bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cloning and in vitro function analysis of codon‐optimized FatI gene
Authors: Sun Xiao‐Feng , Sun Xing‐Hong , Teng Mei‐Li , Liu Huan‐Qi , Min Ling‐Jiang , Pan Qing‐Jie , Qin Guo‐Qing , Shen Wei , Li Lan 
Published: October 2013

AbstractCurrently, n‐3 polyunsaturated fatty acids (n‐3 PUFAs) have attracted great attention because of their biological significance to organisms. In addition, PUFAs show an obvious impact on prevention and treatment of various diseases. Because n‐3 PUFAs cannot be endogenously synthesized by mammals, mammals have to rely on a dietary supplement for sufficient supply. The finding and application of the fatty acid dehydrogenase I (FatI) gene are expected to change the current situation because it can convert n‐6 polyunsaturated fatty acids (n‐6 PUFAs) to n‐3 PUFAs. Meanwhile, the gradual maturation of transgenic technology makes it possible to produce transgenic animals that can synthesize n‐3 PUFAs by themselves. In this study, the DNA coding sequence of FatI was synthesized by a chemical method after codon optimization according to the mammal's codon bias. The synthesized DNA sequence was introduced into Boer goat fetal fibroblasts by the constructed recombinant eukaryotic expression vector pcDNA3.1(+)‐FatI. Boer goat fetal fibroblasts were transfected by electroporation, and the stable transfected cell lines were obtained by G418 selection. Genomic DNA PCR and Southern blot were applied to verify that the foreign gene FatI was integrated into the genome of the Boer goat fibroblasts. RT‐PCR results showed the expression of FatI gene at the mRNA level. The fatty acid profile of cells carrying the FatI gene revealed an increase in total n‐3 PUFAs (from 0.61 to 0.95), but a decrease in n‐6 PUFAs (from 10.34 to 9.85), resulting in a remarkable increase in the n‐3:n‐6 ratio (from 0.059 to 0.096). The n‐3:n‐6 ratio had a 63.49 percent increase, which is a precursor of the response of n‐3 desaturase activity of the FatI gene. The study may provide a practical tool for producing transgenic animals that can produce n‐3 PUFAs by themselves, and we hope that the application will lay the foundation for animals producing n‐3 PUFAs, which will benefit human nutrition and wellness.
Techno‐economic analysis and life‐cycle assessment of cellulosic isobutanol and comparison with cellulosic ethanol and n‐butanol
Authors: Tao Ling , Tan Eric C. D. , McCormick Robert , Zhang Min , Aden Andy , He Xin , Zigler Bradley T. 
Published: October 2013

AbstractThis work presents a detailed analysis of the production design and economics of the cellulosic isobutanol conversion processes and compares cellulosic isobutanol with cellulosic ethanol and n‐butanol in the areas of fuel properties and engine compatibility, fermentation technology, product purification process design and energy consumption, overall process economics, and life cycle assessment. Techno‐economic analysis is used to understand the current stage of isobutanol process development and the impact of key parameters on the overall process economics in a consistent way (i.e. using the same financial assumptions, plant scale, and cost basis). The calculated minimum isobutanol selling price is $3.62/gasoline gallon equivalent ($/GGE) – similar to $3.66/GGE from the n‐butanol process and higher than $3.26/GGE from the cellulosic ethanol conversion process. At the conversion stage, the n‐butanol process emits the most direct CO2, at 26.42 kg CO2/GGE. Isobutanol and ethanol plants have relatively similar CO2 emissions, at 21.91 kg CO2/GGE and 21.01 kg CO2/GGE, respectively. The consumptive water use of the biorefineries increases in the following order: ethanol (8.19 gal/GGE) < isobutanol (8.98 gal/GGE) < n‐butanol (10.84 gal/GGE). Field‐to‐wheel life cycle greenhouse gas (GHG) emissions for the ethanol and n‐butanol conversion processes are similar at 4.3 and 4.5 kg CO2‐eq/GGE, respectively. The life cycle GHG emissions result for the isobutanol conversion process is 5.0 kg CO2‐eq/GGE, approximately 17% higher than that of ethanol. The life cycle fossil fuel consumption is 39 MJ/GGE for n‐butanol, 43 MJ/GGE for ethanol and 51 MJ/GGE for isobutanol. The energy return on investment for each biofuel is also determined and compared: isobutanol (2.2:1) < ethanol (2.7:1) < n‐butanol (2.8:1). © 2013 Society of Chemical Industry and John Wiley & Sons, Ltd
Development of an integrated tactical and operational planning model for supply of feedstock to a commercial‐scale bioethanol plant
Authors: Ebadian Mahmood , Sowlati Taraneh , Sokhansanj Shahab , Smith Lawrence T , Stumborg Mark 
Published: October 2013

AbstractIn this paper, a new modeling approach is proposed to integrate the tactical and operational planning levels in the biomass supply chain. The proposed approach includes an optimization model and a simulation model. The integration is made between these models (i) to assure the fulfillment of the daily biomass demand year‐round for a commercial‐scale cellulosic ethanol plant and (ii) to reduce biomass delivery costs. The optimization model prescribes the design of the supply area in a way that the annual biomass demand is met at a minimum delivery cost for a five‐year planning horizon. Given the design of the supply area, the simulation model schedules the flow of multi‐biomass in the supply chain to meet the daily biomass demand of the ethanol plant subject to the dynamics and uncertainties in the supply chain. If the daily demand cannot be met, the outputs of the simulation model are used to adjust the design in the optimization model to assure the fulfillment of the daily demand. The application of the integrated model to a proposed commercial‐sized bioethanol plant shows the efficiency of the integrated approach to design the supply area in a way that the daily biomass demand is met at the minimum delivery cost possible. The results of the sensitivity analysis reveal that the most influential parameter on the design is biomass yield. In addition, bale bulk density, in‐farm and road transportation operations, and farmer participation rates have the highest impact on delivery cost compared to other input parameters. © 2013 Society of Chemical Industry and John Wiley & Sons, Ltd
Skin uptake and clearance of ciclopirox following topical application
Authors: Nair Anroop B. , Singh Kishan , Al‐Dhubiab Bandar E. , Attimarad Mahesh , Harsha Sree , Alhaider Ibrahim A. 
Published: October 2013

ABSTRACTThe assessment of skin uptake and clearance are important to determine the efficiency and systemic safety of dermatological formulations. The objective of this study was to assess the skin uptake, clearance and possible systemic delivery of ciclopirox following topical application in Wistar rats. In vitro studies (3 h) were carried out in excised pig skin to assess the permeation and retention capacity of ciclopirox in skin layers using gel formulations (1% and 2% w/v). In vivo dermatopharmacokinetics (DPK) parameters were determined by measuring the drug levels in the skin as a function of time post application (0.5, 1, 1.5 and 2 h) and post removal (3, 4, 6 and 8 h) of the formulation in Wistar rats. The plasma drug concentrations were also determined in the same animals. In vitro data indicate the low permeability and high retention of ciclopirox in the stratum corneum. The DPK data observed indicate a higher Cmax value (175.43 ± 25.62 µg/cm2) and AUC (632.14 ± 102.26 µg.h/cm2) with the 2% (w/v) gel formulation. Further, the skin elimination of ciclopirox follows first order kinetics with a short half‐life (t1/2 ~2 h). The fraction of drug reaching the systemic circulation was found to be significantly low (~0.15% of the applied dose). A relation between the drug concentration in the skin layers and the plasma was observed with a short lag period. The topical availability of ciclopirox was found to be relatively low and endured rapid clearance with minimal systemic uptake. Copyright © 2013 John Wiley & Sons, Ltd.
Biodistribution of diclofenac following repeated topical applications of two diclofenac sodium formulations to minipigs
Authors: Wible James H. , Barrett Thomas , Devarakonda Krishna , Giuliani Michael 
Published: October 2013

ABSTRACTThis study evaluated diclofenac concentrations in plasma, selected hind limb tissues and synovial fluid after repeated topical applications of two diclofenac formulations. Group 1 Gottingen minipigs (n = 18) were administered diclofenac sodium 2.0% topical solution twice daily on days 1–6 and once on day 7. Group 2 minipigs (n = 18) were administered diclofenac sodium 1.5% topical solution four times daily on days 1–6 and twice on day 7. Approximately 20 mg of diclofenac was applied daily to a 10 × 15 cm dosing site centered over the patella of the right knee. Plasma and tissue samples were collected throughout and analysed for diclofenac concentrations using liquid chromatography with tandem mass spectrometry. On day 1, diclofenac sodium 2.0% topical solution produced higher plasma concentrations compared with the 1.5% formulation; however, after 24 h and throughout the remainder of the dosing period, plasma concentrations appeared similar, except at the 72 h time point. Twenty‐four hours after the final application, skin treated with diclofenac sodium 2.0% topical solution retained a significantly (p < 0.02) greater amount of diclofenac than the 1.5% formulation. Generally, both formulations produced similar diclofenac concentrations in synovial fluid, underlying muscle, tendon and bone 24 h after the last application. The 2.0% diclofenac formulation applied twice daily delivered similar amounts of diclofenac as the 1.5% formulation administered four times daily. The skin retained a significant portion of the applied dose to serve as a depot for continuous diffusion of diclofenac into underlying tissues and systemic circulation. Copyright © 2013 John Wiley & Sons, Ltd.
ELF magnetic fields do not affect cell survival and DNA damage induced by ultraviolet B
Authors: Mizuno Kohei , Narita Eijiro , Yamada Masaru , Shinohara Naoki , Miyakoshi Junji 
Published: October 2013

AbstractWe investigated whether extremely low frequency (ELF) magnetic field exposure has modification effects on cell survival after ultraviolet B (UV‐B) irradiation and on repair process of DNA damage induced by UV‐B irradiation in WI38VA13 subcloned 2RA and XP2OS(SV) cells. The ELF magnetic field exposure was conducted using a Helmholtz coil‐based system that was designed to generate a sinusoidal magnetic field at 5 mT and 60 Hz. Cell survival was assessed by WST assay after UV‐B irradiation at 20–80 J/m2, ELF magnetic field exposure for 24 h, followed by incubation for 48 h. DNA damage was assessed by quantification of cyclobutane pyrimidine dimer formation and 6‐4 photoproduct formation using ELISA after UV‐B irradiation at 20–80 J/m2 followed by ELF magnetic field exposure for 24 h. No significant changes were observed in cell survival between ELF magnetic field and sham exposures. Similarly, DNA damage induced by UV‐B irradiation did not change significantly following ELF magnetic field exposure. Our results suggest that ELF magnetic field exposure at 5 mT does not have modification effect on cell survival after UV‐B irradiation and on repair process of DNA damage induced by UV‐B irradiation. Bioelectromagnetics. 35:108–115, 2014. © 2013 Wiley Periodicals, Inc.
Electrophoresis–chemiluminescence detection of phenols catalyzed by hemin
Authors: Shu Lu , Zhu Jinkun , Wang Qingjiang , He Pingang , Fang Yuzhi 
Published: October 2013

ABSTRACTBased on the catalytic activity of hemin, an efficient biocatalyst, an indirect capillary electrophoresis–chemiluminescence (CE‐CL) detection method for phenols using a hemin–luminol–hydrogen peroxide system was developed. Through a series of static injection experiments, hemin was found to perform best in a neutral solution rather than an acidic or alkaline medium. Although halide ions such as Br− and F− could further enhance the CL signal catalyzed by hemin, it is difficult to apply these conditions to this CE‐CL detection system because of the self‐polymerization of hemin, as it hinders the CE process. The addition of concentrated ammonium hydroxide to an aqueous/dimethyl sulfoxide solution of hemin–luminol afforded a stable CE‐CL baseline. The indirect CE‐CL detection of five phenols using this method gave the following limits of detections: 4.8 × 10−8 mol/L (o‐sec‐butylphenol), 4.9 × 10−8 mol/L (o‐cresol), 5.4 × 10−8 mol/L (m‐cresol), 5.3 × 10−8 mol/L (2,4‐dichlorophenol) and 7.1 × 10−8 mol/L (phenol). Copyright © 2013 John Wiley & Sons, Ltd.
Photoluminescence in K3Ca2(SO4)3Cl‐doped Eu3+ phosphor
Authors: Baig Nahida , Dhoble N. S. , Pawade V. B. , Kokode N. S. , Dhoble S. J. 
Published: October 2013

ABSTRACTIn this article we report Eu3+ luminescence in novel K3Ca2(SO4)3Cl phosphors prepared by wet chemical methods. The Eu3+ emission was observed at 594 nm and 615 nm, keeping the excitation wavelength constant at 396 nm nearer to light‐emitting diode excitation, Furthermore, phosphors were characterized by X‐ray diffraction for the confirmation of crystallinity. The variation of the photoluminescence intensity with impurity concentration has also been discussed. Thus, prominent emission in the red region makes prepared phosphors more applicable for white light‐emitting diodes. Copyright © 2013 John Wiley & Sons, Ltd.
BMP growth factor signaling in a biomechanical context
Authors: Kopf Jessica , Paarmann Pia , Hiepen Christian , Horbelt Daniel , Knaus Petra 
Published: October 2013

AbstractBone Morphogenetic Proteins (BMPs) are members of the transforming growth factor‐β superfamily of secreted polypeptide growth factors and are important regulators in a multitude of cellular processes. To ensure the precise and balanced propagation of their pleiotropic signaling responses, BMPs and their corresponding signaling pathways are subject to tight control. A large variety of regulatory mechanisms throughout different biological levels combines into a complex network and provides the basis for physiological BMP function. This regulatory network not only includes biochemical factors but also mechanical cues. Both BMP signaling and mechanotransduction pathways are tightly interconnected and represent an elaborate signaling network active during development but also during organ homeostasis. Moreover, its dysregulation is associated with a number of human pathologies. A more detailed understanding of this crosstalk in respect to molecular interactions will be indispensable in the future, in particular to understand BMP‐related diseases as well as with regard to an efficient clinical application of BMP ligands. © 2013 BioFactors, 40(2):171–187, 2014
A principal component analysis of the dynamics of subdomains and binding sites in human serum albumin
Authors: Paris Guillaume , Ramseyer Christophe , Enescu Mironel 
Published: October 2013

ABSTRACTThe conformational dynamics of human serum albumin (HSA) was investigated by principal component analysis (PCA) applied to three molecular dynamics trajectories of 200 ns each. The overlap of the essential subspaces spanned by the first 10 principal components (PC) of different trajectories was about 0.3 showing that the PCA based on a trajectory length of 200 ns is not completely convergent for this protein. The contributions of the relative motion of subdomains and of the subdomains (internal) distortion to the first 10 PCs were found to be comparable. Based on the distribution of the first 3 PC, 10 protein conformers are identified showing relative root mean square deviations (RMSD) between 2.3 and 4.6 Å. The main PCs are found to be delocalized over the whole protein structure indicating that the motions of different protein subdomains are coupled. This coupling is considered as being related to the allosteric effects observed upon ligand binding to HSA. On the other hand, the first PC of one of the three trajectories describes a conformational transition of the protein domain I that is close to that experimentally observed upon myristate binding. This is a theoretical support for the older hypothesis stating that changes of the protein onformation favorable to binding can precede the ligand complexation. A detailed all atoms PCA performed on the primary Sites 1 and 2 confirms the multiconformational character of the HSA binding sites as well as the significant coupling of their motions. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 561–572, 2014.
Limited proteolysis of natively unfolded protein 4E‐BP1 in the presence of trifluoroethanol
Authors: Hackl Ellen V. 
Published: October 2013

ABSTRACTNatively unfolded (intrinsically disordered (ID) proteins) have been attracting an increasing attention due to their involvement in many regulatory processes. Natively unfolded proteins can fold upon binding to their metabolic partners. Coupled folding and binding events usually involve only relatively short motifs (binding motifs). These binding motifs which are able to fold should have an increased propensity to form a secondary structure. The aim of the present work was to probe the conformation of the intrinsically disordered protein 4E‐BP1 in the native and partly folded states by limited proteolysis and to reveal regions with a high propensity to form an ordered structure. Trifuoroethanol (TFE) in low concentrations (up to 15 vol%) was applied to increase the helical population of protein regions with a high intrinsic propensity to fold. When forming helical structures, these regions lose mobility and become more protected from proteases than random/unfolded protein regions. Limited proteolysis followed by mass spectrometry analysis allows identification of the regions with decreased mobility in TFE solutions. Trypsin and V8 proteases were used to perform limited proteolysis of the 4E‐BP1 protein in buffer and in solutions with low TFE concentrations at 37°C and at elevated temperatures (42 and 50°C). Comparison of the results obtained with the previously established 4E‐BP1 structure and the binding motif illustrates the ability of limited proteolysis in the presence of a folding assistant (TFE) to map the regions with high and low propensities to form a secondary structure revealing potential binding motifs inside the intrinsically disordered protein. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 591–602, 2014.
Development and validation of a rapid and high‐sensitivity liquid chromatography–tandem mass spectrometry assay for the determination of neostigmine in small‐volume beagle dog plasma and its application to a pharmacokinetic study
Authors: Cao Di , Li Wenxue , Zhao Xin , Ye Xiaolan , Sun Fanlu , Li Jinying , Song Fenyun , Fan Guorong 
Published: October 2013

ABSTRACTA simple, rapid and high sensitive liquid chromatography–tandem mass spectrometry (LC‐MS/MS) method for the determination of neostigmine in small‐volume beagle dog plasma was developed to assess the plasma pharmacokinetics of neostigmine. After protein precipitation in a Sirocco 96‐well filtration plate, the filtrate was directly injected into the LC‐MS/MS system. The analytes were separated on a Hanbon Hedera CN column (100 × 4.6 mm, 5 µm) with a mobile phase composed of methanol–water (60:40, v/v) and the water containing 0.01% formic acid at a flow rate of 0.6mL/min, with a split ratio of 1:1 flowing 300 μL into the mass spectrometer. The run time was 3 min. Detection was accomplished by electrospray ionization source in multiple reactions monitoring mode with the precursor‐to‐product ion transitions m/z 223.0 → 72.0 and 306.0 → 140.0 for neostigmine and anisodamine (internal standard), respectively. The method was sensitive with a lower limit of quantitation of 0.1 ng/mL, and good linearity in the range 0.1–100ng/mL for neostigmine (r ≥ 0.998). All the validation data, such as accuracy, intra‐run and inter‐run precision, were within the required limits. The method was successfully applied to pharmacokinetic study of neostigmine methylsulfate injection in beagle dogs. Copyright © 2013 John Wiley & Sons, Ltd.
In vitro evaluation of potential complexation between bovine insulin and bovine serum albumin
Authors: Al‐Domi Hayder , Alzweiri Muhammed , Hamdan Imad , Jaradat Ziad 
Published: October 2013

ABSTRACTThe objective of this study was to examine the possible binding of bovine insulin (BI) with bovine serum albumin (BSA) to form a new potential diabetogenic irreversible complex protein. Several preparations of BSA and BI were prepared. Both capillary electrophoresis and spectrophotometric analysis were undertaken to test the possibility of complexation between BI and BSA. HPLC was used to test whether the potential complex of BI and BSA is reversible or irreversible. The optimum deviation between the real and calculated absorbances was observed at a BI/BSA ratio of 2. Moreover, the migration time of BI decreased substantially with increasing ratio of BI to BSA until it became almost constant at equal molar ratio of BI/BSA. While the majority of the 2:1 BI–BSA sample detached during the HPLC analysis, which confirms the reversible character of BI–BSA binding, the HPLC chromatogram also emphasizes the formation of an irreversible complexation between the two proteins. This study provides evidence of the formation of reversible and irreversible new BI–BSA complexes under physiological conditions. This highlights the importance of examining the possible diabetogenicity of BI–BSA complex in genetically susceptible people. Copyright © 2013 John Wiley & Sons, Ltd.
HPLC‐Q‐TOF‐MS/MS for analysis of major chemical constituents of Yinchen–Zhizi herb pair extract
Authors: Fu Zhiwen , Ling Yun , Li Zhixiong , Chen Mingcang , Sun Zhaolin , Huang Chenggang 
Published: October 2013

ABSTRACTThe Yinchen–Zhizi herb pair (YZHP) consists of Herba Artemisiae Scopariae (Yinchen in Chinese) and Fructus Gardeniae (Zhizi in Chinese), and is mainly used to treat icteric hepatitis, itching skin and eczema. However, the bioactive constituents responsible for the pharmacological effects of YZHP are still unclear to date. In this work, a rapid and sensitive method was established to comprehensively study the constituents in YZHP extract by HPLC‐Q‐TOF MS/MS. The analysis was performed on an HPLC system equipped with an Agilent poroshell 120 EC‐C18 column (100 × 2.1 mm, 2.7 mm) working in a gradient elution program coupled to quadrupole‐time‐of‐flight mass spectrometry operating in the negative ion mode. As a result, a total of 46 compounds including 17 from Herba Artemisiae Scopariae and 36 from Fructus Gardeniae were detected and tentatively identified in YZHP extract by comparing the retention time and mass spectrometry and retrieving the reference literature. More importantly, a series of constituents, such as many iridoid glycosides, were reported for the first time in this formula. The HPLC‐Q‐TOF MS/MS method was developed and utilized successfully to identify the major constituents in YZHP extract and would be helpful for further metabolism and pharmacology research on YZHP. Copyright © 2013 John Wiley & Sons, Ltd.