tbuckley/cabot-search huggingface dataset:
An Integrated View of Copy Number and Allelic Alterations in the Cancer Genome Using Single Nucleotide Polymorphism Arrays
Authors: Xiaojun Zhao, Cheng Li, J. Guillermo Paez, Koei Chin, Pasi A. Jänne, Tzu-Hsiu Chen, Luc Girard, John Minna, David Christiani, Chris Leo, Joe W. Gray, William R. Sellers, Matthew Meyerson
Journal: Cancer Research (2004)

Abstract Changes in DNA copy number contribute to cancer pathogenesis. We now show that high-density single nucleotide polymorphism (SNP) arrays can detect copy number alterations. By hybridizing genomic representations of breast and lung carcinoma cell line and lung tumor DNA to SNP arrays, and measuring locus-specific hybridization intensity, we detected both known and novel genomic amplifications and homozygous deletions in these cancer samples. Moreover, by combining genotyping with SNP quantitation, we could distinguish loss of heterozygosity events caused by hemizygous deletion from those that occur by copy-neutral events. The simultaneous measurement of DNA copy number changes and loss of heterozygosity events by SNP arrays should strengthen our ability to discover cancer-causing genes and to refine cancer diagnosis.
Comparative study of MRI and power Doppler ultrasonography of the heel in patients with spondyloarthritis with and without heel pain and in controls
Authors: Antoine Feydy, Marie-Charlotte Lavie-Brion, Laure Gossec, Frédéric Lavie, Henri Guerini, Christelle Nguyen, François Rannou, Jean-Luc Drapé, Maxime Dougados
Journal: Annals of the Rheumatic Diseases (2011)

<h3>Introduction</h3> Imaging of heel enthesopathy in spondyloarthritis (SpA) could potentially be useful for diagnosis and monitoring. The aim of this study was to assess the diagnostic capacities of MRI and power Doppler ultrasonography (PDUS) of the heel to distinguish patients with SpA from controls and to distinguish between patients with SpA with and without enthesopathy. <h3>Methods</h3> A cross-sectional single-centre study was performed in 51 patients (102 heels) with definite SpA according to Amor9s criteria. Patients with degenerative non-inflammatory low back pain (n=24, 48 heels) were included as controls. Bilateral heel MRI and PDUS were performed by two senior musculoskeletal radiologists blinded to the clinical and biological data on the same day as the clinical evaluation. The data were analysed by patient and by heel. <h3>Results</h3> Neither MRI nor PDUS could discriminate between patients with SpA and controls; bone oedema on MRI was the only abnormality specific to SpA (94%), but with a poor sensitivity (22%). However, among patients with SpA, painful heels had more inflammatory abnormalities (81% by MRI, 58% by PDUS) than heels with no pain (56% at MRI, 17% at PDUS). <h3>Conclusion</h3> Heel MRI and PDUS frequently show inflammatory lesions in SpA, particularly in painful heels. However, they were also often abnormal in controls. These results suggest that heel MRI and PDUS cannot be used for the diagnosis of SpA. However, PDUS and MRI may be useful for the depiction and assessment of enthesis inflammatory lesions in patients with SpA with heel pain.
Modulation of tryptophan catabolism by human leukemic cells results in the conversion of CD25− into CD25+ T regulatory cells
Authors: Antonio Curti, Simona Pandolfi, Barbara Valzasina, Michela Aluigi, Alessandro Isidori, Elisa Ferri, Valentina Salvestrini, Giuseppina Bonanno, Sergio Rutella, Ilaria Durelli, Alberto L. Horenstein, Francesca Fiore, Massimo Massaia, Mario P. Colombo, Michele Baccarani, Roberto M. Lemoli
Journal: Blood (2006)
Urokinase-dependent plasminogen activation is required for efficient skeletal muscle regeneration in vivo
Authors: Frederic Lluı́s, Josep Roma, Mònica Suelves, Maribel Parra, Gloria Aniorte, Eduard Gallardo, Isabel Illa, Luciano Rodrı́guez, Simon M. Hughes, Peter Carmeliet, Manuel Roig, Pura Muñoz-Cánoves
Journal: Blood (2001)
The development and validation of the King's Sarcoidosis Questionnaire for the assessment of health status
Authors: Amit Suresh Patel, Richard J Siegert, Daniel Creamer, Genevieve Larkin, Toby M Maher, Elisabetta A Renzoni, Athol U Wells, Irene J Higginson, Surinder S Birring
Journal: Thorax (2012)

<h3>Rationale</h3> Health status is impaired in patients with sarcoidosis. There is a paucity of tools that assess health status in sarcoidosis. The objective of this study was to develop and validate the King9s Sarcoidosis Questionnaire (KSQ), a new modular health status measure. <h3>Methods</h3> Patients with sarcoidosis were recruited from outpatient clinics. The development of the questionnaire consisted of three phases: item generation; item reduction, Rasch analysis to create unidimensional scales and validation; repeatability testing. <h3>Results</h3> 207 patients with sarcoidosis (organ involvement: 184 lung, 54 skin, 45 eye disease) completed a 65-item preliminary questionnaire. 36 items were removed due to redundancy or poor fit to the Rasch model. The final version of the KSQ consisted of five modules (General health status, Lung, Skin, Eye, Medications). Internal consistency assessed with Cronbach9s α coefficient was 0.70–0.93 for KSQ modules. Concurrent validity of the Lung module was high compared with St George9s Respiratory Questionnaire (r=−0.83) and moderate when compared to forced vital capacity (r=0.49). Concurrent validity with skin-specific and eye-specific measures ranged from r=−0.4 to 0.8. The KSQ was repeatable over 2 weeks (n=39), intraclass correlation coefficients for modules were 0.90–0.96. <h3>Conclusions</h3> The KSQ is a brief, valid, self-completed health status measure for sarcoidosis. It can be used in the clinic to assess sarcoidosis from the patients’ perspective.
Molecular markers and biological targeted therapies in metastatic colorectal cancer: expert opinion and recommendations derived from the 11th ESMO/World Congress on Gastrointestinal Cancer, Barcelona, 2009
Authors: E. Van Cutsem, M. Dicato, N. Arber, J. Berlin, A. Cervantes, F. Ciardiello, A. De Gramont, E. Diaz-Rubio, M. Ducreux, R. Geva, B. Glimelius, R. Glynne Jones, A. Grothey, T. Gruenberger, D. Haller, K. Haustermans, R. Labianca, H.J. Lenz, B. Minsky, B. Nordlinger, A. Ohtsu, N. Pavlidis, P. Rougier, W. Schmiegel, C. Van de Velde, H.J. Schmoll, A. Sobrero, J. Tabernero
Journal: Annals of Oncology (2010)
Tuberculosis Control Policies in Major Metropolitan Health Departments in the United States
Authors: DONNA R. LEFF, ALAN R. LEFF
Journal: American Journal of Respiratory and Critical Care Medicine (1997)

Since 1980, we have surveyed at 4-yr intervals the metropolitan health departments initially reporting > 250 cases of tuberculosis to determine the perceived standard of practice for tuberculosis control and the factors affecting formulation of treatment policies. Between 1992 and 1996, use of supervised short-course (6 to 9 mo) intermittent therapy with multiple drugs including isoniazid, ethambutol, pyrazinamide, and rifampin increased from 4.3% to 46% of all new patients. Pyrazinamide use for initial treatment for children has increased substantially and now predominates (74.2% of patients in 1996 versus 48.1% of patients in 1992). Duration of treatment, which was 20 ± 2.1 mo in 1980, is now 8.00 ± 2.29 mo in 1996. The incidence of human immunodeficiency virus–associated tuberculosis, which was virtually unrecognized in 1984, has remained the same between 1992 and 1996 (18.0%). As in previous years, there was a wide variance among health departments in the incidence ( < 5% to > 40%) of HIV-associated tuberculosis. After years of funding decreases, there has been an impressive increase in resources in the past 4 yr. In 1988, mean budget allocation for health departments decreased by 7.9% versus the prior 4 yr and, in 1992, there was no overall change in budget allocation after inflation versus 1988. In 1996, however, funds for treatment increased by 84 ± 33%. This increase in funding has been translated into the greatly expanded use of supervised intermittent therapy and aggressive screening programs, which likely have resulted in the decreased incidence of tuberculosis since the prior survey.
NPHS2, encoding the glomerular protein podocin, is mutated in autosomal recessive steroid-resistant nephrotic syndrome
Authors: Nicolas Boute, Olivier Gribouval, Séverine Roselli, France Benessy, Hyunjoo Lee, Arno Fuchshuber, Karin Dahan, Marie-Claire Gubler, Patrick Niaudet, Corinne Antignac
Journal: Nature Genetics (2000)
Activated Omentum Slows Progression of CKD
Authors: Ignacio Garcia-Gomez, Nishit Pancholi, Jilpa Patel, Krishnamurthy P. Gudehithlu, Periannan Sethupathi, Peter Hart, George Dunea, Jose A.L. Arruda, Ashok K. Singh
Journal: Journal of the American Society of Nephrology (2014)

Stem cells show promise in the treatment of AKI but do not survive long term after injection. However, organ repair has been achieved by extending and attaching the omentum, a fatty tissue lying above the stomach containing stem cells, to various organs. To examine whether fusing the omentum to a subtotally nephrectomized kidney could slow the progression of CKD, we used two groups of rats: an experimental group undergoing 5/6 nephrectomy only and a control group undergoing 5/6 nephrectomy and complete omentectomy. Polydextran gel particles were administered intraperitoneally before suture only in the experimental group to facilitate the fusion of the omentum to the injured kidney. After 12 weeks, experimental rats exhibited omentum fused to the remnant kidney and had lower plasma creatinine and urea nitrogen levels; less glomerulosclerosis, tubulointerstitial injury, and extracellular matrix; and reduced thickening of basement membranes compared with controls. A fusion zone formed between the injured kidney and the omentum contained abundant stem cells expressing stem cell antigen-1, Wilms' tumor 1 (WT-1), and CD34, suggesting active, healing tissue. Furthermore, kidney extracts from experimental rats showed increases in expression levels of growth factors involved in renal repair, the number of proliferating cells, especially at the injured edge, the number of WT-1-positive cells in the glomeruli, and WT-1 gene expression. These results suggest that contact between the omentum and injured kidney slows the progression of CKD in the remnant organ, and this effect appears to be mediated by the presence of omental stem cells and their secretory products.
A CYCLICAL APPEARANCE OF ANTIBODY-PRODUCING CELLS AFTER A SINGLE INJECTION OF SERUM PROTEIN ANTIGEN
Authors: Carole G. Romball, William O. Weigle
Journal: The Journal of Experimental Medicine (1973)

After a single intravenous injection of rabbits with aggregated HuIgG, IgM- and IgG-plaque-forming cells (PFC) in both the spleens and peripheral blood of rabbits peaked 5, 13, and 21 days after injection, while almost no PFC could be detected on days 8 and 16. The available data suggest that the secondary peaks of PFC (days 13 and 21) resulted from stimulation of memory cells by persisting antigen that was localized in the germinal centers in the spleen. No such persistence of antigen occurred in the lymph nodes, and these lymphoid tissues did not exhibit secondary peaks of PFC. The identical kinetic patterns for IgM- and IgG-PFC indicate that the major portion of IgG-PFC did not result from IgM-secreting cells switching to IgG synthesis and secretion. The present data suggest that the antibody produced and present at the site of interaction between committed cells and antigen is responsible for the regulation of antibody synthesis to persisting antigens. Possible cellular events involved in both the regulation and an apparent synchronous appearance of antibody producing cells in the spleens of rabbits were presented.
Two-year results after lung volume reduction surgery in alpha1-antitrypsin deficiency versus smoker's emphysema
Authors: PC Cassina, H Teschler, N Konietzko, D Theegarten, G Stamatis
Journal: European Respiratory Journal (1998)

Lung volume reduction surgery (LVRS) improves exercise capacity and relieves dyspnoea in patients with smoker's emphysema (SE). It is unclear, however, whether LVRS similarly improves lung function in alpha1-antitrypsin-deficiency emphysema (alpha1 E). To address this question, this study prospectively compared the intermediate-term functional outcome in 12 consecutive patients with advanced alpha1E and 18 patients with SE who underwent bilateral LVRS. Before surgery there were no statistically significant differences between the two groups in the six-minute walking distance, dyspnoea score, respiratory mechanics or lung function data, except for the forced expiratory volume in one second, which was lower in the deficient group (24 versus 31% of the predicted value; p&lt;0.05). In both groups, bilateral LRVS produced significant improvements in dyspnoea, the six-minute walking distance, lung function and respiratory mechanics. In the alpha1E group, the functional data, with the exception of the six-minute walking distance, returned to baseline at 6-12 months postoperation and showed further deterioration at 24 months. The functional status of the SE group remained significantly improved over this period. In conclusion, the functional improvements resulting from bilateral lung volume reduction surgery are sustained for at least 2 yrs in most patients with smoker's emphysema, but this type of surgery offers only short-term benefits for most patients with alpha1E.
Use of smokeless tobacco and risk of myocardial infarction and stroke: systematic review with meta-analysis
Authors: P. Boffetta, K. Straif
Journal: BMJ (2009)

<b>Objective</b> To assess whether people who use smokeless tobacco products are at increased risk of myocardial infarction and stroke. <b>Design</b> Meta-analysis of observational studies from Sweden and the United States. <b>Data sources</b> Electronic databases and reference lists. <b>Data extraction</b> Quantitative estimates of the association between use of smokeless tobacco products and risk of myocardial infarction and stroke among never smokers. <b>Review methods</b> Both authors independently abstracted risk estimates and study characteristics. Summary relative risks were estimated on the basis of random effects models. <b>Results</b> 11 studies, mainly in men, were included. Eight risk estimates were available for fatal myocardial infarction: the relative risk for ever use of smokeless tobacco products was 1.13 (95% confidence 1.06 to 1.21) and the excess risk was restricted to current users. The relative risk of fatal stroke, on the basis of five risk estimates, was 1.40 (1.28 to 1.54). The studies from both the United States and Sweden showed an increased risk of death from myocardial infarction and stroke. The inclusion of non-fatal myocardial infarction and non-fatal stroke lowered the summary risk estimates. Data on dose-response were limited but did not suggest a strong relation between risk of dying from either disease and frequency or duration of use of smokeless tobacco products. <b>Conclusion</b> An association was detected between use of smokeless tobacco products and risk of fatal myocardial infarction and stroke, which does not seem to be explained by chance.
Nanotechnology Applications in Cancer
Authors: Shuming Nie, Yun Xing, Gloria J. Kim, Jonathan W. Simons
Journal: Annual Review of Biomedical Engineering (2007)

Cancer nanotechnology is an interdisciplinary area of research in science, engineering, and medicine with broad applications for molecular imaging, molecular diagnosis, and targeted therapy. The basic rationale is that nanometer-sized particles, such as semiconductor quantum dots and iron oxide nanocrystals, have optical, magnetic, or structural properties that are not available from molecules or bulk solids. When linked with tumor targeting ligands such as monoclonal antibodies, peptides, or small molecules, these nanoparticles can be used to target tumor antigens (biomarkers) as well as tumor vasculatures with high affinity and specificity. In the mesoscopic size range of 5-100 nm diameter, nanoparticles also have large surface areas and functional groups for conjugating to multiple diagnostic (e.g., optical, radioisotopic, or magnetic) and therapeutic (e.g., anticancer) agents. Recent advances have led to bioaffinity nanoparticle probes for molecular and cellular imaging, targeted nanoparticle drugs for cancer therapy, and integrated nanodevices for early cancer detection and screening. These developments raise exciting opportunities for personalized oncology in which genetic and protein biomarkers are used to diagnose and treat cancer based on the molecular profiles of individual patients.
Arteriovenous Fistulas among Incident Hemodialysis Patients in Department of Defense and Veterans Affairs Facilities
Authors: Frank P. Hurst, Kevin C. Abbott, Dominic Raj, Mahesh Krishnan, Carlos E. Palant, Lawrence Y. Agodoa, Rahul M. Jindal
Journal: Journal of the American Society of Nephrology (2010)

A higher proportion of patients initiate hemodialysis (HD) with an arteriovenous fistula (AVF) in countries with universal health care systems compared with the United States. Because federally sponsored national health care organizations in the United States, such as the Department of Veterans Affairs (DVA) and the Department of Defense (DoD), are similar to a universal health care model, we studied AVF use within these organizations. We used the US Renal Data System database to perform a cross-sectional analysis of patients who initiated HD between 2005 and 2006. Patients who received predialysis nephrology care had 10-fold greater odds of initiating dialysis with an AVF (adjusted odds ratio [aOR] 10.3; 95% confidence interval [CI] 9.6 to 11.1). DVA/DoD insurance also independently associated with initiating HD with an AVF (aOR 1.4; 95% CI 1.2 to 1.5). Fewer patients initiated HD at a DoD facility, but these patients were also approximately twice as likely to use an AVF (aOR 2.3; 95% CI 1.2 to 4.6). In conclusion, patients in DVA/DoD systems are significantly more likely to use an AVF at initiation of HD than patients with other insurance types, including Medicare. Further study of these federal systems may identify practices that could improve processes of care across health care systems to increase the number of patients who initiate HD with an AVF.
High frequency of HLA class I antigen processing machinery (APM) component upregulation in primary hepatocellular carcinoma tumors
Authors: Fabio Grizzi, Barbara Franceschini, Sonia Di Biccari, Paola Bossi, Maurizio Chiriva-Internati, Soldano Ferrone
Journal: Journal for ImmunoTherapy of Cancer (2013)

Meeting abstracts Malignant transformation of cells is associated with downregulation of HLA class I APM components in most of the tumors. These defects are clinically relevant, since they are frequently associated with the clinical course of the disease. Only in a few tumors malignancy is
Claudin-1 regulates intestinal epithelial homeostasis through the modulation of Notch-signalling
Authors: Jillian L Pope, Ajaz A Bhat, Ashok Sharma, Rizwan Ahmad, Moorthy Krishnan, Mary K Washington, Robert D Beauchamp, Amar B Singh, Punita Dhawan
Journal: Gut (2013)

<h3>Objective</h3> Claudin-1 expression is increased and dysregulated in colorectal cancer and causally associates with the dedifferentiation of colonic epithelial cells, cancer progression and metastasis. Here, we have sought to determine the role claudin-1 plays in the regulation of intestinal epithelial homeostasis. <h3>Design</h3> We have used a novel villin-claudin-1 transgenic (Cl-1Tg) mouse as model (with intestinal claudin-1 overexpression). The effect of claudin-1 expression upon colonic epithelial differentiation, lineage commitment and Notch-signalling was determined using immunohistochemical, immunoblot and real-time PCR analysis. The frequently used mouse model of dextran sodium sulfate (DSS)-colitis was used to model inflammation, injury and repair. <h3>Results</h3> In Cl-1Tg mice, normal colonocyte differentiation programme was disrupted and goblet cell number and mucin-2 (muc-2) expressions were significantly downregulated while Notch- and ERK1/2-signalling were upregulated, compared with the wild type-littermates. Cl-1Tg mice were also susceptible to colonic inflammation and demonstrated impaired recovery and hyperproliferation following the DSS-colitis. Our data further show that claudin-1 regulates Notch-signalling through the regulation of matrix metalloproteinase-9 (MMP-9) and p-ERK signalling to regulate proliferation and differentiation. <h3>Conclusions</h3> Claudin-1 helps regulate intestinal epithelial homeostasis through the regulation of Notch-signalling. An upregulated claudin-1 expression induces MMP-9 and p-ERK signalling to activate Notch-signalling, which in turn inhibits the goblet cell differentiation. Decreased goblet cell number decreases muc-2 expression and thus enhances susceptibility to mucosal inflammation. Claudin-1 expression also induces colonic epithelial proliferation in a Notch-dependent manner. Our findings may help understand the role of claudin-1 in the regulation of inflammatory bowel diseases and CRC.
NAD(P)H oxidase modulates angiogenesis and the development of portosystemic collaterals and splanchnic hyperaemia in portal hypertensive rats
Authors: B. Angermayr, M. Fernandez, M. Mejias, J. Gracia-Sancho, J. C. Garcia-Pagan, J. Bosch
Journal: Gut (2006)

<b>Background:</b> Recent studies have shown the presence of vascular endothelial growth factor (VEGF)-dependent splanchnic angiogenesis in experimental models of portal hypertension, and the role of such neovascularisation on the development of both portosystemic collaterals and hyperdynamic splanchnic circulation. However, the mechanisms modulating angiogenesis in portal hypertension are unknown. Experimental evidence indicates that NAD(P)H oxidase is required for VEGF-induced angiogenesis. Interestingly, we have recently shown that splanchnic NAD(P)H oxidase activity is significantly increased in portal hypertensive rats. Therefore, it could be possible that activated NAD(P)H oxidases modulate angiogenesis in portal hypertension. <b>Aim:</b> To determine the effects of chronic NAD(P)H oxidase inhibition on angiogenesis and splanchnic haemodynamics in portal hypertensive rats. <b>Methods:</b> Partial portal vein-ligated and sham-operated rats were treated with the NAD(P)H oxidase inhibitor apocynin, or with vehicle for 5 days. Then, the expression of angiogenesis markers (western blotting), the formation of portosystemic collaterals (radioactive microspheres) and the production of superoxide anion (lucigenin-enhanced chemiluminescence) were determined. Mean arterial pressure, portal pressure, and superior mesenteric arterial blood flow and resistance were also measured. <b>Results:</b> In portal hypertensive rats, NAD(P)H oxidase blockade significantly decreased portosystemic collateral formation, and superior mesenteric arterial flow. It also reduced the splanchnic expression of VEGF, VEGF receptor-2 and CD31, and attenuated the increased production of superoxide, compared with vehicle. <b>Conclusions:</b> NAD(P)H oxidase plays an important role in experimental portal hypertension, modulating splanchnic angiogenesis, the formation of portosystemic collaterals and the development of splanchnic hyperdynamic circulation. These results suggest that NAD(P)H oxidase may represent a new target in the treatment of portal hypertension.