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Genomes and Genes | Kirk D JonesSummaryAffiliation: University of California Country: USA Publications
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Publications
Histopathologic approach to the surgical lung biopsy in interstitial lung diseaseKirk D Jones
Department of Pathology, University of California San Francisco, San Francisco, CA 94143 0102, USA
Clin Chest Med 33:27-40. 2012..The topic of ILD or diffuse infiltrative lung disease covers several hundred entities. This article is meant to be a launching point in the clinician's approach to the histologic evaluation of lung disease...- An update on lung cancer stagingKirk D Jones
Department of Anatomic Pathology, University of California, San Francisco, 94143, USA
Adv Anat Pathol 17:33-7. 2010.... - A multidimensional index and staging system for idiopathic pulmonary fibrosisBrett Ley
Department of Medicine, University of California, San Francisco, 505 Parnassus Avenue, Box 0111, San Francisco, CA 94143, USA
Ann Intern Med 156:684-91. 2012..Idiopathic pulmonary fibrosis (IPF) is a progressive fibrotic lung disease with an overall poor prognosis. A simple-to-use staging system for IPF may improve prognostication, help guide management, and facilitate research... - Rapidly progressive pulmonary venoocclusive disease in young women taking oral contraceptivesAnatoly Urisman
Department of Pathology, University of California San Francisco, San Francisco, CA 94143 0102, USA
J Heart Lung Transplant 31:1031-6. 2012..The temporal sequence in these 2 patients suggests the thrombogenic action of OCs may contribute to the development of PVOD, with or without underlying connective tissue disease... 
Cleaved cytokeratin-18 is a mechanistically informative biomarker in idiopathic pulmonary fibrosisSeung Ick Cha
Department of Medicine, University of California, San Francisco School of Medicine, San Francisco, CA 94143 0111, USA
Respir Res 13:105. 2012....- Activated Notch1 induces lung adenomas in mice and cooperates with Myc in the generation of lung adenocarcinomaThaddeus D Allen
G W Hooper Research Foundation, University of California, San Francisco, San Francisco, California 94143 0552, USA
Cancer Res 71:6010-8. 2011..These tumor models should be valuable for exploring the role of activated Notch1 in the genesis of NSCLC and for testing therapies targeting either activated Notch1 or its downstream effectors... - Gastroesophageal reflux therapy is associated with longer survival in patients with idiopathic pulmonary fibrosisJoyce S Lee
Department of Medicine, University of California San Francisco, USA
Am J Respir Crit Care Med 184:1390-4. 2011..Gastroesophageal reflux (GER) is highly prevalent in patients with idiopathic pulmonary fibrosis (IPF). Chronic microaspiration secondary to GER may play a role in the pathogenesis and natural history of IPF... - Prevalence and clinical significance of circulating autoantibodies in idiopathic pulmonary fibrosisJoyce S Lee
Department of Medicine at University of California, San Francisco, 505 Parnassus Avenue, Box 0111, San Francisco, CA 94143, USA
Respir Med 107:249-55. 2013..The objective of this study was to determine the frequency and clinical significance of circulating autoantibodies in idiopathic pulmonary fibrosis... - A practical molecular assay to predict survival in resected non-squamous, non-small-cell lung cancer: development and international validation studiesJohannes R Kratz
University of California, San Francisco, CA 94143 1724, USA
Lancet 379:823-32. 2012..We aimed to develop and validate a practical, reliable assay that improves risk stratification compared with conventional staging... 
Low tidal volume reduces epithelial and endothelial injury in acid-injured rat lungsJames A Frank
Cardiovascular Research Institute and the Department of Medicine, University of California, San Francisco, San Francisco, California 94143 0130, USA
Am J Respir Crit Care Med 165:242-9. 2002..The additional decrease in pulmonary edema with a tidal volume of 3 ml/kg is partly accounted for by greater protection of the alveolar epithelium...- Plasma biomarker profiles in acute exacerbation of idiopathic pulmonary fibrosisHarold R Collard
Department of Medicine, University of California San Francisco, San Francisco, California, USA
Am J Physiol Lung Cell Mol Physiol 299:L3-7. 2010..Furthermore, they suggest that acute exacerbation of IPF has a distinct plasma biomarker profile from that of acute lung injury... - Association of large-airway lymphocytic bronchitis with bronchiolitis obliterans syndromeJohn R Greenland
Department of Medicine, University of California at San Francisco, San Francisco, CA 94121, USA
Am J Respir Crit Care Med 187:417-23. 2013..Although acute rejection and lymphocytic bronchiolitis have been identified as risk factors for the development of BOS, it is unclear whether large-airway lymphocytic inflammation conveys the same risk... - Transcript signatures of lymphocytic bronchitis in lung allograft biopsy specimensXiang Xu
Department of Medicine University of California at San Francisco, San Francisco, 94143, USA
J Heart Lung Transplant 24:1055-66. 2005.... - Idiopathic nonspecific interstitial pneumonia: lung manifestation of undifferentiated connective tissue disease?Brent W Kinder
Department of Medicine, University of California School of Medicine, San Francisco, California, USA
Am J Respir Crit Care Med 176:691-7. 2007.... - Interaction between MYC and MCL1 in the genesis and outcome of non-small-cell lung cancerThaddeus D Allen
G W Hooper Research Foundation, University of California, San Francisco, USA
Cancer Res 71:2212-21. 2011..Our findings therefore produce a convergence of mouse and human results that explain how MCL1 can block an important negative consequence of MYC overexpression in both experimental models and clinical cases of NSCLC... - Cough predicts prognosis in idiopathic pulmonary fibrosisChristopher J Ryerson
Department of Medicine, University of California San Francisco, San Francisco, California 94143, USA
Respirology 16:969-75. 2011..The clinical associations and prognostic value of cough in IPF have not been adequately described. The objective of this study was to describe the characteristics and prognostic value of cough in IPF... - Fatal diffuse alveolar damage in two lung transplant patients treated with cetuximabLorriana E Leard
Division of Pulmonary and Critical Care Medicine, University of California at San Francisco, San Francisco, California 94143 0111, USA
J Heart Lung Transplant 26:1340-4. 2007..Both patients died shortly after initiation of cetuximab due to diffuse alveolar damage, suggesting that EGFR inhibitors should be used with extreme caution in lung transplant recipients... - The diagnosis and management of intradiaphragmatic extralobar pulmonary sequestrations: a report of 4 casesAmar Nijagal
Department of Surgery, University of California, San Francisco, CA 94143 0570, USA
J Pediatr Surg 47:1501-5. 2012..We report the largest series of patients with IDEPS and describe the diagnostic and operative challenges associated with this condition... - c-Kit immunophenotyping and metalloproteinase expression profiles of mast cells in interstitial lung diseasesSamuel T Edwards
Cardiovascular Research Institute, University of California, San Francisco, California 94143-0911, USA
J Pathol 206:279-90. 2005..We conclude that ILD microenvironments induce unique c-Kit receptor and metalloproteinase mast cell phenotypes... - Identification of an autoantigen demonstrates a link between interstitial lung disease and a defect in central toleranceAnthony K Shum
1Diabetes Center, University of California, San Francisco, CA 94143, USA
Sci Transl Med 1:9ra20. 2009.... - Evaluation of diffuse liver steatosis by ultrasound, computed tomography, and magnetic resonance imaging: which modality is best?Aliya Qayyum
Department of Radiology, University of California San Francisco, 505 Parnassus Avenue, San Francisco, CA 94143 0628, USA
Clin Imaging 33:110-5. 2009..To compare ultrasound, computed tomography (CT), and magnetic resonance imaging (MRI) determination of diffuse liver steatosis... - Lung pathology in patients with congenital diaphragmatic hernia treated with fetal surgical intervention, including tracheal occlusionAmy E Heerema
Department of Pathology, University of California, San Francisco, 300 Parnassus Avenue, Box 0506, San Francisco, CA 94143 0506, USA
Pediatr Dev Pathol 6:536-46. 2003..The lung remains abnormal with low radial alveolar counts and increased alveolar size. Tracheal occlusion did not prevent development of lung pathology associated with pulmonary hypoplasia... - Death from donor-transmitted malignancy despite emergency liver retransplantationGerald S Lipshutz
Division of Transplantation, Department of Surgery, University of California, San Francisco, CA 94143, USA
Liver Transpl 9:1102-7. 2003..This case of donor-transmitted malignancy underscores the need for vigilance by the procuring surgeon in identifying potential malignancy during organ retrieval and use of a full autopsy on selected donors after organ procurement... - Role of cyclin D1 as a mediator of c-Met- and beta-catenin-induced hepatocarcinogenesisMohini A Patil
Department of Biopharmaceutical Sciences, University of California San Francisco, 513 Parnassus Avenue, San Francisco, CA 94143 0446, USA
Cancer Res 69:253-61. 2009..Moreover, our data suggest that CCND1 expression is not essential for liver tumor development induced by c-Met and beta-catenin... - Distinct pathways of genomic progression to benign and malignant tumors of the liverAaron D Tward
G W Hooper Foundation and Department of Microbiology and Immunology, University of California, San Francisco, CA 94143, USA
Proc Natl Acad Sci U S A 104:14771-6. 2007.... - Lymphangioleiomyomatosis and SZ alpha(1)-antitrypsin disease: a unique combination?Andrew L Chan
University of California, Davis Medical Center, Sacramento, CA, USA
Chest 124:763-5. 2003..The possible mechanisms of interaction resulting from both disease processes are discussed...