A Deep Learning-Based Phenotypic Analysis of Rice Root Distribution from Field Images

Root distribution in the soil determines plants' nutrient and water uptake capacity. Therefore, root distribution is one of the most important factors in crop production. The trench profile method is used to observe the root distribution underground by making a rectangular hole close to the crop, providing informative images of the root distribution compared to other root phenotyping methods. However, much effort is required to segment the root area for quantification. In this study, we present a promising approach employing a convolutional neural network for root segmentation in trench profile images. We defined two parameters, Depth50 and Width50, representing the vertical and horizontal centroid of root distribution, respectively. Quantified parameters for root distribution in rice (Oryza sativa L.) predicted by the trained model were highly correlated with parameters calculated by manual tracing. These results indicated that this approach is useful for rapid quantification of the root distribution from the trench profile images. Using the trained model, we quantified the root distribution parameters among 60 rice accessions, revealing the phenotypic diversity of root distributions. We conclude that employing the trench profile method and a convolutional neural network is reliable for root phenotyping and it will furthermore facilitate the study of crop roots in the field.

Phase II trial of preoperative chemotherapy for breast cancer: Japan Breast Cancer Research Network (JBCRN)-02 trial

BACKGROUND

Neoadjuvant chemotherapy (NAC) is one of the main strategies for patients with locally advanced breast cancer. In our previous study, biological markers such as estrogen receptor (ER), progesterone receptor (PgR), and HER2 were essential predictors of the effectiveness of NAC to help individualize treatment. This study examined the effect of NAC on the disease-free survival (DFS) of breast cancer patients. Furthermore, the study was expanded by adding Ki-67 as a biological marker, and examined the correlation between Ki-67 and the prognosis.

PATIENTS AND METHODS

Between September 2005 and September 2007, 43 patients with breast cancer received NAC and surgery. Four cycles of DC (doxorubicin: 60 mg/m(2) and cyclophosphamide: 500 mg/m(2)) were administered intravenously (i.v.) on day 1 every 21 days, followed by 12 cycles of paclitaxel i.v. (80 mg/m(2)) every 7 days, prior to surgery. The primary endpoint was the pathological complete response (pCR) rate and the secondary endpoint was DFS; the pCR rate was estimated for each groups stratified by the presence or absence of different factors (PcR, ER/PgR, and Ki-67).

RESULTS

The clinical response (cCR+cPR) rate was 81.0%, and the pCR rate was 25.6%. The pCR rate was 75, 50, 9 and 0% in HER2(+)/ER(-), HER2(+)/ER(+), HER2(-)/ER(-), and HER2(-)/ER(+) patients, respectively. The 4-year DFS rate was estimated at 78% for all patients. The HER2 status was an independent predictor of pathological complete response (pCR). The DFS rate of patients with lower Ki-67 values (<15%) was higher than that of patients with higher Ki-67 values (≥15%). The treatment-related adverse events were manageable: the majority were mild, but five patients experienced grade 3 (neutropenia and sensory neuropathy) adverse events.

CONCLUSION

DC followed by weekly paclitaxel is an active and manageable preoperative regimen for breast cancer patients. HER2 overexpression may be a good predictive marker of pCR, and the Ki-67 value after NAC may be a prognostic factor for DFS.

Utility of Breast CT in the Management of Breast Cancer – Results from a Prospective Multi-Institutional Study

Background:In order to obtain negative margins after breast conserving surgery (BCS), even repeated surgery is widely accepted. Before surgery, it is important to conduct a precise assessment of the extent of the breast cancer so that each patient can receive individualized surgery. To evaluate the utility of breast computed tomography (CT) as a tool to manage BCS, a multi-institutional prospective study was conducted in Japan.Patients and Methods:Patients were eligible to participate in this study if they had histologically proven breast cancer and were determined to be BCS candidates based on palpation, mammography (MMG) and ultrasonography (US). Written informed consent was obtained from each patient. First, the surgeon marked the line of planned excision on the skin using information from the MMG and US. Next, an expired angiographic catheter was placed on the mark to show the original surgical margin on the CT image. Breast CT was scanned 60 seconds after the bolus injection of the contrast material in the supine surgical position. The surgeon determined the extent of surgery based on the breast CT results. Surgical specimens were serially sectioned in 5-mm slices.Results:Three hundred and two patients were enrolled in this study. The CT scanners used in this study varied from a single helical CT to a 64-row multidetector CT. The results of the breast CT changed the extent of resection in 14.7% of patients. Among the 5 patients who were recommended to undergo a mastectomy, 4 patients had multicentric tumors pathologically and 1 patient had a widely spread intraductal component. The other patients were recommended to have a quadrantectomy based on the extent of breast cancer that was visualized by CT. Three patients (1%) who required conversion from a lumpectomy to quadrantectomy resulted in overexcision. In short, breast CT correctly changed the extent of surgery in 13.7% of the examined patients.Conclusion:This prospective study suggested that breast CT is useful for hospitals equipped with any type of CT and can be used to provide patients with individualized surgery.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 5021.

Phase II study of AC (doxorubicin and cyclophosphamide) followed by weekly paclitaxel as neoadjuvant chemotherapy in operable patients with primary breast cancer

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Background: The objective of this multi center Phase II clinical study prove the benefit of neoadjuvant combination therapy using anthracycline based AC therapy (doxorubicin and cyclophosphamide), which is useful as a standard therapy, followed by weekly PTX(paclitaxel) in patients with early stage breast cancer. Methods: Forty-seven patients with operable breast cancer were enrolled to the study. Patients received four cycles of AC followed by weekly PTX. The primary endpoint was disease free survival (DFS) stratified by the absence of presence of Quasi-pCR (QpCR: absence of invasive tumor or only focal residual tumor cells). Secondary endpoints were predictors for QpCR, clinical response, breast conservation rate, and safety. The planned sample size was 25. Results: Of 43 assessable patients, 25.6% achieved QpCR. With 28.6 months median follow-up, DFS was estimated at 72% for all patients. 3 year DFS for patients with QpCR was 80% vs. 72% without QpCR. HER2 status and response to AC were independent predictors of QpCR. The overall clinical response was 79%; 58% of patients achieved breast conservation. Nausea was the most common adverse event, observed in 62.8% and 33.3% of patients during AC and PTX respectively. The second common adverse event was peripheral neuritis, observed in 9.3% and 57.1% of patients during AC and PTX respectively. Conclusions: Despite the small sample size, these data shows that AC followed PTX is a highly active neoadjuvant therapy for women with early stage breast cancer.

No significant financial relationships to disclose.

Effects of p27Kip1 on cell cycle status and viability in A549 lung adenocarcinoma cells

p27Kip1 is a cyclin-dependent kinase inhibitor, it negatively regulates G1 progression and is reported to modulate apoptosis. Phosphorylation of this protein is thought to regulate its intracellular localisation and affect its stability. The aim of this study was to regulate p27Kip1 expression levels, and to examine how this protein affects cell cycle status and modulates viability in A549 lung adenocarcinoma cells. In addition, the association between phosphorylation status of p27Kip1 and its intracellular localisation was investigated, using expression vectors with cDNA of p27Kip1 or mutants in which the phosphorylation sites had been mutated. Although overexpression of p27Kip1 reduced cell cycle progression, its removal did not change cell cycle status. Modest induction of p27Kip1 rescued adenovector-induced apoptosis and its removal with short interfering RNA increased spontaneous cell death. It was also observed that p27Kip1 localised mainly in the cytoplasm, and forced expression of p27Kip1 cDNA with the substitution of serine (S) 10, threonine (T) 157 and T198 to glutamate (phosphor-mimetic) induced its cytoplasmic localisation. In conclusion, p27Kip1, when expressed physiologically, exists mainly in the cytoplasm, has little effect on cell cycle status and contributes viability in A549 lung adenocarcinoma cells. It was also surmised that intracellular localisation of p27Kip1 dominates its function and that its localisation was partly determined by its phosphorylation.

Relationship between swallowing function and gas exchange during day and night in patients with obstructive sleep apnea syndrome

Patients with obstructive sleep apnea syndrome (OSAS) are likely to exhibit an impaired swallowing reflex. However, mechanisms of disturbed swallowing reflex have not been determined. Because the upper-airway function is inhibited by hypoxia and hypercapnia, we examined the relationship between the swallowing function and gas exchange during day and night in patients with OSAS. Twenty-four patients with OSAS and 24 age-matched controls were studied. OSAS was diagnosed from overnight polysomnography. The swallowing reflex was judged by the latent time (LT) for swallowing following bolus injection of distilled water at the suprapharynx, the inspiratory suppression time (IST) from swallowing termination to the next onset of inspiration, and the threshold for evoking the swallowing response in terms of a volume of water (TV). Whereas the LT values are positively correlated with PaCO2 but not with PaO2 during the day, the values of IST and TV were not associated with daytime PaCO2 or PaO2. Nocturnal nadir SaO2 was correlated with LT, IST, and TV. These results indicate that oxyhemoglobin desaturation and hypercapnia may be associated with one of the mechanisms of the impaired swallowing function in patients with OSAS.

An in vitro screening system for characterizing the cleft palate-inducing potential of chemicals and underlying mechanisms

An in vitro organ culture system with developing mouse palates was improved to characterize the cleft palate (CP)-inducing potential of chemicals and underlying mechanisms. Palatal explants collected from gestation day 12 mouse fetuses were cultured with various concentrations of teratogens and examined for palatal development after 48 and 72 h of culture to assess effects of the chemicals on growth and/or fusion of palatal shelves. When the explants were exposed to diphenylhydantoin or 5-fluorouracil, palatal growth was inhibited in a concentration-dependent manner at 48 h. Suppression of the expression of proliferative cell nuclear antigen revealed poor cell proliferation. At 72 h, the incidence of explants with CP was significantly increased in the high-dose groups, suggesting that CP induction is mainly attributable to inhibition of palatal growth. By contrast, retinoic acid and hydrocortisone significantly lowered the rates of fused palates at 72 h in all treated groups, while they exhibited no effects on palatal growth at 48 h even at the highest concentration. Because no apoptosis was found in the epithelial cells at the tip of these palates, these chemicals are suggested to inhibit palatal fusion process by preventing apoptosis.

Association of Gc-globulin variation with susceptibility to COPD and diffuse panbronchiolitis

Chronic obstructive pulmonary disease (COPD) and diffuse panbronchiolitis (DPB) are both characterized by chronic airflow limitation. Although the aetiology of these diseases is under investigation, it is commonly hypothesized that neutrophils have a major role in the disease pathogenesis. The variation of the genes related to chemotaxis of neutrophils may confer a risk for the development of both COPD and DPB. In the present report, the authors investigated the association between genetic variation that codes for the 416th and 420th amino acid of Gc-globulin, reported to be associated with chemotaxis of neutrophils, and susceptibility to COPD and DPB. Blood samples obtained from patients with COPD (n=63), DPB (n=82), and-control subjects (n=82) were used for the genotyping assay. The proportion of GC*1F homozygotes was significantly higher in the COPD patients than the control subjects (COPD 36.5% versus control 20.7%), and the odds ratio for GC*IF homozygotes was 2.2 (95%, confidence interval 1.1-4.6) for the COPD group. There was no difference on the distribution of the other genotypes (GC*1F-1S heterozygotes, GC*1S homozvgotes, GC*2-1F heterozygotes, GC*2-1S heterozygotes and GC*2 homozygotes) or the allele frequencies among these groups. These findings suggest that the GC*IF gene polymorphism of Gc-globulin may be one of the risk factors for chronic obstructive pulmonary disease. However, no association between this polymorphism of Gc-globulin and susceptibility to diffuse panbronchiolitis was found.

Extinction of expression of the genes encoding haematopoietic cell-restricted transcription factors in T-lymphoma x fibroblast cell hybrids

We previously reported that expression of the T-cell receptor (TCR) alpha and lck genes is extinguished in hybrids between mouse T-lymphoma EL4 cells and mouse fibroblast B82 cells. In the present study, we found that the activities of the TCRalpha minimum enhancer and the lck promoter monitored by the luciferase or chloramphenicol acetyltransferase (CAT) assays were markedly inhibited in the hybrids. Expression of the TCF-1, LEF-1, GATA-3, Ikaros, c-myb and Fli-1 genes, which encode the haematopoietic cell-restricted transcription factors that appear to be responsible for the activities of the enhancer and the promoter, was fully extinguished or markedly suppressed in the hybrids. On the other hand, expression of the transcription factor genes observed in both parental cells, such as the AML1 and c-ets-1 genes, and that of the genes encoding ubiquitously expressed transcription factors, such as the E2A, CREB and c-ets-2 genes, was not significantly suppressed in the hybrids. These results suggest that the genes encoding haematopoietic cell-restricted transcription factors are targets for negative regulation in fibroblastic background and that the repression of these genes may consequently lead to suppression of the promoter and/or enhancer activities of several T-cell-specific structural genes in T-lymphoma x fibroblast cell hybrids.

Abnormalities of gonadotrophs in the adenohypophysis of infertile male PD rats

Male PD strain rats are sterile in the homozygous condition (pd/pd) due to abnormal spermatogenesis detectable at around nine weeks of age. Previous studies have indicated electron microscopic abnormalities in the Sertoli cells of pd/pd males at three and 12 weeks of age. Since spermatogenesis and Sertoli cell function depend on gonadotropins (luteinizing and follicle-stimulating hormones [LH and FSH]) and testosterone, production and/or secretion of these hormones might be altered in pd/pd males. The aim of the study reported here was to investigate the hormonal status of pd/pd males at three, six, and nine weeks of age. Although alteration was not evident in the LH-immunoreactive cells, FSH-immunoreactive cells in pd/pd males were small in size with scant cytoplasm and were reduced in number and area (73 and 51% of phenotypically normal pd/+ males, respectively) at three weeks of age, although serum FSH concentration was similar to that in pd/+ males. At six and nine weeks of age, percentages of the areas occupied by LH- and FSH-immunoreactive cells in pd/pd males were higher than those in pd/+ males. Serum FSH concentration in pd/pd males was significantly high at nine weeks of age, although a difference in serum LH and testosterone concentration was not evident. These results suggest that FSH production in pd/pd males is decreased at three weeks of age. This might be associated with the Sertoli cell abnormalities and subsequent abnormal spermatogenesis seen in adult life.

[A case of endobronchial tuberculosis associated with bronchial asthma treated with high doses of inhaled corticosteroid]

A 46-year-old woman had been treated with 1,600-2,000 micrograms/day of beclomethasone dipropionate (BDP) and oral theophylline on the basis of a diagnosis of bronchial asthma in 1993. Eosinophilic pneumonia was diagnosed in June 1999, and she was then treated with 40 mg/day of oral prednisolone (PSL), which was gradually tapered off, and then stopped in October 1999. She was referred to our hospital because acid-fast bacilli were found in the sputum on January 18, 2000. Her chest radiographs and CT scans showed partial atelectasis of the right upper lobe, and fiberoptic bronchoscopy revealed bronchial inflammatory changes and whitish mucosal nodular lesions in the walls of the lower trachea, the right main bronchus and the orifice of the right upper lobe bronchus. She was found to have endobronchial tuberculosis. Anti-tuberculosis treatment with isoniazid, rifampicin, streptomycin and pyrazinamide was started. Serum levels of interferon-gamma were markedly elevated on admission. Asthma symptoms improved for a period of one month after the beginning of anti-tuberculosis treatment, despite the termination of inhaled corticosteroid. However, as the tuberculosis improved, the frequency and severity of the asthma increased and so corticosteroid inhalation was started again. Four months after administration of the anti-tuberculosis drug, fiberoptic bronchoscopy revealed that the endobronchial lesions had improved without any stenosis or constrictive changes. It was speculated that high doses of inhaled corticosteroid may have the potential to cause endobronchial tuberculosis whilst, ironically, at the same time preventing bronchial stenosis by endobronchial tuberculosis. This is an interesting case in which the asthma symptoms first decreased during the acute phase of endobronchial tuberculosis and then increased again after the tuberculosis improved.

Isolation and purification of tyrosine hydroxylase from callus cultures of Portulaca grandiflora

Tyrosine hydroxylase was separated from polyphenol oxidase activity and was highly purified from betacyanin producing callus cultures of Portulaca grandiflora. The purified enzyme catalyzed the formation of DOPA (L-3,4-dihydroxyphenylalanine) from tyrosine and required the pterin compounds (6-methyl-5,6,7,8-tetrahydropterin; 5,6,7,8-tetrahydrobiopterin; 6,7-dimethyl-5,6,7,8-tetrahydropterin) as coenzyme. The K(m) values for tyrosine and 6-methyl-5,6,7,8-tetrahydropterin were 0.5 mM and 0.15 mM, respectively. This enzyme was activated by Fe(2+) and Mn(2+), and inhibited by metal chelating agents.

Effects of candesartan on cough and bronchial hyperresponsiveness in mildly to moderately hypertensive patients with symptomatic asthma

BACKGROUND

Candesartan, an AT(1) receptor antagonist, has been reported to have no association with persistent cough in subjects with hypertension, but there has been no study on the safety of its administration to hypertensive patients with symptomatic asthma. The aim of this study was to compare the adverse effects of candesartan and calcium antagonists on cough, pulmonary function, and bronchial hyperresponsiveness in these patients.

METHODS AND RESULTS

Sixty mildly to moderately hypertensive patients with bronchial asthma received either candesartan (n=30) or the calcium antagonists nifedipine or manidipine (n=30) for 6 months. The candesartan group included 5 subjects with a history of ACE inhibitor-induced cough. There were no differences between the 2 groups in patient characteristics, ACE gene polymorphism, pulmonary function, or bronchial hyperresponsiveness to methacholine. Control of hypertension was the primary end point; new cough detected by self-administrated questionnaire and an increase in cough frequency by visual analog scale were the second end point. No patient complained of persistent cough. Neither mean visual analog scale score nor pulmonary functions changed during this study. Bronchial hyperresponsiveness had a tendency to improve in the candesartan group, but there was no difference between the 2 groups.

CONCLUSIONS

Incidence, frequency, and severity of persistent cough, pulmonary functions, and bronchial hyperresponsiveness did not change in either the candesartan or calcium antagonist group. It is suggested that candesartan is as effective and safe as calcium antagonists in the treatment of hypertension associated with symptomatic asthma.

[Effect of inhaled anticholinergic drug on pulmonary function and quality of life in elderly patients with chronic obstructive pulmonary disease]

Effects of inhaled anticholinergic drug on the physiological function of the respiratory system and quality of life (QOL) in elderly patients with chronic obstructive pulmonary disease (COPD) have not been fully elucidated. We examined the pulmonary function, static respiratory pressures, and ventilation during exercise, before and after inhalation of oxitropium bromide (OTB) in 12 male patients with COPD (mean age 82.1 +/- 0.6 years). QOL was measured with a St George's Respiratory Questionnaire (SGRQ) in the patients. Forced expiratory volume in one second was increased by the inhalation of OTB in the patients, whereas the ratio of residual volume to total lung capacity was decreased by the inhalation. Maximum inspiratory pressure was significantly increased after the administration of OTB. Dyspnea sensation during exercise measured on the Borg scale was reduced by the inhalation of OTB. The scores of SGRQ were improved by one-month treatment with OTB. These results suggest that the treatment with OTB are effective for both physiological function and several aspects of QOL in elderly patients with COPD.

Variables pertinent to the efficiency of adeno-associated virus (AAV) vectors mediated gene transfer to human vascular endothelial cells

Factors influencing adeno-associated virus (AAV) - mediated gene transfer to endothelial cells are not fully determined. We tested the variables pertinent to the efficiency of AAV-mediated gene transfer to human vascular endothelial cells (HUVEC) including: (i) kinetics of transduction efficiency of LacZ gene to HUVEC, (ii) the concentration and volume of vector-containing medium, (iii) the period of incubation time of AAV vectors with HUVEC, (iv) the target cell density/proliferation, (v) the duration of transgene expression. There is a dose-response relationship between moi of vectors and transduction efficiency in HUVEC. The higher moi of AAV vectors achieved more than 80% of transduction efficiency in cultured HUVEC. AAV vectors showed incubation time dependent increase in transduction efficiency of LacZ gene to the HUVEC up to 24 h of vector exposure. The foreign gene of AAV vectors preferably transduces the lower density of cells being proliferated. These results indicate that AAV-vector is efficient for gene transfer to HUVEC, and higher moi of vectors or a longer period exposure of vectors to proliferating HUVEC can facilitate efficient tranduction of foreign gene into human vascular endothelial cells in vitro.

Tobacco smoke reduces viability in human lung fibroblasts: protective effect of glutathioneS-transferase P1

Cigarette smoking is thought to be a major risk factor in various lung diseases including lung cancer and emphysema. However, the direct effect of cigarette smoke on the viability of lung-derived cells has not been fully elucidated. In this study, we investigated the viability of human lung fibroblast-derived (HFL1) cells to different concentrations of cigarette smoke extract (CSE). CSE induced apoptosis at lower concentrations (10–25%) and necrosis at higher concentrations (50–100%). We also examined the effects of glutathione S-transferase P1 (GSTP1), one of the xenobiotic metabolizing and antioxidant enzymes in the lung, against the cytotoxicity of CSE. Our results indicated that the level of HFL1 cell death was decreased by transfection with a GSTP1 expression vector and was increased by GSTP1 antisense vector transfection. Therefore, transient overexpression and underexpression of GSTP1 appeared to inhibit and enhance the cytotoxic effects of CSE on HFL1 cells, suggesting that GSTP1 may have protective effects against cigarette smoke in the airway cells.

Distal airspace enlargement in the fawn-hooded rat: influences of aging and alveolar wall destruction

BACKGROUND

A recent study has revealed that the peripheral airspace in the lungs of the fawn-hooded rat (FHR) is enlarged. However, morphological and functional factors of the FHR lung have not been fully investigated.

OBJECTIVE

The purpose of our study was to examine the structural and functional changes in the FHR lung and to investigate the influence of aging on this process. Furthermore, morphological and functional measurements of the lungs of FHRs (4-48 weeks of age) were performed and the results compared with those of age-matched Wistar control rats (WCRs).

METHODS

All animals were studied under controlled conditions, and morphological and functional changes of the lungs were examined. Measurements of body and lung weights were recorded, and the lungs were subjected to morphological evaluation. Morphological measurements: mean linear intercept (MLI) and destructive index were determined. Functional evaluation of the lungs: total lung capacity, pressure-volume curve, and exponential constant (K) which describes the shape of the curve were analyzed. In addition, right ventricular hypertrophy measurements were performed to assess the severity of pulmonary hypertension. Statistical analysis was performed using the unpaired t test, analysis of variance, and the Fisher post hoc test (p < 0.05).

RESULTS

Morphological analysis revealed a significant increase in airspace size (MLI) in all FHRs as compared with the WCRs which was evident from an early age (4 weeks). The increase in MLI did not progress age dependently in the FHR, whereas a tendency for an age-dependent increase in MLI was observed in the WCR. The destructive index measurements revealed that the increase in MLI of FHR was not accompanied by alveolar wall destruction. Concerning the functional examination, a leftward and upward shift of the pressure-volume curve was observed in the FHRs as compared with the WCRs at all ages. As compared with the WCRs, a higher K value was observed in all FHRs which was evident from an early age (4 weeks). Age-dependent changes similar to those in MLI were observed in the K in both rat strains.

CONCLUSIONS

The results of our study suggest that FHRs manifest characteristics of distal airspace enlargement accompanied by increased lung distensibility without alveolar wall destruction at an early age and that the changes do not progress age dependently. Neither an accelerated aging process nor destruction of the alveolar walls appears to be the mechanism responsible for the enlarged airspace in this rat strain.

[Genetic variation of NADPH/NADH oxidase and susceptibility to diffuse panbronchiolitis (DPB) and chronic obstructive pulmonary disease (COPD)]

Diffuse panbronchiolitis (DPB) and chronic obstructive pulmonary disease (COPD) are both characterized by chronic airflow obstruction of unknown etiology. It is hypothesized that neutrophils play the major role in the pathogenesis of these diseases. Recent studies have suggested that genetic factors may be related to individual susceptibility to these diseases. We have investigated the association between the C 242 T polymorphism of p 22 phox, a critical subunit of superoxide-generating NADH/NADPH oxidase, and susceptibility to DPB and COPD. Blood samples obtained from both patients with DPB (n = 82), COPD (n = 53), and control subjects (n = 82) were used for this genotyping assay; and the polymerase chain reaction (PCR) and restriction fragment length polymorphism (RFLP) were performed to genotype the gene. The frequency of the C allele was 0.91, 0.92, 0.92 in the DPB, COPD, and control groups, respectively. There were no differences in the distribution of the genotype of p 22 phox among these groups, either. We concluded that there is no association between the C 242 T polymorphism of p 22 phox, and susceptibility to DPB and COPD.