bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Cd101 as a Susceptibility Gene for Novosphingobium aromaticivorans-Induced Liver Autoimmunity
Authors: Mohammed Javid P. , Fusakio Michael E. , Rainbow Daniel B. , Moule Carolyn , Fraser Heather I. , Clark Jan , Todd John A. , Peterson Laurence B. , Savage Paul B. , Wills-Karp Marsha , Ridgway William M. , Wicker Linda S. , Mattner Jochen 
Published: May 2011

Abstract
Environmental and genetic factors define the susceptibility of an individual to autoimmune disease. Although common genetic pathways affect general immunological tolerance mechanisms in autoimmunity, the effects of such genes could vary under distinct immune challenges within different tissues. In this study, we demonstrate this by observing that autoimmune type 1 diabetes-protective haplotypes at the insulin-dependent diabetes susceptibility region 10 (Idd10) introgressed from chromosome 3 of C57BL/6 (B6) and A/J mice onto the NOD background increase the severity of autoimmune primary biliary cirrhosis induced by infection with Novosphingobium aromaticivorans, a ubiquitous alphaproteobacterium, when compared with mice having the NOD and NOD.CAST Idd10 type 1 diabetes-susceptible haplotypes. Substantially increased liver pathology in mice having the B6 and A/J Idd10 haplotypes correlates with reduced expression of CD101 on dendritic cells, macrophages, and granulocytes following infection, delayed clearance of N. aromaticivorans, and the promotion of overzealous IFN-γ– and IL-17–dominated T cell responses essential for the adoptive transfer of liver lesions. CD101-knockout mice generated on the B6 background also exhibit substantially more severe N. aromaticivorans-induced liver disease correlating with increased IFN-γ and IL-17 responses compared with wild-type mice. These data strongly support the hypothesis that allelic variation of the Cd101 gene, located in the Idd10 region, alters the severity of liver autoimmunity induced by N. aromaticivorans.
Constructions of Chiral Polytopes of Small Rank
Authors: D’Azevedo Antonio Breda , Jones Gareth A. , Schulte Egon 
Published: May 2011

AbstractAn abstract polytope of rank n is said to be chiral if its automorphism group has precisely two orbits on the flags, such that adjacent flags belong to distinct orbits. This paper describes a general method for deriving new finite chiral polytopes from old finite chiral polytopes of the same rank. In particular, the technique is used to construct many new examples in ranks 3, 4, and 5.
Quandle Cocycle Invariants for Spatial Graphs and Knotted Handlebodies
Authors: Ishii Atsushi , Iwakiri Masahide 
Published: May 2011

Abstract We introduce a flow of a spatial graph and see how invariants for spatial graphs and handlebody-links are derived from those for flowed spatial graphs. We define a new quandle (co)homology by introducing a subcomplex of the rack chain complex. Then we define quandle colorings and quandle cocycle invariants for spatial graphs and handlebody-links.
A Proposed Methodology for the Assessment of Glaucoma Awareness in Greece: Introduction of the EIT-8G Scale
Authors: Labiris Georgios , Katsanos Andreas , Fanariotis Michael , Koutsogianni Anna , Giarmoukakis Athanassios , Chatzoulis Dimitrios , Kozobolis Vassilios P. 
Published: May 2011

Purpose To develop a reliable and practical questionnaire for glaucoma awareness and evaluate the impact of potential determinants. Methods Patients with primary open-angle, pigmentary, and exfoliation glaucoma, as well as healthy controls, were recruited. The instrument included questions about demographic characteristics, as well as 8 questions assessing the participant's familiarity with glaucoma. Rasch analysis was used for the validation of the questionnaire. The effect of demographics as potential determinants of awareness was examined with a multivariate logistic regression analysis. Bonferroni-corrected statistical significance was tested with the Mann-Whitney U test or one-way analysis of variance. Association between demographics and questionnaire scores was examined with Spearman correlation. Results As indicated by power analysis, responses from 175 patients (mean age 65.5 years) and 314 controls (mean age 43.3 years) were analyzed. Rasch analysis indicated no multidimensionality and good item-person targeting. Mean ± SD awareness scores for the glaucoma and control groups were 4.43±2.10 and 4.20±2.11, respectively (p=0.207). Sex and residence were not predictors of disease awareness, whereas educational level was only a determinant in the control group (p<0.001). Income was a predictor only for patients (r=0.357, p<0.001), whereas family history was predictive for both groups (p<0.001). Logistic regression analysis revealed that only family history was associated with increased awareness (χ2=4.61, p=0.03, odds ratio 1.98). Conclusions This study introduces a practical and valid instrument for the assessment of glaucoma awareness.
Precision, Morphology, and Histology of Corneal Flap Cuts Using a 200-kHz Femtosecond Laser
Authors: Khoramnia Ramin , Salgado Josefina P. , Lohmann Chris P. , Kobuch Karin A. , von Mohrenfels Christoph Winkler 
Published: May 2011

Purpose Laser-assisted in situ keratomileusis (LASIK) requires precise corneal flap cutting. Especially the creation of thin flaps has recently gained importance for thin-flap LASIK. Currently, there is a trend towards faster femtosecond lasers that can produce flaps in a short period of time. We analyzed flaps created with a 200-kHz femtosecond laser concerning their cut precision, morphology, and histology. Methods Femtosecond laser flap cutting was performed on 36 porcine cadaver eyes using the prototype 200-kHz femtosecond laser UltraFlap (WaveLight GmbH, Erlangen, Germany). The eyes were assigned to 3 thickness groups, with a cut depth of 100 µm, 130 µm, or 180 µm, respectively. Additionally, flap diameters were varied, ranging from 8.0 mm to 9.5 mm. Flap thicknesses were determined with a micrometer gauge. Flap diameters were measured with a sliding caliper. Furthermore, flaps were created for histologic examination. Results There were no complications during flap creation. The mean flap thickness and standard deviation was (in micrometers) 96.33±7.45 (intended thickness: 100), 134.67±4.96 (intended thickness: 130), and 174.59±9.35 (intended thickness: 180), respectively. The flap diameter revealed a mean (in mm) of 8.03±0.15 (intended diameter: 8.0), 8.56±0.10 (intended diameter: 8.5), 9.09±0.10 (intended diameter: 9.0), and 9.54±0.15 (intended diameter: 9.5), respectively. Histologic examination showed very little to almost no changes in the structure of the corneal stroma. Conclusions Flap creation could be performed easily without any complications. The morphology and accuracy of the cuts were very reliable and precise. Histology showed a smooth cut.
Permeability and partition coefficient of aqueous sodium chloride in soft contact lenses
Authors: Guan L. , Jiménez M. E. González , Walowski C. , Boushehri A. , Prausnitz J. M. , Radke C. J. 
Published: May 2011

AbstractTransport of physiologic saline through soft contact lenses is important to on‐eye behavior. Using a specially designed Stokes‐diaphragm cell, we measure aqueous NaCl permeabilities through commercial soft contact lenses at 35°C. The permeabilities increase exponentially with the water content of the lenses spanning a range from 10−7 to 10−5 cm2/s. Equilibrium partition coefficients are obtained by the back‐extraction of lenses initially immersed in 1M aqueous NaCl. Partition coefficients also increase with lens water content but over a smaller range, from 0.1 to 0.7. Because the partition coefficient values are smaller than the water content of the lenses, ideal theory is not followed. Donnan exclusion, bound water, and excluded volume are proposed explanations. The diffusion coefficients of aqueous NaCl through soft contact lenses increase with increasing lens water content following free‐volume theory. Aqueous NaCl diffusivities in the lower water‐content lenses are smaller than the diffusion coefficient of NaCl in water by factors up to 100 indicating very tortuous diffusion paths. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Effects of copper‐containing layered double hydroxide on thermal and smoke behavior of poly(vinyl chloride)
Authors: Zhu Hong , Wang Winson , Liu Tianxi 
Published: May 2011

AbstractThermal and smoke properties of poly(vinyl chloride)/copper‐containing layered double hydroxide (MgCuAl‐LDH) composites were studied in this article. Highly crystallized LDH with platelet size at micrometer scale was prepared via urea hydrolysis and further intercalated with a variety of anions. X‐ray diffraction results indicated an enlargement of basal spacing to 2.54 nm for dodecylsulfonate‐intercalated LDH. The effects of LDHs on thermal stability and degradation behavior of PVC were investigated by Congo Red tests and thermogravimetric analysis (TGA). By incorporating 3 wt % LDHs, the thermal stability times of carbonated MgAl‐LDH and MgCuAl‐LDH/PVC composites were even three and five times of that of neat PVC. The TGA showed an increase of polyene sequences and char residues formed during PVC pyrolysis. MgCuAl‐LDH/PVC composites gave the best reduction in maximum density of smoke, i.e., 25% lower than that of MgAl‐LDH/PVC composites. However, the organomodification of LDH by anion exchange gave no contribution to improvement of thermal stability of PVC. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Dye adsorption and desorption properties of Mentha pulegium in single and binary systems
Authors: Mahmoodi Niyaz Mohammad , Hayati Bagher , Bahrami Hajir , Arami Mokhtar 
Published: May 2011

AbstractThis article deals with the dye adsorption and desorption properties of Mentha pulegium (MP) from single and binary (mixture of dyes) systems. Direct Red 80 (DR80) and Acid Black 26 (AB26) were used as model dyes. The Fourier transform infrared (FTIR) was used to investigate the biosorbent characteristics. The effects of biosorbent dosage, contact time, dye concentration, salt, and pH on dye removal were studied. The biosorption isotherms, kinetics, and thermodynamic were studied. In addition, dye desorption was carried out to study adsorbent recovery. The results showed that the isotherm data of single and binary systems of dyes followed the Langmuir isotherm. The adsorption kinetic of the dyes was found to conform to a pseudosecond order kinetic model. Desorption tests showed maximum dye releasing of 97% for DR80 and 95% for AB26 in single system and 92% for DR80 and 94% for AB26 in binary system of dyes at pH 12. The thermodynamic data showed that the biosorption process is spontaneous, endothermic, and a physisorption reaction. It can be concluded that MP is an ecofriendly biosorbent to remove dyes from single and binary systems. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
Synthesis, characterization, and enzymatic degradation of chitosan/PEG hydrogel films
Authors: Altinisik Aylin , Yurdakoc Kadir 
Published: May 2011

AbstractPoly(ethyleneglycol) (PEG)/tartaric acid (TA)‐crosslinked chitosan hydrogel (CPT) films were prepared, and the formation of the PEG/TA‐crosslinked structure was confirmed by Fourier transformed infrared (FTIR), nuclear magnetic resonance (NMR), and scanning electron microscope (SEM) measurements. The thermal properties of the crosslinked films were also determined with thermogravimetric analysis (TGA) and differential scanning calorimeter (DSC) analysis. The swelling properties of the films were investigated at different temperature and pH values. It was found that the swelling ratio increased with the decrease of pH value of the surrounding buffer solutions, amount of PEG, and with the increase of temperature. Swelling behavior of the PEG/TA‐crosslinked chitosan hydrogel films depended on pH and reversible with the temperature. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2011
The Effects of Castration and Hormone Replacement on the Cross‐Sectional Area of Pubococcygeus Muscle Fibers in the Female Rat
Authors: Lara‐García Miguel , Alvarado Mayvi , Cuevas Estela , Cortés‐sol Albertina , Domínguez Andrés , Tovar Anibal , Pacheco Pablo 
Published: May 2011

AbstractIn this study, we analyzed the effect of ovariectomy and gonadal hormone replacement on the cross‐sectional area of pubococcygeus (Pcm) fibers. It was found that in comparison to intact animals, ovariectomized animals [for 2 or 6 weeks] had an increased cross‐sectional area average in Pcm fibers. Ovariectomy also reduced the percentage of fibers with smaller cross‐sectional area. In ovariectomized animals after 4 weeks of hormone replacement with an empty Silastic capsule or filled with testosterone propionate or dihydrotestosterone, significantly increased the cross‐sectional area average and the percentage of fibers with larger size. However, 17β‐estradiol but not estradiol benzoate treatment reduced the cross‐sectional area average and increased the percentage of Pcm fibers with smaller size. Progesterone did not have an effect on the cross‐sectional area of this muscle. We conclude that Pcm fibers of female rats are sensitive to gonadal hormones, and contrary to male castration, ovariectomy promotes an increase in their cross‐sectional area. Also, we discuss according to other studies that an external mechanism which lies within the neuromuscular periphery could also participate in the modulatory hormonal effect on mass or muscle fiber size. Furthermore, in this process, estradiol is likely to regulate the fiber cross‐sectional area growing produced by androgens. Anat Rec, 2011. © 2011 Wiley‐Liss, Inc.
Expression, purification, and characterization of protective MPT64 antigen protein and identification of its multimers isolated from nontoxic Mycobacterium tuberculosis H37Ra
Authors: Chu Teng‐Ping J. , Yuann Jeu‐Ming P. 
Published: May 2011

AbstractMPT64, a secreted protein of Mycobacterium tuberculosis (MTB), stimulates the immune reactions within cells and is a protective antigen that is lost by the bacilli Calmette–Guérin (BCG) vaccine during propagation. To minimize the toxicity caused by MTB, we used the MPT64 gene encoded by nontoxic H37Ra MTB to carry out genetic expansion via polymerase chain reaction and gene clone MPT64. The plasmid DNA encoded MPT64 was expressed at 20°C for 22 H, and a large quantity of MPT64 was obtained. In the absence of urea, MPT64 multimers with subunits being covalently connected via disulfide bonds were detected by Western blot showing strong protein–protein interactions, as evidenced by the formation of MPT64 tetramers. Finally, with urea of decreasing concentrations, we refolded MPT64 purified in the presence of urea and determined its secondary structures using circular dichroism. MPT64 was found to contain 2.2% α‐helix, 50.9% β‐sheet, 19.5% turn, and 27.4% random coil. The molecular weight of MPT64 was determined by a matrix‐assisted laser desorption ionization‐time of flight mass spectrometer and found to be 23,497 Da, very close to the theoretical molecular weight of MPT64. The results presented here provide a sound basis for future biochemical and biophysical studies of MPT64 or any other proteins encoded by nontoxic H37Ra MTB.
An in silico approach for the discovery of CDK5/p25 interaction inhibitors
Authors: Zhang Bing , Corbel Caroline , Guéritte Françoise , Couturier Cyril , Bach Stéphane , Tan Vincent B. C. 
Published: May 2011

AbstractThe lack of selectivity of all existing ATP competitive inhibitors for a single cyclin‐dependent kinase (CDK) has led us to redirect the structure‐based molecule design from targeting the classic ATP‐binding pocket in CDK5 toward the CDK5/p25 interface. The aim was to seek novel inhibition mechanisms to interrupt protein‐protein interactions. A combined strategy of alanine‐scanning calculations for locating binding sites, virtual screening for small molecules, molecular dynamics simulations for examining the binding stability of virtual screening hits and bio‐assays for testing the level of inhibition was set up and used to explore novel inhibitors capable of interrupting the interactions between the proteins, and consequently of inhibiting the kinase activity. Two compounds were shown to inhibit the complex formation between CDK5 and p25 through p25 binding. They could open avenues for the discovery of new types of structures that prevent interactions between CDK5 and p25 or other CDK and activator proteins, and, more importantly, provide leads in the development of selective inhibitors among CDKs.Accompanying article Corbel et al.
Promoter methylation and transgene copy numbers predict unstable protein production in recombinant chinese hamster ovary cell lines
Authors: Osterlehner Andrea , Simmeth Silke , Göpfert Ulrich 
Published: May 2011

AbstractMammalian cell lines for recombinant protein production need to maintain productivity over extended cultivation times. Long‐term stability studies are time and resource intensive, but are widely performed to identify and eliminate unstable candidates during cell line development. Production instability of manufacturing cell lines can be associated with methylation and silencing of the heterologous promoter. We have identified CpG dinucleotides within the human cytomegalovirus major immediate early promoter/enhancer (hCMV‐MIE) that are frequently methylated in unstable antibody‐producing Chinese hamster ovary (CHO) cell lines. We have established methylation‐specific real‐time qPCR for the rapid and sensitive measurement of hCMV‐MIE methylation in multiple cell lines and provide evidence that hCMV‐MIE methylation and transgene copy numbers can be used as early markers to predict production instability of recombinant CHO cell lines. These markers should provide the opportunity to enrich stable producers early in cell line development and allow developers to put more emphasis on other criteria, such as product quality and bioprocess robustness. Biotechnol. Bioeng. 2011;108: 2670–2681. © 2011 Wiley Periodicals, Inc.
Transforming growth factor‐β1 is constitutively secreted by chinese hamster ovary cells and is functional in human cells
Authors: Beatson Richard , Sproviero Daisy , Maher John , Wilkie Scott , Taylor‐Papadimitriou Joyce , Burchell Joy M. 
Published: May 2011

AbstractChinese hamster ovary (CHO) cells are widely used for the production of recombinant proteins for clinical use as well as academic research. They are particularly important for the production of glycoproteins where bacteria cannot be used. TGFβ1 is a potent cytokine highly conserved across species with multiple immunological and non‐immunological effects. We have discovered that CHOK1, the CHO clone most commonly used by the pharmaceutical industry, constitutively secretes latent TGFβ1 and that this hamster TGFβ1 is active on human cells inducing profound immunological effects. As far as we are aware, the production of TGFβ1 by CHOK1 cells has not been reported before in the literature. As TGFβ1 exerts powerful and pleiotropic effects on diverse cell types, and as CHO cells are used to produce a large number of clinical and non‐clinical products, our findings are highly relevant to studies that rely on recombinant proteins. Biotechnol. Bioeng. 2011;108: 2759–2764. © 2011 Wiley Periodicals, Inc.
Utilization of non‐AUG initiation codons in a flow cytometric method for efficient selection of recombinant cell lines
Authors: Cairns Victor R. , DeMaria Christine T. , Poulin Francis , Sancho José , Liu Ping , Zhang Jin , Campos‐Rivera Juanita , Karey Kenneth P. , Estes Scott 
Published: May 2011

AbstractHere we describe a method that couples flow cytometric detection with the attenuated translation of a reporter protein to enable efficient selection of CHO clones producing high levels of recombinant proteins. In this system, a small cell surface reporter protein is expressed from an upstream open reading frame utilizing a non‐AUG initiation (alternate start) codon. Due to the low translation initiation efficiency of this alternate start codon, the majority of translation initiation events occur at the first AUG of the downstream open reading frame encoding the recombinant protein of interest. While translation of the reporter is significantly reduced, the levels are sufficient for detection using flow cytometric methods and, in turn, predictive of protein expression from the gene of interest since both ORFs are translated from the same mRNA. Using this system, CHO cells have been sorted to obtain enriched pools producing significantly higher levels of recombinant proteins than the starting cell population and clones with significantly better productivity than those generated from limiting dilution cloning. This method also serves as an effective screening tool during clone expansion to enable resources to be focused solely on clones with both high and stable expression. Biotechnol. Bioeng. 2011;108: 2611–2622. © 2011 Wiley Periodicals, Inc.
The role of polymer nanolayer architecture on the separation performance of anion‐exchange membrane adsorbers: Part II. DNA and virus separations
Authors: Bhut Bharat V. , Weaver Justin , Carter Andrew R. , Wickramasinghe S. Ranil , Husson Scott M. 
Published: May 2011

AbstractThe surface‐initiated polymerization protocol developed in part I was used to prepare strong anion‐exchange membranes with variable polymer chain graft densities and degrees of polymerization for DNA and virus particle separations. A focus of part II was to evaluate the role of polymer nanolayer architecture on DNA and virus binding. Salmon sperm‐DNA (SS‐DNA) was used as model nucleic acid to measure the dynamic‐binding capacities at 10% breakthrough. The dynamic‐binding capacity increases linearly with increasing poly ([2‐(methacryloyloxy)ethyl]trimethylammonium chloride) chain density up to the highest chain density used in this study. The new membranes yielded threefold higher SS‐DNA‐binding capacity (30 mg/mL) than a leading commercial membrane with the same functional group chemistry. Elution of bound DNA yielded a sharp peak, and resulted in a 13‐fold increase relative to the feed concentration. This concentration effect further demonstrates the highly favorable transport properties of the newly designed Q‐type membranes. However, unlike findings in part I on protein binding, SS‐DNA binding was not fully reversible. Minute virus of mice (MVM) was used as model virus to evaluate the virus clearance performance of newly designed Q‐type membranes. Log reduction of virus (LRV) of MVM increased with increasing polymer chain density. Membranes exhibited >4.5 LRV for the given MVM impurity load and may be capable of higher LRV values, as the MVM concentration in the flow‐through fraction of these samples was below the limit of detection of the assay. Biotechnol. Bioeng. 2011;108: 2654–2660. © 2011 Wiley Periodicals, Inc.