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Recent advances in molecular targets and treatment of idiopathic pulmonary fibrosis: focus on TGFbeta signaling and the myofibroblast
FAK-related nonkinase is a multifunctional negative regulator of pulmonary fibrosis
Tissue inhibitor of metalloproteinase-3 is up-regulated by transforming growth factor-beta1 in vitro and expressed in fibroblastic foci in vivo in idiopathic pulmonary fibrosis
Bleomycin and IL-1beta-mediated pulmonary fibrosis is IL-17A dependent
Defective histone acetylation is responsible for the diminished expression of cyclooxygenase 2 in idiopathic pulmonary fibrosis
EZH2 enhances the differentiation of fibroblasts into myofibroblasts in idiopathic pulmonary fibrosis
y-Herpes virus-68, but not Pseudomonas aeruginosa or influenza A (H1N1), exacerbates established murine lung fibrosis
Microarray identifies ADAM family members as key responders to TGF-beta1 in alveolar epithelial cells
Diagnostic Values For Club Cell Secretory Protein (CC16) in Serum of Patients of Combined Pulmonary Fibrosis and Emphysema
Anti-pulmonary fibrotic activity of salvianolic acid B was screened by a novel method based on the cyto-biophysical properties
miR-26a suppresses EMT by disrupting the Lin28B/let-7d axis: potential cross-talks among miRNAs in IPF
Targeting genes for treatment in idiopathic pulmonary fibrosis: challenges and opportunities, promises and pitfalls
Th1/Th2 cytokine gene polymorphisms in patients with idiopathic pulmonary fibrosis
VCAM-1 is a TGF-b1 inducible gene upregulated in idiopathic pulmonary fibrosis
Hsp90 regulation of fibroblast activation in pulmonary fibrosis
Integrated analyses identify the involvement of microRNA-26a in epithelial-mesenchymal transition during idiopathic pulmonary fibrosis
Upregulation of alveolar levels of activin B, but not activin A, in lungs of west highland white terriers with idiopathic pulmonary fibrosis and diffuse alveolar damage
Roles for insulin-like growth factor I and transforming growth factor-beta in fibrotic lung disease
Epigenetic Regulation of Caveolin-1 Gene Expression in Lung Fibroblasts
Combined inhibition of TGFb and PDGF signaling attenuates radiation-induced pulmonary fibrosis
Targeting of Discoidin Domain Receptor 2 (DDR2) Prevents Myofibroblast Activation and Neovessel Formation During Pulmonary Fibrosis
Glucagon like peptide-1 attenuates bleomycin-induced pulmonary fibrosis, involving the inactivation of NF-kB in mice
Carbon monoxide-bound hemoglobin-vesicles for the treatment of bleomycin-induced pulmonary fibrosis
Protease activated receptor-1 regulates macrophage-mediated cellular senescence: a risk for idiopathic pulmonary fibrosis
Control of virus reactivation arrests pulmonary herpesvirus-induced fibrosis in IFN-gamma receptor-deficient mice
Epithelial Cell Mitochondrial Dysfunction and PINK1 Are Induced by Transforming Growth Factor- Beta1 in Pulmonary Fibrosis
MiR-185/AKT and miR-29a/collagen 1a pathways are activated in IPF BAL cells
Regulation of TGF-b storage and activation in the human idiopathic pulmonary fibrosis lung
Interleukin-17 induces human alveolar epithelial to mesenchymal cell transition via the TGF-b1 mediated Smad2/3 and ERK1/2 activation
Tubastatin ameliorates pulmonary fibrosis by targeting the TGFb-PI3K-Akt pathway
Prognostic factors for idiopathic pulmonary fibrosis: clinical, physiologic, pathologic, and molecular aspects
The lncRNA H19 Mediates Pulmonary Fibrosis by Regulating the miR-196a/COL1A1 Axis
Progressive transforming growth factor beta1-induced lung fibrosis is blocked by an orally active ALK5 kinase inhibitor
Toll-like receptor 4 activation attenuates profibrotic response in control lung fibroblasts but not in fibroblasts from patients with IPF
Significant involvement of CCL2 (MCP-1) in inflammatory disorders of the lung
Pirfenidone inhibits the expression of HSP47 in TGF-beta1-stimulated human lung fibroblasts
Free radical generation induces epithelial-to-mesenchymal transition in lung epithelium via a TGF-b1-dependent mechanism
Methylation-mediated BMPER expression in fibroblast activation in vitro and lung fibrosis in mice in vivo
Inhibition of PHGDH Attenuates Bleomycin-induced Pulmonary Fibrosis
Effects of particulate matter from straw burning on lung fibrosis in mice
BARD1 mediates TGF-b signaling in pulmonary fibrosis
Upregulation of activin-B and follistatin in pulmonary fibrosis - a translational study using human biopsies and a specific inhibitor in mouse fibrosis models
Resveratrol inhibits transforming growth factor-b-induced proliferation and differentiation of ex vivo human lung fibroblasts into myofibroblasts through ERK/Akt inhibition and PTEN restoration
Effects of doxycycline on production of growth factors and matrix metalloproteinases in pulmonary fibrosis
Renin is an angiotensin-independent profibrotic mediator: role in pulmonary fibrosis
Regulation of myofibroblast differentiation by miR-424 during epithelial-to-mesenchymal transition
MS80, a novel sulfated oligosaccharide, inhibits pulmonary fibrosis by targeting TGF-beta1 both in vitro and in vivo
Association of HLA and cytokine gene polymorphisms with idiopathic pulmonary fibrosis
Oxidant-antioxidant imbalance as a potential contributor to the progression of human pulmonary fibrosis
Up-regulation of heparan sulfate 6-O-sulfation in idiopathic pulmonary fibrosis
Mechanisms of fibrosis in coal workers' pneumoconiosis
Transforming Growth Factor Beta 1 Activation, Storage, and Signaling Pathways in Idiopathic Pulmonary Fibrosis in Dogs
Effect of substrate stiffness on pulmonary fibroblast activation by TGF-b
A translational preclinical model of interstitial pulmonary fibrosis and pulmonary hypertension: mechanistic pathways driving disease pathophysiology
Epithelial cell alpha3beta1 integrin links beta-catenin and Smad signaling to promote myofibroblast formation and pulmonary fibrosis
Role for alpha3 integrin in EMT and pulmonary fibrosis
Shikonin suppresses pulmonary fibroblasts proliferation and activation by regulating Akt and p38 MAPK signaling pathways
Pirfenidone for the treatment of idiopathic pulmonary fibrosis
Interactions between b-catenin and transforming growth factor-b signaling pathways mediate epithelial-mesenchymal transition and are dependent on the transcriptional co-activator cAMP-response element-binding protein (CREB)-binding protein (CBP)
Gremlin-mediated decrease in bone morphogenetic protein signaling promotes pulmonary fibrosis
Molecular targets in pulmonary fibrosis: the myofibroblast in focus
miR-92a regulates TGF-b1-induced WISP1 expression in pulmonary fibrosis
Transgelin is a direct target of TGF-beta/Smad3-dependent epithelial cell migration in lung fibrosis
Uncoupling of the profibrotic and hemostatic effects of thrombin in lung fibrosis
Studies of hepatocyte growth factor in bronchoalveolar lavage fluid in chronic interstitial lung diseases
Syndecan-2 exerts antifibrotic effects by promoting caveolin-1-mediated transforming growth factor-b receptor I internalization and inhibiting transforming growth factor-b1 signaling
Compromised peroxisomes in idiopathic pulmonary fibrosis, a vicious cycle inducing a higher fibrotic response via TGF-b signaling
Increased alveolar soluble annexin V promotes lung inflammation and fibrosis
Simvastatin attenuates TGF-b1-induced epithelial-mesenchymal transition in human alveolar epithelial cells
Expression of 150-kDa oxygen-regulated protein (ORP150) stimulates bleomycin-induced pulmonary fibrosis and dysfunction in mice
Kinase inhibitors fail to induce mesenchymal-epithelial transition in fibroblasts from fibrotic lung tissue
The small heat-shock protein aB-crystallin is essential for the nuclear localization of Smad4: impact on pulmonary fibrosis
Developmental Reprogramming in Mesenchymal Stromal Cells of Human Subjects with Idiopathic Pulmonary Fibrosis
Blockade of the Wnt/b-catenin pathway attenuates bleomycin-induced pulmonary fibrosis
Epithelial stem cell exhaustion in the pathogenesis of idiopathic pulmonary fibrosis
Re-evaluation of fibrogenic cytokines in lung fibrosis
Autoimmunity to Vimentin Is Associated with Outcomes of Patients with Idiopathic Pulmonary Fibrosis
Lung myofibroblasts are characterized by down-regulated cyclooxygenase-2 and its main metabolite, prostaglandin E2
CUX1/Wnt signaling regulates epithelial mesenchymal transition in EBV infected epithelial cells
Mode of action of nintedanib in the treatment of idiopathic pulmonary fibrosis
Idiopathic pulmonary fibrosis: an altered fibroblast proliferation linked to cancer biology
Lower expression of platelet derived growth factor is associated with better overall survival rate of patients with idiopathic nonspecific interstitial pneumonia
Elevated expression of NEU1 sialidase in idiopathic pulmonary fibrosis provokes pulmonary collagen deposition, lymphocytosis, and fibrosis
TGF-beta 1, but not TGF-beta 2 or TGF-beta 3, is differentially present in epithelial cells of advanced pulmonary fibrosis: an immunohistochemical study
A critical role for the mTORC2 pathway in lung fibrosis
Cthrc1 lowers pulmonary collagen associated with bleomycin-induced fibrosis and protects lung function
Pigment epithelium-derived factor in idiopathic pulmonary fibrosis: a role in aberrant angiogenesis
Cytoskeletal protein modulation in pulmonary alveolar myofibroblasts during idiopathic pulmonary fibrosis
Increased expression of 5-hydroxytryptamine2A/B receptors in idiopathic pulmonary fibrosis: a rationale for therapeutic intervention
Signaling pathways and their miRNA regulators involved in the etiopathology of idiopathic pulmonary fibrosis (IPF) and hypersensitivity pneumonitis (HP)
Alveolar epithelial cells express mesenchymal proteins in patients with idiopathic pulmonary fibrosis
TGF-b1 induces tissue factor expression in human lung fibroblasts in a PI3K/JNK/Akt-dependent and AP-1-dependent manner
Inhibitory effects of amines from Citrus reticulata on bleomycin-induced pulmonary fibrosis in rats
Focal adhesion kinase signaling determines the fate of lung epithelial cells in response to TGF-b
Amplification of TGFb Induced ITGB6 Gene Transcription May Promote Pulmonary Fibrosis
Fibrotic myofibroblasts manifest genome-wide derangements of translational control
Inhibition and role of let-7d in idiopathic pulmonary fibrosis
Beyond TGFb - Novel ways to target airway and parenchymal fibrosis
Rapamycin increases CCN2 expression of lung fibroblasts via phosphoinositide 3-kinase
Induction of epithelial-mesenchymal transition in alveolar epithelial cells by transforming growth factor-beta1: potential role in idiopathic pulmonary fibrosis
The profibrotic cytokine transforming growth factor-b1 increases endothelial progenitor cell angiogenic properties
Tannic acid attenuates TGF-b1-induced epithelial-to-mesenchymal transition by effectively intervening TGF-b signaling in lung epithelial cells
Predisposition for disrepair in the aged lung
Differential expression of alpha E beta 7 integrins on bronchoalveolar lavage T lymphocyte subsets: regulation by alpha 4 beta 1-integrin crosslinking and TGF-beta
MicroRNA regulatory networks in idiopathic pulmonary fibrosis
Elevated sL1-CAM levels in BALF and serum of IPF patients
Macrophage Bone Morphogenic Protein Receptor 2 (BMPR2) depletion in Idiopathic Pulmonary Fibrosis (IPF) and Group III Pulmonary Hypertension
Wnt coreceptor Lrp5 is a driver of idiopathic pulmonary fibrosis
The potential application of strategic released apigenin from polymeric carrier in pulmonary fibrosis
Immunomodulation by mesenchymal stem cells in treating human autoimmune disease-associated lung fibrosis
Pirfenidone inhibits myofibroblast differentiation and lung fibrosis development during insufficient mitophagy
Epithelial-to-mesenchymal transition and its role in EGFR-mutant lung adenocarcinoma and idiopathic pulmonary fibrosis
Resveratrol-Mediated Repression and Reversion of Prostatic Myofibroblast Phenoconversion
Genetic partitioning of interleukin-6 signalling in mice dissociates Stat3 from Smad3-mediated lung fibrosis
Effects of thymosin b4 and its N-terminal fragment Ac-SDKP on TGF-b-treated human lung fibroblasts and in the mouse model of bleomycin-induced lung fibrosis
Transcription factor GATA-6 is expressed in quiescent myofibroblasts in idiopathic pulmonary fibrosis
Epithelial contribution to the pro-fibrotic stiff microenvironment and myofibroblast population in lung fibrosis
The matricellular protein CCN1 enhances TGF-b1/SMAD3-dependent profibrotic signaling in fibroblasts and contributes to fibrogenic responses to lung injury
[Idiopathic pulmonary fibrosis and lung cancer]
MicroRNA-326 regulates profibrotic functions of transforming growth factor-b in pulmonary fibrosis
Role of caveolin-1 in fibrotic diseases
Latent cytomegalovirus infection exacerbates experimental pulmonary fibrosis by activating TGF-b1
Significance of elevated procollagen-III-peptide and transforming growth factor-beta levels of bronchoalveolar lavage fluids from idiopathic pulmonary fibrosis patients
The latent form of TGFbeta(1) is induced by TNFalpha through an ERK specific pathway and is activated by asbestos-derived reactive oxygen species in vitro and in vivo
Sunitinib, a Small-Molecule Kinase Inhibitor, Attenuates Bleomycin-Induced Pulmonary Fibrosis in Mice
Endogenous Semaphorin-7A Impedes Human Lung Fibroblast Differentiation
Protective role of gambogic acid in experimental pulmonary fibrosis in vitro and in vivo
An ex vivo model to induce early fibrosis-like changes in human precision-cut lung slices
Differing Expression of Cytokines and Tumor Markers in Combined Pulmonary Fibrosis and Emphysema Compared to Emphysema and Pulmonary Fibrosis
Differential effects of human neutrophil peptide-1 on growth factor and interleukin-8 production by human lung fibroblasts and epithelial cells
miR-18a-5p Inhibits Sub-pleural Pulmonary Fibrosis by Targeting TGF-b Receptor II
Human placental mesenchymal stem cells of fetal origins-alleviated inflammation and fibrosis by attenuating MyD88 signaling in bleomycin-induced pulmonary fibrosis mice
Caveolin-1: a critical regulator of lung fibrosis in idiopathic pulmonary fibrosis
TGF-beta driven lung fibrosis is macrophage dependent and blocked by Serum amyloid P
Lysocardiolipin acyltransferase regulates TGF-b mediated lung fibroblast differentiation
Fibroblasts from idiopathic pulmonary fibrosis and normal lungs differ in growth rate, apoptosis, and tissue inhibitor of metalloproteinases expression
Phosphatase and tensin homolog deleted on chromosome 10 contributes to phenotype transformation of fibroblasts in idiopathic pulmonary fibrosis via multiple pathways
Release of biologically active TGF-beta1 by alveolar epithelial cells results in pulmonary fibrosis
Azithromycin attenuates myofibroblast differentiation and lung fibrosis development through proteasomal degradation of NOX4
[Potential role of cytokines in idiopathic pulmonary fibrosis]
Overproduction of collagen and diminished SOCS1 expression are causally linked in fibroblasts from idiopathic pulmonary fibrosis
Thalidomide reduces IL-18, IL-8 and TNF-alpha release from alveolar macrophages in interstitial lung disease
The potential role of PDGF, IGF-1, TGF-beta expression in idiopathic pulmonary fibrosis
Pathogenesis pathways of idiopathic pulmonary fibrosis in bleomycin-induced lung injury model in mice
Hyper-responsiveness of IPF/UIP fibroblasts: interplay between TGFbeta1, IL-13 and CCL2
VEGF ameliorates pulmonary hypertension through inhibition of endothelial apoptosis in experimental lung fibrosis in rats
Genomewide RNA expression profiling in lung identifies distinct signatures in idiopathic pulmonary arterial hypertension and secondary pulmonary hypertension
Transforming growth factor-b1 downregulates vascular endothelial growth factor-D expression in human lung fibroblasts via the Jun NH2-terminal kinase signaling pathway
Corilagin attenuates aerosol bleomycin-induced experimental lung injury
Bleomycin induces molecular changes directly relevant to idiopathic pulmonary fibrosis: a model for "active" disease
Cytokine profiles in idiopathic pulmonary fibrosis suggest an important role for TGF-beta and IL-10
Therapeutic targets in fibrotic pathways
Protective Effect of Ginsenoside Rg1 on Bleomycin-Induced Pulmonary Fibrosis in Rats: Involvement of Caveolin-1 and TGF-b1 Signal Pathway
Suppression of plasminogen activator inhibitor-1 by RNA interference attenuates pulmonary fibrosis
Pirfenidone exerts antifibrotic effects through inhibition of GLI transcription factors
Long-acting human serum albumin-thioredoxin fusion protein suppresses bleomycin-induced pulmonary fibrosis progression
Profibrotic role of WNT10A via TGF-b signaling in idiopathic pulmonary fibrosis
Mesenchymal Stem Cells Correct Inappropriate Epithelial-mesenchyme Relation in Pulmonary Fibrosis Using Stanniocalcin-1
Angiotensin-TGF-beta 1 crosstalk in human idiopathic pulmonary fibrosis: autocrine mechanisms in myofibroblasts and macrophages
microRNA-1343 attenuates pathways of fibrosis by targeting the TGF-b receptors
miR-199a-5p Is upregulated during fibrogenic response to tissue injury and mediates TGFbeta-induced lung fibroblast activation by targeting caveolin-1
Increased expression of protease nexin-1 in fibroblasts during idiopathic pulmonary fibrosis regulates thrombin activity and fibronectin expression
Plasma CCN2 (connective tissue growth factor; CTGF) is a potential biomarker in idiopathic pulmonary fibrosis (IPF)
Cysteine-rich protein 1 is regulated by transforming growth factor-b1 and expressed in lung fibrosis
Microencapsulation of lefty-secreting engineered cells for pulmonary fibrosis therapy in mice
Accelerated epithelial cell senescence in IPF and the inhibitory role of SIRT6 in TGF-b-induced senescence of human bronchial epithelial cells
Effect of Renshen Pingfei Decoction, a traditional Chinese prescription, on IPF induced by Bleomycin in rats and regulation of TGF-b1/Smad3
M2 macrophages induce EMT through the TGF-b/Smad2 signaling pathway
Pleural mesothelial cell transformation into myofibroblasts and haptotactic migration in response to TGF-beta1 in vitro
Exercise Reduces Lung Fibrosis Involving Serotonin/Akt Signaling
p63 - Key molecule in the early phase of epithelial abnormality in idiopathic pulmonary fibrosis
Chop Deficiency Protects Mice Against Bleomycin-induced Pulmonary Fibrosis by Attenuating M2 Macrophage Production
miR -221 targets HMGA2 to inhibit bleomycin -induced pulmonary fibrosis by regulating TGF -b1/Smad3-induced EMT
Increased interleukin-1 receptor antagonist in idiopathic pulmonary fibrosis
Transforming Growth Factor (TGF)-b Promotes de Novo Serine Synthesis for Collagen Production
Autophagy in idiopathic pulmonary fibrosis
Molecular pathogenesis of interstitial pneumonitis with TNF-alpha transgenic mice
Overexpression of Sulf2 in idiopathic pulmonary fibrosis
Wilms' tumor 1 (Wt1) regulates pleural mesothelial cell plasticity and transition into myofibroblasts in idiopathic pulmonary fibrosis
Two-Way Conversion between Lipogenic and Myogenic Fibroblastic Phenotypes Marks the Progression and Resolution of Lung Fibrosis
Matrix metalloproteinase (MMP)-19 deficient fibroblasts display a profibrotic phenotype
Epithelium-specific deletion of TGF-b receptor type II protects mice from bleomycin-induced pulmonary fibrosis
[Pulmonary fibrosis--a therapeutic dilemma?]
Bleomycin in the setting of lung fibrosis induction: From biological mechanisms to counteractions
Signaling pathways in the epithelial origins of pulmonary fibrosis
Assessment of the effect of potential antifibrotic compounds on total and aVb6 integrin-mediated TGF-b activation
FGF-1 reverts epithelial-mesenchymal transition induced by TGF-{beta}1 through MAPK/ERK kinase pathway
The anti-fibrotic effect of inhibition of TGFb-ALK5 signalling in experimental pulmonary fibrosis in mice is attenuated in the presence of concurrent y-herpesvirus infection
Plasminogen activator inhibitor 1, fibroblast apoptosis resistance, and aging-related susceptibility to lung fibrosis
Antifibrotic properties of receptor for advanced glycation end products in idiopathic pulmonary fibrosis
Participation of miR-200 in pulmonary fibrosis
Genetic polymorphism in matrix metalloproteinase-9 and transforming growth factor-b1 and susceptibility to combined pulmonary fibrosis and emphysema in a Chinese population
Proteasomal regulation of pulmonary fibrosis
Inhibition of HSP27 blocks fibrosis development and EMT features by promoting Snail degradation
Berberine attenuates bleomycin induced pulmonary toxicity and fibrosis via suppressing NF-kB dependant TGF-b activation: a biphasic experimental study
Transforming growth factor-b inhibits IQ motif containing guanosine triphosphatase activating protein 1 expression in lung fibroblasts via the nuclear factor-kB signaling pathway
Role of CD248 as a potential severity marker in idiopathic pulmonary fibrosis
Immunoglobulin A in serum: an old acquaintance as a new prognostic biomarker in idiopathic pulmonary fibrosis
Defect of hepatocyte growth factor secretion by fibroblasts in idiopathic pulmonary fibrosis
Normal Human Lung Epithelial Cells Inhibit Transforming Growth Factor-b Induced Myofibroblast Differentiation via Prostaglandin E2
The JAK2 pathway is activated in idiopathic pulmonary fibrosis
Inhibition of the KCa3.1 Channel Alleviates Established Pulmonary Fibrosis in a Large Animal Model
Possible involvement of pirfenidone metabolites in the antifibrotic action of a therapy for idiopathic pulmonary fibrosis
Effect of pirfenidone on proliferation, TGF-b-induced myofibroblast differentiation and fibrogenic activity of primary human lung fibroblasts
Olodaterol shows anti-fibrotic efficacy in in vitro and in vivo models of pulmonary fibrosis
Human lung myofibroblast TGFb1-dependent Smad2/3 signalling is Ca(2+)-dependent and regulated by KCa3.1 K(+) channels
AKT2 Regulates Pulmonary Inflammation and Fibrosis via Modulating Macrophage Activation
[Quantifying plasma levels of transforming growth factor beta1 in idiopathic pulmonary fibrosis]
Transforming growth factor-beta1 in sarcoidosis
BAX inhibitor-1-associated V-ATPase glycosylation enhances collagen degradation in pulmonary fibrosis
The anti-fibrotic effects of microRNA-153 by targeting TGFBR-2 in pulmonary fibrosis
Cytokines in human lung fibrosis
MicroRNA-101 attenuates pulmonary fibrosis by inhibiting fibroblast proliferation and activation
Idiopathic pulmonary fibrosis: pathobiology of novel approaches to treatment
Novel pharmacological approaches to manage interstitial lung fibrosis in the twenty-first century
De-ubiquitinating enzyme, USP11, promotes transforming growth factor b-1 signaling through stabilization of transforming growth factor b receptor II
SPARC suppresses apoptosis of idiopathic pulmonary fibrosis fibroblasts through constitutive activation of beta-catenin
Cartilage oligomeric matrix protein in idiopathic pulmonary fibrosis
Aortic carboxypeptidase-like protein (ACLP) enhances lung myofibroblast differentiation through transforming growth factor b receptor-dependent and -independent pathways
IL-4 polymorphisms, HRCT score and lung tissue markers in idiopathic pulmonary fibrosis
TGF-beta1 induces human alveolar epithelial to mesenchymal cell transition (EMT)
NADPH oxidase-4 mediates myofibroblast activation and fibrogenic responses to lung injury
TGF-beta 1 as an enhancer of Fas-mediated apoptosis of lung epithelial cells
Novel Mechanisms for the Antifibrotic Action of Nintedanib
MicroRNA-29c regulates apoptosis sensitivity via modulation of the cell-surface death receptor, Fas, in lung fibroblasts
Insulin-like growth factor binding proteins 3 and 5 are overexpressed in idiopathic pulmonary fibrosis and contribute to extracellular matrix deposition
Bile acids induce activation of alveolar epithelial cells and lung fibroblasts through farnesoid X receptor-dependent and independent pathways
Determining the True Selectivity Profile of av Integrin Ligands Using Radioligand Binding: Applying an Old Solution to a New Problem
Fibroblastic foci, covered with alveolar epithelia exhibiting epithelial-mesenchymal transition, destroy alveolar septa by disrupting blood flow in idiopathic pulmonary fibrosis
Connective tissue growth factor expression and induction by transforming growth factor-beta is abrogated by simvastatin via a Rho signaling mechanism
Increased Galectin-9 Concentration and Number of CD4+Foxp3high+Cells in Bronchoalveolar Lavage Fluid of Patients with Cryptogenic Organizing Pneumonia
Cytokine gene polymorphisms in idiopathic pulmonary fibrosis
Regulation of human lung fibroblast C1q-receptors by transforming growth factor-beta and tumor necrosis factor-alpha
Sorafenib ameliorates bleomycin-induced pulmonary fibrosis: potential roles in the inhibition of epithelial-mesenchymal transition and fibroblast activation
Matrix metalloproteinase 3 is a mediator of pulmonary fibrosis
Microarray profiling reveals suppressed interferon stimulated gene program in fibroblasts from scleroderma-associated interstitial lung disease
Effects of antifibrotic agents on TGF-beta1, CTGF and IFN-gamma expression in patients with idiopathic pulmonary fibrosis
NOX4/NADPH oxidase expression is increased in pulmonary fibroblasts from patients with idiopathic pulmonary fibrosis and mediates TGFbeta1-induced fibroblast differentiation into myofibroblasts
[The expressions and meanings of BMP-7 and TGF-b in idiopathic pulmonary fibrosis and idiopathic nonspecific interstitial pneumonia]
Increased deposition of chondroitin/dermatan sulfate glycosaminoglycan and upregulation of b1,3-glucuronosyltransferase I in pulmonary fibrosis
Identification and validation of differentially expressed transcripts by RNA-sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis
Increased TGF-beta1 in the lungs of asbestos-exposed rats and mice: reduced expression in TNF-alpha receptor knockout mice
Discovery and validation of extracellular/circulating microRNAs during idiopathic pulmonary fibrosis disease progression
Idiopathic pulmonary fibrosis in relation to gene polymorphisms of transforming growth factor-b1 and plasminogen activator inhibitor 1
Comparative study of transforming growth factor-b signalling and regulatory molecules in human and canine idiopathic pulmonary fibrosis
TGF-b1 T869C polymorphism may affect susceptibility to idiopathic pulmonary fibrosis and disease severity
Inhibition of PI3K prevents the proliferation and differentiation of human lung fibroblasts into myofibroblasts: the role of class I P110 isoforms
Medical treatment for pulmonary fibrosis: current trends, concepts, and prospects
Ubiquitin carboxyl-terminal hydrolase-L5 promotes TGFb-1 signaling by de-ubiquitinating and stabilizing Smad2/Smad3 in pulmonary fibrosis
Contribution of the anaphylatoxin receptors, C3aR and C5aR, to the pathogenesis of pulmonary fibrosis
Comparison between conventional and "clinical" assessment of experimental lung fibrosis
MOXIBUSTION HAS A POSITIVE EFFECT ON PULMONARY FIBROSIS: AN ALTERNATIVE APPROACH
Intratracheal bleomycin causes airway remodeling and airflow obstruction in mice
Role of endoplasmic reticulum stress in age-related susceptibility to lung fibrosis
Transforming growth factor b1 (TGFb1)-induced CD44V6-NOX4 signaling in pathogenesis of idiopathic pulmonary fibrosis
Increased levels of prostaglandin E-major urinary metabolite (PGE-MUM) in chronic fibrosing interstitial pneumonia
Cub domain containing protein 1 (CDCP1) negatively regulates TGFb signaling and myofibroblast differentiation
The mannose-6-phosphate analogue, PXS64, inhibits fibrosis via TGF-b1 pathway in human lung fibroblasts
Reduced Ets Domain-containing Protein Elk1 Promotes Pulmonary Fibrosis via Increased Integrin avb6 Expression
Pirfenidone inhibits TGF-b1-induced over-expression of collagen type I and heat shock protein 47 in A549 cells
N-acetylcysteine inhibits alveolar epithelial-mesenchymal transition
BAL cytokine profile in different interstitial lung diseases: a focus on systemic sclerosis
Expression of RXFP1 Is Decreased in Idiopathic Pulmonary Fibrosis
Anti-fibrotic effects of nintedanib in lung fibroblasts derived from patients with idiopathic pulmonary fibrosis
Effect of an immunotoxin to folate receptor beta on bleomycin-induced experimental pulmonary fibrosis
Pulmonary fibrosis: pathogenesis, etiology and regulation
Smooth muscle alpha-actin expression and myofibroblast differentiation by TGFbeta are dependent upon MK2
Modulation of CD11c+ lung dendritic cells in respect to TGF-b in experimental pulmonary fibrosis
Microsatellite instability in transforming growth factor-beta 1 type II receptor gene in alveolar lining epithelial cells of idiopathic pulmonary fibrosis
Profibrotic role of miR-154 in pulmonary fibrosis
miR-323a-3p regulates lung fibrosis by targeting multiple profibrotic pathways
Single-cell RNA sequencing identifies diverse roles of epithelial cells in idiopathic pulmonary fibrosis
Expression of suppressor of cytokine signaling 1 in the peripheral blood of patients with idiopathic pulmonary fibrosis
The Anti-fibrotic Effects and Mechanisms of MicroRNA-486-5p in Pulmonary Fibrosis
Prostaglandin F(2alpha) receptor signaling facilitates bleomycin-induced pulmonary fibrosis independently of transforming growth factor-beta
Low-dose paclitaxel ameliorates pulmonary fibrosis by suppressing TGF-b1/Smad3 pathway via miR-140 upregulation
IPF lung fibroblasts have a senescent phenotype
Sphingosine-1-phosphate lyase is an endogenous suppressor of pulmonary fibrosis: role of S1P signalling and autophagy
Roles of p38 MAPK and JNK in TGF-b1-induced human alveolar epithelial to mesenchymal transition
The role of microRNA-155/liver X receptor pathway in experimental and idiopathic pulmonary fibrosis
Sphingosine-1-phosphate is increased in patients with idiopathic pulmonary fibrosis and mediates epithelial to mesenchymal transition
MiR-338* targeting smoothened to inhibit pulmonary fibrosis by epithelial-mesenchymal transition
MAP3K19 Is a Novel Regulator of TGF-b Signaling That Impacts Bleomycin-Induced Lung Injury and Pulmonary Fibrosis
Nitric oxide attenuates epithelial-mesenchymal transition in alveolar epithelial cells
N-acetyl-L-cysteine inhibits TGF-beta1-induced profibrotic responses in fibroblasts
Sirtuin 7 is decreased in pulmonary fibrosis and regulates the fibrotic phenotype of lung fibroblasts
Evaluation of permeability alteration and epithelial-mesenchymal transition induced by transforming growth factor-b1 in A549, NCI-H441, and Calu-3 cells: Development of an in vitro model of respiratory epithelial cells in idiopathic pulmonary fibrosis
Dysregulated Collagen Homeostasis by Matrix Stiffening and TGF-b1 in Fibroblasts from Idiopathic Pulmonary Fibrosis Patients: Role of FAK/Akt
Hydrogen peroxide is a diffusible paracrine signal for the induction of epithelial cell death by activated myofibroblasts
TGF-b1 stimulates HDAC4 nucleus-to-cytoplasm translocation and NADPH oxidase 4-derived reactive oxygen species in normal human lung fibroblasts
Effects of a leukotriene B4 receptor antagonist on bleomycin-induced pulmonary fibrosis
Fibrogenic Lung Injury Induces Non-Cell-Autonomous Fibroblast Invasion
Raised serum levels of IGFBP-1 and IGFBP-2 in idiopathic pulmonary fibrosis
Sphingolipids in pulmonary fibrosis
Inhibition of NF-kappaB signaling reduces virus load and gammaherpesvirus-induced pulmonary fibrosis
Sustained PI3K Activation exacerbates BLM-induced Lung Fibrosis via activation of pro-inflammatory and pro-fibrotic pathways
Triptolide suppresses paraquat induced idiopathic pulmonary fibrosis by inhibiting TGFB1-dependent epithelial mesenchymal transition
N-acetylcysteine downregulation of lysyl oxidase activity alleviating bleomycin-induced pulmonary fibrosis in rats
Cytokine gene polymorphisms and BALF cytokine levels in interstitial lung diseases
[The morphology and molecular bases of damage to the stem cell niche of respiratory acini in idiopathic interstitial pneumonias]
Lactic acid is elevated in idiopathic pulmonary fibrosis and induces myofibroblast differentiation via pH-dependent activation of transforming growth factor-b
Differential mRNA expression of insulin-like growth factor-1 splice variants in patients with idiopathic pulmonary fibrosis and pulmonary sarcoidosis
The hedgehog system machinery controls transforming growth factor-b-dependent myofibroblastic differentiation in humans: involvement in idiopathic pulmonary fibrosis
Neutrophil elastase promotes myofibroblast differentiation in lung fibrosis
Effects and mechanisms of pirfenidone, prednisone and acetylcysteine on pulmonary fibrosis in rat idiopathic pulmonary fibrosis models
Sustained Activation of Toll-Like Receptor 9 Induces an Invasive Phenotype in Lung Fibroblasts: Possible Implications in Idiopathic Pulmonary Fibrosis
PPAR-y ligands repress TGFb-induced myofibroblast differentiation by targeting the PI3K/Akt pathway: implications for therapy of fibrosis
WISP1 mediates IL-6-dependent proliferation in primary human lung fibroblasts
BALF N-acetylglucosaminidase and beta-galactosidase activities in idiopathic pulmonary fibrosis
Melatonin attenuates TGFb1-induced epithelial-mesenchymal transition in lung alveolar epithelial cells
Transglutaminase 2 and its role in pulmonary fibrosis
The role of cytokines in human lung fibrosis
JAK2 mediates lung fibrosis, pulmonary vascular remodelling and hypertension in idiopathic pulmonary fibrosis: an experimental study
Ambroxol hydrochloride in the management of idiopathic pulmonary fibrosis: Clinical trials are the need of the hour
Reactive oxygen species are required for maintenance and differentiation of primary lung fibroblasts in idiopathic pulmonary fibrosis
MiR-5100 targets TOB2 to drive epithelial-mesenchymal transition associated with activating smad2/3 in lung epithelial cells
IL-17A deficiency mitigates bleomycin-induced complement activation during lung fibrosis
Inhibitory effect of receptor for advanced glycation end products (RAGE) on the TGF-b-induced alveolar epithelial to mesenchymal transition
miR-9-5p suppresses pro-fibrogenic transformation of fibroblasts and prevents organ fibrosis by targeting NOX4 and TGFBR2
Extracellular Matrix Metalloproteinase Inducer (EMMPRIN) promotes lung fibroblast proliferation, survival and differentiation to myofibroblasts
Regulation of 26S Proteasome Activity in Pulmonary Fibrosis
TGF-beta-induced EMT: mechanisms and implications for fibrotic lung disease
Membrane-anchored Serine Protease Matriptase Is a Trigger of Pulmonary Fibrogenesis
Pleural mesothelial cells in pleural and lung diseases
Pleural mesothelial cell differentiation and invasion in fibrogenic lung injury
Absence of Thy-1 results in TGF-b induced MMP-9 expression and confers a profibrotic phenotype to human lung fibroblasts
[Different cytokine profiles in usual interstitial pneumonia and nonspecific interstitial pneumonia]
Signalling pathways from NADPH oxidase-4 to idiopathic pulmonary fibrosis
Essential role for the ATG4B protease and autophagy in bleomycin-induced pulmonary fibrosis
Interplay between RAGE, CD44, and focal adhesion molecules in epithelial-mesenchymal transition of alveolar epithelial cells
Deregulation of selective autophagy during aging and pulmonary fibrosis: the role of TGFb1
Are mast cells instrumental for fibrotic diseases? Idiopathic pulmonary fibrosis (IPF) is a fatal lung disorder of unknown etiology characterized by accumulation of lung fibroblasts and extracellular matrix deposition, ultimately leading to compromised tissue architecture and lung function capacity
Association between cytokine removal by polymyxin B hemoperfusion and improved pulmonary oxygenation in patients with acute exacerbation of idiopathic pulmonary fibrosis
The Role of PPARs in Lung Fibrosis
Increased production and immunohistochemical localization of transforming growth factor-beta in idiopathic pulmonary fibrosis
TNF-alpha, PDGF, and TGF-beta(1) expression by primary mouse bronchiolar-alveolar epithelial and mesenchymal cells: tnf-alpha induces TGF-beta(1)
MiR-338* suppresses fibrotic pathogenesis in pulmonary fibrosis through targeting LPA1
Metformin attenuates lung fibrosis development via NOX4 suppression
Investigation of bone marrow mesenchymal stem cells (BM MSCs) involvement in Idiopathic Pulmonary Fibrosis (IPF)
Anchorage-independent colony growth of pulmonary fibroblasts derived from fibrotic human lung tissue
The pathogenesis of idiopathic pulmonary fibrosis
Interstitial fibrosis and growth factors
Overexpression of squamous cell carcinoma antigen in idiopathic pulmonary fibrosis: clinicopathological correlations
TIAM1 inhibits lung fibroblast differentiation in pulmonary fibrosis
Intrinsic defence capacity and therapeutic potential of natriuretic peptides in pulmonary hypertension associated with lung fibrosis
Role of integrin-mediated TGFbeta activation in the pathogenesis of pulmonary fibrosis
Microsomal prostaglandin E synthase-1 deficiency exacerbates pulmonary fibrosis induced by bleomycin in mice
Antifibrotic effects of cyclosporine A on TGF-b1-treated lung fibroblasts and lungs from bleomycin-treated mice: role of hypoxia-inducible factor-1a
Preventive and therapeutic effects of thymosin b4 N-terminal fragment Ac-SDKP in the bleomycin model of pulmonary fibrosis
The role of halofuginone in fibrosis: more to be explored? Fibrosis, which can be defined as an abnormal or excessive accumulation of extracellular matrix (ECM), particularly fibrillar collagens, is a key driver of progressive organ dysfunction in many inflammatory and metabolic diseases, including idiopathic pulmonary fibrosis (IPF), cirrhosis, nephropathy, and oral submucous fibrosis (OSF)
Leucine-rich a-2 glycoprotein promotes lung fibrosis by modulating TGF-b signaling in fibroblasts
Forkhead Box F1 (FOXF1) represses cell growth, COL1 and ARPC2 expression in lung fibroblasts in vitro
Nitrated fatty acids reverse pulmonary fibrosis by dedifferentiating myofibroblasts and promoting collagen uptake by alveolar macrophages
Serpin B4 isoform overexpression is associated with aberrant epithelial proliferation and lung cancer in idiopathic pulmonary fibrosis
Modulation of specific beta cell gene (re)expression during in vitro expansion of human pancreatic islet cells
Dehydroepiandrosterone has strong antifibrotic effects and is decreased in idiopathic pulmonary fibrosis
Regulation of the effects of TGF-beta 1 by activation of latent TGF-beta 1 and differential expression of TGF-beta receptors (T beta R-I and T beta R-II) in idiopathic pulmonary fibrosis
MiR-541-5p regulates lung fibrosis by targeting cyclic nucleotide phosphodiesterase 1A
Lipoxin A4 Attenuates Constitutive and TGF-b1-Dependent Profibrotic Activity in Human Lung Myofibroblasts
Establishment of the mouse model of acute exacerbation of idiopathic pulmonary fibrosis
CCN5 overexpression inhibits profibrotic phenotypes via the PI3K/Akt signaling pathway in lung fibroblasts isolated from patients with idiopathic pulmonary fibrosis and in an in vivo model of lung fibrosis
Spiruchostatin A inhibits proliferation and differentiation of fibroblasts from patients with pulmonary fibrosis
Periostin promotes fibrosis and predicts progression in patients with idiopathic pulmonary fibrosis
Tumor necrosis factor superfamily 14 (LIGHT) controls thymic stromal lymphopoietin to drive pulmonary fibrosis
High levels of IL-6 and IL-8 characterize early-on idiopathic pulmonary fibrosis acute exacerbations
Mast cell chymase: an indispensable instrument in the pathological symphony of idiopathic pulmonary fibrosis? Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive and fatal lung disease with no known etiology and treatment options
Defect of pro-hepatocyte growth factor activation by fibroblasts in idiopathic pulmonary fibrosis
Lung infection with gamma-herpesvirus induces progressive pulmonary fibrosis in Th2-biased mice
Role of von Hippel-Lindau protein in fibroblast proliferation and fibrosis
miR-21 mediates fibrogenic activation of pulmonary fibroblasts and lung fibrosis
Amplified canonical transforming growth factor-b signalling<i>via</i>heat shock protein 90 in pulmonary fibrosis
Pirfenidone attenuates bleomycin-induced pulmonary fibrosis in mice by regulating Nrf2/Bach1 equilibrium
miR-31 is a negative regulator of fibrogenesis and pulmonary fibrosis
Cytokine gene polymorphisms and serum cytokine levels in patients with idiopathic pulmonary fibrosis
Thalidomide prevents bleomycin-induced pulmonary fibrosis in mice
Reduced expression of BMP3 contributes to the development of pulmonary fibrosis and predicts the unfavorable prognosis in IIP patients
The antifibrotic effects and mechanisms of microRNA-26a action in idiopathic pulmonary fibrosis
The K+ channel KCa3.1 as a novel target for idiopathic pulmonary fibrosis
The Epstein-Barr virus latent membrane protein 1 and transforming growth factor--b1 synergistically induce epithelial--mesenchymal transition in lung epithelial cells
An inhibitor of NADPH oxidase-4 attenuates established pulmonary fibrosis in a rodent disease model
TRPV4 mediates myofibroblast differentiation and pulmonary fibrosis in mice
Cigarette Smoke Enhances the Expression of Profibrotic Molecules in Alveolar Epithelial Cells
Pleiotropic effect of the proton pump inhibitor esomeprazole leading to suppression of lung inflammation and fibrosis
Activated human T lymphocytes inhibit TGFb-induced fibroblast to myofibroblast differentiation via prostaglandins D2 and E2
Sputum biomarkers in IPF: Evidence for raised gene expression and protein level of IGFBP-2, IL-8 and MMP-7
STAT3-mediated signaling dysregulates lung fibroblast-myofibroblast activation and differentiation in UIP/IPF
Peripheral depletion of NK cells and imbalance of the Treg/Th17 axis in idiopathic pulmonary fibrosis patients
Bone morphogenetic protein-4 inhibitor gremlin is overexpressed in idiopathic pulmonary fibrosis
TGF-b1 induces Fstl1 via the Smad3-c-Jun pathway in lung fibroblasts
Role of protease-activated receptor-2 in idiopathic pulmonary fibrosis
Type V collagen induced tolerance suppresses collagen deposition, TGF-b and associated transcripts in pulmonary fibrosis
Syndecan-2 is a novel target of insulin-like growth factor binding protein-3 and is over-expressed in fibrosis
Matrix regulation of idiopathic pulmonary fibrosis: the role of enzymes
Epithelial-mesenchymal transition in chronic hypersensitivity pneumonitis
Idiopathic Pulmonary Fibrosis: Aging, Mitochondrial Dysfunction, and Cellular Bioenergetics
HSP27 regulates TGF-b mediated lung fibroblast differentiation through the Smad3 and ERK pathways
Inhibition of mechanosensitive signaling in myofibroblasts ameliorates experimental pulmonary fibrosis
Extracellular superoxide dismutase has a highly specific localization in idiopathic pulmonary fibrosis/usual interstitial pneumonia
Early growth response transcription factors: key mediators of fibrosis and novel targets for anti-fibrotic therapy
[A role for mesothelial cells in the genesis of idiopathic pulmonary fibrosis?]
Effects of the tumor suppressor PTEN on the pathogenesis of idiopathic pulmonary fibrosis in Chinese patients
Different effects of growth factors on proliferation and matrix production of normal and fibrotic human lung fibroblasts
The impact of TGF-b on lung fibrosis: from targeting to biomarkers
Pathogenesis of idiopathic pulmonary fibrosis
SNAI transcription factors mediate epithelial-mesenchymal transition in lung fibrosis
TGF-b activation and lung fibrosis
Herpes virus infection is associated with vascular remodeling and pulmonary hypertension in idiopathic pulmonary fibrosis
N-acetylcysteine inhibits TNF-alpha, sTNFR, and TGF-beta1 release by alveolar macrophages in idiopathic pulmonary fibrosis in vitro
Recombinant human serum amyloid P in healthy volunteers and patients with pulmonary fibrosis
Protective role of andrographolide in bleomycin-induced pulmonary fibrosis in mice
Transforming growth factor beta1 induces epithelial-to-mesenchymal transition of A549 cells
[The potential role of cytokines expression in idiopathic pulmonary fibrosis]
X-linked inhibitor of apoptosis regulates lung fibroblast resistance to Fas-mediated apoptosis
Idiopathic pulmonary fibrosis: immunohistochemical analysis provides fresh insights into lung tissue remodelling with implications for novel prognostic markers
PI3K p110y overexpression in idiopathic pulmonary fibrosis lung tissue and fibroblast cells: in vitro effects of its inhibition
Alveolar epithelial cell injury with Epstein-Barr virus upregulates TGFbeta1 expression
CXCL9 Regulates TGF-b1-Induced Epithelial to Mesenchymal Transition in Human Alveolar Epithelial Cells
Expression of mucosa-related integrin alphaEbeta7 on alveolar T cells in interstitial lung diseases
Effects of cigarette smoke extract on A549 cells and human lung fibroblasts treated with transforming growth factor-beta1 in a coculture system
Nuclear factor erythroid 2-related factor 2 nuclear translocation induces myofibroblastic dedifferentiation in idiopathic pulmonary fibrosis
Rapamycin regulates connective tissue growth factor expression of lung epithelial cells via phosphoinositide 3-kinase
Autophagy and inflammation in chronic respiratory disease
Bone morphogenetic protein-inducer tilorone identified by high-throughput screening is antifibrotic in vivo
Peptide-mediated inhibition of mitogen-activated protein kinase-activated protein kinase-2 ameliorates bleomycin-induced pulmonary fibrosis
Reviews and prospectives of signaling pathway analysis in idiopathic pulmonary fibrosis
Membrane type-matrix metalloproteinases in idiopathic pulmonary fibrosis
Endothelin-1 induces alveolar epithelial-mesenchymal transition through endothelin type A receptor-mediated production of TGF-beta1
Effect of glycosides based standardized fenugreek seed extract in bleomycin-induced pulmonary fibrosis in rats: Decisive role of Bax, Nrf2, NF-kB, Muc5ac, TNF-a and IL-1b
Simvastatin inhibits growth factor expression and modulates profibrogenic markers in lung fibroblasts
Lung fibrotic tenascin-C upregulation is associated with other extracellular matrix proteins and induced by TGFb1
Activated MCTC mast cells infiltrate diseased lung areas in cystic fibrosis and idiopathic pulmonary fibrosis
EMT and interstitial lung disease: a mysterious relationship
Type II alveolar epithelial cells and interstitial fibroblasts express connective tissue growth factor in IPF
Anti-fibrotic Role of aB-crystallin Inhibition in Pleural and Subpleural Fibrosis
Fibrosis of two: Epithelial cell-fibroblast interactions in pulmonary fibrosis
Lysyl oxidases regulate fibrillar collagen remodelling in idiopathic pulmonary fibrosis
Crosstalk between TGF-b1 and complement activation augments epithelial injury in pulmonary fibrosis
RhoA signaling modulates cyclin D1 expression in human lung fibroblasts; implications for idiopathic pulmonary fibrosis
MicroRNAs in idiopathic pulmonary fibrosis
Titration of non-replicating adenovirus as a vector for transducing active TGF-beta1 gene expression causing inflammation and fibrogenesis in the lungs of C57BL/6 mice
Yin yang 1 is a novel regulator of pulmonary fibrosis
Age-driven developmental drift in the pathogenesis of idiopathic pulmonary fibrosis
Current and novel drug therapies for idiopathic pulmonary fibrosis
Proliferation of pulmonary interstitial fibroblasts is mediated by transforming growth factor-beta1-induced release of extracellular fibroblast growth factor-2 and phosphorylation of p38 MAPK and JNK
Secreted protein acidic and rich in cysteine (SPARC) is upregulated by transforming growth factor (TGF)-b and is required for TGF-b-induced hydrogen peroxide production in fibroblasts
Semaphorin 7a+ regulatory T cells are associated with progressive idiopathic pulmonary fibrosis and are implicated in transforming growth factor-b1-induced pulmonary fibrosis
Regulation of transforming growth factor-b1-driven lung fibrosis by galectin-3
Reduced transcription of the Smad4 gene during pulmonary carcinogenesis in idiopathic pulmonary fibrosis
Abrogation of TGF-beta1-induced fibroblast-myofibroblast differentiation by histone deacetylase inhibition
Curcumin inhibits fibrosis-related effects in IPF fibroblasts and in mice following bleomycin-induced lung injury
Targeting sphingosine kinase 1 attenuates bleomycin-induced pulmonary fibrosis
Data on CUX1 isoforms in idiopathic pulmonary fibrosis lung and systemic sclerosis skin tissue sections
Arsenic trioxide inhibits transforming growth factor-b1-induced fibroblast to myofibroblast differentiation in vitro and bleomycin induced lung fibrosis in vivo
Expression of WNT5A in Idiopathic Pulmonary Fibrosis and Its Control by TGF-b and WNT7B in Human Lung Fibroblasts
Negative regulation of myofibroblast differentiation by PTEN (Phosphatase and Tensin Homolog Deleted on chromosome 10)
This diff could not be displayed because it is too large.
# missing word embeddings:
29c
14
31
26a
beta1
486
profibrotic
92a
29a
matricellular
155
13
b1
etiopathology
nexin
avb6
21
19
acetylglucosaminidase
326
dermatan
1b
p38
47
68
3p
dedifferentiating
alpha3beta1
chymase
2alpha
90
7d
5100
18a
1a
alpha3
150
1343
140
541
fibrogenesis
221
mitophagy
b4
p63
10
5p
haptotactic
nonkinase
farnesoid
lymphopoietin
7a
18
338
1beta
424
199a
154
smad2
17
185
bronchoalveolar
101
profibrogenic
153
gambogic
ubiquitinating
p110y
200
323a
196a
dysregulates
fibrogenic
salvianolic
# missing MI weights:
Tumor
sTNFR
Compromised
Modulating
Renin
Invasive
Cytokine
D1
C3aR
Prostaglandin
Diagnostic
HLA
Interstitial
Transforming
Phenotypes
Up
Clinical
TGFb
Interplay
Animal
Decoction
Foxp3high
Leucine
CCL2
SDKP
IL
Correct
Elk1
Participation
Azithromycin
Amplification
1A
Endothelin
Kinase
Possible
Associated
MicroRNA
sL1
Action
For
Development
Establishment
Extracellular
Epstein
MUM
Serine
Interactions
Macrophage
Pseudomonas
Cytokines
IGFBP
Calu
PI3K
B4
Chinese
Cigarette
BALF
NK
alphaEbeta7
microRNAs
Gene
True
Pneumonia
CUX1
miRNA
Ubiquitin
Wnt
CDCP1
Barr
ORP150
Curcumin
aB
Myofibroblast
JNK
Aortic
L5
Hsp90
Smoke
IFN
Reactive
Significance
aVb6
Th2
Constitutive
Melatonin
Mediates
AP
Lindau
ALK5
AKT2
EMT
Reversion
Patients
Solution
Focal
Immunoglobulin
RhoA
Neutrophil
BMPR2
CXCL9
Lower
Olodaterol
Lavage
Induces
Induced
Beyond
MMP
Fstl1
cAMP
Aging
SPARC
Activity
ECM
Human
Fibrotic
Repression
Prostatic
NOX4
Against
Discovery
Resveratrol
Interleukin
Deleted
Differentiation
Spiruchostatin
Insulin
PXS64
MCTC
HP
Triptolide
Values
Differential
Lysyl
FGF
Promote
Yin
Tissue
BMP
CAM
Discoidin
Overproduction
Wilms
Regulates
Reduced
Mesenchymal
Inflammation
PINK1
Release
E2
CD44V6
TGFbeta1
Rg1
H441
kDa
M2
Expression
Data
Contribution
Negative
Nintedanib
Pulmonary
Emphysema
Intrinsic
17A
Marks
26S
RXFP1
Neovessel
Genetic
Protective
Tensin
Inducer
Like
Determining
Increased
Microsatellite
Sphingosine
TRPV4
Club
Methylation
Phenoconversion
Serpin
Activated
Muc5ac
MyD88
Glucagon
IPF
SIRT6
Rapamycin
Essential
TNFalpha
Corilagin
Sorafenib
Epithelial
T869C
Induction
Long
Wt1
Molecules
TGFBR2
P110
Nuclear
Old
Targeting
WNT7B
Thy
Potential
TGF
Tubastatin
Semaphorin
Attenuating
Smad
Pigment
Homolog
Binding
microRNA
C57BL
Regulating
Implications
Hydrogen
BARD1
A549
Homeostasis
Selectivity
Medical
Model
Cytoskeletal
Differing
BMP3
Enhances
NADPH
Fibrogenesis
Defect
Two
FAK
RNA
Quantifying
Epigenetic
Profibrotic
Ambroxol
Trigger
Titration
Transcription
Regulation
Mitochondrial
H1N1
Recent
BMPER
PPARs
VCAM
Microsomal
Hippel
Renshen
Absence
Anchorage
Applying
Free
OSF
PGE
Tannic
Plasminogen
TGFBR
Channel
Age
Cell
Connective
Proteasomal
RAGE
Bach1
Pirfenidone
Outcomes
GATA
Small
Autoimmunity
III
VEGF
Control
HSP27
Cartilage
Periostin
Idiopathic
COL1A1
CBP
Bronchoalveolar
Crosstalk
Amplified
Evidence
Simvastatin
Sphingolipids
Mechanisms
JAK2
Rats
Mice
Protease
From
LPA1
Collagen
Carbon
Molecular
Stat3
Genomewide
Stem
S1P
Novel
EBV
Serum
Abrogation
That
Pingfei
Stromal
Current
Molecule
MAP3K19
Decisive
Protein
Fluid
HDAC4
Angiotensin
SOCS1
Different
Membrane
Domain
Secretory
Signalling
NCI
Bax
ADAM
Are
Beta1
Activation
Problem
Prognostic
II
Sputum
Phosphatase
Inhibition
Profile
Dogs
HRCT
lncRNA
Storage
Nitrated
Box
Forkhead
CREB
Sirtuin
Cryptogenic
Decreased
Inhibits
Formation
MK2
Comparison
Mediated
Latent
Recombinant
Microencapsulation
PHGDH
Organizing
Dysfunction
Way
Using
Peripheral
Markers
MiR
Anti
Studies
May
Significant
Morphogenic
Low
Lactic
Overexpression
Protects
Arsenic
Caveolin
pH
Inhibit
Proteasome
MicroRNAs
Toll
Herpes
CTGF
Normal
Defective
CD44
Large
Ligands
Axis
NH2
Progression
Smad3
Phenotype
Ets
Identification
kB
Role
Relation
Mode
Developmental
Fibrosis
Stanniocalcin
WNT10A
Integrated
Syndecan
Metalloproteinase
TOB2
USP11
WISP1
Dysregulated
Th17
Progressive
Key
Subpleural
Mast
Rho
Growth
Upregulation
Alleviates
Re
Preventive
ITGB6
Fibroblasts
ATG4B
Comparative
Cthrc1
mRNA
Peptide
SNAI
BM
ATPase
AKT
Fibroblastic
Matriptase
Sub
Sustained
Pleiotropic
New
Regulator
Receptor
Therapeutic
Vimentin
IGF
Cells
LIGHT
Production
D2
Dehydroepiandrosterone
Lin28B
Antifibrotic
Raised
Proliferation
Dependent
COL1
Lysocardiolipin
Epithelium
STAT3
Prevents
Th1
NF
CCN5
Snail
Myogenic
CD4
Akt
TGFb1
Accelerated
PDGF
Intratracheal
TGFB1
Cysteine
Oxidant
Effect
Reprogramming
IIP
MS80
FOXF1
Promotes
Assessment
BLM
CC16
BAL
CD248
Ginsenoside
Secreted
Association
IQ
mTORC2
Established
The
Combined
Jun
UIP
Sulf2
Thalidomide
Bioenergetics
TNF
CCN2
NEU1
Attenuates
HMGA2
Group
Conversion
Predisposition
Transglutaminase
Pathway
Reviews
Treg
DDR2
Autophagy
Hyper
Bile
Sunitinib
Stiffening
Signal
Resolution
De
Type
Factor
Smad2
Single
PPAR
WNT5A
Novo
An
EGFR
Cub
GLI
HSP47
Early
ERK1
TGFbeta
Deficiency
hydroxytryptamine2A
BAX
Inhibitory
Integrin
Suppression
Shikonin
SMAD3
Effects
Metformin
F1
MAPK
Modulation
Bleomycin
Injury
Elevated
Cellular
Radioligand
Citrus
TIAM1
Subjects
Lung
ARPC2
H19
EZH2
Pathways
Is
Microarray
Fas
CCN1
Ac
miRNAs
Myofibroblasts
FFPE
Inhibitor
During
Matrix
Nrf2
Immunomodulation
C5aR
Gremlin
High
Concentration
Evaluation
Roles
Number
Bone
ACLP
Hypertension
Lipogenic
Uncoupling
Signaling
Lrp5
Berberine
A4
CD11c
miR
Chop
Galectin
Alveolar
Transition
Plasma
Impacts
Smad4
Its
Pathogenesis
Inappropriate
Investigation
Beta
Ca
ERK
Deregulation
MSCs
PTEN
Lipoxin
Nitric
C1q
KCa3
kappaB
Involvement
MCP
Pleural
EMMPRIN
Smooth
Synthesis
Blockade
Compared
Transgelin
No preview for this file type
# missing word embeddings:
profibrogenic
199a
p38
beta1
68
etiopathology
1343
lymphopoietin
29c
185
5p
17
dermatan
1a
13
424
101
p63
140
b1
fibrogenic
gambogic
nonkinase
21
alpha3
154
2alpha
chymase
18a
196a
5100
smad2
7d
541
1b
acetylglucosaminidase
326
47
dysregulates
92a
200
29a
90
31
mitophagy
b4
3p
nexin
dedifferentiating
155
150
ubiquitinating
10
486
19
avb6
fibrogenesis
farnesoid
haptotactic
alpha3beta1
14
323a
matricellular
7a
profibrotic
bronchoalveolar
26a
18
salvianolic
338
1beta
p110y
221
153
# missing MI weights:
Compared
Are
True
Ambroxol
Diagnostic
Alveolar
Smad2
Neovessel
RXFP1
Normal
Shikonin
Spiruchostatin
ORP150
Tubastatin
That
Bone
WISP1
Wt1
Smad4
ECM
Syndecan
Radioligand
BAX
De
FAK
Prevents
Endothelin
kB
Promote
Reversion
Determining
Cytokines
Glucagon
Pathways
Myogenic
SOCS1
Investigation
Regulating
Targeting
Decoction
Stromal
PPARs
HP
Focal
Transgelin
Association
Effects
EGFR
Gene
Human
Metalloproteinase
Lower
Rg1
Binding
Therapeutic
Mesenchymal
CD248
Formation
Cysteine
Caveolin
Type
Signaling
Molecular
Alleviates
Early
Transforming
Potential
COL1A1
Plasminogen
Factor
Semaphorin
CC16
Integrated
Like
Stat3
Tissue
Signalling
Phenotype
TGFBR2
Homolog
III
MiR
Lactic
Pulmonary
Fibroblastic
Defect
Molecules
Yin
MCP
MicroRNA
LIGHT
Beyond
Recombinant
Compromised
Ginsenoside
P110
Production
Lipogenic
HRCT
Its
Implications
Problem
NH2
Fibrogenesis
TOB2
SMAD3
Lin28B
Significance
Differential
Cytokine
Progressive
Solution
Identification
Peptide
Synthesis
Protein
Macrophage
PDGF
Repression
CREB
Cellular
Plasma
A4
Latent
Wnt
Proteasome
Kinase
Proteasomal
Pathway
Sirtuin
MSCs
D2
Absence
Cells
Thalidomide
Regulation
Hippel
pH
Chinese
Th17
Uncoupling
Periostin
Promotes
Amplification
Smad
Profibrotic
Patients
Subpleural
Cytoskeletal
Progression
Lavage
Angiotensin
Domain
Peripheral
Inhibitor
Associated
Involvement
Serum
Toll
Activation
SPARC
Attenuating
Resveratrol
PI3K
Induced
Matrix
Leucine
BALF
Defective
Negative
JNK
Receptor
Reprogramming
CD11c
Nuclear
hydroxytryptamine2A
Is
Sustained
Essential
Beta
CBP
miRNA
Pathogenesis
Aging
Neutrophil
Nitrated
Resolution
Signal
Low
New
Contribution
Homeostasis
HLA
Sub
26S
HMGA2
Treg
Significant
Blockade
HSP27
Clinical
Th1
Triptolide
Dependent
Inflammation
VEGF
PINK1
H1N1
E2
Discovery
Interplay
Secretory
CCL2
Dehydroepiandrosterone
Modulation
Mechanisms
MMP
Mediated
H19
Morphogenic
Ac
Corilagin
Tannic
Hypertension
WNT10A
MCTC
Possible
Studies
Pigment
Wilms
Hydrogen
Azithromycin
Number
Transglutaminase
Outcomes
NCI
RNA
WNT5A
Mice
Methylation
Novel
Nitric
Cell
HSP47
TRPV4
Protease
Release
For
Ligands
TGF
Epithelium
Aortic
NADPH
Herpes
Bach1
Ca
Dysregulated
Membrane
TGFBR
Connective
Decreased
TIAM1
Serpin
Fstl1
CCN1
BLM
Sphingosine
C57BL
Data
Dogs
Organizing
IGF
COL1
CD44V6
BMPER
ARPC2
Galectin
Lindau
Inappropriate
Microencapsulation
Oxidant
M2
Renshen
Sputum
Snail
Inducer
Prognostic
Storage
MAPK
Citrus
PPAR
Collagen
Matriptase
Arsenic
Long
F1
Deleted
Genomewide
PXS64
Lysyl
ERK
Calu
MyD88
aB
Activity
Applying
Secreted
Control
BM
Mitochondrial
Age
EZH2
Overproduction
Way
The
DDR2
1A
Rho
Bronchoalveolar
TGFbeta1
Akt
ERK1
Novo
Curcumin
FGF
C5aR
17A
Lysocardiolipin
Protects
Predisposition
Thy
C1q
Nintedanib
High
KCa3
Olodaterol
Reviews
Proliferation
Immunomodulation
Attenuates
Gremlin
Cthrc1
Vimentin
Elk1
Lipoxin
IQ
Roles
BAL
Relation
Autophagy
IGFBP
Inhibition
BMP
Anchorage
ITGB6
Mode
Modulating
miRNAs
Inhibit
PHGDH
Up
Phosphatase
TGFbeta
C3aR
Pseudomonas
Comparative
Reduced
Crosstalk
Conversion
Injury
Phenotypes
CD4
MicroRNAs
Regulates
TNFalpha
Pirfenidone
Raised
Old
Cartilage
Prostaglandin
BMP3
BARD1
Deficiency
RhoA
AKT2
NF
Cigarette
GATA
MAP3K19
sTNFR
NK
Different
Subjects
Autoimmunity
Mast
Single
Microsomal
WNT7B
MK2
TGFb1
CCN2
Growth
Prostatic
PGE
Abrogation
Stem
EBV
Microsatellite
Nrf2
Epstein
Club
TGFB1
ATG4B
Differentiation
EMMPRIN
Smad3
Genetic
Sorafenib
IFN
Impacts
Key
Activated
AKT
Th2
PTEN
USP11
IL
Effect
HDAC4
Free
Sunitinib
Established
Fluid
Decisive
Inhibits
Marks
mTORC2
Trigger
Concentration
Intratracheal
Participation
Against
Expression
kappaB
Role
Rats
Intrinsic
Epigenetic
Smooth
NOX4
Tumor
Rapamycin
microRNA
Overexpression
Current
Muc5ac
Combined
II
D1
Accelerated
Regulator
Pleural
Invasive
alphaEbeta7
From
MUM
Immunoglobulin
Beta1
Small
Sphingolipids
Stiffening
FFPE
miR
LPA1
B4
Two
Extracellular
Enhances
Evaluation
Recent
Elevated
Re
IIP
CD44
Interactions
CXCL9
Protective
Ets
Preventive
Establishment
ALK5
Increased
Values
kDa
Large
May
Transcription
ACLP
Cryptogenic
Ubiquitin
GLI
L5
Discoidin
Bleomycin
Carbon
Renin
CUX1
Correct
Constitutive
SNAI
Bile
Assessment
Fibrotic
Differing
Development
Channel
Simvastatin
CAM
Fibroblasts
Melatonin
SIRT6
STAT3
Tensin
Pingfei
Stanniocalcin
Bax
Group
mRNA
Selectivity
Emphysema
Barr
Berberine
Metformin
Hsp90
CDCP1
T869C
EMT
ADAM
Cub
Pneumonia
Induces
FOXF1
Upregulation
H441
RAGE
Myofibroblasts
JAK2
Interstitial
Amplified
Fibrosis
Microarray
Developmental
CTGF
Serine
Integrin
AP
Fas
During
CCN5
Insulin
Pleiotropic
TGFb
Evidence
Phenoconversion
Comparison
Smoke
Box
microRNAs
Anti
Suppression
A549
Chop
Jun
Myofibroblast
Dysfunction
Axis
IPF
MS80
S1P
Inhibitory
Interleukin
Action
Bioenergetics
Transition
Hyper
Lrp5
Model
cAMP
Medical
SDKP
UIP
Animal
Forkhead
lncRNA
Lung
Antifibrotic
Induction
Titration
Epithelial
OSF
ATPase
Reactive
TNF
aVb6
Molecule
NEU1
Deregulation
Idiopathic
An
Using
Quantifying
BMPR2
Foxp3high
sL1
Profile
Sulf2
Mediates
Markers
VCAM
#!/usr/bin/python
# -*- coding: latin-1 -*-
# Python2.7
import numpy as np
import logging
import os
from functools import partial
from pdb import set_trace as st
logging.basicConfig(format='%(asctime)s : %(levelname)s : %(message)s',
level=logging.INFO)
class wisse(object):
""" Both the TFIDFVectorizer and the word embedding model must be pretrained, either from the local
sentence corpus or from model persintence.
"""
def __init__(self, embeddings, vectorizer, tf_tfidf, combiner = "sum"):
self.tokenize = vectorizer.build_tokenizer()
self.tfidf = vectorizer
self.embedding = embeddings
self.pred_tfidf = tf_tfidf
if combiner.startswith("avg"):
self.comb = partial(np.mean, axis = 0)
else:
self.comb = partial(np.sum, axis = 0)
def fit(self, X, y = None): # Scikit-learn template
if isinstance(X, list):
self.sentences = X
return self
def transform(self, X):
if isinstance(X, list):
return self.fit(X)
elif isinstance(X, str):
return self.infer_sentence(X)
def fit_transform(self, X, y=None):
return self.transform(X)
def infer_sentence(self, sent):
ss = self.tokenize(sent)
missing_bow = []
missing_cbow = []
series = {}
if not ss == []:
self.weights, m = self.infer_tfidf_weights(ss)
else:
return None
missing_bow += m
for w in self.weights:
try:
series[w] = (self.weights[w], self.embedding[w])
except KeyError:
series[w] = None
missing_cbow.append(w)
continue
except IndexError:
continue
if self.weights == {}: return None
# Embedding the sentence... :
sentence = np.array([series[w][1] for w in series if not series[w] is None])
series = {}
return missing_cbow, missing_bow, self.comb(sentence)
def infer_tfidf_weights(self, sentence):
existent = {}
missing = []
if not self.tfidf:
for word in sentence:
existent[word] = 1.0
return existent, missing
if self.pred_tfidf:
unseen = self.tfidf.transform([" ".join(sentence)]).toarray()
for word in sentence:
try:
existent[word] = unseen[0][self.tfidf.vocabulary_[word]]
except KeyError:
missing.append(word)
continue
else:
for word in sentence:
try:
weight = vectorizer.idf_[vectorizer.vocabulary_[word]]
existent[word] = weight if weight > 2 else 0.01
except KeyError:
missing.append(word)
continue
return existent, missing
def __iter__(self):
for s in self.sentences:
yield self.transform(s)
def save_dense(directory, filename, array):
directory=os.path.normpath(directory) + '/'
# try:
if filename.isalpha():
np.save(directory + filename, array)
else:
return None
# except UnicodeEncodeError:
# return None
def load_dense(filename):
return np.load(filename)
def load_sparse_bsr(filename):
loader = np.load(filename)
return bsr_matrix((loader['data'], loader['indices'], loader['indptr']),
shape=loader['shape'])
def save_sparse_bsr(directory, filename, array):
# note that .npz extension is added automatically
directory=os.path.normpath(directory) + '/'
if word.isalpha():
array=array.tobsr()
np.savez(directory + filename, data=array.data, indices=array.indices,
indptr=array.indptr, shape=array.shape)
else:
return None
class vector_space(object):
def __init__(self, directory, sparse = False):
self.sparse = sparse
ext = ".npz" if sparse else ".npy"
if directory.endswith(".tar.gz"):
self._tar = True
import tarfile
self.tar = tarfile.open(directory)
file_list = self.tar.getnames() #[os.path.basename(n) for n in self.tar.getnames()]
self.words = {os.path.basename(word).replace(ext, ''): word
for word in file_list}
else:
self._tar = False
directory = os.path.normpath(directory) + '/'
file_list = os.listdir(directory)
self.words = {word.replace(ext, ''): directory + word
for word in file_list}
def __getitem__(self, item):
if self.sparse:
if self._tar:
member = self.tar.getmember(self.words[item])
word = self.tar.extractfile(member)
else:
word = self.words[item]
#return load_sparse_bsr(self.words[item])
return load_sparse_bsr(word)
else:
if self._tar:
member = self.tar.getmember(self.words[item])
word = self.tar.extractfile(member)
else:
word = self.words[item]
#return load_sparse_bsr(self.words[item])
return load_dense(word)
def keyed2indexed(keyed_model, output_dir = "word_embeddings/", parallel = True, n_jobs = -1):
output_dir = os.path.normpath(output_dir) + '/'
if not os.path.exists(output_dir):
os.makedirs(output_dir)
if parallel:
from joblib import Parallel, delayed
Parallel(n_jobs = n_jobs, verbose = 10)(delayed(save_dense)(output_dir, word, keyed_model[word])
for word, _ in keyed_model.vocab.items())
else:
for word, _ in keyed_model.vocab.items():
save_dense(output_dir, word, keyed_model[word])
class streamer(object):
def __init__(self, file_name):
self.file_name = file_name
def __iter__(self):
for s in open(self.file_name):
yield s.strip()
No preview for this file type
#!/usr/bin/python
# -*- coding: latin-1 -*-
# Python2.7
from gensim.models.keyedvectors import KeyedVectors as vDB
from sklearn.feature_extraction.text import TfidfVectorizer
import numpy as np
#import numexpr as ne
import argparse
#import _pickle as pickle
#import cPickle as pickle
import logging
import os
from functools import partial
import wisse
load_vectors = vDB.load_word2vec_format
logging.basicConfig(format='%(asctime)s : %(levelname)s : %(message)s',
level=logging.INFO)
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="""This use example shows sentence
embedding by using WISSE. The input is a text file which has a sentece in
each of its rows. The output file has two tab-separated columns: the index
line of the sentece in the input file and the sentence vector representation
.""")
parser.add_argument("--idfmodel", help = """Input file containing IDF
pre-trained weights. If not provided,
all word vector weights will be set to
1.0. If 'local' tf-idf weights will be
computed locally from the input file
(pickled sklearn object).""",
default = None)
parser.add_argument("--embedmodel", help = """Input file containing word
embeddings model (binary and text
are allowed).""", required = True)
parser.add_argument("--output", help = """Output file containing the sentence
embeddings.""", default = "")
parser.add_argument("--input", help = """Input file containing a sentence
by row.""", required = True)
parser.add_argument("--comb", help = """Desired word vector combination for
sentence representation {sum, avg}.
(default = 'sum')""", default = "sum")
parser.add_argument("--suffix", nargs = '?', help = """A suffix to be added
to the output file (default = '')""",
default = "", required = False)
parser.add_argument("--tfidf", help="""To predict TFIDF complete weights
('tfidf') or use only partial IDFs
('idf'). (default = 'tfidf')""",
default = "tfidf")
parser.add_argument("--localw", help = """TFIDF word vector weights
computed locally from the input file of
sentences {freq, binary, sublinear}
(default='none').""", default = "none")
parser.add_argument("--stop", help = """Toggles stripping stop words in
locally computed word vector weights.""",
action = "store_true")
parser.add_argument("--format", help = """The format of the embedding model
file: {binary, text, wisse}.
default = 'binary'""", default = "binary")
args = parser.parse_args()
if not args.format.startswith("wisse"):
if not os.path.isfile(args.embedmodel):
logging.info("""Embedding model file does not exist (EXIT):
\n%s\n ...""" % args.embedmodel)
exit()
elif not os.path.exists(args.embedmodel):
logging.info("""Embedding model directory does not exist (EXIT):
\n%s\n ...""" % args.embedmodel)
exit()
if not os.path.isfile(args.idfmodel) and not args.idfmodel.startswith("local"):
logging.info("""IDF model file does not exist (EXIT):
\n%s\n ...""" % args.idfmodel)
exit()
if not os.path.isfile(args.input):
logging.info("""Input file does not exist (EXIT):
\n%s\n ...""" % args.input)
exit()
if args.output != "":
if os.path.dirname(args.output) != "":
if not os.path.exists(os.path.dirname(args.output)):
logging.info("""Output directory does not exist (EXIT):
\n%s\n ...""" % args.output)
exit()
else:
output_name = args.output
else:
output_name = args.output
else:
suffix = "_".join([embedding_name,
args.comb,
args.tfidf,
"local" if args.idfmodel.startswith("local") else tfidf_name,
args.suffix]).strip("_")
output_name = args.input + ".output_" + suffix
if args.tfidf.startswith("tfidf"):
pred_tfidf = True
elif args.tfidf.startswith("idf"):
pred_tfidf = False
else:
pred_tfidf = False
tfidf = False
vectorizer = TfidfVectorizer(min_df = 1,
encoding = "latin-1",
decode_error = "replace",
lowercase = True,
binary = True if args.localw.startswith("bin") else False,
sublinear_tf = True if args.localw.startswith("subl") else False,
stop_words = "english" if args.stop else None)
sentences = wisse.streamer(args.input)
if args.idfmodel.startswith("local"):
logging.info("Fitting local TFIDF weights from: %s ..." % args.input)
tfidf = vectorizer.fit(sentences)
elif os.path.isfile(args.idfmodel):
logging.info("Loading global TFIDF weights from: %s ..." % args.idfmodel)
with open(args.idfmodel, 'rb') as f:
tfidf = pickle.load(f)#, encoding = 'latin-1')
else:
tfidf = False
try:
if args.format.startswith("bin"):
embedding = load_vectors(args.embedmodel, binary = True,
encoding = "latin-1")
elif args.format.startswith("tex"):
embedding = load_vectors(args.embedmodel, binary = False,
encoding = "latin-1")
else:
embedding = wisse.vector_space(args.embedmodel, sparse = False)
except:
logging.info(
"""Error while loading word embedding model. Verify if the file
is broken (EXIT)...\n%s\n""" % args.embedmodel)
exit()
embedding_name = os.path.basename(args.embedmodel).split(".")[0]
tfidf_name = os.path.basename(args.idfmodel).split(".")[0]
missing_bow = [] # Stores missing words in the TFIDF model
missing_cbow = [] # Stores missing words in the W2V model
sidx = 0 # The index of the sentence according to the input file
logging.info("\n\nEmbedding sentences and saving then to a the output file..\n%s\n" % output_name)
with open(output_name, "w") as fo:
for sent in sentences:
sidx += 1
series = wisse.wisse(embeddings = embedding, vectorizer = tfidf,
tf_tfidf = True, combiner='sum')
try:
mc, mb, vector = series.transform(sent)
except TypeError:
continue
# At this point you can use the embedding 'vector' for any application as it
# is a numpy array. Also you can simply save the vectors in text format as
# follows:
missing_cbow += mc
missing_bow += mb
fo.write("%d\t%s\n" % (sidx, np.array2string(vector,
formatter = {'float_kind':lambda x: "%.6f" % x},
max_line_width = 20000).strip(']').strip('[') ))
missing_name = (os.path.basename(args.input).split(".")[0] + "_" +
embedding_name + "_" +
tfidf_name + ".missing")
logging.info("\n\nSaving missing vocabulary to %s ..\n\n" % missing_name)
with open(missing_name, "w") as f:
f.write("# missing word embeddings:\n")
for w in set(missing_cbow):
f.write("%s\n" % w)
f.write("# missing MI weights:\n")
for w in set(missing_bow):
f.write("%s\n" % w)
logging.info("FINISHED! \n")