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Yu YB, Li YQ. Enteric glial cells and their role in the intestinal epithelial barrier. World J Gastroenterol 2014; 20:11273-11280. [PMID: 25170211 PMCID: PMC4145765 DOI: 10.3748/wjg.v20.i32.11273] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2014] [Revised: 03/11/2014] [Accepted: 05/14/2014] [Indexed: 02/06/2023] Open
Abstract
The intestinal epithelium constitutes a physical and functional barrier between the external environment and the host organism. It is formed by a continuous monolayer of intestinal epithelial cells maintained together by intercellular junctional complex, limiting access of pathogens, toxins and xenobiotics to host tissues. Once this barrier integrity is disrupted, inflammatory disorders and tissue injury are initiated and perpetuated. Beneath the intestinal epithelial cells lies a population of astrocyte-like cells that are known as enteric glia. The morphological characteristics and expression markers of these enteric glia cells were identical to the astrocytes of the central nervous system. In the past few years, enteric glia have been demonstrated to have a trophic and supporting relationship with intestinal epithelial cells. Enteric glia lesions and/or functional defects can be involved in the barrier dysfunction. Besides, factors secreted by enteric glia are important for the regulation of gut barrier function. Moreover, enteric glia have an important impact on epithelial cell transcriptome and induce a shift in epithelial cell phenotype towards increased cell adhesion and cell differentiation. Enteric glia can also preserve epithelial barrier against intestinal bacteria insult. In this review, we will describe the current body of evidence supporting functional roles of enteric glia on intestinal barrier.
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Yu YB, He GZ, Zhang X. Synthesis of α,α-Difluoromethylene Alkynes by Palladium-Catalyzedgem-Difluoropropargylation of Aryl and Alkenyl Boron Reagents. Angew Chem Int Ed Engl 2014; 53:10457-61. [DOI: 10.1002/anie.201405204] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/28/2014] [Indexed: 01/16/2023]
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Yu YB, He GZ, Zhang X. Synthesis of α,α-Difluoromethylene Alkynes by Palladium-Catalyzedgem-Difluoropropargylation of Aryl and Alkenyl Boron Reagents. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201405204] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Liu Y, Zhang MH, Yu YB, Sun Z, Zhen Z, Gao XJ. Event-Specific Qualitative and Quantitative Detection in Transgenic Soybean OsDREB3 Based on the 5′ Flanking Sequence. FOOD BIOTECHNOL 2014. [DOI: 10.1080/08905436.2013.871289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Yu Y, Wang Z, Zhang X. Pd-catalyzed cross-coupling of polyfluoroarenes with cyclic vinyl triflates. Sci China Chem 2013. [DOI: 10.1007/s11426-013-5024-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Wang C, Yu YB, Fan S, Zhang X. Pd-Catalyzed Direct Arylation of Nitro(pentafluorosulfanyl)benzenes with Aryl Bromides. Org Lett 2013; 15:5004-7. [DOI: 10.1021/ol4023326] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Dong YY, Chen FX, Yu YB, Du C, Qi QQ, Liu H, Li YQ. A school-based study with Rome III criteria on the prevalence of functional gastrointestinal disorders in Chinese college and university students. PLoS One 2013; 8:e54183. [PMID: 23349820 PMCID: PMC3548818 DOI: 10.1371/journal.pone.0054183] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2012] [Accepted: 12/07/2012] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Functional gastrointestinal disorders, including functional dyspepsia, irritable bowel syndrome and functional constipation are very common worldwide. OBJECTIVE This research aims to estimate the prevalence and associated factors involved in functional gastrointestinal disorders in Chinese college and university students using the Rome III criteria. METHODS A total of 5000 students from Shandong University in China were asked in January-May 2012 to complete questionnaires, including the Rome III questionnaire, hospital anxiety and depression scale, and negative life events scale. RESULTS Based on the 4638 students who completed the questionnaire, the prevalence of functional dyspepsia, irritable bowel syndrome and functional constipation in college and university students of North China worked out to be 9.25%, 8.34% and 5.45% respectively. They were more frequent in female students. The factors of anxiety (OR 1.07; 95% CI 0.99 to 1.16, P=0.002<0.05) and depression (OR 0.55; 95% CI 0.15 to 1.05, P=0.045<0.05) indicated a high risk of causing irritable bowel syndrome. CONCLUSION Functional dyspepsia, irritable bowel syndrome and functional constipation were common in college and university students of North China. Psychological disorders such as anxiety and depression provide significant risk factors for irritable bowel syndrome patients.
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Song S, Zhu SF, Yu YB, Zhou QL. Carboxy-Directed Asymmetric Hydrogenation of 1,1-Diarylethenes and 1,1-Dialkylethenes. Angew Chem Int Ed Engl 2012; 52:1556-9. [DOI: 10.1002/anie.201208606] [Citation(s) in RCA: 99] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2012] [Indexed: 11/06/2022]
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Song S, Zhu SF, Yu YB, Zhou QL. Carboxy-Directed Asymmetric Hydrogenation of 1,1-Diarylethenes and 1,1-Dialkylethenes. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201208606] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Yu YB, Fan S, Zhang X. Copper- and Phosphine-Ligand-Free Palladium-Catalyzed Direct Allylation of Electron-Deficient Polyfluoroarenes with Allylic Chlorides. Chemistry 2012; 18:14643-8. [DOI: 10.1002/chem.201202824] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2012] [Revised: 09/15/2012] [Indexed: 11/10/2022]
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Zhu SF, Yu YB, Li S, Wang LX, Zhou QL. Enantioselective Hydrogenation of α-Substituted Acrylic Acids Catalyzed by Iridium Complexes with Chiral Spiro Aminophosphine Ligands. Angew Chem Int Ed Engl 2012. [DOI: 10.1002/ange.201204363] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Zhu SF, Yu YB, Li S, Wang LX, Zhou QL. Enantioselective Hydrogenation of α-Substituted Acrylic Acids Catalyzed by Iridium Complexes with Chiral Spiro Aminophosphine Ligands. Angew Chem Int Ed Engl 2012; 51:8872-5. [DOI: 10.1002/anie.201204363] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2012] [Indexed: 11/11/2022]
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Lee YY, Yu YB, Gunawardena HP, Xie L, Chen X. BCLAF1 is a radiation-induced H2AX-interacting partner involved in γH2AX-mediated regulation of apoptosis and DNA repair. Cell Death Dis 2012; 3:e359. [PMID: 22833098 PMCID: PMC3406578 DOI: 10.1038/cddis.2012.76] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
H2AX, a histone H2A variant, has a key role in the cellular response to DNA double-strand breaks (DSBs). H2AX senses DSBs through rapid serine 139 phosphorylation, concurrently leading to the formation of phospho-(γ)H2AX foci with various proteins. However, in the cells with different sensitivity to ionizing radiation (IR)-induced DSBs, still incomplete are those specific proteins selectively recruited by γH2AX to decide different cell fates. Because the abundance of γH2AX indicates the extent of DSBs, we first identified IR-induced dose-dependent H2AX-interacting partners and found that Bcl-2-associated transcription factor 1 (BCLAF1/Btf) showed enhanced association with γH2AX only under high-dose radiation. In acutely irradiated cells, BCLAF1 promoted apoptosis of irreparable cells through disturbing p21-mediated inhibition of Caspase/cyclin E-dependent, mitochondrial-mediated pathways. Meanwhile, BCLAF1 co-localized with γH2AX foci in nuclei and stabilized the Ku70/DNA-PKcs complex therein, facilitating non-homologous end joining (NHEJ)-based DSB repair in surviving cells. In tumor cells, BCLAF1 was intrinsically suppressed, leading to formation of anti-apoptotic Ku70-Bax complexes and disruption of Ku70/DNA-PKcs complexes, all of which contribute to tumor-associated apoptotic resistance and cell survival with defective NHEJ DNA repair. For the first time, our studies reveal that, based on the extent of DNA damage, BCLAF1 is involved in the γH2AX-mediated regulation of apoptosis and DNA repair, and is a γH2AX-interacting tumor suppressor.
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Yang S, Zhu SF, Zhang CM, Song S, Yu YB, Li S, Zhou QL. Enantioselective iridium-catalyzed hydrogenation of α-arylcinnamic acids and synthesis of (S)-equol. Tetrahedron 2012. [DOI: 10.1016/j.tet.2012.03.118] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Yu YB, Zuo XL, Zhao QJ, Chen FX, Yang J, Dong YY, Wang P, Li YQ. Brain-derived neurotrophic factor contributes to abdominal pain in irritable bowel syndrome. Gut 2012; 61:685-94. [PMID: 21997550 DOI: 10.1136/gutjnl-2011-300265] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
OBJECTIVE Brain-derived neurotrophic factor (BDNF), a member of the neurotrophin family, may play a critical role in many chronic pain conditions. The possible involvement of BDNF in the altered gut sensation in patients with irritable bowel syndrome (IBS) was investigated in the present study. METHODS Rectosigmoid biopsies were collected from 40 patients with IBS fulfilling the Rome II criteria and 21 healthy controls. Abdominal pain was quantified by a validated questionnaire. The presence of BDNF and nerve fibres in the mucosa was assessed by immunohistochemistry. The structure of mucosal nerve fibres was assessed by transmission electron microscopy. Mucosal BDNF release was measured by ELISA and correlated with abdominal pain scores. Animal studies using BDNF(+/-) mice were carried out to evaluate visceral sensitivity, mucosal nerve fibre density and ultrastructural changes. Alterations of visceral sensitivity and TrkB expression in dorsal root ganglia were examined in BDNF(+/+) mice following different doses of BDNF administration. RESULTS Biopsies from patients with IBS revealed a significant upregulation of BDNF (p=0.003), as compared with controls. Total nerve fibres were also substantially increased in patients with IBS. Electron microscopy showed ultrastructural damage on the mucosal nerve fibres (eg, swollen mitochondria and nerve axons). Elevated BDNF release was significantly correlated with the abdominal pain scores. Meanwhile, abdominal withdrawal reflex scores to colorectal distension and mucosal protein gene product 9.5 immunoreactivity were significantly lowered in BDNF(+/-) than in BDNF(+/+) mice. Electron microscopy showed degenerative changes on the mucosal nerve fibres in BDNF(+/-) mice. Exogenous BDNF induced an obvious dose-dependent increase in TrkB expression in dorsal root ganglia and dose-dependent decrease in threshold pressure in BDNF(+/+) mice. CONCLUSIONS The increased expression of BDNF in colonic mucosa, together with the structural alterations of mucosal innervation, may contribute to the visceral hyperalgesia in IBS.
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Yu YB, Wang HJ, Xiao M, Zhu SN. Directly produced three-color entanglement by quasi-phase-matched third-harmonic generation. OPTICS EXPRESS 2011; 19:13949-13956. [PMID: 21934755 DOI: 10.1364/oe.19.013949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
A new scheme is presented to directly produce fundamental, second-, and third-harmonic three-color continuous-variable (CV) entangled beams by cascaded quasi-phase-matched third-harmonic generation (THG) in an optical cavity. THG can be achieved with high efficiency through a coupled sum-frequency process between the second-harmonic and the fundamental fields. It is demonstrated that the three beams (fundamental, second-, and third-harmonic fields) are entangled with each other according to the CV entanglement criterion. In this scheme, only one crystal and one pump field can generate three-color CV entangled beams separated by an octave in frequency through quasi-phase-matched cascaded nonlinear process, which may be very useful for the applications in quantum communication and computation networks.
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Yu YB, Jia XJ, Gao Y, Song GC, Luo J, Wang RS, Pan XM. Theoretical investigation on the reaction mechanism of CF 3OCHF 2 + O( 1D). Mol Phys 2011. [DOI: 10.1080/00268976.2010.524170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Dong YY, Zuo XL, Li CQ, Yu YB, Zhao QJ, Li YQ. Prevalence of irritable bowel syndrome in Chinese college and university students assessed using Rome III criteria. World J Gastroenterol 2010; 16:4221-6. [PMID: 20806442 PMCID: PMC2932929 DOI: 10.3748/wjg.v16.i33.4221] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To estimate the prevalence of irritable bowel syndrome (IBS) in college and university students of North China and certain related factors for IBS.
METHODS: A total of 2500 students from Shandong University in North China were asked in February-March 2009 to complete questionnaires, including the Rome III questionnaire, hospital anxiety and depression scale, and IBS-quality of life questionnaire (IBS-QOL).
RESULTS: Among the 2126 students with complete data, the prevalence of IBS was 7.85% according to the Rome III criteria, with a female/male ratio of 1.78:1. Most students had the IBS-constipation subtype (36.5%), followed by IBS-diarrhea subtype (31.1%) and IBS-mixed subtype (23.9%). The students with IBS had a higher anxiety and depression score than those without IBS. Low exercise level and anxiety indicated a high risk for IBS. The mean score of IBS patients was 74.2 ± 4.242 on the IBS-QOL.
CONCLUSION: The prevalence of IBS is 7.85% in Chinese college and university students according to the Rome III criteria. Low exercise level and anxiety may be the risk factors for IBS.
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Yu YB, Yang J, Zuo XL, Gao LJ, Wang P, Li YQ. Transient receptor potential vanilloid-1 (TRPV1) and ankyrin-1 (TRPA1) participate in visceral hyperalgesia in chronic water avoidance stress rat model. Neurochem Res 2010; 35:797-803. [PMID: 20182791 DOI: 10.1007/s11064-010-0137-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2010] [Indexed: 12/13/2022]
Abstract
Stressfull life events have powerful influences on visceral perception of certain IBS patients. In the present study, we aimed to examine the involvement of TRPV1 and TRPA1 in the stress-induced visceral hyperalgesia. Rats were exposed to 1-h water avoidance stress (WAS) daily for 10 consecutive days. The abdominal withdrawal reflex (AWR) to colorectal distension was assessed at the end of the 10-day period. Western-blotting analysis was applied to investigate the alterations of TRPV1 and TRPA1 in the colonic afferent dorsal root ganglia (DRG). Compared with control rats, the WAS-treated rats demonstrated a significant increase in the AWR with the pressure > or = 40 mm Hg (P < 0.05). Meanwhile, in the WAS-treated rats, western-blotting analysis showed significant upregulation of TRPV1 and TRPA1 in the colonic afferent DRG. The results indicate that WAS could induce the upregulation of TRPV1 and TRPA1 in the colonic afferent DRG, and both receptors may be candidate molecules involved in the stress-induced visceral hyperalgesia in rats.
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Sun YJ, Li N, Zheng ZB, Liu L, Yu YB, Qin ZH, Fu B. Highly Enantioselective FriedelâCrafts Reaction of Indole with Alkylidenemalonates Catalyzed by Heteroarylidene Malonate-Derived Bis(oxazoline) Copper(II) Complexes. Adv Synth Catal 2009. [DOI: 10.1002/adsc.200900669] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Flinders KT, Yu YB, Flynn PF. The effect of a side chain-backbone swap on protein stability. THE JOURNAL OF PEPTIDE RESEARCH 2008; 63:17-22. [PMID: 14984569 DOI: 10.1046/j.1399-3011.2004.00099.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
To assess the relative importance of backbone hydrogen bonding (H-bonding) vs. side chain hydrophobicity in protein structural formation, a method called side chain-backbone swap is proposed. Such a method swaps the side chain and backbone portions of certain amino acid residues, such as Asp, Glu, Asn, Gln, Lys, and Arg. Such a swap retains the sequence of a polypeptide and preserves the identity of the backbone linkage. On the other hand, the swap disrupts backbone H-bonding geometry because of the introduction of extra methylene groups into the peptide backbone. In this project, we chose the two-stranded alpha-helical coiled-coil to implement side chain-backbone swap. A pair of 36-residue peptides was designed. The two peptides have identical sequence with four residues in each heptad repeat occupied by glutamyl residues. Each glutamic acid was incorporated either as alpha-glutamyl residue (the peptide is denoted as alpha-Glu-36) or as gamma-glutamyl residue (the peptide is denoted as gamma-Glu-36). The inter-conversion between the two peptides constitutes a side chain-backbone swap. Residues constituting the hydrophobic core of the coiled-coil, however, are left unchanged. The peptide pair was characterized by circular dichroism spectroscopy, reversed-phase liquid chromatography (RPLC), and two-dimensional nuclear magnetic resonance (NMR). The results indicate that alpha-Glu-36 is a two-stranded alpha-helical coiled-coil while gamma-Glu-36 lacks stable structural elements. It is concluded that, at least for coiled-coils where hydrophobic interactions are predominantly long-range, local backbone H-bonding is a required for structural formation, consistent with a hierarchic folding mechanism. The methodological implication of side chain-backbone swap is also discussed.
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Yu YB, Zang P, Fu YH, Zhang LD, Yan YL, Chen B. [The rapid analysis of fatty acids in vegetable oils by near infrared spectrum]. GUANG PU XUE YU GUANG PU FEN XI = GUANG PU 2008; 28:1554-1558. [PMID: 18844159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
In this research, The functional components of vegetable oils were analyzed by near infrared (NIR) spectral technology. The optimum conditions of mathematics model of four components (C16 : 0, C18 : 0, C18 : 1, C18 : 2) were studied, including the sample set selection, chemical value analysis, the detection methods and condition. Chemical value was analyzed by HPLC. 52 samples were selected, 41 for modeling set and 11 for testing set. All samples were placed in 5mm thick sample pools and swept by near infrared (NIR) with discrimination factor 8 cm(-1) without any other disposal. Using PLS methods sated model. Data were processed by first derivative method and centering method. 5 000-9 000 cm(-1) spectral region was analyzed. Correlating index (r), RMSECV and RMSEP were chose as evaluation index. The result demonstrated that the correlation between the reference value of the modeling sample set and the near infrared predictive value were r(C16 : 0) = 0.891, r(C18 : 0) = 0.837, r(C18 : 1) = 0.982, r(C18 : 2) = 0.971, respectively. And the correlation between the reference value of the testing sample set and the near infrared predictive value were 0.921, 0.891, 0.946 and 0.949, respectively. It proved that the near infrared predictive value was linear with chemical value and the mathematical model established for components of vegetable oils was feasible. For validation, 8 unknown samples were selected to be analysis by infrared (NIR). The result demonstrated that error between predict value and chemical value was less than 10%. That was to say infrared (NIR) had a good veracity in analysis components of vegetable oil. Because infrared (NIR) spectral technology is convenient, rapid than HPLC in oil components analysis, moreover, infrared (NIR) can analyze many components at the same time. It must have great application prospect in vegetable oil components analysis.
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Boukchina R, Choi E, Kim S, Yu YB, Cheung YJ. Strategy for olive mill wastewater treatment and reuse with a sewage plant in an arid region. WATER SCIENCE AND TECHNOLOGY : A JOURNAL OF THE INTERNATIONAL ASSOCIATION ON WATER POLLUTION RESEARCH 2007; 55:71-8. [PMID: 17564372 DOI: 10.2166/wst.2007.308] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
This study was conducted to evaluate the treatability of OMW (olive mill wastewater) with sewage and sewage sludge, which could supplement nutrients and microbes required for OMW treatment and reduce its possible toxicity. The amount of OMW added to an aeration tank was based on the loading difference between the designed and actual COD loads, while the amount added to anaerobic digestion for energy recovery was determined by CH4 production. The COD removal efficiencies were 70-85% for both systems. Compost of OMW with dried sewage sludge also showed a similar temperature profile without OMW addition. This strongly suggested that OMW can be treated at a sewage plant without pretreatment and the treated effluent can be reused in irrigation for an arid region.
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Wang W, Yu YB. Algorithmic Generation of Freely Jointed Hard Sphere Chains and Properties of Inertial Tensors. J Biomol Struct Dyn 2004; 21:805-12. [PMID: 15107002 DOI: 10.1080/07391102.2004.10506970] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A statistical algorithm, capable of generating a large number of freely jointed hard sphere chains, is presented. This is the first of a series of algorithms being developed to model unfolded proteins by different modes of hard sphere chains. The aim of these studies is to systematically investigate the effects of different factors, such as atomic radii, bond angles, torsion angles, chain length, etc., on the conformation of unfolded proteins and other random polymers. As continuous models, various types of hard sphere chains enable one to isolate the aforementioned factors one at a time for investigation and thus are advantageous over discrete lattice models. In particular, the freely jointed hard sphere chain model allows one to evaluate the excluded volume effect. As a first step in this endeavor, the average determinant D(N, r) and the average trace T(N, r) of the inertial tensor A of the random chains were calculated at various sphere radii r and chain lengths N. It is found that both the average determinant D(N, r) and the average trace T(N, r) scale linearly with chain length N after logarithmic transformation. However, the critical exponent of D(N, r) increases with r faster than that of T(N, r) as a result of the non-commutativity between the det operator and the average operator < >. The significance of the algorithm and the results obtained on understanding random polypeptide chains are discussed.
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Abstract
It is pointed out that even though the standard state for solutions is a fictitious state, it nonetheless should be thermodynamically self-consistent. Using a volumetric constraint, it is shown that the biochemical standard state concentration of 1M is too high for macromolecules like proteins and nucleic acids that it violates volumetric self-consistency. Also, at 1 M standard state, the mole fraction of these macromolecular solutes is not the commonly held value of 1/55.5, but rather a meaningless negative number. Thus, the ideal mixing entropy (also called cratic entropy) cannot be meaningfully calculated for macromolecules at such a standard state. The relevance of this conclusion to the interpretation of standard bimolecular binding entropy is discussed.
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