to understand the psychological adjustment to Rheumatoid Arthritis (RA). Coping strategies of other inflammatory arthritis (IA) have been less extensively studied and have not been compared to each other. Moreover, biologics could dramatically influence coping strategies. <h3>Objectives</h3> To describe and compare the coping strategies of 3 groups of patients with IA treated by biologics: RA, Axial Spondyloarthritis (AS) and Psoriatic arthritis (PsA). <h3>Methods</h3> Data were obtained from a national cross-sectional survey aimed at studying self-care skills of patients treated by biologics for IA. To be as representative as possible of the patients treated by biologics, rheumatologists were randomly sampled from the national directory. They were invited to include 3 consecutive patients. All patients completed sociodemographic and clinical data, quality of life (SF12) and coping style (Brief Cope) self-administered questionnaires. The Brief Cope, a 28-item questionnaire determines the frequency with which people engage in 14 different coping mechanisms (self-distraction, active coping, denial, substance use, using emotional support, behavioural disengagement, religion, acceptance, venting, using instrumental support, positive reframing, self-blame, planning, humour). Scores on each subscale range from 2 to 8. The 3 IA were compared with analyses of variance. <h3>Results</h3> Of the 671 patients included, 67% were women, 61% had RA, 31% AS and 9% PsA, 63% were treated by subcutaneous antiTNF, 20% by non antiTNF biologics. The mean age was 53±13 years old, the SF12 physical and mental component summaries were 43.2±8.8, and 47.4±7.1 respectively. The coping strategies the most frequently used (median &gt;5) were acceptance, active coping, self-distraction, positive reframing and planning. Among the 14 coping mechanisms, only 4 were different (Table). PsA patients used more humour and less behavioural disengagement strategies. RA patients used more religion strategy and AS used less acceptance strategy. Scores were not associated with age (r &lt;0.15); humour was more frequently used by men and religion by women. After adjustment on sex, religion and humour dimensions were no more different between IA. <h3>Conclusions</h3> The differences of coping strategies between RA, AS and PsA patients treated by biologics are negligible. Biologics probably reduce these differences. These results help physicians to better understand coping strategies of patients with IA to better care for them in their adaptation to their chronic disease. <h3>Disclosure of Interest</h3> None declared <h3>DOI</h3> 10.1136/annrheumdis-2014-eular.4178
Abstract 74: Genome-wide DNA methylation analysis of pT1a renal cell carcinoma and renal oncocytomas
Authors: Ilsiya Ibragimova, Gowrishankar Banumathy, Tahseen Al-Saleem, Robert G. Uzzo, Paul Cairns
Journal: Cancer Research (2011)

Abstract Nephron sparing surgery (partial nephrectomy) is currently performed on small renal masses (4cm or less in size) confined to the kidney (pT1a). Up to 25% of small renal masses are benign, the majority being oncocytomas. Benign oncocytomas lack distinct radiographic findings on computerized tomography (CT) and cannot be diagnosed accurately using imaging alone. No difference in tumor size at presentation or tumor growth rate was noted between oncocytoma and RCC in a review of the literature. A needle biopsy or non-invasive urine based differential diagnosis of a benign lesion potentially would allow patients with equivocal renal lesions to avoid unnecessary surgery as well as anxiety if under active surveillance. The epigenetic alteration of aberrant DNA methylation has potential benefits as a choice of a biomarker because aberrant methylation occurs frequently and early in tumorgenesis and can be detected at extremely sensitive and specific levels by currently available technology. It is known that aberrant hypermethylation of the VHL gene occurs in a subset of clear cell RCC but is absent in oncocytoma. We hypothesized that additonal genes with a differential methylation status between benign oncocytoma and RCC could be identified. In this study, we performed genome-wide detection of DNA methylation in 25 RCC (pT1a), 25 oncocytomas of 4cm or less in size, and 4 age-matched histologically normal kidney tissues using the Infinium HumanMethylation27 BeadChip. To date, we have evidence that the profile of aberrant gene methylation is different between benign and malignant small renal masses matched for median size. Infinium-identified differentially methylated genes are validated using direct bisulfite sequencing, then a qMSP assay designed. If the panel of differentially methylated genes we have identified are verified in an independent set of small renal masses, we can then determine the predictive value of methylation-based detection of benign oncocytoma versus malignant RCC. 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 74. doi:10.1158/1538-7445.AM2011-74
Abstract 3482: Directly Detect High Risk HPV Oncogenes E6/E7 mRNAs from Pap Smear Samples without RNA Purification and RT-PCR.
Authors: Aiguo Zhang, Lulu Zhang, Rachel Chuang, Xining Zhu, Rachel Diaz, Lily Chen
Journal: Cancer Research (2013)

Abstract Cervical cancer is one of the most common cancers in women, with about 450,000 new cases diagnosed each year. Nearly all the cervical cancers are from Papillomaviruses (HPV) infection. HPV are DNA-based viruses that infect the skin and mucous membranes of humans and many other animals. Most cancers of the vulva and vagina are induced by oncogenic HPV types. In precancerous lesions, most HPV genomes persist in an episomal state whereas, in many high-grade lesions and carcinomas, genomes are found integrated into the host chromosome. Two viral genes, E6 and E7, are invariably expressed in HPV-positive cancer cells. Their gene products are known to inactivate the major tumour suppressors, p53 and retinoblastoma protein (pRB), respectively. In addition, E6 oncoprotein is also capable to up regulate the expression of inhibitors of apoptosis, and E6 and E7 cooperate to effectively immortalise primary epithelial cells. It has been demonstrated that HPV E6/E7 expression level plays a key role in the progression of invasive carcinoma of the uterine cervix via the deregulation of cellular genes controlling tumour cell proliferation. HPV E6/E7 oncogenes have been proved to be good biological markers for prognosis assessment and specific therapy of the disease. We have developed a sandwich nucleic acid hybridization assay using branched DNA to amplify the signals. The assay can simultaneously detect E6/E7 mRNAs of all 14 high risk HPV subtypes directly from Pap smear samples without RNA purification and RT-PCR. All HPV mRNA targets are captured through cooperative hybridization of multiple probes and probe set design determines the specificity of each HPV subtype of E6/E7 mRNA. Probe set oligonucleotides bind a contiguous region of the target E6/E7 mRNAs and selectively capture target RNAs to a solid surface during hybridization. Signal amplification is performed via sequential hybridization of Pre-Amplifier, Amplifier and label probe. The assay is highly specific and sensitive, which can detect as low as 50 transcript molecules. Citation Format: Aiguo Zhang, Lulu Zhang, Rachel Chuang, Xining Zhu, Rachel Diaz, Lily Chen. Directly Detect High Risk HPV Oncogenes E6/E7 mRNAs from Pap Smear Samples without RNA Purification and RT-PCR. [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 3482. doi:10.1158/1538-7445.AM2013-3482
Reply to Fan et al.
Authors: Seung-Woo Lee, Jeong-Seon Ji, Kang-Moon Lee
Journal: Endoscopy (2014)

First, there is indeed a typographical error in Table 4. As pointed out by Fan et al., stalk diameter should be ≤ 10 mm and > 10 mm, and not ≤ 1.0 mm and > 1.0 mm, respectively, as shown. An erratum has been published in issue 9.[*]
783 HBV-SPECIFIC CD8+ T CELLS AND NK CELLS MEDIATE THEIR ANTIVIRAL EFFECT PRIMARILY VIA PERFORIN/GRANZYME DEPENDENT CYTOLYSIS
Authors: D. Grimm, M. Heeg, N. Kersting, H.E. Blum, A. Bertoletti, R. Thimme
Journal: Journal of Hepatology (2012)
Paradoxical Restoration of Hepatic Uptake of Ga-67 After Aggressive Chemotherapy in a Case of Mesenteric Malignant Lymphoma
Authors: KAZUYOSHI SUGA, YUKO ISHIKAWA, KAZUKO MOTOYAMA, NORIHIKO KUME, NAOFUMI MATSUNAGA
Journal: Clinical Nuclear Medicine (2000)

Aggressive or recent antineoplastic chemotherapy will reduce hepatic uptake of Ga-67. The authors describe a patient with mesenteric lymphoma in whom a paradoxical increase of hepatic uptake of Ga-67 occurred after aggressive chemotherapy. Before treatment, the mesenteric vessels were involved extensively by the lymphoma mass, and hepatic uptake of Ga-67 was markedly diminished despite the fact that the patient had a normal serum transferrin concentration and no history of blood transfusions. After treatment, the vessels were normalized as a result of a marked regression of the lymphoma mass. Alterations of Ga-67 delivery to the liver through the mesenteric or portal vessels may cause paradoxical improvements of hepatic Ga-67 uptake after chemotherapy.
Diagnosis of focal pancreas lesions with CEUS and EUS
Authors: X Xie, M Lu, Y Cui, X Xie, Z Xu
Journal: Endoscopy (2006)

Objective: CEUS (contrast enhanced ultrasound) is very limited researches on the focal pancreas lesions. The aim of this study is to characterize the enhancement patterns of focal pancreas lesions with CEUS and to compare to the accuracy of CEUS and EUS in diagnosis.
Abstract LB-270: Targeting USP1 decreases glioblastoma stem cell survival and tumor growth.
Authors: Young Taek M. Oh, Eunhee Kim, Jeongwu Lee, Do-Hyun Nam
Journal: Cancer Research (2013)

Abstract Glioblastoma multiforme (GBM) is the most common and lethal primary brain tumor. GBM cells are highly resistant to standard-of-care therapies including radiation and chemotherapy, indicating an urgent need for the development of novel therapeutics. Recent evidence suggests that deubiquitinating enzymes are overexpressed or activated in various cancers, and they contribute to tumor progression and recurrence. Here, we report that the deubiquitinating enzyme ubiquitin-specific peptidase 1 (USP1) is highly expressed in GBMs and the targeting USP1 decreases cell survival and tumor growth. Targeting USP1 by RNA interference or treatment with a chemical USP1 inhibitor attenuated self-renewal and survival of GSCs. As one of the molecular mechanism that link USP1 to pro-tumorigenic roles, we found that the USP1 stabilized the inhibitor of DNA binding protein1 (ID1) and checkpoint kinase 1 (CHEK1), both of which are positive GSC regulators and implicated in radioresistance. Inhibition of USP1 in GBM cells leads to hypersensitivity to ionizing radiation through the decrease in DNA damage repair capacity. Finally, USP1 inhibition in orthotopic GBM xenografts significantly reduced tumor growth and prolonged the survival of tumor bearing mice. Together, our findings suggest that USP1 is a promising therapeutic target for GBMs and provide a rationale for positioning USP1 inhibitor as a GBM radiosensitizer. Citation Format: Young Taek M. Oh, Eunhee Kim, Jeongwu Lee, Do-Hyun Nam. Targeting USP1 decreases glioblastoma stem cell survival and tumor growth. [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 LB-270. doi:10.1158/1538-7445.AM2013-LB-270
IMPS-02EXPRESSION OF MULTIPLE ANTIGENS IN INDIVIDUAL GLIOBLASTOMA PATIENT SAMPLES EVALUATED BY IMMUNOCHEMISTRY
Authors: Michael Barish, Lihong Weng, Yubo Zhai, Massimo D'Apuzzo, Behnam Badie, Stephen Forman, Christine Brown
Journal: Neuro-Oncology (2015)

Cellular heterogeneity is a hallmark characteristic of ostensibly similar cell populations occurring during neural and glial development, and during tumorigenesis and tumor progression. For the latter case, large collections of formalin-fixed paraffin embedded (FFPE) clinical specimens are a valuable resource for evaluating gene expression across large study cohorts. Many of these patient samples consist of serial tumor sections each stained for a single antigen by chromogenic immunohistochemistry (IHC), as is standard clinical pathology practice. Quantifying multiple tumor related antigens in the context of GBM tissue is an essential step towards understanding the fundamental biology of these tumors as well as developing novel targeted therapies. Towards this end, we have developed methods for combining semi-quantitative analysis of IHC processed tumor sections with regional annotation by a clinical pathologist. This has allowed us to consider patterns of antigen co-expression as well as spatial relationships with tumor structures and physiological status. We will present our observations on expression of tumor-associated antigens IL13Rα2, HER2 and EGFR, and associations with proliferation as indicated by Ki67 expression and the vasculature as marked by the endothelial cell marker CD34.
P31 Intelligence Based Information System (ibis) Reduces Respiratory Patients' Use Of Secondary Health Care Resources
Authors: S. Harlow, J. Tollit, M. Irvin-Sellers
Journal: Thorax (2014)

<h3>Background</h3> IBIS is a database developed by South East Coast Ambulance Service (SECAmb) to facilitate communication of individual patient care plans between SECAmb, the Respiratory Care Team (RCT) and secondary care. It aims to reduce the number of patients conveyed to hospital. <h3>Aims and objectives</h3> The investigation aimed to establish the impact of IBIS on respiratory patients’ use of secondary care in our locality. <h3>Methods</h3> Respiratory patients uploaded into IBIS between May and November 2013 were included. Data were collected from the Patient Administration System including, number of A&amp;E attendances and admissions in the three months preceding and three months after patient care plans were included in IBIS. Data were analysed with descriptive statistics and Wilcoxon Paired Test utilising SPSS version 22. <h3>Results</h3> 65 patients were included in the study. Table 1 demonstrates the impact of IBIS on A&amp;E attendances and admissions. There was a significant reduction in admissions (p = 0.011). A reduction in A&amp;E attendances was observed (p = 0.064). A sub-analysis of patients already utilising secondary care resources was undertaken. In this patient group a significant reduction in both A&amp;E attendances (p = 0.000) and admissions (p = 0.000) was observed. <h3>Conclusions</h3> IBIS assists in reducing respiratory patients A&amp;E attendances and admissions. The impact of IBIS is more profound in patients who have already utilised secondary health care resources.