Genomes and Genes
Kirk D Jones
Affiliation: University of California
- 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....
- 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...
- Idiopathic pulmonary fibrosis: CT and risk of deathBrett Ley
From the Departments of Medicine B L, J S L, T E K, H R C, Radiology B M E, Epidemiology and Biostatistics E V, and Pathology K D J, University of California San Francisco, 505 Parnassus Ave, Box 0111, San Francisco, CA 94143 Departments of Radiology T E H and Medicine J H R, Mayo Clinic, Rochester, Minn Department of Medicine, University of British Columbia, Vancouver, BC, Canada C J R and Department of Respiratory Medicine, University of Southampton, Southampton, England L R
Radiology 273:570-9. 2014....
- 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...
- 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....
- 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...
- The effect of bronchodilators on forced vital capacity measurement in patients with idiopathic pulmonary fibrosisDeborah Assayag
Department of Medicine, University of California San Francisco, San Francisco, CA, United States Electronic address
Respir Med 109:1058-62. 2015..We hypothesize that reversible airflow limitation co-exists in a subgroup of patients with IPF, and that bronchodilator use will improve the performance characteristics of FVC...
- 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...
- 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...
- Pathogenesis of idiopathic pulmonary fibrosisPaul J Wolters
Department of Medicine, School of Medicine, University of California, San Francisco, California 94143 email
Annu Rev Pathol 9:157-79. 2014..We then discuss the pathologic changes within IPF fibroblasts and the extracellular matrix, and we conclude with a summary of how these profibrotic pathways may be interrelated. ..
- 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...
- Mast cells in a murine lung ischemia-reperfusion model of primary graft dysfunctionJohn R Greenland
Medical Service, VA Medical Center, San Francisco, CA, USA
Respir Res 15:95. 2014..These findings predict that mast cells, although activated in lungs injured by ischemia and reperfusion, are not necessary for the development of PGD. ..
- Pulmonary interstitial emphysema in adults: a clinicopathologic study of 53 lung explantsSara M Barcia
Departments of Pathology Surgery, University of California San Francisco, San Francisco, CA
Am J Surg Pathol 38:339-45. 2014..A correlation was seen between prior ventilation and/or biopsy. These findings may indicate that PIE is a result of medical intervention; however, in the remainder of cases the disease process itself may have been a contributing factor. ..
- 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..Early detection is hindered by inadequate tests and an incomplete understanding of the molecular events preceding or accompanying graft deterioration...
- 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...
- 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....
- Multidisciplinary Approach to Hypersensitivity PneumonitisBrett M Elicker
Departments of Radiology and Biomedical Imaging Pathology Internal Medicine, University of California San Francisco, San Francisco, CA Department of Radiology and Imaging Sciences, Emory University School of Medicine, Atlanta, GA
J Thorac Imaging 31:92-103. 2016..The goal of this paper is to discuss recent advances in HP and to present the spectrum of clinical, radiographic, and pathologic findings. ..
- MicroRNA-494 within an oncogenic microRNA megacluster regulates G1/S transition in liver tumorigenesis through suppression of mutated in colorectal cancerLionel Lim
Department of Cell and Tissue Biology, University of California San Francisco, San Francisco, CA Department of Medicine, University of California San Francisco, San Francisco, CA
Hepatology 59:202-15. 2014..miR-494 inhibition in human HCC cell lines decreases cellular transformation, and anti-miR-494 treatment of primary MYC-driven liver tumor formation significantly diminishes tumor size...
- Whence lepidic?: the history of a Canadian neologismKirk D Jones
From the Department of Pathology, University of California, San Francisco
Arch Pathol Lab Med 137:1822-4. 2013..This historical perspective traces the history of the term lepidic from its origins at McGill University in Montreal, Canada, through its uses in English pathologic descriptions, to its current state in pulmonary pathology. ..
- Data set for reporting of lung carcinomas: recommendations from International Collaboration on Cancer ReportingKirk D Jones
Department of Pathology, University of California San Francisco, San Francisco, USA
Arch Pathol Lab Med 137:1054-62. 2013..The resultant standardization of cancer reporting would be expected to benefit not only those countries directly involved in the collaboration but also others not in a position to develop their own data sets...
- 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...
- 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...
- 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...
- Pulmonary interstitial glycogenosis: an unrecognized etiology of persistent pulmonary hypertension of the newborn in congenital heart disease?Monique R Radman
Department of Pediatrics, University of California, 513 Parnassus Avenue, Box 1346, San Francisco, CA 94143 1346, USA
Pediatr Cardiol 34:1254-7. 2013..Pulmonary interstitial glycogenosis (PIG) arises from a developmental disorder of the pulmonary mesenchyme and presents clinically with reversible neonatal respiratory distress and/or persistent pulmonary hypertension of the newborn (PPHN)...
- Pulmonary pathology in connective tissue diseaseAnatoly Urisman
Department of Pathology, University of California San Francisco, San Francisco, California
Semin Respir Crit Care Med 35:201-12. 2014..Acquired autoimmune connective tissue diseases will be covered in this review, while lung involvement in vasculitides, heritable connective tissue disorders, and drug-induced CTD-like conditions will not be discussed. ..
- 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....
- 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...
- 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...
- 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....
- 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...
- 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...