Publications by authors named "Zhanyong Wang"

37 Publications

Comparability of thyroid-stimulating hormone immunoassays using fresh frozen human sera and external quality assessment data.

PLoS One 2021 15;16(6):e0253324. Epub 2021 Jun 15.

Department of Clinical Laboratory, Beijing Chaoyang Hospital, Beijing Center for Clinical Laboratories, The Third Clinical Medical College of Capital Medical University, Beijing, P.R. China.

Background: This study aimed to assess the comparability among assays using freshly frozen human sera and external quality assessment (EQA) data in China.

Methods: Twenty-nine serum samples and two commercial EQA materials, obtained from the National Center for Clinical Laboratories (NCCL), were analyzed in triplicate using eight routine TSH assays. The commutability of commercial EQA materials (NCCL materials) was evaluated in accordance with the CLSI EP30-A and IFCC bias analysis. Median values obtained for the NCCL EQA materials were used to determine the systematic and commutability-related biases among immunoassays through back-calculation. The comparability of TSH measurements from a panel of clinical samples and NCCL EQA data was determined on the basis of Passing-Bablok regression. Furthermore, human serum pools were used to perform commutable EQA.

Results: NCCL EQA materials displayed commutability among three or five of seven assay combinations according CLSI or IFCC approach, respectively. The mean of systematic bias ranged from -13.78% to 9.85% for the eight routine TSH assays. After correcting for systematic bias, averaged commutability-related biases ranged between -42.26% and 12.19%. After correction for systematic and commutability -related biases, the slopes indicating interassay relatedness ranged from 0.801 to 1.299 using individual human sera, from 0.735 to 1.254 using NCCL EQA data, and from 0.729 to 1.115 using pooled human serum EQA(the commutable EQA).

Conclusions: The harmonization of TSH measurement is challenging; hence, systematic and commutability-related biases should be determined and corrected for accurate comparisons among assays when using human individual serum and the commercial EQA materials.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0253324PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8205121PMC
June 2021

Investigation on Crystallization and Magnetic Properties of (Nd, Pr, Ce)FeB/α-Fe Nanocomposite Magnets by Microwave Annealing Treatment.

Materials (Basel) 2021 May 22;14(11). Epub 2021 May 22.

Department Key Laboratory for Advanced Metals and Materials, University of Science and Technology Beijing, Beijing 100083, China.

In the present work, the structures and magnetic properties of (Nd, Pr, Ce) FeB/α-Fe nanocomposite magnets were thoroughly investigated. The microwave annealing was applied to achieve a uniform heating effect and uniform grains. Microwave annealing is more favorable to obtain α-Fe phase than conventional annealing, which leads to the enhanced coercivity of hysteresis loops. The coercivity of nanocomposite magnets was 245 kA/m after annealing at 2000 W for 10 min.
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http://dx.doi.org/10.3390/ma14112739DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8196883PMC
May 2021

Using a distributed air sensor network to investigate the spatiotemporal patterns of PM concentrations.

Environ Pollut 2020 Sep 19;264:114549. Epub 2020 Apr 19.

State Environmental Protection Key Laboratory of the Formation and Prevention of Urban Air Pollution Complex, Shanghai Academy of Environmental Sciences, Shanghai, 200233, China.

Spatiotemporal variations in PM are a key factor affecting personal pollution exposure levels in urban areas. However, fixed-site monitoring stations are so sparsely distributed that they hardly capture the dynamic and fine-scale variations in PM in urban areas with complex geographical features and urban forms. Recently, a distributed air sensor network (DASN) was deployed in Dezhou city, China, to monitor fine-scale air pollution information and obtain deep insight into variations in PM. Based on the data collected by the DASN, this paper investigated the spatiotemporal patterns of PM using the time-series clustering method. The results demonstrated that there were four stages of PM daily variations, i.e., accumulation, continuous pollution, dispersion, and cleaning. Generally, the stage of dispersion occurred more rapidly than the stage of accumulation, and PM accumulated easily in warm and humid weather with low wind speeds. However, the stage of dispersion was affected mainly by high wind speeds and precipitation. Additionally, the results suggested that four variation stages did not strictly correspond to seasonal divisions. The spatial distributions of PM revealed that the main pollution source was located in a southeastern industrial park, which exhibited a significant impact throughout the four stages. Considering both the temporal and spatial characteristics of PM, this study successfully identified pollution hotspots and confirmed the effect of industrial parks. The study demonstrates that the DASN has high prospective applicability for assessing the fine-scale spatial distribution of PM, and the time-series clustering method can also assist environmental researchers in further exploring the spatiotemporal characteristics of urban air pollution.
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http://dx.doi.org/10.1016/j.envpol.2020.114549DOI Listing
September 2020

Preparation of porous materials by selective enzymatic degradation: effect of in vitro degradation and in vivo compatibility.

Sci Rep 2020 04 27;10(1):7031. Epub 2020 Apr 27.

College of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Fushun, 113001, China.

Poly(butylene succinate) (PBS) and poly(lactic acid) (PLA) were melt-blended and formed into a film by hot press forming. The film was selectively degraded by cutinase and proteinase K to form a porous material. The porous materials were characterized with respect to their pore morphology, pore size, porosity and hydrophilicity. The porous materials were investigated in vitro degradation and in vivo compatibility. The results show that the pore size of the prepared porous materials could be controlled by the proportion of PBS and the degradation time. When the PBS composition of PBS/PLA blends was changed from 40 wt% to 50 wt%, the mean pore diameter of the porous materials significantly increased from 6.91 µm to 120 µm, the porosity improved from 81.52% to 96.90%, and the contact angle decreased from 81.08° to 46.56°. In vitro degradation suggests that the PBS-based porous materials have a good corrosion resistance but the PLA-based porous materials have degradability in simulated body fluid. Subcutaneous implantation of the porous materials did not cause intense inflammatory response, which revealed good compatibility. The results of hematoxylin and eosin and Masson's trichrome staining assays demonstrated that the porous materials promote chondrocyte production. Porous materials have great potential in preparing implants for tissue engineering applications.
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http://dx.doi.org/10.1038/s41598-020-63892-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7184588PMC
April 2020

Enzymatic hydrolysis of polyester: Degradation of poly(ε-caprolactone) by Candida antarctica lipase and Fusarium solani cutinase.

Int J Biol Macromol 2020 Feb 13;144:183-189. Epub 2019 Dec 13.

College of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Fushun 113001, China. Electronic address:

Poly(ε-caprolactone) (PCL) particles were melt-pressed into films using a hot press and then subjected to degradation by lipase from Candida antarctica and cutinase from Fusarium solani, respectively. The differences in weight loss, degradation modes, thermal stability, and crystallization were investigated after degradation by two kinds of enzymes. The result showed that mass loss of PCL films degraded by lipase was higher than that degraded by cutinase at the same enzyme concentrations. The degradation mode of PCL films is layered for cutinase degradation and penetrated for lipase degradation. Crystallinity of PCL had no obvious decrease after degradation by cutinase, but it markedly decreased after lipase-degradation. PCL films occurred one-step decomposition during heating and the cutinase-degraded products had similar thermal stability. Whereas the thermal stability of lipase-degraded PCL decreased significantly and the weight loss of the PCL occurred in several steps with increasing lipase hydrolysis time.
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http://dx.doi.org/10.1016/j.ijbiomac.2019.12.105DOI Listing
February 2020

Multi-Responsive Behaviors of Copolymers Bearing N-Isopropylacrylamide with or without Phenylboronic Acid in Aqueous Solution.

Polymers (Basel) 2018 Mar 9;10(3). Epub 2018 Mar 9.

School of Environmental and Biological Engineering, Liaoning Shihua University, Fushun 113001, China.

Continuing efforts to develop novel smart materials are anticipated to upgrade the quality of life of humans. Thermo-responsive poly(-isopropylacrylamide) and glucose-responsive phenylboronic acid-typical representatives-are often integrated as multi-stimuli-sensitive materials, but few are available for side-by-side comparisons with their properties. In this study, both copolymers bearing -isopropylacrylamide (NIPAAm), with or without 3-acrylamidophenylboronic acid (AAPBA), were synthesized by free radical polymerization, and characterized by Fourier transform infrared spectrometry, nuclear magnetic resonance hydrogen spectroscopy and gel permeation chromatography. Dynamic light scattering was used to analyze and compare the responsive behaviors of the copolymers in different aqueous solutions. Atomic force microscopy was also employed to investigate the apparent morphology changes with particle sizes. The results demonstrated that the introduction of NIPAAm endowed the composite materials with thermosensitivity, whereas the addition of AAPBA lowered the molecular weight of the copolymers, intensified the intermolecular aggregation of the nanoparticles, reduced the lower critical solution temperature (LCST) of the composites, and accordingly allowed the copolymers to respond to glucose. It was also concluded that the responding of smart copolymers to operating parameters can be activated only under special conditions, and copolymer dimension and conformation were affected by inter/intramolecular interactions.
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http://dx.doi.org/10.3390/polym10030293DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6415023PMC
March 2018

Selective enzymatic degradation and porous morphology of poly(butylene succinate)/poly(lactic acid) blends.

Int J Biol Macromol 2019 Apr 23;126:436-442. Epub 2018 Dec 23.

College of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Fushun 113001, China; Department of Microbiology, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY 14853, USA. Electronic address:

Poly(butylene succinate) (PBS) and poly(lactic acid) (PLA) were melt-blended in different proportions and selectively degraded by cutinase and proteinase K, respectively. The selective enzymatic degradation process was systematically investigated. The degraded PBS/PLA blends were analyzed via scanning electron microscopy, Fourier-transform infrared spectroscopy, powder X-ray diffraction, and differential scanning calorimetry. The results of the weight loss of PBS/PLA blends degraded by cutinase and proteinase K suggested that PLA hindered the cutinase-catalyzed degradation of PBS, whereas the addition of PBS in the blends accelerated the degradation of PLA within a specific PBS/PLA ratio. The change in crystallinity after degradation was closely related to the different way of degradation. The characterization of PBS/PLA blends after degradation showed that selective enzymatic degradation could not completely degrade PBS or PLA component. After degradation, the pores formed by proteinase K were more uniform and larger than those formed by cutinase. This work provides a new insight into the selective enzymatic degradation processes of the porous materials, which will be used in tissue engineering or oil-water separation in the future.
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http://dx.doi.org/10.1016/j.ijbiomac.2018.12.168DOI Listing
April 2019

Preparation, characterization, and biodegradation of poly(butylene succinate)/cellulose triacetate blends.

Int J Biol Macromol 2018 Jul 27;114:373-380. Epub 2018 Mar 27.

College of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Fushun 113001, China. Electronic address:

Poly(butylene succinate) (PBS) and cellulose triacetate (CT) were blended using chloroform as solvent. The solid-state properties of PBS/CT blends were confirmed by Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), X-ray diffraction (XRD), thermogravimetric analysis, scanning electron microscopy (SEM), and water contact angle measurements. FTIR results show that PBS and CT were physically blended. Tensile strength was not distinguished when the weight percent of CT was <15%, and Young's modulus increased gradually with increasing CT. DSC and XRD results show that the crystals were homogeneous, and crystallinity had no apparent decrease when <10% CT was added to the PBS matrix. However, the addition of more CT components could destroy the crystal behavior of PBS. SEM showed that no phase separation occurred between the two materials. The addition of CT increased the hydrophilicity of PBS/CT1-15 blends. The weight loss was nearly 90% after 16h of degradation for PBS/CT10. The appropriate proportion of PBS to CT was 90:10.
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http://dx.doi.org/10.1016/j.ijbiomac.2018.03.151DOI Listing
July 2018

Extraction and characterization of collagen hydrolysates from the skin of .

3 Biotech 2018 Mar 14;8(3):181. Epub 2018 Mar 14.

College of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Fushun, 113001 China.

The production of Hasma generates plentiful non-edible by-products in China and Central Asia. As one of main by-products, the skin of is discarded as waste without utilization. In this work, skin collagen (RCSC) hydrolysates were extracted using pepsin under acidic conditions. The yield of RCSC is 15.1% (w/w). Amino acid analysis revealed that RCSC contained glycine (204.5/1000 residues) and imino acids (182/1000 residues). RCSC exhibited high solubility in acidic pH (1-4) and low NaCl concentrations (< 2%, w/v). Differential scanning calorimetry indicated that the denaturation temperature of RCSC was 33.5 °C. Scanning electron microscopy analysis confirmed their well-defined fibril morphologies. The results indicated that the skin of is an alternative source of collagen hydrolysates, and RCSC can serve as a potential source applying in foodstuff and medical industry.
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http://dx.doi.org/10.1007/s13205-018-1198-yDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5851943PMC
March 2018

Enzymatic degradation of poly(butylene succinate) with different molecular weights by cutinase.

Int J Biol Macromol 2018 May 31;111:1040-1046. Epub 2018 Jan 31.

College of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Fushun 113001, China. Electronic address:

Poly(butylene succinate) (PBS) films with different molecular weights were enzymatically degraded by cutinase. Changes in the properties of the films before and after enzymatic degradation were studied through scanning electron microscopy, differential scanning calorimetry, thermogravimetry, X-ray powder diffraction, proton nuclear magnetic resonance, and gel-permeation chromatography analysis. The weight loss of the films initially decreased and then increased with increasing molecular weight. Crystallinity was inversely proportional to weight loss and tended to decrease with prolonged degradation time. Crystalline and amorphous regions were simultaneously degraded. The thermal stability of PBS films decreased after enzymatic degradation. PBS was the main component of the enzymatically degraded polymers. The molecular weights of the films did not considerably change before and after degradation by cutinase.
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http://dx.doi.org/10.1016/j.ijbiomac.2018.01.107DOI Listing
May 2018

Effect of Hydroxyl Monomers on the Enzymatic Degradation of Poly(ethylene succinate), Poly(butylene succinate), and Poly(hexylene succinate).

Polymers (Basel) 2018 Jan 18;10(1). Epub 2018 Jan 18.

College of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Fushun 113001, China.

Poly(ethylene succinate) (PES), poly(butylene succinate) (PBS), and poly(hexylene succinate) (PHS), were synthesized using succinic acid and different dihydric alcohols as materials. Enzymatic degradability by cutinase of the three kinds of polyesters was studied, as well as their solid-state properties. The biodegradation behavior relied heavily on the distance between ester groups, crystallinity, and the hydrophilicity-hydrophobicity balance of polyester surfaces. The weight loss through degradation of the three kinds of polyesters with different hydroxyl monomers took place in the order PHS > PBS > PES. The degradation behavior of the polyesters before and after degradation was analyzed by scanning electron microscopy, differential scanning calorimetry, powder X-ray diffraction, Fourier transform infrared spectroscopy, gel permeation chromatography, and thermogravimetric analysis. The decrease in relative intensity at 1800⁻1650 estedpolyesters were degraded simultaneously. The frequencies of the crystalline and amorphous bands were almost identical before and after degradation. Thus, enzymatic degradation did not change the crystalline structure but destroyed it, and the degree of crystallinity markedly decreased. The molecular weight and polydispersity index only changed slightly. The thermal stability of the three kinds of polyesters decreased during enzymatic degradation.
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http://dx.doi.org/10.3390/polym10010090DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6414858PMC
January 2018

Performance assessment of a portable nephelometer for outdoor particle mass measurement.

Environ Sci Process Impacts 2018 Feb;20(2):370-383

School of Engineering, Sun Yat-sen University, Guangdong Provincial Key Laboratory of Intelligent Transportation System, Guangzhou 510006, China.

The availability of portable nephelometers has improved assessment of exposure to atmospheric particles at a high resolution regarding space and time. However, nephelometer performance has seldom been evaluated for outdoor measurements, especially in Chinese cities. During 37 days of measurements at four outdoor sites in Shanghai, we assessed a popular nephelometer called SidePak (TSI Inc., USA) for PM, PM and PM mass measurements and compared them to US federal reference methods (FRMs) based on different measurement principles. The nephelometer showed high measurement precision and stability and was strongly correlated with FRMs, making it superior to the portable light scattering monitors reported in the past and thus indicating the maturity of this principle. The nephelometer measurements overestimated all those of FRMs by a factor of two, which is higher than in evaluations in other international cities. This overestimation showed a descending order for PM (2.9-fold), PM (2.2-fold) and PM (1.9-fold) relative to the FRMs of tapered element oscillating microbalance or beta attenuation combined with nephelometry, based on whole samples. Sites that are far from direct pollution sources showed very good agreement between the nephelometer and FRMs for PM mass measurements, while, by comparison, the roadside site showed a lower SidePak/FRM PM ratio, which is likely due to higher abundance of elemental carbon in roadside particles. Relative humidity (RH) was shown to be a key factor that distorted the measurement of the nephelometer. An empirical formula incorporating an RH adjustment developed to correct the nephelometer could produce a reasonable result, even across the various sites. This study demonstrates the great potential of the nephelometer for outdoor particle mass measurements, but for accurate and comparable data, a site-specific calibration is strongly recommended before using.
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http://dx.doi.org/10.1039/c7em00336fDOI Listing
February 2018

Biodegradation of P(3HB--4HB) powder by for preparation low-molecular-mass P(3HB--4HB).

3 Biotech 2017 Oct 16;7(5):281. Epub 2017 Aug 16.

College of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Fushun, 113001 Liaoning China.

Poly(3-hydroxybutyrate--4-hydroxybutyrate) (P(3HB--4HB)) is a biodegradable plastic that is extensively utilized in many fields. In this work, P(3HB--4HB) powder was degraded by for the preparation of low-molecular-mass (LMW) P(3HB--4HB). After degradation, the remaining P(3HB--4HB) powder was analyzed via gel permeation chromatography (GPC), differential scanning calorimetry (DSC), X-ray powder diffraction (XRD), Fourier transform infrared (FTIR) spectroscopy, and proton nuclear magnetic resonance (H NMR) spectroscopy. The degradation of P(3HB--4HB) by occurred in two stages: the fast degradation stage (0-8 h) and the slow degradation stage (8-24 h). GPC analysis showed that the molecular weight of P(3HB--4HB) gradually decreased with degradation time. After 24 h of degradation, the weight-average molecular weight of P(3HB--4HB) was reduced to 4-5 kDa. DSC and XRD analyses both verified that the degree of crystallinity decreased with prolonged degradation time. The melting temperature of the degraded powder, however, remained unchanged. FTIR and H NMR analyses of the degraded powder showed that no new material was produced during degradation. Thus, the degradation of P(3HB--4HB) by could be used to produce LMW P(3HB--4HB) for use in various applications, such as the synthesis of amphiphilic block copolymers.
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http://dx.doi.org/10.1007/s13205-017-0824-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5559386PMC
October 2017

IPED2: Inheritance Path Based Pedigree Reconstruction Algorithm for Complicated Pedigrees.

IEEE/ACM Trans Comput Biol Bioinform 2017 Sep-Oct;14(5):1094-1103. Epub 2017 Mar 28.

Reconstruction of family trees, or pedigree reconstruction, for a group of individuals is a fundamental problem in genetics. The problem is known to be NP-hard even for datasets known to only contain siblings. Some recent methods have been developed to accurately and efficiently reconstruct pedigrees. These methods, however, still consider relatively simple pedigrees, for example, they are not able to handle half-sibling situations where a pair of individuals only share one parent. In this work, we propose an efficient method, IPED2, based on our previous work, which specifically targets reconstruction of complicated pedigrees that include half-siblings. We note that the presence of half-siblings makes the reconstruction problem significantly more challenging which is why previous methods exclude the possibility of half-siblings. We proposed a novel model as well as an efficient graph algorithm and experiments show that our algorithm achieves relatively accurate reconstruction. To our knowledge, this is the first method that is able to handle pedigree reconstruction from genotype data when half-sibling exists in any generation of the pedigree.
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http://dx.doi.org/10.1109/TCBB.2017.2688439DOI Listing
May 2018

Optimization Extraction Process of Polysaccharides from Suillus granulatus and Their Antioxidant and Immunological Activities In vitro.

Pharmacogn Mag 2016 May 11;12(Suppl 2):S277-84. Epub 2016 May 11.

Department of Biotechnology, College of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Fushun, P.R. China.

Background: Suillus granulatus is an edible and medicinal fungus in China. S. granulatus polysaccharide (SGP) was considered as the main bioactivity compounds in S. granulatus. Therefore, the extraction of SGP and their antioxidant activities were studied in this work.

Materials And Methods: Fruiting bodies of S. granulatus were purchased from a local market (Fushun, China). Response surface methodology was adopted to optimize the extraction conditions of SGP. The antioxidant and immunological activities in vitro were also assayed.

Results: The extraction of SGP was optimized by a Box-Behnken design. The optimal conditions for the extraction of polysaccharides were as follows: Pre-extraction time, 2 h; extraction temperature, 94°C; ratio of water to raw material, 25; and extraction frequency, 2. Under these conditions, the experimental yield of polysaccharides was 5.38% ±0.15%, which agreed with the predicted yield. The antioxidant assay in vitro showed that SGPs had relatively high scavenging ability for hydroxyl radicals and higher scavenging ability for 1,1-diphenyl-2-picrylhydrazyl radical. However, the scavenging ability of SGPs for superoxide anion radical and reducing power was relatively low. The polysaccharides also significantly increased splenocyte proliferation in vitro.

Conclusion: SGP possessed good antioxidant and immunological activities in vitro and explored as a novel natural antioxidant or functional food.

Summary: The predictive model of Suillus granulatus polysaccharide (SGP) extraction is adequate for the extraction processSGP possessed a good antioxidant activity in vitroLymphocyte proliferation in vitro was significantly increased by SGPPictorial abstract (in MS Powerpoint Format) is submitted as a separated file in the online submission system. Abbreviation used: SGP: Suillus granulatus polysaccharides, RSM: Response surface methodology, BBD: Box-Behnken design, Vc: Ascorbic acid, DPPH: 1,1-diphenyl-2-picrylhydrazyl, MTT: 3-(4,5- dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide, ConA: Concanavalin A, LPS: lipopolysaccharide, RPMI-1640: Roswell Park Memorial Institute-1640.
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http://dx.doi.org/10.4103/0973-1296.182161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4883092PMC
May 2016

Preparation of Fe-doped colloidal SiO(2) abrasives and their chemical mechanical polishing behavior on sapphire substrates.

Appl Opt 2015 Aug;54(24):7188-94

Abrasives are one of key influencing factors on surface quality during chemical mechanical polishing (CMP). Silica sol, a widely used abrasive in CMP slurries for sapphire substrates, often causes lower material removal rate (MRRs). In the present paper, Fe-doped colloidal SiO2 composite abrasives were prepared by a seed-induced growth method in order to improve the MRR of sapphire substrates. The CMP performance of Fe-doped colloidal SiO2 abrasives on sapphire substrates was investigated using UNIPOL-1502 CMP equipment. Experimental results indicate that the Fe-doped colloidal SiO2 composite abrasives exhibit lower surface roughness and higher MRR than pure colloidal SiO2 abrasives for sapphire substrates under the same testing conditions. Furthermore, the acting mechanism of Fe-doped colloidal SiO2 composite abrasives in sapphire CMP was analyzed by x-ray photoelectron spectroscopy. Analytical results show that the Fe in the composite abrasives can react with the sapphire substrates to form aluminum ferrite (AlFeO3) during CMP, which promotes the chemical effect in CMP and leads to improvement of MRR.
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http://dx.doi.org/10.1364/AO.54.007188DOI Listing
August 2015

Characterization and antioxidant activity in vitro and in vivo of polysaccharide purified from Rana chensinensis skin.

Carbohydr Polym 2015 Aug 21;126:17-22. Epub 2015 Mar 21.

College of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Fushun 113001, China.

Preliminary characterization and antioxidant activity in vitro and in vivo investigation of the polysaccharide fraction named as RCSP II, which was extracted from Rana chensinensis skin, were performed. Results indicated that RCSP II comprised glucose, galactose, and mannose in a molar ratio of 87.82:2.77:1.54 with a molecular weight of 12.8 kDa. Antioxidant activity assay in vitro showed that RCSP II exhibited 75.2% scavenging activity against 2,2'-azino-bis(3-ethylbenz-thiazoline-6-sulfonic acid) radicals at the concentration of 2500 mg/L and 85.1% against chelated ferrous ion at 4000 mg/L. Antioxidant activity assay in vivo further showed that RCSP II increased the activities of antioxidant enzymes, decreased the levels of malondialodehyde, and enhanced total antioxidant capabilities in livers and sera of d-galactose induced mice. These results suggested that RCSP II could have potential antioxidant applications as medicine or functional food.
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http://dx.doi.org/10.1016/j.carbpol.2015.03.031DOI Listing
August 2015

Gene-Gene Interactions Detection Using a Two-stage Model.

J Comput Biol 2015 Jun 14;22(6):563-76. Epub 2015 Apr 14.

1Computer Science Department, University of California Los Angeles, Los Angeles, California.

Genome-wide association studies (GWAS) have discovered numerous loci involved in genetic traits. Virtually all studies have reported associations between individual single nucleotide polymorphisms (SNPs) and traits. However, it is likely that complex traits are influenced by interaction of multiple SNPs. One approach to detect interactions of SNPs is the brute force approach which performs a pairwise association test between a trait and each pair of SNPs. The brute force approach is often computationally infeasible because of the large number of SNPs collected in current GWAS studies. We propose a two-stage model, Threshold-based Efficient Pairwise Association Approach (TEPAA), to reduce the number of tests needed while maintaining almost identical power to the brute force approach. In the first stage, our method performs the single marker test on all SNPs and selects a subset of SNPs that achieve a certain significance threshold. In the second stage, we perform a pairwise association test between traits and pairs of the SNPs selected from the first stage. The key insight of our approach is that we derive the joint distribution between the association statistics of a single SNP and the association statistics of pairs of SNPs. This joint distribution allows us to provide guarantees that the statistical power of our approach will closely approximate the brute force approach. We applied our approach to the Northern Finland Birth Cohort data and achieved 63 times speedup while maintaining 99% of the power of the brute force approach.
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http://dx.doi.org/10.1089/cmb.2014.0163DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4449719PMC
June 2015

Data-driven encoding for quantitative genetic trait prediction.

BMC Bioinformatics 2015 18;16 Suppl 1:S10. Epub 2015 Feb 18.

Motivation: Given a set of biallelic molecular markers, such as SNPs, with genotype values on a collection of plant, animal or human samples, the goal of quantitative genetic trait prediction is to predict the quantitative trait values by simultaneously modeling all marker effects. Quantitative genetic trait prediction is usually represented as linear regression models which require quantitative encodings for the genotypes: the three distinct genotype values, corresponding to one heterozygous and two homozygous alleles, are usually coded as integers, and manipulated algebraically in the model. Further, epistasis between multiple markers is modeled as multiplication between the markers: it is unclear that the regression model continues to be effective under this. In this work we investigate the effects of encodings to the quantitative genetic trait prediction problem.

Results: We first showed that different encodings lead to different prediction accuracies, in many test cases. We then proposed a data-driven encoding strategy, where we encode the genotypes according to their distribution in the phenotypes and we allow each marker to have different encodings. We show in our experiments that this encoding strategy is able to improve the performance of the genetic trait prediction method and it is more helpful for the oligogenic traits, whose values rely on a relatively small set of markers. To the best of our knowledge, this is the first paper that discusses the effects of encodings to the genetic trait prediction problem.
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http://dx.doi.org/10.1186/1471-2105-16-S1-S10DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4571493PMC
May 2015

Extraction and antioxidant activity of polysaccharides from Rana chensinensis skin.

Carbohydr Polym 2015 Jan 2;115:25-31. Epub 2014 Sep 2.

College of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Fushun 113001, China.

The extraction process of polysaccharides from Rana chensinensis skin was optimized by using a Box-Behnken design. The optimum extraction conditions were as follows: extraction time, 4.96h; extraction temperature, 100°C; ratio of water to raw material, 60; and extraction frequency, 1. Under these conditions, the experimental polysaccharide yield was 2.03±0.14%, which agreed with the predicted yield. The purified polysaccharide RCSP II was successfully obtained by diethylaminoethanol-Sepharose and Sepharose CL-6B column chromatography. In vitro experiments showed that RCSP II exhibited a strong scavenging activity against superoxide anion and 1,1-diphenyl-2-picrylhydrazyl radicals but a weak scavenging activity against hydroxyl radicals. RCSP II also showed a strong reducing capacity. Thus, this polysaccharide can be used as a natural antioxidant in functional foods or medicines.
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http://dx.doi.org/10.1016/j.carbpol.2014.08.082DOI Listing
January 2015

Antioxidant and immunological activities of polysaccharides from Gentiana scabra Bunge roots.

Carbohydr Polym 2014 Nov 4;112:114-8. Epub 2014 Jun 4.

College of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Fushun 113001, PR China.

Two polysaccharide fractions, GSP I-a and GSP II-b, were isolated from Gentiana scabra Bunge roots. Both GSP I-a and GSP II-b comprised seven monosaccharides: fructose, mannose, rhamnose, galacturonic acid, glucose, galactose, and fucose. Ultraviolet and infrared analyses show that GSP I-a and GSP II-b are proteoglycans. In vitro evaluation of the antioxidant activity suggests that GSP I-a and GSP II-b scavenge 1,1-diphenyl-2-picrylhydrazyl radicals. However, the scavenging activity of the latter is stronger than that of the former. GSP I-a and GSP II-b have relatively low reducing powers and scavenging activities toward superoxide anions and hydroxyls. GSP I-a and GSP II-b significantly increase lymphocyte proliferation when lipopolysaccharide is used as a mitogen for lymphocytes, but only GSP I-a can significantly increase lymphocyte proliferation within the test-dosage range when concanavalin A is used as a mitogen.
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http://dx.doi.org/10.1016/j.carbpol.2014.05.077DOI Listing
November 2014

Optimization of medium composition for 3-hydroxycarboxylic acid production by Pseudomonas mendocina-biodegraded polyhydroxybutyrate.

Biotechnol Appl Biochem 2015 Mar-Apr;62(2):260-7. Epub 2014 Nov 11.

College of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Fushun, People's Republic of China.

We optimized the culture medium for 3-hydroxycarboxylic acid production by Pseudomonas mendocina DS-04-T-biodegraded polyhydroxybutyrate (PHB) using the Plackett-Burman design, steepest ascent method, and Box-Behnken design. The optimized concentrations of the constituents of the culture medium were as follows: PHB (7.57 g/L), NH4 Cl (5.0 g/L), KH2 PO4 (2.64 g/L), Na2 HPO4 ·12H2 O (12 g/L), MgSO4 ·7H2 O (0.5 g/L), and CaCl2 ·2H2 O (5 mg/L). The yield of 3-hydroxycarboxylic acid obtained using the optimized culture medium was 56.8 ± 1.64%, which was 2.5-fold higher than that obtained when the unoptimized culture medium was used.
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http://dx.doi.org/10.1002/bab.1257DOI Listing
January 2016

G protein-coupled receptor 56 regulates matrix production and motility of lung fibroblasts.

Exp Biol Med (Maywood) 2014 Jun;239(6):686-96

Idiopathic pulmonary fibrosis is a chronic, progressive, and fatal fibrotic lung disease with a poor prognosis, but no effective treatment is available. G protein-coupled receptor 56 (GPR56) plays a role in cell adhesion and tumor progression, but its function in fibrogenesis has not been explored. In this in vitro study, we found that GPR56 in IPF fibroblasts was lower than in normal fibroblasts. GPR56 regulated the production of fibronectin and type I collagen, and also changed the migratory and invasive capacity of lung fibroblasts. However, it was not sufficient to activate some classic markers of fibroblast and myofibroblast, such as α-smooth muscle actin and fibroblast specific protein 1. These findings demonstrate that reduced expression of GPR56 in lung fibroblasts may be an important link with pulmonary fibrosis, playing a role in regulating some important fibroblast functions.
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http://dx.doi.org/10.1177/1535370214529395DOI Listing
June 2014

Optimization of medium composition for exopolysaccharide production by Phellinus nigricans.

Carbohydr Polym 2014 May 5;105:200-6. Epub 2014 Feb 5.

College of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Fushun 113001, China.

Using Plackett-Burman design, steepest ascent method, and Box-Behnken design, we carried out sequential statistical optimization of the Phellinus nigricans culture medium for maximizing the production of exopolysaccharides. The concentrations of the constituents of culture medium as optimized by this method were: 51.67g/L glucose, 6.96g/L peptone, 1.0g/L yeast extract, 5mg/L thiamine, 1.0g/L KH2PO4, and 0.5g/L MgSO4. The yield of exopolysaccharides obtained using the optimized culture medium was 1.89±0.13g/L-2.3-fold higher than that obtained when unoptimized culture medium was used. The exopolysaccharide of P. nigricans (PNEP) is comprised by glucose and mannose with the molar ratio 1:2.63. PNEP thus produced scavenged superoxide anion radical, 1,1-diphenyl-2-picrylhydrazyl radical, and hydroxyl radical; showed antioxidant properties; and had reducing power.
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http://dx.doi.org/10.1016/j.carbpol.2014.01.099DOI Listing
May 2014

Antioxidant and immunological activity in vitro of polysaccharides from Phellinus nigricans mycelia.

Int J Biol Macromol 2014 Mar 7;64:139-43. Epub 2013 Dec 7.

College of Chemistry, Chemical Engineering and Environmental Engineering, Liaoning Shihua University, Fushun 113001, PR China.

Three polysaccharide fractions, namely, PNMP 1, PNMP2, and PNMP3, were isolated from Phellinus nigricans mycelia. The average molecular weights of PNMP1, PNMP2, and PNMP3 were approximately 28.4, 31.5, and 26.1 kDa, respectively. PNMP2 and PNMP3 comprised six monosaccharides: arabinose, fucose, glucose, galactose, mannose, and xylose. PNMP1 comprised only four monosaccharides: glucose, galactose, mannose, and xylose. In vitro antioxidant tests showed that PNMP2 and PNMP3 significantly scavenged superoxide radical, hydroxyl radical, and 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical. PNMP1 effectively inhibited DPPH radical. Lymphocyte proliferation was significantly increased by PNMP1, PNMP2, and PNMP3, particularly by PNMP2 and PNMP3 in the presence of concanavalin A or lipopolysaccharide as mitogens for lymphocytes.
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http://dx.doi.org/10.1016/j.ijbiomac.2013.11.038DOI Listing
March 2014

Extraction of polysaccharides from Phellinus nigricans mycelia and their antioxidant activities in vitro.

Carbohydr Polym 2014 Jan 28;99:110-5. Epub 2013 Aug 28.

School of Environmental and Biological Engineering, Liaoning Shihua University, Fushun 113001, China. Electronic address:

In this study, response surface methodology was employed to optimize the extraction of polysaccharides from Phellinus nigricans mycelia. A central composite design was adopted to determine optimum parameters (extraction time, extraction temperature, extraction frequency, and ratio of water to raw material) that could yield a maximum polysaccharide. Results revealed the following optimum extraction conditions: extraction time, 2.8h; ratio of water to raw material, 28; extraction frequency, 5; and extraction temperature, 95 °C. Under optimized conditions, the experimental yield of P. nigricans mycelia polysaccharides was 15.33 ± 0.21%, which is consistent with the predicted yield. The antioxidant activity assay in vitro showed that the polysaccharides exhibited a high scavenging activity against superoxide anion, hydroxyl, and 1,1-diphenyl-2-picrylhydrazyl radicals. These polysaccharides also exhibited a strong reducing power. Thus, these polysaccharides can be used as natural antioxidants in functional foods or medicine.
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http://dx.doi.org/10.1016/j.carbpol.2013.08.073DOI Listing
January 2014

IPED: inheritance path-based pedigree reconstruction algorithm using genotype data.

J Comput Biol 2013 Oct;20(10):780-91

1 IBM T.J. Watson Research , Yorktown Heights, New York.

The problem of inference of family trees, or pedigree reconstruction, for a group of individuals is a fundamental problem in genetics. Various methods have been proposed to automate the process of pedigree reconstruction given the genotypes or haplotypes of a set of individuals. Current methods, unfortunately, are very time-consuming and inaccurate for complicated pedigrees, such as pedigrees with inbreeding. In this work, we propose an efficient algorithm that is able to reconstruct large pedigrees with reasonable accuracy. Our algorithm reconstructs the pedigrees generation by generation, backward in time from the extant generation. We predict the relationships between individuals in the same generation using an inheritance path-based approach implemented with an efficient dynamic programming algorithm. Experiments show that our algorithm runs in linear time with respect to the number of reconstructed generations, and therefore, it can reconstruct pedigrees that have a large number of generations. Indeed it is the first practical method for reconstruction of large pedigrees from genotype data.
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http://dx.doi.org/10.1089/cmb.2013.0080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3791035PMC
October 2013

Purification and characterization of two extracellular polyhydroxyalkanoate depolymerases from Pseudomonas mendocina.

Biotechnol Lett 2013 Nov 24;35(11):1919-24. Epub 2013 Jul 24.

School of Environmental and Biological Engineering, Liaoning Shihua University, Fushun, 113001, China.

Two polyhydroxyalkanoate depolymerases, PHAase I and PHAase II, were purified to homogeneity from the culture supernatant of an effective PHA-degrading bacterium, Pseudomonas mendocina DS04-T. The molecular masses of PHAase I and PHAase II were determined by SDS-PAGE as 59.4 and 33.8 kDa, respectively. Their optimum pH values were 8.5 and 8, respectively. Enzymatic activity was optimal at 50 °C. Both purified enzymes could degrade PHB, PHBV, and P(3HB-co-4HB). Addition of Na(+) and K(+) slightly increased the rate of PHAase II. EDTA significantly inhibited PHAase II but not PHAase I. Mercaptoethanol and H2O2 also inhibited the activities of both enzymes.
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http://dx.doi.org/10.1007/s10529-013-1288-1DOI Listing
November 2013

Leveraging reads that span multiple single nucleotide polymorphisms for haplotype inference from sequencing data.

Bioinformatics 2013 Sep 3;29(18):2245-52. Epub 2013 Jul 3.

Department of Computer Science and Inter-Departmental Program in Bioinformatics, University of California, Los Angeles, CA 90095, USA.

Motivation: Haplotypes, defined as the sequence of alleles on one chromosome, are crucial for many genetic analyses. As experimental determination of haplotypes is extremely expensive, haplotypes are traditionally inferred using computational approaches from genotype data, i.e. the mixture of the genetic information from both haplotypes. Best performing approaches for haplotype inference rely on Hidden Markov Models, with the underlying assumption that the haplotypes of a given individual can be represented as a mosaic of segments from other haplotypes in the same population. Such algorithms use this model to predict the most likely haplotypes that explain the observed genotype data conditional on reference panel of haplotypes. With rapid advances in short read sequencing technologies, sequencing is quickly establishing as a powerful approach for collecting genetic variation information. As opposed to traditional genotyping-array technologies that independently call genotypes at polymorphic sites, short read sequencing often collects haplotypic information; a read spanning more than one polymorphic locus (multi-single nucleotide polymorphic read) contains information on the haplotype from which the read originates. However, this information is generally ignored in existing approaches for haplotype phasing and genotype-calling from short read data.

Results: In this article, we propose a novel framework for haplotype inference from short read sequencing that leverages multi-single nucleotide polymorphic reads together with a reference panel of haplotypes. The basis of our approach is a new probabilistic model that finds the most likely haplotype segments from the reference panel to explain the short read sequencing data for a given individual. We devised an efficient sampling method within a probabilistic model to achieve superior performance than existing methods. Using simulated sequencing reads from real individual genotypes in the HapMap data and the 1000 Genomes projects, we show that our method is highly accurate and computationally efficient. Our haplotype predictions improve accuracy over the basic haplotype copying model by ∼20% with comparable computational time, and over another recently proposed approach Hap-SeqX by ∼10% with significantly reduced computational time and memory usage.

Availability: Publicly available software is available at http://genetics.cs.ucla.edu/harsh

Contact: [email protected] or [email protected]
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http://dx.doi.org/10.1093/bioinformatics/btt386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3753566PMC
September 2013

Extraction of crude polysaccharides from Gomphidius rutilus and their antioxidant activities in vitro.

Carbohydr Polym 2013 Apr 23;94(1):479-86. Epub 2013 Jan 23.

School of Environmental and Biological Engineering, Liaoning Shihua University, Fushun 113001, China.

Response surface methodology was used to optimize the extraction of crude polysaccharides from the fruiting bodies of Gomphidius rutilus. A central composite design was adopted to determine the combination of factors (extraction time, extraction temperature, extraction frequency, and ratio of water to raw material) that resulted in the maximum crude polysaccharide production. Results showed that the optimum extraction conditions were as follows: extraction temperature, 95°C; ratio of water to raw material, 16; extraction time, 2.5 h; and extraction frequency, 4. Under these conditions, the experimental yield of crude polysaccharides was 8.02±0.15%, which well agreed with the predicted yield. Evaluation of the antioxidant activity in vitro suggested that the crude polysaccharides had high scavenging activity for superoxide anion, hydroxyl, and 1,1-diphenyl-2-picrylhydrazyl radicals. The crude polysaccharides also showed strong reducing power. Thus, they can be used as natural antioxidants in functional foods or medicine.
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http://dx.doi.org/10.1016/j.carbpol.2013.01.034DOI Listing
April 2013