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Abstract The discovery of aerobic and anammox bacteria capable of generating methane in bio-filters in freshwater aquaculture systems is generating interest in studies to understand the activity, diversity, distribution and roles of these environmental bacteria. In this study, we used microbial enrichment of bio-filters to assess their effect on water quality. Profiles of ammonia-oxidizing bacterial communities generated using nested PCR methods and DGGE were used to assess the expression of 16S rRNA genes using DNA sequencing. Five dominant ammonia-oxidizing bacterial strains–clones; KB.13, KB.15, KB.16, KB.17 and KB.18—were isolated and identified by phylogenetic analysis as environmental samples closely related to genera Methylobacillus, Stanieria, Nitrosomonas, and Heliorestis. The methyl ammonia-oxidizing microbes thereby found suggest a biochemical pathway involving electron donors and carbon sources, and all strains were functional in freshwater aquaculture systems. Environmental parameters including TN (2.69–20.43); COD (9.34–31.47); NH4 +-N (0.44–11.78); NO2 −N (0.00–3.67); NO3 −N (0.05–1.82), mg/L and DO (1.47–10.31 µg/L) assessed varied in the ranges in the different tanks. Principal component analysis revealed that these water quality parameters significantly influenced the ammonia oxidizing microbial community composition. Temperature rises to about 40 °C significantly affected environmental characteristics—especially DO, TN and NH4 +-N—and directly or indirectly affected the microbial communities. Although the nested PCR design was preferred due to its high sensitivity for amplifying specific DNA regions, a more concise method is recommended, as an equimolar mixture of degenerate PCR primer pairs, CTO189f-GC and CTO654r, never amplified only 16S rRNA of ammonia-oxidizing bacteria.

In this paper, we study the spatial propagation dynamics of a parabolic–elliptic chemotaxis system with logistic source which reduces to the well‐known Fisher‐KPP equation without chemotaxis. It is known that for fast decaying initial functions, this system has a finite spreading speed. For slowly decaying initial functions, we show that the accelerating propagation will occur and chemotaxis does not affect the propagation mode determined by slowly decaying initial functions if the logistic damping is strong, that is, the system has the same upper and lower bounds of the accelerating propagation as for the classical Fisher‐KPP equation. The main new idea of proving our results is the construction of auxiliary equations to overcome the lack of comparison principle due to chemotaxis. [ABSTRACT FROM AUTHOR]

Objective BAG3 -related myopathy is a rare condition so far reported in twenty patients worldwide. The purpose of this study was to draw attention to this rare disease and to the fact that BAG3 -related myopathy should be considered as a rare differential diagnosis of hypercapnia. Methods We report a sporadic case of a 14-year-old Chinese girl with a de novo p.Pro209Leu mutation in BAG3 and reviewed the literatures for reported cases related to this mutation. Results We described a 14-year-old Chinese girl who presented with gradually appearing symptoms of hypercapnia that required assisted ventilation. The muscle biopsy and the blood whole-exome sequencing results confirmed the diagnosis of myofibrillar myopathy with a de novo p.Pro209Leu mutation in BAG3 . Totally twenty-one patients from twenty families with a confirmed diagnosis of BAG3 -related myopathy were reported to date, including this patient and literature review. The male to female ratio was 11:10 and most showed initial symptoms in the first decade of life. Most patients presented toe/clumsy walking or running as the onset symptom, followed by muscle weakness or atrophy. Creatine kinase levels were elevated in fourteen patients and were normal in three. Eighteen patients developed respiratory insufficiency during the disease course and thirteen (one could not tolerate non-invasive assisted ventilation) required non-invasive assisted ventilation for treatment. Except for one not reported, heart involvement was found in seventeen patients during the disease course and seven underwent heart transplantation. Z-disk streaming and aggregation could be observed in most of the patients' muscle histology. In the long-term follow-up, five patients died of cardiac or respiratory failure. Conclusion BAG3 -associated myopathy is a rare type of myofibrillar myopathy. It should be considered as a rare differential diagnosis of hypercapnia.

Objectives: The aims of the study were to evaluate the effectiveness of bronchoalveolar lavage (BAL) for diagnosing pulmonary infection in patients with rheumatic autoimmune diseases and lung infiltrates and to evaluate factors that affect the diagnostic yield., Methods: A retrospective study was performed in patients with rheumatic autoimmune diseases and lung infiltrates whose BALs were sent for microbial assays at Peking Union Medical College Hospital from January 2009 to June 2013. Patient characteristics, clinical symptoms, medication history, laboratory parameters, radiographic findings, lung lobe lavaged, and diagnostic yield were retrieved., Results: Seventy BALs were performed in 69 patients. The overall diagnostic yield of BAL for pulmonary infection was 17.1% (12/70), sensitivity was 35.5%, and specificity was 97.4%. Twelve microorganisms were isolated from 12 different BALs conforming to diagnostic criteria, including 4 Aspergillus, 3 Pneumocystis jirovecii, 3 gram-negative bacilli, 1 gram-positive coccus, and 1 mycobacterium. Patients with clinical symptoms of fever, cough, or expectoration had a higher diagnostic yield than patients without either symptom (25.6% vs 3.7%, P = 0.042). Patients with ground-glass opacity, mass, or consolidation radiographically had a higher yield than did patients with reticular or nodular infiltrates (20.3% vs 0, P < 0.001)., Conclusions: Bronchoalveolar lavage is a useful tool for patients with rheumatic autoimmune diseases and lung infiltrates, especially in cases where initial antimicrobial therapy is ineffective. Opportunistic pathogens are important in patients with rheumatic autoimmune diseases and lung infiltrates and should be considered when antibacterial treatment is ineffective.

Objective: To improve understanding of the clinical characteristics and diagnosis of hypersensitivity pneumonitis (HP)., Methods: We retrospectively analyzed the clinical data, including clinical symptoms, laboratory tests, exposure, pulmonary function tests, chest CT imaging and cytological classification of bronchoalveolar lavage (BAL) of 96 patients with HP from Jan 2001 to Jun 2011 in Peking Union Medical College Hospital. We divided the patients into 2 groups: a pathologically-confirmed group and a clinically-suspected group., Results: There were 58 females and 41 males. The median age at the diagnosis was 53 years. The most common exposures were low-molecular-weight chemicals (42.7%) and animal proteins (37.5%). Common clinical symptoms included dyspnea on exertion (90.6%) and cough (76.0%). Pulmonary function test showed diffusion abnormality (73.5%) and restrictive ventilatory impairment (59.7%). Chest CT scan revealed patchy or diffuse bilateral ground-glass opacities (64.6%), centrilobular nodules (21.9%), and air trapping (15.6%). Reticulation (45.8%), traction bronchiectasis (21.9%) and honeycombing(9.4%) were present in chronic HP. BAL lymphocyte counts > 0.2 and CD4/CD8 < 0.9 were more commonly seen in patients with a disease course of less than 1 year. The pathologically-confirmed group and the clinically-suspected group shared many similar characteristics including age at diagnosis, gender, clinical manifestation, pulmonary function impairments and imaging findings, but significant differences existed in certain parameters. In the pathologically- confirmed group, the duration of disease was longer (24 months vs 6 months, Z = -2.492, P = 0.013) and clubbed fingers were more common (23.4% vs 8.2%, χ(2) = 4.227, P = 0.040). Diffusion abnormality was present in more patients of this group (90.7% vs 44.0%, χ(2) = 35.219, P < 0.01). By CT scan, reticulation, traction bronchiectasis and honeycombing (57.5% vs 26.5%, χ(2) = 9.434, P < 0.01) were more evident as compared to the clinically-suspected group. The value of transbronchial lung biopsy for diagnosing HP was limited, with a positive result of only 8.2%. Surgical lung biopsy was needed in uncertain cases., Conclusion: The diagnosis of HP was difficult. In some cases a clinical diagnosis can be made by combination of history of exposure, CT manifestations and cell classification of BAL. For atypical cases a multi-disciplinary approach including pathologists, radiologists and pulmonologists is needed.

Objective: This study was to evaluate the efficacy and limitation of CT-guided percutaneous cutting needle lung biopsy in the diagnosis of diffuse parenchymal lung diseases (DPLD)., Methods: A total of 481 patients admitted in Peking Union Medical College Hospital from January 2000 to December 2008 underwent CT-guided percutaneous cutting needle lung biopsy. The patients were evaluated by clinical history, physical examination and lung HRCT. Those with localized opacity or lesions in a single lung in the CT scan were excluded. Finally, 248 patients with DPLD in HRCT were enrolled for this study., Results: The study patients included 114 males and 134 females, and the mean (± SD) age at diagnosis was 50 ± 16 (range from 13 - 78) years. Confirmed diagnosis by percutaneous needle lung biopsy was obtained in 130 patients (52.4%), including pulmonary infection (35.4%, 46/130), pulmonary malignant diseases (25.4%, 33/130), bronchiolitis obliterans organizing pneumonia/organizing pneumonia (22.3%, 29/130), pulmonary vasculitis (6.2%, 8/130), granulomatous lesions (4.6%, 6/130), pulmonary sarcoidosis (2.3%, 3/130), acute interstitial pneumonia (1.5%, 2/130), pulmonary amyloidosis (1.5%, 2/130), and pulmonary alveolar proteinosis (0.8%, 1/130). Open lung biopsy/video-assisted thoracoscopic surgery was performed in 37 out of 118 cases for which the diagnosis was undetermined by percutaneous lung biopsy. Confirmed diagnosis was obtained in 36 patients, including non-specific interstitial pneumonia (NSIP, 33.3%, 12/36), usual interstitial pneumonia (UIP, 8.3%, 3/36), pulmonary infection (16.7%, 6/36), neoplasm (8.3%, 3/36), lymphoid interstitial pneumonia, pulmonary vasculitis (5.6% 2/36), hypersensitivity pneumonitis (5.6%, 2/36), and pulmonary sarcoidosis, allergic bronchopulmonary aspergillosis, pulmonary hyalinizing granuloma, pneumoconiosis, Castleman's disease, and lymphoproliferative disorder (1 case respectively)., Conclusion: CT-guided percutaneous cutting needle lung biopsy can provide confirmed diagnosis in half of patients with DPLD, and has a high diagnostic yield in patients with infectious or neoplastic diseases, but it is not a good method for diagnosis of interstitial lung diseases such as NSIP and UIP.

The low efficiency of somatic cell nuclear transfer (SCNT) is a significant barrier to the production of highly valuable transgenic livestock. It is generally believed that the principal cause of the low SCNT efficiency is the aberrant nuclear epigenetic reprogramming of donor somatic cell. DNA methylation is a major epigenetic modification of the genome and plays a crucial role in nuclear reprogramming during SCNT. In order to assess whether the abnormal epigenetic modifications of the imprinted gene in placenta are correlated with the development abnormality and death of the cloned transgenic calves, the DNA methylation patterns of PEG10 were compared in the placentas from different kinds of cattle. This comparison included transgenic cloned calves died during perinatal stage and showed developmental defects (Death group), transgenic cloned calves survived and lived on healthily (Live group) and the normal reproduced calves (N group) used as the control group analyzed by Bisulfite Sequencing PCR (BSP) method and Combined Bisulfite Restriction Analy-sis (COBRA). Comparing to the control group, PEG10 gene in the Death group showed abnormal hypermethylation, but was not significant different in methylation level from the Live group. It can be postulated from the results that the incom-plete or abnormal DNA methylation epigenetic reprogramming of imprinting gene in placenta may be one of the main causes of the abnormal development and death of the transgenic cloned cattle.

Bioaerosol samples were collected using an Andersen sampler from Jul. 2009 to Nov. 2009 in the Qingdao coastal region. Total microbe (including 'culturable microbe' and 'non-culturable microbe'), the terrigenous and marine microbe were analyzed by the counting methods of fluorescence microscope and Petri dishes containing agar media. The results showed that the proportion of non-culturable microbe to total microbe was as high as 99.58% of total on average, while the average proportion of culturable microbe to total microbe was 0.42%. The average proportions of marine bacteria/fungi did to the culturable microbe (18.99% and 45.47% respectively) were more than that of terrigenous bacteria/fungi (16.91% and 18.63% respectively), therefore marine bacteria/fungi contributed more to the microbe than terrigenous bacteria/fungi. It could be seen that the composition and concentration distribution were greatly affected by the ocean in the Qingdao coastal region. The average concentrations of total microbe were higher in Autumn (181 682.5 CFU/m3) than that in Summer (159 704.2 CFU/m3), and that of terrigenous bacteria, marine bacteria/fungi were also higher in Autumn than in Summer. The particle sizes of total microbe presented a log-normal distribution in summer and autumn, and the total microbe mainly existed in coarse particles larger than 2.1 microm. There was the highest proportion of total microbe in 3.3-4.7 microm particles, the lowest one in 0.65-1.1 microm. The terrigenous and marine bacterial particle sizes showed a skew distribution with a higher value in large particles (> 7 microm) and a lower one in fine particles (0.65-1.1 microm). The terrigenous and marine fungal particle sizes showed a log-normal distribution in summer and autumn, and the highest concentration proportion existed in particles with diameter of 2.1-3.3 microm.

Objective: To study the clinical characteristics and diagnosis of primary ciliary dyskinesia (PCD)., Methods: Four cases diagnosed as PCD by cilia electron microscopy examination from Jan. 2007 to Aug. 2009 in this hospital were retrospectively analyzed, and the related literature was reviewed., Results: In the 4 patients, there were 1 male and 3 females. The age at disease onset was 0 - 10 years, and the age at diagnosis was 15 - 53 years. The most common symptoms were productive cough (4/4), sinusitis (3/4), and shortness of breath (3/4). Other manifestations included situs inversus (2/4), infertility (1/4), and tympanitis (1/4). Hypoxemia was found in 3 cases. Obstructive ventilatory impairment accompanied with diffusion dysfunction was observed in 2 cases, while the pulmonary function tests were normal in the other 2 cases. All 4 cases received chest CT scan, and bronchiectasis was present in all of them. Bilateral diffuse micronodules and patchy infiltrates were found in 3 and 2 cases respectively. Electron microscopic examination of the endobronchial biopsy specimen showed lack of dynein arms in 4, lack of muco-cilia in 2, and abnormal arrangement of microtubules in 2 cases., Conclusions: The Kartagener syndrome is relatively easy to be diagnosed, because it is characterized by the triad of sinusitis, bronchiectasis and situs inversus. However, PCD without situs inversus often goes unrecognized. PCD should be considered in patients with childhood onset disease, bronchiectasis, centrilobular micronodules or tree-in-bud signs in CT scan. Examination of the ciliary ultrastructure is essential to the confirmation of the diagnosis.

Objective: The purpose of this paper was to investigate the clinical and radiological features of pulmonary tuberculosis presenting as interstitial lung diseases (ILD)., Methods: We analyzed the data of cases suspected of diffuse parenchyma lung diseases at this hospital between October 2003 and October 2007. The diagnosis of active pulmonary tuberculosis was based on epithelioid granuloma or positive acid-fast bacilli in lung biopsy and changes on serial radiographs obtained during treatment., Results: The data of a series of 230 consecutive patients with suspected ILD were retrospectively analyzed. The diagnosis was confirmed by lung biopsy. Twelve patients were confirmed to have pulmonary tuberculosis. There were 5 males and 7 females with a mean age of 38 +/- 11 years (range, 17 - 68). The median course of disease in these patients was 3 months (range, 0.5 - 18 months). Patients with pulmonary tuberculosis presented with fever (11/12), cough (9/12), weight loss (7/12), dyspnea (7/12), lymphadenopathy (4/12), and splenohepatomegaly (2/12). On chest CT scan, ground-glass attenuation was identified in 4, bilateral patchy infiltration in 5, tree-in-bud appearance 1, and centrilobular lesions in 2 of the 12 patients. During the follow-up period (median, 9 month, range from 3 to 12 month), 11 patients improved, but 1 died of diabetic ketoacidosis., Conclusion: The diagnosis of pulmonary tuberculosis should be considered in suspected ILD patients presenting with fever, splenohepatomegaly and lymphadenopathy.

Objective: To evaluate the diagnostic specificity of dynamic assessment and monitoring using a portable spirometer in diagnosis and differential diagnosis of asthma., Methods: We retrospectively reviewed the results of dynamic monitoring of spirometry in 145 symptomatic patients with physician-diagnosed asthma. Flow-volume curve and simultaneous symptoms and mood were measured in a fixed-time thrice-daily assessment schedule for 2 weeks. Patients were allowed to make additional measurements in case of symptom exacerbations., Results: The clinical data of 51 males and 94 females with a mean age of (39.1 +/- 13.0) years (ranged from 10 to 65 years) were analyzed. Duration of asthma before study was (6.7 +/- 9.9) years. Of 145 patients with physician-diagnosed asthma, 126 (87%) could be conclusively confirmed for a diagnosis of asthma. Asthma was misdiagnosed in 14 patients (9.7%). Overdiagnosis of asthma was observed in 5 patients (3.4%)., Conclusion: Dynamic assessment and monitoring using a portable spirometer by revealing variability and reversibility of airway obstruction may provide an additional tool for diagnosis and differential diagnosis of asthma.

Objective: To enhance the knowledge about Churg-Strauss syndrome (CSS)., Methods: The clinical data of 16 CSS patients were analyzed. Follow-up was conducted for 42 (14 - 76) months., Results: All patients had the symptom of asthma. As in other case series, the lung, peripheral nervous system, and skin were the most commonly involved organs. During the active stage of the disease, most of the patients exhibited peripheral blood eosinophilia and elevated serum total IgE level. Two patients were treated with pulse treatment of methylprednisolone followed by prednisone with tapering dose and cyclophosphamide, nine patients were treated with corticosteroids and cyclophosphamide, and the others were treated with corticosteroids alone. Several patients were treated with the following drugs in combination: methotrexate, hydroxychloroquine, azathioprine, ciclosporin, common Threewingnut root, and intravenous injection of IgG. Symptom relief was seen in all patients after treatment. Two patients were lost to follow-up. Seven patients showed sustained remission, of which 3 had discontinued the medication, 3 were treated with low-dose corticosteroids and immunity inhibitors, and 1 continued to be treated with low-dose corticosteroids. Six patients suffered from relapse 1.7 times due to withdrawal of corticosteroid treatment or tapering of corticosteroid dose and they regained remission once more after increasing the corticosteroid dose and combination of cyclophosphamide. Four of these 6 patients were treated with corticosteroids of low or medium dose as maintenance doses, and the other 2 with medium-dose corticosteroids and cyclophosphamide. One patient committed suicide because of family dissension 1 year after treatment., Conclusions: The clinical manifestations and course of CSS vary considerably. Its clinical manifestations may range from mild symptoms to life-threatening conditions. Corticosteroids and cyclophosphamide are both effective remedies. Despite relapses in several cases, the general prognosis is good.