tbuckley/cabot-search huggingface dataset:
Abstract 3853: Unique pattern of copy number changes including chromothripsis in pulmonary adenocarcinoma with EML4-ALK fusion
Authors: Hironori Ninomiya, Motohiro Kato, Seishi Ogawa, Noriko Motoi, Kengo Takeuchi, Tatsushi Kodama, Hiroshi Sakamoto, Nobuya Ishii, Mutsunori Fujiwara, Yuichi Ishikawa
Journal: Cancer Research (2015)

Abstract Background: A subset of lung adenocarcinomas harbors an ALK fusion gene resulting in dominant oncogenic activity. Gene inversion may play a main role in forming the fusion, not producing copy number changes. But its detailed mechanism leading to gene fusion remains unsolved. MATERIAL AND METHODS: To elucidate the underlying mechanisms resulting in gene fusion, two cancer cell lines positive for EML4-ALK fusion and surgically resected frozen specimens (33 ALK fusion-positive and 95 ALK fusion-negative adenocarcinomas) were analyzed using Affymetrix CytoScan HD Array with Chromosome Analysis Suite (ChAS) software for cell lines (JFCR-LC649 and JFCR-LC654) and Affymetrix GeneChip Mapping 250K arrays for surgical specimens. RESULTS: One (JFCR-LC649) of the two cell lines with gene fusion showed an extremely frequent change of copy number, or “copy number oscillation”, which we thought was chromothripsis. In surgical materials, 30% (10/33) of adenocarcinomas with ALK fusion harbored frequent copy number changes at various degrees, but not like the “oscillation” pattern. None of the 95 resected cases without ALK fusion showed similar genomic aberrations. These results from the JFCR-LC649 line and the 10 surgical cases indicated that genomic changes resulting in copy number alterations (including chromothripsis) as well as a simple inversion may cause gene fusion. CONCLUSION: As well as genome inversion, copy number alterations such as chromothripsis contribute to gene rearrangements resulting in the EML4-ALK fusion. Citation Format: Hironori Ninomiya, Motohiro Kato, Seishi Ogawa, Noriko Motoi, Kengo Takeuchi, Tatsushi Kodama, Hiroshi Sakamoto, Nobuya Ishii, Mutsunori Fujiwara, Yuichi Ishikawa. Unique pattern of copy number changes including chromothripsis in pulmonary adenocarcinoma with EML4-ALK fusion. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3853. doi:10.1158/1538-7445.AM2015-3853
Genetic Determination of Sex-Specific Antigens&lt;xref ref-type="fn" rid="FN1"&gt;2&lt;/xref&gt;
Authors: Allen S. Fox
Journal: JNCI Journal of the National Cancer Institute (1959)

The results of an immunogenetic analysis of the effects of the X and Y chromosomes on tissue antigens (proteins) in Drosophila melanogaster are presented, and are used to formulate by analogy the genetic problems involved in the analysis of sex-specific antigens, particularly those connected with the Eichwald-Silmser effect in mice (rejection of male isografts by females). In Drosophila, 2 male-specific antigens (♂-1 and ♂-2) and 2 female-specific antigens (♀ -1 and ♀ -2) are demonstrated by means of agar-diffusion techniques. These differences between males and females are attributable to the difference in number of X chromosomes (1 in males and 2 in females) rather than to the presence or absence of the Y chromosome, thus suggesting involvement of the sex-determining genes carried by the X. The heterochromatic Y chromosome has no detected effect on the antigenic specificity of proteins, but it does exert a maternal influence on the immunological (precipitating) and physical properties of at least one protein (Y-1). The presence or absence of a Y chromosome in the oocytes of a female prior to meiosis determines the properties of Y-1 produced in her progeny after fertilization. Thus, questions regarding X-chromosomal dosage, presence or absence of the Y chromosome, and matrocliny must all be answered in the genetic analysis of sex-specific antigens. Description is given of experiments designed to fulfill these requirements in the case of the Eichwald-Silmser effect.
Early-life ozone exposure associated with asthma without sensitization in Latino children
Authors: Katherine K. Nishimura, Kensho Iwanaga, Sam S. Oh, Maria Pino-Yanes, Celeste Eng, Anjeni Keswani, Lindsey A. Roth, Elizabeth A. Nguyen, Shannon M. Thyne, Harold J. Farber, Denise Serebrisky, Kelley Meade, Michael A. LeNoir, William Rodriguez-Cintron, Luisa N. Borrell, Kirsten Bibbins-Domingo, Fred Lurmann, Śaunak Sen, Jose R. Rodriguez-Santana, Emerita Brigino-Buenaventura, Pedro C. Avila, John R. Balmes, Rajesh Kumar, Esteban G. Burchard
Journal: Journal of Allergy and Clinical Immunology (2016)
Asia-Pacific consensus on the management of gastro-oesophageal reflux disease: an update focusing on refractory reflux disease and Barrett's oesophagus
Authors: Kwong Ming Fock, Nicholas Talley, Khean Lee Goh, Kentaro Sugano, Peter Katelaris, Gerald Holtmann, John E Pandolfino, Prateek Sharma, Tiing Leong Ang, Michio Hongo, Justin Wu, Minhu Chen, Myung-Gyu Choi, Ngai Moh Law, Bor-Shyang Sheu, Jun Zhang, Khek Yu Ho, Jose Sollano, Abdul Aziz Rani, Chomsri Kositchaiwat, Shobna Bhatia
Journal: Gut (2016)

<h3>Objective</h3> Since the publication of the Asia-Pacific consensus on gastro-oesophageal reflux disease in 2008, there has been further scientific advancement in this field. This updated consensus focuses on proton pump inhibitor-refractory reflux disease and Barrett9s oesophagus. <h3>Methods</h3> A steering committee identified three areas to address: (1) burden of disease and diagnosis of reflux disease; (2) proton pump inhibitor-refractory reflux disease; (3) Barrett9s oesophagus. Three working groups formulated draft statements with supporting evidence. Discussions were done via email before a final face-to-face discussion. We used a Delphi consensus process, with a 70% agreement threshold, using Grading of Recommendations Assessment, Development and Evaluation (GRADE) criteria to categorise the quality of evidence and strength of recommendations. <h3>Results</h3> A total of 32 statements were proposed and 31 were accepted by consensus. A rise in the prevalence rates of gastro-oesophageal reflux disease in Asia was noted, with the majority being non-erosive reflux disease. Overweight and obesity contributed to the rise. Proton pump inhibitor-refractory reflux disease was recognised to be common. A distinction was made between refractory symptoms and refractory reflux disease, with clarification of the roles of endoscopy and functional testing summarised in two algorithms. The definition of Barrett9s oesophagus was revised such that a minimum length of 1 cm was required and the presence of intestinal metaplasia no longer necessary. We recommended the use of standardised endoscopic reporting and advocated endoscopic therapy for confirmed dysplasia and early cancer. <h3>Conclusions</h3> These guidelines standardise the management of patients with refractory gastro-oesophageal reflux disease and Barrett9s oesophagus in the Asia-Pacific region.
AB1008 Screening of Free Carnitine and Acyl-Carnitine Status in Patients with Familial Mediterranean Fever
Authors: E. Kiykim, K. Barut, A.C. Aktuglu-Zeybek, T. Zubarioglu, S. Cansever, A. Aydin, O. Kasapcopur
Journal: Annals of the Rheumatic Diseases (2015)

<h3>Background</h3> Familial Mediterranean fever (FMF) is an autosomal recessive disease characterized by recurring self-limited fever, abdominal pain and chest pain caused by serositis (1). FMF mainly affects Middle-East populations with a high prevalence in Sephardic Jews, Turkish, Arabs and Armenians (2). Carnitine is an important molecule in cellular energy metabolism. Secondary carnitine deficiency can be detected in chronic diseases by either renal loss or increased needs (3). <h3>Objectives</h3> Our hypothesis was that FMF patients would have lower free carnitine levels than their healthy age and gender matched controls due to increased need of carnitine because of recurrent auto-inflammation. The present study was conducted to determine the patterns of free carnitine and acyl-carnitine esters in FMF patients. <h3>Methods</h3> This is a cross-sectional study of 205 FMF patients who were attending the outpatient Pediatric Rheumatology clinic of Cerrahpasa Medical Faculty Children9s Hospital. The patients were selected by random sampling and FMF diagnosis was confirmed by a pediatric rheumatologist according to Yalcınkaya criteria. 50 healthy subsects were enrolled to the present study. A fasting died blood sample was taken for studying free carnitine and acyl-carnitine esters with tandem mass spectrometry from children in both groups. <h3>Results</h3> Acyl-carnitine analyses in spot dried blood samples with ESI-MS/MS were performed in all patients and control group. Screening of acyl-carnitine profile revealed free carnitine, C16-OH and C18:2 carnitine levels were higher (p&lt;0,0001, p&lt;0,0001 and p=0,003 respectively), while C4-OH and C4DC carnitine levels were lower (p&lt;0,0001) in FMF patients than the control group. <h3>Conclusions</h3> In the present study we were not able to define secondary carnitine deficiency in FMF patients, therefore usage of carnitine in all patients with FMF is not recommended. <h3>References</h3> Ozen S, Bilginer Y. A clinical guide to autoinflammatory diseases: familial Mediterranean fever and next-of-kin. Nat Rev Rheumatol. 2014;10(3):135-47. Yilmaz E, Ozen S, Balci B, Duzova A, Topaloglu R, Besbas N et al. Mutation frequency of Familial Mediterranean Fever and evidence for a high carrier rate in the Turkish population. Eur J Hum Genet 2001;9:553–5. Stanley CA. Carnitine deficiency disorders in children. Ann N Y Acad. Sci.2004; 1033:42–51. <h3>Disclosure of Interest</h3> None declared
Results of Allogeneic Transplantation As First Line Rescue Therapy in Patients with Multiple Myeloma Relapsing to a Prior Autograft: Role of Conditioning Regimen
Authors: Jose A. Perez-Simon, Francisco J Marquez-Malaver, Cora Knol, Simona Iacobelli, Didier Blaise, Noel-Jean Milpied, Ellen Meijer, Peter Dreger, Yener Koc, Eefke Petersen, Mauricette Michallet, Laurent Garderet, Nicolaus Kroeger
Journal: Blood (2015)
Nilotinib For Steroid-Refractory Chronic Graft Versus Host Disease (SR-cGVHD): Preliminary Results Of a Phase I-II GITMO Study (Gruppo Italiano Trapianto di Midollo Osseo)
Authors: Attilio Olivieri, Michele Cimminiello, Ivana Latesoriere, Pietro Leoni, Francesco Onida, Roberta Fedele, Paolo Corradini, Vincenzo Pavone, Roberta Nuccorini, Sara Pasquina Pascale, Jacopo Olivieri, Giorgia Mancini, Sonia Mammoliti, Alessandro Rambaldi
Journal: Blood (2013)
Glucose Metabolism of Tumors Induced by Rous Sarcoma Virus. III. Carbohydrate Metabolic Enzymes in Rous Sarcoma&lt;xref ref-type="fn" rid="FN1"&gt;2&lt;/xref&gt;
Authors: Weber, George, Banerjee, Gouri, Levine, Alvin S., Ashmore, James
Journal: JNCI Journal of the National Cancer Institute (1961)

Journal Article Glucose Metabolism of Tumors Induced by Rous Sarcoma Virus. III. Carbohydrate Metabolic Enzymes in Rous Sarcoma Get access George Weber, George Weber Departments of Pharmacology and Microbiology, Indiana University School of Medicine, Indianapolis, Indiana Search for other works by this author on: Oxford Academic PubMed Google Scholar Gouri Banerjee, Gouri Banerjee Departments of Pharmacology and Microbiology, Indiana University School of Medicine, Indianapolis, Indiana Search for other works by this author on: Oxford Academic PubMed Google Scholar Alvin S. Levine, Alvin S. Levine Departments of Pharmacology and Microbiology, Indiana University School of Medicine, Indianapolis, Indiana Search for other works by this author on: Oxford Academic PubMed Google Scholar James Ashmore James Ashmore Departments of Pharmacology and Microbiology, Indiana University School of Medicine, Indianapolis, Indiana Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 27, Issue 4, October 1961, Pages 869–873, https://doi.org/10.1093/jnci/27.4.869 Published: 01 October 1961 Article history Received: 19 June 1961 Published: 01 October 1961
First human case of West Nile virus neuroinvasive infection in Italy, September 2008 – case report
Authors: G Rossini, F Cavrini, A Pierro, P Macini, A C Finarelli, C Po, G Peroni, A Di Caro, M R Capobianchi, L Nicoletti, M P Landini, V Sambri
Journal: Eurosurveillance (2008)

On 20 September 2008, the laboratory of the Regional Reference Centre for Microbiological Emergencies (Centro di Riferimento Regionale per le Emergenze Microbiologiche, CRREM) in Bologna, reported the detection of specific IgM and IgG antibodies against West Nile virus (WNV) in the serum of a female patient in her eighties who lived in a rural area between Ferrara and Bologna, Italy.
The Future of Tissue Culture in Relation to Morphology&lt;xref ref-type="fn" rid="FN1"&gt;2&lt;/xref&gt;
Authors: H B FELL
Journal: JNCI Journal of the National Cancer Institute (1957)

Journal Article The Future of Tissue Culture in Relation to Morphology Get access Honor B. Fell Honor B. Fell Strangeways Research Laboratory, Cambridge, England Search for other works by this author on: Oxford Academic PubMed Google Scholar JNCI: Journal of the National Cancer Institute, Volume 19, Issue 4, October 1957, Pages 643–662, https://doi.org/10.1093/jnci/19.4.643 Published: 01 October 1957 Article history Received: 28 May 1957 Published: 01 October 1957
Multimodality Treatment of the Hyperkinetic Child
Authors: Anne C. Feighner, John P. Feighner
Journal: American Journal of Psychiatry (1974)

This paper describes a comprehensive program for the diagnosis and treatment of hyperkinetic children. The program is an intensive but short-term undertaking and includes a complete evaluation of the child, pharmacotherapy, behavior modification, curriculum counseling, training for parents and teachers, parent-child interaction videotaping and feedback sessions, and a coordination of the treatment effort with the child, his family, and his school. The program allows for a progression at the child's pace in order to ensure continuity of both care and development.
SP0024 Challenges in Supporting Behavior Change in a Two-Year Real-Life Physical Activity Program
Authors: B. Nordgren
Journal: Annals of the Rheumatic Diseases (2015)

Promoting physical activity (PA) in rheumatoid Arthritis (RA) is important for improved health outcomes, and is usually performed in a clinical setting. Considering that RA is a lifelong disease, self-management of PA outside health care should be encouraged. The purpose of the Physical Activity in Rheumatoid Arthritis (PARA) study, was to study whether persons with RA would be able to manage their PA in a real life environment, outside health care with limited support from a physical therapist. The 2-year program, performed in public training centers, was based on PA recommendations. The first year consisted of three main components; daily PA, two weekly circuit training sessions including aerobic and strength exercises and bi-weekly support group meetings. The meetings were based on existing evidence on social cognitive theory using individual goal setting, action planning, feedback on performance and provision of social support in a group format. The meetings were led by physical therapists, trained prior the intervention in coaching skills and strategies to support PA behavior. During the second year, the meetings were optional with the participant9s in charge. High retention and reasonable adherence indicated good feasibility of the program. Circuit training at public gyms, PA in daily life, prompts by text messages and professional coaching were highly valued by the participants. Tailoring coaching to the participant9s preferences regarding setting, exercise format and behavioral support was a major challenge as was also the mixed previous experience of exercise and the individual9s physical condition. <h3>Disclosure of Interest</h3> None declared
Effect of Tumor Necrosis Factor in Normal Subjects
Authors: J N Bavinck, A M Kootte, F J van der Woude, J P Vandenbroucke, B J Vermeer, F H Claas
Journal: New England Journal of Medicine (1990)

To the Editor: Considering that there is now a consensus on the central role of tumor necrosis factor in the pathogenesis of septic shock, the study by van der Poll et al. (June 7 issue),1 in which normal subjects were administered tumor necrosis factor, is both timely and important. I agree with their deduction — based on the increased levels of the activation peptide of factor X and prothrombin fragment F1+2 — that the common coagulation pathway is probably activated initially by tissue factor. However, their conclusion that the intrinsic pathway, particularly the contact system, was not activated is.
AB0522 Use of Steroids and Immunosuppressors in Primary SjÖgren's Syndrome and Its Relation with Damage Accrual: Table 1
Authors: G. Hernandez-Molina, D. Faz-Muñoz
Journal: Annals of the Rheumatic Diseases (2015)

<h3>Background</h3> Primary Sjögren9s syndrome (pSS) is a multisystem autoimmune disease that encompasses extraglandular features that are traditionally managed with steroids and immunosuppresors. <h3>Objectives</h3> To assess the use of prednisone (PDN) and immunosuppressors in a retrospective pSS cohort and to evaluate their association with damage accrual. <h3>Methods</h3> We reviewed the medical records of 155 pSS patients who regularly attended our Institution (2010-2014) with at least 6 months of follow-up. We used a standardized form to register demographics, glandular (oral/ocular symptoms, parotid enlargement) and extraglandular features. We specifically reviewed data regarding the use of PDN and immunosuppresors from the diagnosis until the last visit. We also scored the SSDI at the last visit (n=116). We used descriptive statistics, Chi-square test and logistic regression analysis reporting OR and 95%C.I. <h3>Results</h3> Patients were 92.2% females, mean age 57.4±14.7 years and median follow-up 11 years (0.5-47.9). Fifty-one patients (32.9%) were free of treatment and 104 (67%) had ever received PDN and/or immunosuppressors. The latter group presented more parotid enlargement (55.8% vs. 37.3%, p=0.04), lymphadenopathy (34.6% vs. 13.7%, p=0.007), arthritis (45.2% vs. 9.8%, p&lt;0.0001), autoimmune hepatitis (9.6% vs. 0%, p=0.02), pulmonary (16.3% vs. 3.9%, p=0.03) and hematologic involvement (44.2% vs. 25.5%, p=0.03). The percentage of use, median number of use periods, maximum dose, main indication and percentage of toxicity are shown at Table 1. Some patients with isolated parotid enlargement (PDN 3%, AZA 2%, antimalarial 1%, MTX 0.6%) or oral/ocular dryness (PDN 1.9%, antimalarial 7%, AZA and MTX 0.6% for each) also received treatment. The overall median SSDI score was 3 (0-8). Patients with a SSDI&gt;2 (n=60) used more frequently cyclophosphamide (15% vs. 0%, p=0.003) and less often antimalarials (35% vs. 55%, p=0.02). At the regression logistic analysis adjusted by disease duration, a SSDI &gt;2 was associated with the presence of any extraglandular feature (OR 4.4, 95% C.I. 1.39-13.9, p=0.01) whereas the use of antimalarials was protective (OR 0.36, 95% C.I. 0.16-0.82, p=0.01). <h3>Conclusions</h3> More than 50% of pSS patients received PDN and/or immunosuppresors during their follow-up. This fact confirms the systemic nature of the disease and should alert physicians of secondary adverse events with the use of this treatment. The use of antimalarial seemed to protect against damage accrual, an observation that needs further validation in another cohorts. <h3>Disclosure of Interest</h3> None declared
Allogeneic HY Antibodies 3 Months Following Sex-Mismatched HCT Predicts Chronic Graft-Versus-Host Disease and Non-Relapse Mortality
Authors: Hideki Nakasone, Lu Tian, Takakazu Kawase, Bita Sahaf, Rakesh Popli, Joyce Lee, Kelsi Schoenrock, Spenser Perloff, Fang Wu, Joanne M Otani, Andrea M. H. Towlerton, Shoko Satoh, Edus H. Warren, David B. Miklos
Journal: Blood (2013)
A Revolution in Treatment for Hepatitis C Infection: Mitigating the Budgetary Impact
Authors: Elliot Marseille, James G. Kahn
Journal: PLoS Medicine (2016)

The new generation of direct-acting antiviral drugs for hepatitis C (HCV) are extraordinarily effective, safe and well tolerated.With a relatively short 12-week course of treatment costing approximately US$84,000 in the United States, they are also extraordinarily costly [1].In their study in PLOS Medicine, Suzanne Hill and colleagues address important economic implications of the new HCV therapies in 26 Organisation for Economic Cooperation and Development (OECD) member countries plus four low-and middle-income countries (LMICs).Given medicine prices specific to each country and the recommended 12-week treatment, the authors calculated total drug costs, which they compared with the total pharmaceutical expenditure (TPE) and the average annual wage in each country.By these measures of affordability, the authors argue that the new drug regimens ". ..threaten the sustainability of health systems in many countries and prevent large scale provision of treatment."They call for fairer prices that would allow countries to invest in more treatment and thus lower the burden of HCV.Lower prices would ease the budgetary impact of these drugs and accelerate access.However, we believe that even with the current price structure, in each country the budgetary impact need not be as severe as suggested.In this Perspective, we compare the history of the pricing and availability of antiviral therapy for HIV with that of HCV.Elucidating points of similarity, and particularly differences, may aid in understanding the challenges and opportunities associated with the HCV therapies.Both HIV anti-retroviral therapy (ART) and the new HCV therapies are highly effective, revolutionizing the responses to these diseases.While no cure, ART famously had the "Lazarus effect" of bringing patients back from the brink of death.With subsequent refinement of the regimens, patients may live as long as their HIV-negative counterparts and with a tolerable sideeffect profile [2,3].Similarly, the new generation of HCV treatments are very effective, with cure rates of 95%.The other similarity is the very high price.At an annual cost of US$12,000 in the early days of ART, these prices ensured that ART could not be implemented at scale in LMICs, even with assistance from donors.Similarly, at a list price for HCV therapies of about US $84,000 in high-income countries, the onerous short-term budgetary impact guarantees that the new therapies will not be immediately available to all those who might benefit in rich countries, let alone LMICs.But here the similarities end, and the differences are more illuminating. Multi-tiered Pricing from the StartStarting in 1997, the pharmaceutical industry resisted calls by activists for lower ART prices in LMICs, citing trade agreements, law, and the long-standing practice of having one global price
Endocrine and Anatomical Correlations in Human Ovarian Pathology
Authors: A. F. Haney
Journal: Environmental Health Perspectives (1987)

Knowledge of normal gonadal hormone production and function provides the basis for understanding the ovarian pathologic effects resulting from perturbations in endocrine balance and feedback. A precisely timed, complex, and well-coordinated cascade of ovarian steroidogenesis accompanies normal cyclical follicular function. This cascade involves both estrogens and androgens. Alterations in the hormonal milieu are associated with specific morphological changes in the ovary. While predictable hormonal changes accompany commencement of menopause, several disease states are associated with ovarian dysfunction. These diseases include polycystic ovarian syndrome and hyperthecosis, both associated with androgenization. Ovarian tumors may also be associated with morphological and clinical alterations. While endocrinologically inert ovarian tumors are associated with morphologic evidence of stromal activation, endocrinologically active ovarian tumors may cause differentiation along either male or female lines as a consequence of differential productions of androgens and estrogens.