Journal articles: 'Deep MCCA'

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Yang, Hai, Rui Chen, Dongdong Li, and Zhe Wang. "Subtype-GAN: a deep learning approach for integrative cancer subtyping of multi-omics data." Bioinformatics 37, no. 16 (February 18, 2021): 2231–37. http://dx.doi.org/10.1093/bioinformatics/btab109.

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Abstract Motivation The discovery of cancer subtyping can help explore cancer pathogenesis, determine clinical actionability in treatment, and improve patients' survival rates. However, due to the diversity and complexity of multi-omics data, it is still challenging to develop integrated clustering algorithms for tumor molecular subtyping. Results We propose Subtype-GAN, a deep adversarial learning approach based on the multiple-input multiple-output neural network to model the complex omics data accurately. With the latent variables extracted from the neural network, Subtype-GAN uses consensus clustering and the Gaussian Mixture model to identify tumor samples' molecular subtypes. Compared with other state-of-the-art subtyping approaches, Subtype-GAN achieved outstanding performance on the benchmark datasets consisting of ∼4000 TCGA tumors from 10 types of cancer. We found that on the comparison dataset, the clustering scheme of Subtype-GAN is not always similar to that of the deep learning method AE but is identical to that of NEMO, MCCA, VAE and other excellent approaches. Finally, we applied Subtype-GAN to the BRCA dataset and automatically obtained the number of subtypes and the subtype labels of 1031 BRCA tumors. Through the detailed analysis, we found that the identified subtypes are clinically meaningful and show distinct patterns in the feature space, demonstrating the practicality of Subtype-GAN. Availabilityand implementation The source codes, the clustering results of Subtype-GAN across the benchmark datasets are available at https://github.com/haiyang1986/Subtype-GAN. Supplementary information Supplementary data are available at Bioinformatics online.

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Huang, Dian, Chen Yu, Zongze Shao, Minmin Cai, Guangyu Li, Longyu Zheng, Ziniu Yu, and Jibin Zhang. "Identification and Characterization of Nnematicidal Volatile Organic Compounds from Deep-Sea Virgibacillus dokdonensis MCCC 1A00493." Molecules 25, no. 3 (February 9, 2020): 744. http://dx.doi.org/10.3390/molecules25030744.

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Root-knot nematode diseases cause severe yield and economic losses each year in global agricultural production. Virgibacillus dokdonensis MCCC 1A00493, a deep-sea bacterium, shows a significant nematicidal activity against Meloidogyne incognita in vitro. However, information about the active substances of V. dokdonensis MCCC 1A00493 is limited. In this study, volatile organic compounds (VOCs) from V. dokdonensis MCCC 1A00493 were isolated and analyzed through solid-phase microextraction and gas chromatography–mass spectrometry. Four VOCs, namely, acetaldehyde, dimethyl disulfide, ethylbenzene, and 2-butanone, were identified, and their nematicidal activities were evaluated. The four VOCs had a variety of active modes on M. incognita juveniles. Acetaldehyde had direct contact killing, fumigation, and attraction activities; dimethyl disulfide had direct contact killing and attraction activities; ethylbenzene had an attraction activity; and 2-butanone had a repellent activity. Only acetaldehyde had a fumigant activity to inhibit egg hatching. Combining this fumigant activity against eggs and juveniles could be an effective strategy to control the different developmental stages of M. incognita. The combination of direct contact and attraction activities could also establish trapping and killing strategies against root-knot nematodes. Considering all nematicidal modes or strategies, we could use V. dokdonensis MCCC 1A00493 to set up an integrated strategy to control root-knot nematodes.

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Niu, Siwen, Dong Liu, Zongze Shao, Jiang Huang, Aili Fan, and Wenhan Lin. "Chlorinated metabolites with antibacterial activities from a deep-sea-derived Spiromastix fungus." RSC Advances 11, no. 47 (2021): 29661–67. http://dx.doi.org/10.1039/d1ra05736g.

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Morshed, Ahsan, Prem Prakash Jayaraman, Timos Sellis, Dimitrios Georgakopoulos, Massimo Villari, and Rajiv Ranjan. "Deep Osmosis: Holistic Distributed Deep Learning in Osmotic Computing." IEEE Cloud Computing 4, no. 6 (November 2017): 22–32. http://dx.doi.org/10.1109/mcc.2018.1081070.

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Geng, Huantong, and Liangchao Geng. "MCCS-LSTM: Extracting Full-Image Contextual Information and Multi-Scale Spatiotemporal Feature for Radar Echo Extrapolation." Atmosphere 13, no. 2 (January 25, 2022): 192. http://dx.doi.org/10.3390/atmos13020192.

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Precipitation nowcasting has been gaining importance in the operational weather forecast, being essential for economic and social development. Conventional methods of precipitation nowcasting are mainly focused on the task of radar echo extrapolation. In recent years, deep learning methods have been used in this task. Nevertheless, raising the accuracy and extending the lead time of prediction remains as a challenging problem. To address the problem, we proposed a Multi-Scale Criss-Cross Attention Context Sensing Long Short-Term Memory (MCCS-LSTM). In this model, Context Sensing framework (CS framework) focuses on contextual correlations, and Multi-Scale Spatiotemporal block (MS block) with criss-cross attention is designed to extract multi-scale spatiotemporal feature and full-image dependency. To validate the effectiveness of our model, we conduct experiments on CIKM AnalytiCup 2017 data sets and Guangdong Province of China radar data sets. By comparing with existing deep learning models, the results demonstrate that the MCCS-LSTM has the best prediction performance, especially for predicting accuracy with longer lead times.

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Xiao, Jing, Yingxue Luo, Shujie Xie, and Jun Xu. "Serinicoccus profundi sp. nov., an actinomycete isolated from deep-sea sediment, and emended description of the genus Serinicoccus." International Journal of Systematic and Evolutionary Microbiology 61, no. 1 (January 1, 2011): 16–19. http://dx.doi.org/10.1099/ijs.0.019976-0.

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A Gram-reaction-positive bacterial strain of the genus Serinicoccus, designated MCCC 1A05965T, was isolated from a deep-sea (5368 m) sediment of the Indian Ocean. Comparison of 16S rRNA gene sequences revealed that the isolate shared 97.6 % sequence similarity with Serinicoccus marinus JC1078T, the type strain of the only described species of the genus Serinicoccus. The DNA–DNA relatedness between these two strains was 46.2 % (standard deviation 1.86 %). The cell wall contained alanine, glycine, serine, l-ornithine and glutamic acid, which corresponds to the description of the genus Serinicoccus. The acyl type of the glycan chain of the peptidoglycan was glycolyl. Other characteristics of strain MCCC 1A05965T were consistent with those of the genus Serinicoccus. Cells were coccoid, moderately halophilic, oxidase-negative, catalase-positive and non-spore-forming. The major menaquinone was MK-8(H4). The predominant cellular fatty acids were iso-C15 : 0 (34.7 %) and iso-C16 : 0 (17.0 %). The polar lipids were phosphatidylglycerol, diphosphatidylglycerol, phosphatidylcholine, phosphatidylinositol and an unknown glycolipid. The DNA G+C content was 72 mol%. Strain MCCC 1A05965T (=0714S6-1T =DSM 21363T =CGMCC 4.5582T) is assigned as the type strain of a novel species, for which the name Serinicoccus profundi sp. nov. is proposed.

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Niu, Siwen, Chun-Lan Xie, Tianhua Zhong, Wei Xu, Zhu-Hua Luo, Zongze Shao, and Xian-Wen Yang. "Sesquiterpenes from a deep-sea-derived fungus Graphostroma sp. MCCC 3A00421." Tetrahedron 73, no. 52 (December 2017): 7267–73. http://dx.doi.org/10.1016/j.tet.2017.11.013.

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Mehta, Sanket, Nicholas C. Danford, Venkat Boddapati, Bonnie Y. Chien, and Justin K. Greisberg. "Discriminative Ability for Adverse Outcomes in Traumatic Ankle Fracture: A Comparison of the Modified Charlson Comorbidity Index, Elixhauser Comorbidity Measure, and Modified Frailty Index." Foot & Ankle Orthopaedics 7, no. 4 (October 2022): 2473011421S0080. http://dx.doi.org/10.1177/2473011421s00803.

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Category: Trauma; Ankle Introduction/Purpose: The modified Charlson Comorbidity Index (mCCI), Elixhauser comorbidity measure (ECM), and 5- factor modified Frailty Index (mFI-5) have been validated for the purpose of outcome prediction in foot and ankle orthopedic care. However, from the perspective of clinical utility, no study has sought to compare the predictive performance of these measures specifically following traumatic ankle fracture. The present study compares the discriminative ability of the mCCI, ECM, and mFI-5, as well as various demographic characteristics, such as age, gender, and race, to predict in-hospital mortality and complications after the surgical management of traumatic ankle fracture. Methods: We performed a retrospective cohort study of adult patients registered in the National Trauma Data Bank (NTDB) 2011-2016 experiencing ankle trauma as malleolar fracture and undergoing surgical management. Patients missing baseline or comorbidity information, dead on arrival, or with a pilon fracture or stress fracture were excluded. Enhanced ICD-9 algorithms were used to calculate mCCI, ECM, and mFI-5 as has been done in prior orthopedic literature. The discriminative ability of the indices for adverse outcomes was assessed using area under the curve analysis from receiver operating characteristic curves. Outcomes included death, severe adverse events (death, deep surgical site infection (SSI), myocardial infarction (MI), cardiac arrest, deep vein thrombosis (DVT), pulmonary embolism (PE), sepsis, stroke, compartment syndrome), minor adverse events (acute kidney injury (AKI), pneumonia, superficial SSI, urinary tract infection (UTI)), infectious events (deep SSI, organ/space SSI, superficial SSI, pneumonia, UTI, catheter-related bloodstream infection, osteomyelitis, sepsis), and any adverse event. Results: In total, 171,097 patients met inclusion criteria. The median age was 50 years and 49% of patients were male. Compared to ECM and mFI-5, mCCI had the largest discriminative ability for the outcome of in-hospital mortality (P=0.02 versus ECM, P<0.001 versus mFI-5, Table I). ECM, however, had a larger discriminative ability for major adverse event, minor adverse event, infectious event, and any complication during the hospitalization (P<0.001, all comparisons). In an analysis of demographic factors, age demonstrated higher discriminative ability for in-hospital mortality compared to gender (P<0.001) and race (P<0.001). Race had sole or shared inferior discriminative ability for all outcomes. The most discriminative comorbidity index (ECM) outperformed the most discriminative demographic factor (age, gender) for any complication, minor adverse event, and infectious events. A combination analysis of the most predictive comorbidity index and the most predictive demographic factor resulted in discriminative improvements in all five outcome variables. Conclusion: Among comorbidity indices, the mCCI demonstrated significantly greater discriminative ability for mortality and the ECM demonstrated significantly greater discriminative ability for multiple adverse events during hospitalization. The use of these indices in conjunction with easily accessible demographic factors, such as age, resulted in further improvements in discrimination ability. These findings suggest that increased use of the mCCI and ECM may assist in the identification and management of patients at risk of death and postoperative complications, respectively, and thereby help optimize risk stratification, inform patient expectations, and guide outcomes-based reimbursements in the management of traumatic ankle fracture.

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Chen, Wen, Jinping Wang, Dian Huang, Wanli Cheng, Zongze Shao, Minmin Cai, Longyu Zheng, Ziniu Yu, and Jibin Zhang. "Volatile Organic Compounds from Bacillus aryabhattai MCCC 1K02966 with Multiple Modes against Meloidogyne incognita." Molecules 27, no. 1 (December 24, 2021): 103. http://dx.doi.org/10.3390/molecules27010103.

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Plant-parasitic nematodes cause severe losses to crop production and economies all over the world. Bacillus aryabhattai MCCC 1K02966, a deep-sea bacterium, was obtained from the Southwest Indian Ocean and showed nematicidal and fumigant activities against Meloidogyne incognita in vitro. The nematicidal volatile organic compounds (VOCs) from the fermentation broth of B. aryabhattai MCCC 1K02966 were investigated further using solid-phase microextraction gas chromatography-mass spectrometry. Four VOCs, namely, pentane, 1-butanol, methyl thioacetate, and dimethyl disulfide, were identified in the fermentation broth. Among these VOCs, methyl thioacetate exhibited multiple nematicidal activities, including contact nematicidal, fumigant, and repellent activities against M. incognita. Methyl thioacetate showed a significant contact nematicidal activity with 87.90% mortality at 0.01 mg/mL by 72 h, fumigant activity in mortality 91.10% at 1 mg/mL by 48 h, and repellent activity at 0.01–10 mg/mL. In addition, methyl thioacetate exhibited 80–100% egg-hatching inhibition on the 7th day over the range of 0.5 mg/mL to 5 mg/mL. These results showed that methyl thioacetate from MCCC 1K02966 control M. incognita with multiple nematicidal modes and can be used as a potential biological control agent.

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He, Zhi-Hui, Jia Wu, Lin Xu, Man-Yi Hu, Ming-Ming Xie, You-Jia Hao, Shu-Jin Li, Zong-Ze Shao, and Xian-Wen Yang. "Chemical Constituents of the Deep-Sea-Derived Penicillium solitum." Marine Drugs 19, no. 10 (October 17, 2021): 580. http://dx.doi.org/10.3390/md19100580.

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A systematic chemical investigation of the deep-sea-derived fungus Penicillium solitum MCCC 3A00215 resulted in the isolation of one novel polyketide (1), two new alkaloids (2 and 3), and 22 known (4–25) compounds. The structures of the new compounds were established mainly on the basis of exhaustive analysis of 1D and 2D NMR data. Viridicatol (13) displayed moderate anti-tumor activities against PANC-1, Hela, and A549 cells with IC50 values of around 20 μM. Moreover, 13 displayed potent in vitro anti-food allergic activity with an IC50 value of 13 μM, compared to that of 92 μM for the positive control, loratadine, while indole-3-acetic acid methyl ester (9) and penicopeptide A (10) showed moderate effects (IC50 = 50 and 58 μM, respectively).

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Niu, Siwen, Jin-Mei Xia, Zengpeng Li, Long-He Yang, Zhi-Wei Yi, Chun-Lan Xie, Guizhen Peng, Zhu-Hua Luo, Zongze Shao, and Xian-Wen Yang. "Aphidicolin Chemistry of the Deep-Sea-Derived Fungus Botryotinia fuckeliana MCCC 3A00494." Journal of Natural Products 82, no. 8 (August 12, 2019): 2307–31. http://dx.doi.org/10.1021/acs.jnatprod.9b00705.

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Liu, Chih-Yi, Nai-Wen Kang, Kengo Takeuchi, and Shih-Sung Chuang. "Combined Merkel Cell Carcinoma with Nodal Presentation: Report of a Case Diagnosed with Excisional but Not Incisional Biopsy and Literature Review." Diagnostics 13, no. 3 (January 26, 2023): 449. http://dx.doi.org/10.3390/diagnostics13030449.

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Merkel cell carcinoma (MCC) is a rare primary neuroendocrine carcinoma (NEC) of the skin. As compared to pure MCCs, combined MCCs are aggressive and exhibit a higher probability of metastasis. A correct diagnosis might be missed, especially when the biopsy sample is too small or too superficial. We report a 79-year-old Taiwanese male who presented with lymphadenopathy suspicious for lymphoma. A nodal biopsy showed metastatic NEC. A skin tumor in the lower back was identified, and an incisional biopsy showed only squamous cell carcinoma (SCC). A subsequent excisional biopsy was performed based on the advice of the senior pathologist because of the presence of metastatic nodal NEC. Finally, a diagnosis of combined MCC and SCC was confirmed. Our literature review identified 13 cases of combined MCC with nodal metastasis as initial presentations, all with an aggressive clinical course. Both the MCC and non-MCC components could be present in the metastatic nodes. Metastases of pure MCC cells were observed in three combined MCCs in sun-protected areas, probably pointing to a distinct pathogenesis. Excision or punch biopsy to include the deep dermal NEC component is recommended as timely diagnosis is mandatory for appropriate management of patients with this rare skin cancer.

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Niu, Siwen, Shuhuan Huang, Bihong Hong, Qixi Huang, Xiupian Liu, Zongze Shao, and Gaiyun Zhang. "Antiviral Cyclopropane Acids from Deep-Sea-Derived Fungus Aspergillus sydowii." Marine Drugs 20, no. 7 (June 23, 2022): 410. http://dx.doi.org/10.3390/md20070410.

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Four novel monocyclic cyclopropane acids, namely, sydocyclopropanes A–D (1–4), along with one known congener hamavellone B (5), were isolated from the Aspergillus sydowii MCCC 3A00324 fungus, which was isolated from the deep-sea sediment. The gross structures of novel compounds were established by detailed analyses of the spectroscopic data (HRESIMS and NMR spectra), and their absolute configurations were resolved on the basis of the quantum chemical calculations of ECD and NMR data, in association with DP4+ probability analyses. Sydocyclopropanes A–D, featuring the 1,1,2,3-tetrasubstituted cyclopropane nucleus with different lengthy alkyl side chains, were discovered in nature for the first time. All compounds exhibited antiviral activities against A/WSN/33 (H1N1), with IC50 values ranging from 26.7 to 77.2 μM, of which compound 1 exhibited a moderate inhibitory effect (IC50 = 26.7 μM).

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Donizy, Piotr, Joanna P. Wróblewska, Dora Dias-Santagata, Katarzyna Woznica, Przemyslaw Biecek, Mark C. Mochel, Cheng-Lin Wu, et al. "Merkel Cell Carcinoma of Unknown Primary: Immunohistochemical and Molecular Analyses Reveal Distinct UV-Signature/MCPyV-Negative and High Immunogenicity/MCPyV-Positive Profiles." Cancers 13, no. 7 (March 31, 2021): 1621. http://dx.doi.org/10.3390/cancers13071621.

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Background: Merkel cell carcinomas of unknown primary (MCC-UPs) are defined as deep-seated tumors without an associated cutaneous tumor. Although the distinction has important clinical implications, it remains unclear whether these tumors represent primary tumors of lymph nodes or metastatic cutaneous primaries. Methods: We compared the immunohistochemical profiles of four groups of MCCs (Merkel cell polyomavirus (MCPyV)-positive UP, MCPyV-negative UP, MCPyV-positive known primary (KP), and MCPyV-negative KP) using B-cell and pre-B-cell markers, cell cycle regulating proteins, follicular stem cell markers, and immune markers, and performed next generation and Sanger sequencing. Results: Virus-positive and virus-negative MCC-UPs exhibited an immunoprofile similar to virus-positive and virus-negative primary cutaneous MCCs, respectively. MCC-UP tumors (both virus-positive and -negative) were immunogenic with similar or even higher tumoral PD-L1 expression and intratumoral CD8 and FoxP3 infiltrates in comparison to MCPyV-positive cutaneous tumors. In addition, similar to primary cutaneous MCCs, MCPyV-negative MCC-UPs exhibited UV signatures and frequent high tumor mutational burdens, whereas few molecular alterations were noted in MCPyV-positive MCC-UPs. Conclusions: Our results showed distinct UV-signatures in MCPyV-negative tumors and high immunogenicity in MCPyV-positive tumors. Although additional studies are warranted for the MCPyV-positive cases, our findings are supportive of a cutaneous metastatic origin for MCPyV-negative MCC-UP tumors.

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Xing, Cui-Ping, Dan Chen, Chun-Lan Xie, Qingmei Liu, Tian-Hua Zhong, Zongze Shao, Guangming Liu, Lian-Zhong Luo, and Xian-Wen Yang. "Anti-Food Allergic Compounds from Penicillium griseofulvum MCCC 3A00225, a Deep-Sea-Derived Fungus." Marine Drugs 19, no. 4 (April 16, 2021): 224. http://dx.doi.org/10.3390/md19040224.

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Ten new (1–10) and 26 known (11–36) compounds were isolated from Penicillium griseofulvum MCCC 3A00225, a deep sea-derived fungus. The structures of the new compounds were determined by detailed analysis of the NMR and HRESIMS spectroscopic data. The absolute configurations were established by X-ray crystallography, Marfey’s method, and the ICD method. All isolates were tested for in vitro anti-food allergic bioactivities in immunoglobulin (Ig) E-mediated rat basophilic leukemia (RBL)-2H3 cells. Compound 13 significantly decreased the degranulation release with an IC50 value of 60.3 μM, compared to that of 91.6 μM of the positive control, loratadine.

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Hao, You-Jia, Zheng-Biao Zou, Ming-Min Xie, Yong Zhang, Lin Xu, Hao-Yu Yu, Hua-Bin Ma, and Xian-Wen Yang. "Ferroptosis Inhibitory Compounds from the Deep-Sea-Derived Fungus Penicillium sp. MCCC 3A00126." Marine Drugs 21, no. 4 (April 10, 2023): 234. http://dx.doi.org/10.3390/md21040234.

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Two new xanthones (1 and 2) were isolated from the deep-sea-derived fungus Penicillium sp. MCCC 3A00126 along with 34 known compounds (3–36). The structures of the new compounds were established by spectroscopic data. The absolute configuration of 1 was validated by comparison of experimental and calculated ECD spectra. All isolated compounds were evaluated for cytotoxicity and ferroptosis inhibitory activities. Compounds 14 and 15 exerted potent cytotoxicity against CCRF-CEM cells, with IC50 values of 5.5 and 3.5 μM, respectively, whereas 26, 28, 33, and 34 significantly inhibited RSL3-induced ferroptosis, with EC50 values of 11.6, 7.2, 11.8, and 2.2 μM, respectively.

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Zhang, Yu, Jianguo Yao, and Haibing Guan. "Intelligent Cloud Resource Management with Deep Reinforcement Learning." IEEE Cloud Computing 4, no. 6 (November 2017): 60–69. http://dx.doi.org/10.1109/mcc.2018.1081063.

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Xie, Chun-Lan, Qingmei Liu, Jin-Mei Xia, Yuanyuan Gao, Quan Yang, Zong-Ze Shao, Guangming Liu, and Xian-Wen Yang. "Anti-Allergic Compounds from the Deep-Sea-Derived Actinomycete Nesterenkonia flava MCCC 1K00610." Marine Drugs 15, no. 3 (March 14, 2017): 71. http://dx.doi.org/10.3390/md15030071.

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Niu, Siwen, Manli Xia, Mingliang Chen, Xiupian Liu, Zengpeng Li, Yunchang Xie, Zongze Shao, and Gaiyun Zhang. "Cytotoxic Polyketides Isolated from the Deep-Sea-Derived Fungus Penicillium chrysogenum MCCC 3A00292." Marine Drugs 17, no. 12 (December 5, 2019): 686. http://dx.doi.org/10.3390/md17120686.

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The chemical examination of the solid cultures of the deep-sea-derived fungus Penicillium chrysogenum MCCC 3A00292 resulted in the isolation of three new versiol-type analogues, namely peniciversiols A–C (1–3), and two novel lactone derivatives, namely penicilactones A and B (6 and 7), along with 11 known polyketides. The planar structures of the new compounds were determined by the comprehensive analyses of the high-resolution electrospray ionization mass spectroscopy (HRESIMS) and nuclear magnetic resonance (NMR) data, while their absolute configurations were resolved on the basis of comparisons of the experimental electronic circular dichroism (ECD) spectra with the calculated ECD data. Compound 1 is the second example of versiols featuring a 2,3-dihydropyran-4-one ring. Additionally, compounds 6 and 7 are the first representatives of γ-lactone derivatives constructed by a 1,3-dihydroxy-5-methylbenzene unit esterifying with the α-methyl-γ-hydroxy-γ-acetic acid α,β-unsaturated-γ-lactone moiety and α-hydroxy-γ-methyl-γ-acetic acid α,β-unsaturated-γ-lactone unit, respectively. All of the isolated compounds were evaluated for their cytotoxic activities against five human cancer cell lines of BIU-87, ECA109, BEL-7402, PANC-1, and Hela-S3. Compound 1 exhibited a selective inhibitory effect against the BIU-87 cell line (IC50 = 10.21 μM), while compounds 4, 5, 8, and 12–16 showed inhibitory activities against the ECA109, BIU-87, and BEL-7402 cell lines with the IC50 values ranging from 7.70 to > 20 μM.

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Ma, Xin-hua, Wei-min Zheng, Kai-hui Sun, Xiao-fan Gu, Xian-ming Zeng, Hai-tao Zhang, Tian-hua Zhong, Zong-ze Shao, and Yong-hong Zhang. "Two new phenylspirodrimanes from the deep-sea derived fungus Stachybotrys sp. MCCC 3A00409." Natural Product Research 33, no. 3 (March 23, 2018): 386–92. http://dx.doi.org/10.1080/14786419.2018.1455041.

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Xing, Cui-Ping, Jia Wu, Jin-Mei Xia, Shao-Qiang Fan, and Xian-Wen Yang. "Steroids and anthraquinones from the deep-sea-derived fungus Aspergillus nidulans MCCC 3A00050." Biochemical Systematics and Ecology 83 (April 2019): 103–5. http://dx.doi.org/10.1016/j.bse.2018.12.012.

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Niu, Siwen, Zuowang Fan, Xixiang Tang, Qingmei Liu, Zongze Shao, Guangming Liu, and Xian-Wen Yang. "Cyclopiane-type diterpenes from the deep-sea-derived fungus Penicillium commune MCCC 3A00940." Tetrahedron Letters 59, no. 4 (January 2018): 375–78. http://dx.doi.org/10.1016/j.tetlet.2017.12.045.

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van der Pas, J. W. G. M., W. E. Walker, V. A. W. J. Marchau, G. P. Van Wee, and D. B. Agusdinata. "Exploratory MCDA for handling deep uncertainties: the case of intelligent speed adaptation implementation." Journal of Multi-Criteria Decision Analysis 17, no. 1-2 (January 2010): 1–23. http://dx.doi.org/10.1002/mcda.450.

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Marco Ivaldi, Andrea Ciavattini, and Cugliari Giovanni. "Heart rate analysis during very deep dives in flooded caves: single case study." International Journal of Physical Education, Fitness and Sports 9, no. 3 (August 30, 2020): 9–17. http://dx.doi.org/10.34256/ijpefs2032.

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The purpose of this study is to investigate the heart rate adaptations during deep dave diving with MCCR (mechanical closed circuit rebreather). Previous studies on this matter have not been conducted to the depths reached in this study and most of them have been conducted inside hyperbaric chambers trying to recreate the immersion conditions. The data collection took place during the exploration of two hydrogeological sites by a professional cave diver. The recordings were made using a SCUBAPRO GALILEO SOL® dive computer capable of monitoring the heart rate, with a sampling interval of 0,25 Hz. The data collected confirm a direct relationship between the increase in diving depth and the increase in the detected heart rate.

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Antonsdottir, Inga, Quincy Samus, Melissa Reuland, Deirdre Johnston, Morgan Spliedt, and Danetta Sloan. "Staff Perspectives on Lessons Learned From an Interdisciplinary Memory Care Coordination Program." Innovation in Aging 5, Supplement_1 (December 1, 2021): 325. http://dx.doi.org/10.1093/geroni/igab046.1263.

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Abstract MIND at Home is a home-based care coordination program for persons living with dementia (PLWD) and their informal care partners (CP). Assessments, care planning and coordination is delivered by trained non-clinical Memory Care Coordinators (MCCs), working together on an interdisciplinary team with nurses and geriatric psychiatrists. We report qualitative results from program staff (two nurses and eight MCCs) who implemented the program in the context of two clinical trials. Care team respondents answered open-ended questions covering 5 domains pertaining to: helpful skillsets; positive and challenging factors aspects of care coordination; barriers to care coordination for clients; and improvements suggestions/resources to strengthen the program. Compassion, finding common ground, listening, organization, and time management were reported as critical skills. Staff enjoyed team collaboration, being in and learning about the community, increasing CP confidence and mastery when caring for a PLWD. Reported challenges included documentation in EHR, accessing/navigating resources, driving long distances, unsafe neighborhoods, ambiguous assessment tools, and working with low engagement clients. Common barriers faced by clients (as reported by staff) were financial struggles/poverty, and lack of insurance coverage for needed services. Staff suggested several improvements: better communication strategies, integration with LTSS services and medical providers, 24-hour program hotline, continuous education for staff, simplified data collection and care delivery tracking process. This presentation on the experience of MIND at Home trained nurses and MCCs provides deep insight on how this and similar care coordination programs might be successfully implemented or strengthened.

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Taylor, H., J. McDonald, J. I. Serrano Contreras, J. Li, J. Marchesi, and A. Hart. "DOP08 Deep remission in paediatric Crohn’s disease is associated with increased abundance of dialister species and increased valerate." Journal of Crohn's and Colitis 14, Supplement_1 (January 2020): S045—S046. http://dx.doi.org/10.1093/ecco-jcc/jjz203.047.

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Abstract Background Deep remission, or the absence of mucosal inflammation on endoscopy, is associated with improved long-term outcomes in paediatric Crohn’s disease (pCD). In pCD faecal calprotectin level <100 mg/l is a validated non-invasive marker of deep remission and is a therapeutic target used in clinical practice. The microbiome in pCD has been extensively compared with controls and is known to have reduced diversity, high instability, and depleted short-chain fatty acid (SCFA) producers. This study investigates variation in microbiome, metabolome and protease activity associated with deep remission. Methods Children aged 3–18 years with established pCD on infliximab were recruited. Stool samples were cooled immediately, aliquoted, and frozen at −80oC within 4 h. Deep remission status was assigned if the calprotectin level was under 100 mg/l. 16S sequencing and analysis used Illumina MiSeq (V1-2 primers), DADA2, and STAMP. ¹H-NMR spectral profiles were used to develop partial-least-squares discriminant-analysis with Monte-Carlo cross-validation (MCCV-PLS-DA) models. Metabolome microbiome correlation used Storey’s method for multiple testing correction and a threshold of │RHO│≥ 0.5 with q < 0.05. Protease activity was assayed by comparing the breakdown of fluorescein labelled casein against trypsin standards. Results Twenty-one children were included; 10 were in deep remission and 11 had active disease. There were no significant differences in age, disease duration, treatment, or BMI between groups. Mean height z score was lower in those with active disease (p = 0.015). There was no significant difference in α diversity between groups, and non-metric multidimensional scaling of weighted unifrac distance identified no difference in community composition (PERMANOVA p = 0.317). The relative abundance of Dialister species was higher in those with deep remission (3.4 vs. 0.4%, q = 0.033). Dialister abundance was positively correlated with valerate concentration. MCCV–PLS-DA was able to effectively discriminate metabolome profiles from active and deep remission patients (R2 = 0.87, Q2 = 0.51); valerate and glutamate were increased in deep remission, ethanol and lysine were decreased. There was a trend towards increased protease activity in patients with active disease (p = 0.054). Conclusion Dialister species are enriched in pCD in deep remission and are associated with significant metabolome changes, including increased valerate. Valerate, like other SCFAs, has known anti-inflammatory properties and has previously been implicated in effective C. difficile treatment. This study supports an association between Dialister abundance, valerate and mucosal healing in pCD. A trend towards higher protease activity in active disease also warrants further investigation.

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Tang, Xi-Xiang, Shun-Zhi Liu, Xia Yan, Bo-Wen Tang, Mei-Juan Fang, Xiu-Min Wang, Zhen Wu, and Ying-Kun Qiu. "Two New Cytotoxic Compounds from a Deep-Sea Penicillum citreonigrum XT20-134." Marine Drugs 17, no. 9 (August 29, 2019): 509. http://dx.doi.org/10.3390/md17090509.

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Penicillum citreonigrum XT20-134 (MCCC 3A00956) is a fungus with cytotoxic activity, derived from deep-sea sediment. Five new compounds, adeninylpyrenocine (1), 2-hydroxyl-3-pyrenocine-thio propanoic acid (2), ozazino-cyclo-(2,3-dihydroxyl-trp-tyr) (3), 5,5-dichloro-1-(3,5-dimethoxyphenyl)-1,4-dihydroxypentan-2-one (4), and 2,3,4-trihydroxybutyl cinnamate (5), together with 19 known compounds (6–24), were isolated from an ethyl acetate (EtOAc) extract of its fermentation. The structures of the new compounds were comprehensively characterized by high-resolution electrospray ionization-mass spectrometry (HR-ESI-MS), 1D and 2D nuclear magnetic resonance (NMR). All isolates were evaluated for their cytotoxic activities. The heteroatom-containing new compounds 2 and 4 showed potent cytotoxicity to the human hepatoma tumor cell Bel7402 with IC50 values of 7.63 ± 1.46, 13.14 ± 1.41 μM and the human fibrosarcoma tumor cell HT1080 with IC50 values of 10.22 ± 1.32, 16.53 ± 1.67 μM, respectively.

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Zou, Zheng-Biao, Gang Zhang, Yu-Qi Zhou, Chun-Lan Xie, Ming-Min Xie, Lin Xu, You-Jia Hao, et al. "Chemical Constituents of the Deep-Sea-Derived Penicillium citreonigrum MCCC 3A00169 and Their Antiproliferative Effects." Marine Drugs 20, no. 12 (November 24, 2022): 736. http://dx.doi.org/10.3390/md20120736.

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Six new citreoviridins (citreoviridins J–O, 1–6) and twenty-two known compounds (7–28) were isolated from the deep-sea-derived Penicillium citreonigrum MCCC 3A00169. The structures of the new compounds were determined by spectroscopic methods, including the HRESIMS, NMR, ECD calculations, and dimolybdenum tetraacetate-induced CD (ICD) experiments. Citreoviridins J−O (1–6) are diastereomers of 6,7-epoxycitreoviridin with different chiral centers at C-2–C-7. Pyrenocine A (7), terrein (14), and citreoviridin (20) significantly induced apoptosis for HeLa cells with IC50 values of 5.4 μM, 11.3 μM, and 0.7 μM, respectively. To be specific, pyrenocine A could induce S phase arrest, while terrein and citreoviridin could obviously induce G0-G1 phase arrest. Citreoviridin could inhibit mTOR activity in HeLa cells.

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Lai, Qiliang, Liping Wang, Yuhui Liu, Jun Yuan, Fengqin Sun, and Zongze Shao. "Parvibaculum indicum sp. nov., isolated from deep-sea water." International Journal of Systematic and Evolutionary Microbiology 61, no. 2 (February 1, 2011): 271–74. http://dx.doi.org/10.1099/ijs.0.021899-0.

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A taxonomic study was carried out on strain P31T, which was isolated from a polycyclic aromatic hydrocarbon (PAH)-degrading consortium enriched with deep-sea water of the Indian Ocean. The isolate was Gram-reaction-negative, rod-shaped, motile by means of a polar flagellum and incapable of reducing nitrate to nitrite. Growth was observed at 0.5–8 % NaCl and at 10–41 °C. Strain P31T was unable to degrade Tween 80 or gelatin. The major respiratory quinone was ubiquinone 11 (Q-11). The dominant fatty acids were C18 : 1 ω7c (39.79 %), 11-methyl C18 : 1 ω7c (17.84 %), C19 : 0 cyclo ω8c (12.05 %) and C18 : 0 (6.09 %). The G+C content of the chromosomal DNA was 62.1 mol%. A phylogenetic tree based on 16S rRNA gene sequence analysis showed that strain P31T and Parvibaculum lavamentivorans DS-1T formed a distinct lineage in the family Phyllobacteriaceae; these two strains showed 95.7 % sequence similarity, while similarities between P31T and other members of the genus Parvibaculum were below 93 %. Based on the genotypic and phenotypic data, strain P31T represents a novel species of the genus Parvibaculum, for which the name Parvibaculum indicum sp. nov. is proposed. The type strain is P31T (=CCTCC AB 208230T =LMG 24712T =MCCC 1A01132T).

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Lai, Qiliang, Yuanyuan Fu, Jianning Wang, Shuangxi Chen, Huanzi Zhong, Fengqin Sun, and Zongze Shao. "Citreicella marina sp. nov., isolated from deep-sea sediment." International Journal of Systematic and Evolutionary Microbiology 61, no. 4 (April 1, 2011): 728–31. http://dx.doi.org/10.1099/ijs.0.022376-0.

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A taxonomic study was carried out on a novel strain, designated CK-I3-6T, which was isolated from deep-sea sediment of the south-west Indian Ocean Ridge. Cells were Gram-reaction-negative, oxidase- and catalase-positive, rod-shaped and non-motile. Growth was observed at 4–38 °C and in 1–12 % (w/v) NaCl. Cells were able to degrade gelatin and oxidize thiosulfate but did not reduce nitrate. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain CK-I3-6T belonged to the genus Citreicella with a sequence similarity of 97.3 % to Citreicella thiooxidans CHLG 1T, while similarities with other taxa were <95.7 %. DNA–DNA hybridization showed that strain CK-I3-6T and C. thiooxidans CHLG 1T showed a low DNA–DNA relatedness (48±3 %). The principal fatty acids were C16 : 0 (7.8 %), C18 : 1ω7c (66.6 %), summed feature 3 (C16 : 1ω6c and/or C16 : 1ω7c; 6.3 %) and C19 : 0ω8c cyclo (10.0 %). The chromosomal DNA G+C content was 67.5 mol%. On the basis of the combined genotypic and phenotypic data, strain CK-I3-6T represents a novel species of the genus Citreicella, for which the name Citreicella marina sp. nov. is proposed. The type strain is CK-I3-6T ( = CCTCC AB 209064T = LMG 25230T = MCCC 1A03060T).

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Lai, Qiliang, Zhiwei Yu, Jun Yuan, Fengqin Sun, and Zongze Shao. "Nitratireductor indicus sp. nov., isolated from deep-sea water." International Journal of Systematic and Evolutionary Microbiology 61, no. 2 (February 1, 2011): 295–98. http://dx.doi.org/10.1099/ijs.0.022962-0.

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A taxonomic study was carried out on a novel bacterial strain, designated C115T, isolated from a crude-oil-degrading consortium, enriched from deep-sea water of the Indian Ocean. Cells were Gram-negative short rods, mobile by means of a monopolar flagellum. Growth was observed at salinities of 0–7 % and at 10–43 °C. It was unable to degrade Tween 80 or gelatin. 16S rRNA gene sequence analysis showed that strain C115T was related most closely to Nitratireductor aquibiodomus NL21T (96.5 % similarity), Nitratireductor kimnyeongensis KY 101T (96.4 %) and Nitratireductor basaltis J3T (96.2 %). The predominant fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c, 81.8 %) and C18 : 0 (7.0 %). The G+C content of the chromosomal DNA of strain C115T was 59 mol%. Based on its morphology, physiology and fatty acid composition together with 16S rRNA gene sequence comparisons, the novel strain most appropriately belongs to the genus Nitratireductor, but can be distinguished readily from recognized species of the genus. Strain C115T is therefore considered to represent a novel species of the genus Nitratireductor, for which the name Nitratireductor indicus sp. nov. is proposed. The type strain is C115T (=RC92-7T =CCTCC AB 209298T =LMG 25540T =MCCC 1A01260T).

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Xu, Hui, Yuanyuan Fu, Ning Yang, Zhixin Ding, Qiliang Lai, and Runying Zeng. "Flammeovirga pacifica sp. nov., isolated from deep-sea sediment." International Journal of Systematic and Evolutionary Microbiology 62, Pt_4 (April 1, 2012): 937–41. http://dx.doi.org/10.1099/ijs.0.030676-0.

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Strain WPAGA1T was isolated from marine sediment of the west Pacific Ocean. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belonged to the genus Flammeovirga . Strain WPAGA1T exhibited highest 16S rRNA gene sequence similarity with Flammeovirga yaeyamensis NBRC 100898T (98.1 %) and lower sequence similarity with Flammeovirga arenaria IFO 15982T (94.6 %) and other members of the genus Flammeovirga (<94.2 %). DNA–DNA relatedness studies showed that strain WPAGA1T was distinct from F. yaeyamensis NBRC 100898T and F. arenaria NBRC 15982T (43±4 % and 32±2 % relatedness values, respectively). Strain WPAGA1T could be distinguished from all known members of the genus Flammeovirga by a number of phenotypic features. However, the dominant fatty acids of strain WPAGA1T (iso-C15 : 0, C16 : 0 and C20 : 4ω6,9,12,15c), the major polyamine (cadaverine) and the G+C content of the chromosomal DNA (32.9 mol%) were consistent with those of members of the genus Flammeovirga . Based on phenotypic and chemotaxonomic features and 16S rRNA gene sequences, strain WPAGA1T can be assigned to the genus Flammeovirga as a representative of a novel species, for which the name Flammeovirga pacifica sp. nov. is proposed; the type strain is WPAGA1T ( = CCTCC AB 2010364T = LMG 26175T = DSM 24597T = MCCC 1A06425T).

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Li, Guizhen, Qiliang Lai, Yaping Du, Xiupian Liu, Fengqin Sun, and Zongze Shao. "Marinibacterium profundimaris gen. nov., sp. nov., isolated from deep seawater." International Journal of Systematic and Evolutionary Microbiology 65, Pt_11 (November 1, 2015): 4175–79. http://dx.doi.org/10.1099/ijsem.0.000557.

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A taxonomic study was carried out on strain 22II1-22F33T, which was isolated from deep seawater of the Atlantic Ocean. The bacterium was Gram-stain-negative, oxidase-positive and weakly catalase-positive, oval in shape without flagellum. Growth was observed at salinities of 0–12 % and at temperatures of 4–41 °C. The isolate was capable of hydrolysing aesculin and Tween 80 and reduction of nitrate to nitrite, but unable to hydrolyse gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22II1-22F33T belongs to the family Rhodobacteraceae, with highest sequence similarity to Pseudooceanicola marinus AZO-CT (96.5 %). The principal fatty acids (>10 %) were summed feature 8 (C18 : 1ω7c/ω6c) (73.8 %). The G+C content of the genomic DNA was 66.2 mol%. The respiratory quinone was Q-10 (100 %). Phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), two unidentified aminolipids (ALs), six unidentified phospholipids (PLs) and one unidentified lipid (L) were present. The combined genotypic and phenotypic data show that strain 22II1-22F33T represents a novel species within a new genus, for which the name Marinibacterium profundimaris gen. nov., sp. nov. is proposed. The type strain of Marinibacterium profundimaris is 22II1-22F33T ( = LMG 27151T = MCCC 1A09326T).

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Niu, Siwen, Longhe Yang, Tingting Chen, Bihong Hong, Shengxiang Pei, Zongze Shao, and Gaiyun Zhang. "New Monoterpenoids and Polyketides from the Deep-Sea Sediment-Derived Fungus Aspergillus sydowii MCCC 3A00324." Marine Drugs 18, no. 11 (November 17, 2020): 561. http://dx.doi.org/10.3390/md18110561.

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Chemical study of the secondary metabolites of a deep-sea-derived fungus Aspergillus sydowii MCCC 3A00324 led to the isolation of eleven compounds (1–11), including one novel (1) and one new (2) osmane-related monoterpenoids and two undescribed polyketides (3 and 4). The structures of the metabolites were determined by comprehensive analyses of the NMR and HRESIMS spectra, in association with quantum chemical calculations of the 13C NMR, ECD, and specific rotation data for the configurational assignment. Compound 1 possessed a novel monoterpenoid skeleton, biogenetically probably derived from the osmane-type monoperpenoid after the cyclopentane ring cleavage and oxidation reactions. Additionally, compound 3 was the first example of the α-pyrone derivatives bearing two phenyl units at C-3 and C-5, respectively. The anti-inflammatory activities of 1–11 were tested. As a result, compound 6 showed potent inhibitory nitric oxide production in lipopolysaccharide (LPS)-activated BV-2 microglia cells with an inhibition rate of 94.4% at the concentration of 10 µM. In addition, a plausible biosynthetic pathway for 1 and 2 was also proposed.

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Niu, Siwen, Dong Liu, Zongze Shao, Peter Proksch, and Wenhan Lin. "Eutypellazines A–M, thiodiketopiperazine-type alkaloids from deep sea derived fungus Eutypella sp. MCCC 3A00281." RSC Advances 7, no. 53 (2017): 33580–90. http://dx.doi.org/10.1039/c7ra05774a.

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Li, Guizhen, Qiliang Lai, Yaping Du, Xiupian Liu, Fengqin Sun, and Zongze Shao. "Aestuariivita atlantica sp. nov., isolated from deep-sea sediment." International Journal of Systematic and Evolutionary Microbiology 65, Pt_10 (October 1, 2015): 3281–85. http://dx.doi.org/10.1099/ijsem.0.000406.

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A novel strain, 22II-S11-z3T, was isolated from the deep-sea sediment of the Atlantic Ocean. The bacterium was aerobic, Gram-staining-negative, oxidase-positive and catalase-negative, oval- to rod-shaped, and non-motile. Growth was observed at salinities of 1–9 % NaCl and temperatures of 10–45 °C. The isolate could hydrolyse aesculin and Tweens 20, 40 and 80, but not gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22II-S11-z3T belonged to the genus Aestuariivita, with highest sequence similarity to Aestuariivita boseongensis KCTC 42052T (97.5 %). The average nucleotide identity and digital DNA–DNA hybridization values between strain 22II-S11-z3T and A. boseongensis KCTC 42052T were 71.5 % and 20.0 ± 2.3 %, respectively. The G+C content of the chromosomal DNA was 65.5 mol%. The principal fatty acids (>5 %) were summed feature 8 (C18 : 1ω7c/ω6c) (35.2 %), C19 : 0 cyclo ω8c (20.9 %), C16 : 0 (11.8 %), 11-methyl C18 : 1ω7c (11.4 %) and C12 : 1 3-OH (9.4 %). The respiratory quinone was determined to be Q-10. Diphosphatidylglycerol, phosphatidylcholine, phosphatidylglycerol, nine unidentified phospholipids, one unidentified aminolipid and two unidentified lipids were present. The combined genotypic and phenotypic data show that strain 22II-S11-z3T represents a novel species of the genus Aestuariivita, for which the name Aestuariivita atlantica sp. nov. is proposed, with the type strain 22II-S11-z3T ( = KCTC 42276T = MCCC 1A09432T).

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Li, Jianyang, Mingming Qi, Qiliang Lai, Guangyi Wang, and Zongze Shao. "Sunxiuqinia indica sp. nov., isolated from deep sea." International Journal of Systematic and Evolutionary Microbiology 70, no. 7 (July 1, 2020): 4186–92. http://dx.doi.org/10.1099/ijsem.0.004273.

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A Gram-stain-negative, facultative anaerobic, red-pigmented, rod-shaped and non-motile strain (RC1_OXG_1FT) was isolated from deep sea water of the Indian Ocean. It was able to grow at pH 5–8 (optimum, pH 7), at 5–37 °C (optimum, 30 °C), and at salinity (% NaCl, w/v) of 0.5–5 % (optimum, 1–2 %). Catalase- and oxidase-positive. It had highest 16S rRNA gene similarity (96.7 %) to ‘ Sunxiuqinia dokdonensis ’ DH1T, followed by Sunxiuqinia faeciviva JAM-BA0302T (96.6 %), Sunxiuqinia elliptica CGMCC 1.9156T (96.2 %), Sunxiuqinia rutila HG677T (96.0 %) and species (less than 92.3 %) of other genera. It belongs to the genus Sunxiuqinia within the phylum Bacteroidetes , based on the phylogenetic analysis. The results of digital DNA–DNA hybridization and average nucleotide identity analyses indicated that the strain belonged to a novel species. Its genome size is 5,250, 885 bp, with DNA G+C content of 40.5 mol%. Genome analysis revealed that the strain possessed many genes involved in polysaccharide degradation, especially hemicellulose degradation, indicating that the strain could maintain its normal metabolism by using recalcitrant organic matter in the oligotrophic deep sea environment. Its principal fatty acids were anteiso-C15 : 0 and iso-C15 : 0 and the major polar lipids were phosphatidylethanolamine, two unidentified glycolipids, three unidentified phospholipids and two unidentified polar lipids. The isoprenoid quinone was MK-7. Based on the phenotypic, chemotaxonomic and genotypic data, the strain represents a novel species within the genus Sunxiuqinia , for which the name Sunxiuqinia indica sp. nov. is proposed. The type strain is RC1_OXG_1FT (=MCCC 1A13858T=KCTC 62805T).

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de Groot, Jos, and Steven Hijink. "Verslaggeving over ‘in-control’ door Nederlandse beursvennootschappen." Maandblad Voor Accountancy en Bedrijfseconomie 94, no. 11/12 (December 15, 2020): 477–93. http://dx.doi.org/10.5117/mab.94.59763.

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De onderwerpen ‘in control’ en de ‘in-control statement’ worden in de praktijk op verschillende manieren geïnterpreteerd en uitgelegd. Tegelijkertijd is in het afgelopen jaar vanuit verschillende invalshoeken (hernieuwde) belangstelling getoond voor nieuwe regelgeving voor verslaggeving over ‘in-control’ zijn. Dit praktijkonderzoek van 91 jaarverslagen over 2019 van Nederlandse beursvennootschappen toont aan dat de bestuursverklaring uit de Code 2016 op alle vier de sub-elementen voor het overgrote deel wordt gevolgd door de AEX-, AMX- en AScX-fondsen. Bij de lokale beursvennootschappen behorende tot de overige-fondsen is dat significant lager. Van de 91 onderzochte beursvennootschappen nemen er 41 in het bestuursverslag 2019 een expliciete ‘in-control verklaring’ over het effectief functioneren van de interne risicobeheersings- en controlesystemen op, ondanks dat dit sinds de Code 2016 niet meer wordt voorgeschreven. Consistentie is in de ‘in-control verklaringen’ ver te zoeken; ze zijn een cocktail van toepassing van de best practice bepalingen uit de Code 2003, de Interpretatie Frijns (MCCG 2005), de Code 2008 en het Herzieningsvoorstel Code 2016 (MCCG 2016a).

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Shao, Rui, Qiliang Lai, Xiupian Liu, Fengqin Sun, Yaping Du, Guangyu Li, and Zongze Shao. "Zunongwangia atlantica sp. nov., isolated from deep-sea water." International Journal of Systematic and Evolutionary Microbiology 64, Pt_1 (January 1, 2014): 16–20. http://dx.doi.org/10.1099/ijs.0.054007-0.

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A taxonomic study was carried out on strain 22II14-10F7T, which was isolated from the deep-sea water of the Atlantic Ocean with oil-degrading enrichment. The bacterium was Gram-stain-negative, oxidase- and catalase-positive and rod-shaped. Growth was observed at salinities from 0.5 to 15 % and at temperatures from 4 to 37 °C; it was unable to hydrolyse Tween 40, 80 or gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain 22II14-10F7T represented a member of the genus Zunongwangia , with highest sequence similarity of 97.3 % to Zunongwangia profunda SM-A87T, while the similarities to other species were all below 94.0 %. The DNA–DNA hybridization estimate of the similarity between strain 22II14-10F7T and Z. profunda SM-A87T was 27.20±2.43 % according to their genome sequences. The principal fatty acids were iso-C15 : 0, anteiso-C15 : 0 , iso-C15 : 1 G, iso-C17 : 0 3-OH, summed feature 3 (C16 : 1ω7c/ω6c) and summed feature 9 (iso-C17 : 1ω9c or C16 : 0 10-methyl). The G+C content of the chromosomal DNA was 35.5 mol%. The major respiratory quinone was determined to be MK-6. Phosphatidylethanolamine (PE), two aminolipids (AL1 and AL2) and five unknown lipids (L1–L5) were present. The combined genotypic and phenotypic data show that strain 22II14-10F7T represents a novel species of the genus Zunongwangia , for which the name Zunongwangia atlantica sp. nov. is proposed, with the type strain 22II14-10F7T ( = CGMCC1.12470T = LMG 27421T = MCCC 1A06481T).

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Ozrazgat-Baslanti, Tezcan, Tyler J. Loftus, Yuanfang Ren, Matthew M. Ruppert, and Azra Bihorac. "Advances in artificial intelligence and deep learning systems in ICU-related acute kidney injury." Current Opinion in Critical Care 27, no. 6 (September 16, 2021): 560–72. http://dx.doi.org/10.1097/mcc.0000000000000887.

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Xie, Chun-Lan, Qingmei Liu, Zhi-Hui He, Ying-Bao Gai, Zheng-Biao Zou, Zong-Ze Shao, Guang-Ming Liu, Hai-Feng Chen, and Xian-Wen Yang. "Discovery of andrastones from the deep-sea-derived Penicillium allii-sativi MCCC 3A00580 by OSMAC strategy." Bioorganic Chemistry 108 (March 2021): 104671. http://dx.doi.org/10.1016/j.bioorg.2021.104671.

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Niu, Siwen, Ting-Ting Zhou, Chun-Lan Xie, Gai-Yun Zhang, and Xian-Wen Yang. "Microindolinone A, a Novel 4,5,6,7-Tetrahydroindole, from the Deep-Sea-Derived Actinomycete Microbacterium sp. MCCC 1A11207." Marine Drugs 15, no. 7 (July 19, 2017): 230. http://dx.doi.org/10.3390/md15070230.

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Huang, Dian, Zong-Ze Shao, Yi Yu, Min-Min Cai, Long-Yu Zheng, Guang-Yu Li, Zi-Niu Yu, Xian-Feng Yi, Ji-Bin Zhang, and Fu-Hua Hao. "Identification, Characteristics and Mechanism of 1-Deoxy-N-acetylglucosamine from Deep-Sea Virgibacillus dokdonensis MCCC 1A00493." Marine Drugs 16, no. 2 (February 7, 2018): 52. http://dx.doi.org/10.3390/md16020052.

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Niu, Siwen, Ning Wang, Chun-Lan Xie, Zuowang Fan, Zhuhua Luo, Hai-Feng Chen, and Xian-Wen Yang. "Roquefortine J, a novel roquefortine alkaloid, from the deep-sea-derived fungus Penicillium granulatum MCCC 3A00475." Journal of Antibiotics 71, no. 7 (April 4, 2018): 658–61. http://dx.doi.org/10.1038/s41429-018-0046-y.

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Niu, Siwen, Qingmei Liu, Jin-Mei Xia, Chun-Lan Xie, Zhu-Hua Luo, Zongze Shao, Guangming Liu, and Xian-Wen Yang. "Polyketides from the Deep-Sea-Derived Fungus Graphostroma sp. MCCC 3A00421 Showed Potent Antifood Allergic Activities." Journal of Agricultural and Food Chemistry 66, no. 6 (February 2, 2018): 1369–76. http://dx.doi.org/10.1021/acs.jafc.7b04383.

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Lai, Qiliang, Junwei Cao, Jun Yuan, Fuying Li, and Zongze Shao. "Celeribacter indicus sp. nov., a polycyclic aromatic hydrocarbon-degrading bacterium from deep-sea sediment and reclassification of Huaishuia halophila as Celeribacter halophilus comb. nov." International Journal of Systematic and Evolutionary Microbiology 64, Pt_12 (December 1, 2014): 4160–67. http://dx.doi.org/10.1099/ijs.0.069039-0.

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A taxonomic study was carried out on strain P73T, which was isolated from deep-sea sediment of the Indian Ocean by enrichment of polycyclic aromatic hydrocarbons. The strain was able to degrade biphenyl, naphthalene, 2-methylnaphthalene, 2,6-dimethylnaphthalene, acenaphthene, anthracene, phenanthrene, dibenzothiophene, dibenzofuran, fluorene, 4-methyldibenzothiophene and fluoranthene, but not pyrene or chrysene. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain P73T formed a clade with the genera Celeribacter and Huaishuia within the family Rhodobacteraceae , with highest sequence similarity of 96.98 % to Celeribacter neptunius H 14T, followed by Huaishuia halophila ZXM137T (96.42 %). The bacterium was Gram-stain-negative, oxidase- and catalase-positive, rod-shaped and non-motile. Growth was observed at salinities from 0.5 to 12 % and at temperatures from 10 to 41 °C. The principal fatty acids (>10 %) of strain P73T were summed feature 8 (C18 : 1ω7c/ω6c) and C19 : 0ω8c cyclo. The sole respiratory quinone was Q-10. The major lipids were phosphatidylglycerol, one unknown aminolipid, one unknown phospholipid and one unknown lipid; a second unknown phospholipid and one unknown glycolipid were present as minor components. The G+C content of the chromosomal DNA was 66.0 mol%. The combined genotypic and phenotypic data show that strain P73T represents a novel species of the genus Celeribacter , for which the name Celeribacter indicus sp. nov. is proposed. The type strain is P73T ( = MCCC 1A01112T = LMG 27600T = DSM 27257T). Phylogenetic study and existing phenotypic information also show that Huaishuia halophila should be transferred to the genus Celeribacter as Celeribacter halophilus comb. nov. (type strain ZXM137T = MCCC 1A06432T = CGMCC 1.8891T = LMG 24854T).

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Yang, Shanshan, Xuegong Li, Xiang Xiao, Guangjiao Zhuang, and Yu Zhang. "Sphingomonas profundi sp. nov., isolated from deep-sea sediment of the Mariana Trench." International Journal of Systematic and Evolutionary Microbiology 70, no. 6 (June 1, 2020): 3809–15. http://dx.doi.org/10.1099/ijsem.0.004235.

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A Gram-stain-negative, short rod-shaped, yellow bacterium (strain LMO-1T) was isolated from deep-sea sediment of the Mariana Trench, Challenger Deep. Phylogenetic analysis based on the 16S rRNA gene sequence showed that strain LMO-1T belonged to genus Sphingomonas , with the highest sequence similarity to Sphingomonas formosensis CC-Nfb-2T (96.3 %), followed by Sphingomonas prati W18RDT (96.1 %), Sphingomonas arantia 6PT (96.0 %) and Sphingomonas montana W16RDT (95.9 %). The predominant polar lipids were phosphatidylethanolamine, sphingoglycolipid, phosphatidylglycerol and phosphatidylcholine. The main cellular fatty acids were summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c), C16 : 0 and C14 : 0 2-OH. The major polyamine was sym-homospermidine and the predominant isoprenoid quinone was ubiquinone-10. The genome DNA G+C content of strain LMO-1T was 69.2 mol%. The average nucleotide identity and DNA–DNA hybridization values between strain LMO-1T and CC-Nfb-2T were 75.9 and 20.5 %, respectively. Based on these data, LMO-1T should be classified as representing a novel species of the genus Sphingomonas , for which the name Sphingomonas profundi sp. nov. is proposed. The type strain is LMO-1T (=MCCC 1K04066T=JCM 33666T).

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Li, Chongping, Qiliang Lai, Yuanyuan Fu, Shuangxi Chen, and Zongze Shao. "Galbibacter marinus sp. nov., isolated from deep-sea sediment." International Journal of Systematic and Evolutionary Microbiology 63, Pt_4 (April 1, 2013): 1427–30. http://dx.doi.org/10.1099/ijs.0.044305-0.

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A taxonomic study was carried out on a novel bacterium, designated strain ck-I2-15T, which was isolated from deep-sea sediment collected from the South-west Indian Ocean Ridge. Cells of strain ck-I2-15T were Gram-reaction-negative, rod-shaped, non-motile, moderately halophilic and capable of denitrification. Growth was observed with 0–9 % (w/v) NaCl and at temperatures of 10–37 °C. The novel strain was unable to degrade gelatin. The dominant cellular fatty acids were iso-C15 : 0, iso-C17 : 0 3-OH and summed feature 9 (iso-C17 : 1ω9c and/or 10-methyl C16 : 0). The major respiratory quinone was MK6 and the polar lipid profile comprised phosphatidylethanolamine, one unidentified phospholipid, two unidentified aminolipids, one unidentified glycolipid and four other unidentified lipids. The G+C content of the genomic DNA was 38 mol%. 16S rRNA gene sequence comparison indicated that strain ck-I2-15T was most closely related to Galbibacter mesophilus Mok-17T (92.9 % sequence similarity), followed by ‘Joostella atrarenae’ M1-2 (92.8 %), Joostella marina En5T (92.7 %) and Zhouia amylolytica HN-171T (91.6 %). Phylogenetic analyses based on 16S rRNA gene sequences showed that strain ck-I2-15T formed a clade with the genus Galbibacter , within the family Flavobacteriaceae . Several phenotypic properties allowed strain ck-I2-15T to be distinguished from its closest phylogenetic relatives. On the basis of the phenotypic and phylogenetic data, strain ck-I2-15T represents a novel species of the genus Galbibacter , for which the name Galbibacter marinus is proposed. The type strain is ck-I2-15T ( = CCTCC AB 209062T = LMG 25228T = MCCC 1A03044T).

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Li, Yi, Xiao-Meng Sun, Jian Li, Xiao-Yan Song, Qi-Long Qin, Hai-Nan Su, Xiu-Lan Chen, Yu-Zhong Zhang, Shou-Jin Fan, and Xi-Ying Zhang. "Marinomonas profundi sp. nov., isolated from deep seawater of the Mariana Trench." International Journal of Systematic and Evolutionary Microbiology 70, no. 11 (November 1, 2020): 5747–52. http://dx.doi.org/10.1099/ijsem.0.004472.

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A Gram-stain-negative, aerobic, polarly flagellated, straight or curved rod-shaped bacterium, designated strain M1K-6T, was isolated from deep seawater samples collected from the Mariana Trench. The strain grew at −4 to 37 °C (optimum, 25–30 °C), at pH 5.5–10.0 (optimum, pH 7.0) and with 0.5–14.0 % (w/v) NaCl (optimum, 2.0 %). It did not reduce nitrate to nitrite nor hydrolyse gelatin or starch. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain M1K-6T was affiliated with the genus Marinomonas , sharing 93.1–97.0 % sequence similarity with the type strains of recognized Marinomonas species. The major cellular fatty acids were summed feature 3 (C16 : 1 ω6c/C16 : 1 ω7c), summed feature 8 (C18 : 1 ω7c/C18 : 1 ω6c), C16 : 0, C10 : 0 3-OH and C18 : 0. The predominant respiratory quinone was ubiquinone-8. Polar lipids of strain M1K-6T included phosphatidylethanolamine, phosphatidylglycerol and two unidentified lipids. The genomic G+C content of strain M1K-6T was 46.0 mol%. Based on data from the present polyphasic study, strain M1K-6T was considered to represent a novel species within the genus Marinomonas , for which the name Marinomonas profundi sp. nov. is proposed. The type strain is M1K-6T (=KCTC 72501T=MCCC 1K03890T).

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Lai, Qiliang, Nan Qiao, Changliang Wu, Fengqin Sun, Jun Yuan, and Zongze Shao. "Stappia indica sp. nov., isolated from deep seawater of the Indian Ocean." International Journal of Systematic and Evolutionary Microbiology 60, no. 4 (April 1, 2010): 733–36. http://dx.doi.org/10.1099/ijs.0.013417-0.

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A taxonomic study was carried out on strain B106T, which was isolated from a polycyclic aromatic hydrocarbon-degrading consortium, enriched with deep seawater from the Indian Ocean. The isolate was Gram-negative, oxidase- and catalase-positive, rod-shaped and motile by means of one polar flagellum. Growth was observed at salinities of 0.5–11 % and at temperatures of 4–42 °C, and the strain was capable of nitrate reduction, but was unable to degrade Tween 80 or gelatin. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain B106T belonged to the genus Stappia, with a highest sequence similarity of 97.7 % to Stappia stellulata IAM 12621T; similarity to other strains was below 95.2 %. DNA–DNA hybridization between strain B106T and S. stellulata IAM 12621T was 43 %. The major fatty acids were C16 : 0 (6.10 %), C18 : 1 ω7c (62.58 %), C18 : 0 (5.17 %), C18 : 1 ω7c 11-methyl (14.48 %) and C19 : 0 ω8c cyclo (4.70 %). The G+C content of the chromosomal DNA was 65.9 mol%. The combined genotypic and phenotypic data showed that strain B106T represents a novel species of the genus Stappia, for which the name Stappia indica sp. nov. is proposed, with the type strain B106T (=PR56-8T=CCTCC AB 208228T=LMG 24625T=MCCC 1A01226T).

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