bluuebunny/crossref_metadata_2025_split huggingface dataset:
Immune recognition of exposed xenoantigens on the surface of PEGylated bovine red blood cells
Authors: Gundersen Sharon I. , Kennedy Melanie S. , Palmer Andre F. 
Published: March 2008

AbstractDue to potential problems that can occur during blood transfusion and increasing blood shortages, our group engineered methoxypolyethylene glycol conjugated bovine red blood cells (mPEG‐bRBCs) as a potential universal oxygen therapeutic. This current work investigates the immunological properties of mPEG‐bRBCs incubated with human plasma (hP) and correlates these properties to exposed Galα(1,3)Gal xenoantigens. After mPEG‐bRBCs were incubated with hP, the amount of bound IgG and IgM was assessed via flow cytometry. Flow cytometry also assessed the amount of GS‐IB4 bound to exposed Galα(1,3)Gal xenoantigens. The results of this study demonstrate that most hP samples strongly promote agglutination of mPEG‐bRBCs regardless of the extent of mPEG surface coverage or donor blood type. IgG and IgM from hP bound strongly to mPEG‐bRBCs. In general, the Galα(1,3)Gal xenoantigen remains exposed at all levels of PEG surface coverage. PEGylation did block some of the xenoantigens as the amount of exposed Galα (1,3)Gal decreased with increased mPEG surface coverage. However, this was not sufficient to prevent a strong agglutination reaction. Taken together, the results of this study indicate that the current strategy for PEGylating bRBCs is unsatisfactory for the development of immunologically silent oxygen therapeutics. Biotechnol. Bioeng. 2008;101: 337–344. © 2008 Wiley Periodicals, Inc.
The Renewable Chemicals Industry
Authors: Christensen Claus Hviid , Rass‐Hansen Jeppe , Marsden Charlotte C. , Taarning Esben , Egeblad Kresten 
Published: March 2008

AbstractThe possibilities for establishing a renewable chemicals industry featuring renewable resources as the dominant feedstock rather than fossil resources are discussed in this Concept. Such use of biomass can potentially be interesting from both an economical and ecological perspective. Simple and educational tools are introduced to allow initial estimates of which chemical processes could be viable. Specifically, fossil and renewables value chains are used to indicate where renewable feedstocks can be optimally valorized. Additionally, C factors are introduced that specify the amount of CO2 produced per kilogram of desired product to illustrate in which processes the use of renewable resources lead to the most substantial reduction of CO2 emissions. The steps towards a renewable chemicals industry will most likely involve intimate integration of biocatalytic and conventional catalytic processes to arrive at cost‐competitive and environmentally friendly processes.
Genotoxic effects of formaldehyde in the human lung cell line A549 and in primary human nasal epithelial cells
Authors: Speit Günter , Schmid Oliver , Neuss Simone , Schütz Petra 
Published: March 2008

AbstractThe alkaline comet assay was used to further characterize the induction of DNA‐protein crosslinks (DPX) by formaldehyde (FA) and their removal in the human lung cell line A549 and in primary human nasal epithelial cells (HNEC). DPX were indirectly measured as the reduction of γ ray – induced DNA migration. FA induced DPX in A549 cells in a concentration‐related manner in the range of 100–300 μM. This result is in agreement with previous studies using different mammalian cell lines. The main new findings of the present study are: (i) Determination of cytotoxicity in relation to genotoxicity strongly depend on the method used. Cytotoxicity measured as the reduction in cell counts 48 hr after addition of FA to the cultures occurred parallel to the induction of DPX while colony forming ability was already reduced at 10 times lower FA concentrations; (ii) DPX induced by a 1‐hr FA treatment were completely removed within 8 hr cultivation in fresh medium while in the presence of FA in the medium DPX levels remained unchanged for 24 hr; (iii) Induction and removal of DPX did not fundamentally differ between exponentially growing and confluent A549 cultures; (iv) Slowly proliferating HNEC showed the same sensitivity towards FA‐induced DPX as A549 cells (i.e. the same FA concentrations induced DPX under the same experimental conditions) and removed DPX with a similar efficiency. In summary, these results contribute to a better understanding of the genotoxic activity of FA in vitro and indicate that the tested cultured primary and permanent human cells do not differ fundamentally with regard to the processing of FA‐induced primary genotoxic effects. Environ. Mol. Mutagen., 2008. © 2008 Wiley‐Liss, Inc.
Waste elimination processes of iron oxide red
Authors: Wang Xiaojun , Xu Jinhua , Xiao Ding , Chen Sili 
Published: March 2008

AbstractA new process of mixing acid iron oxide red was studied. The process uses an inoculating seed of sulfuric acid method after purification and enrichment, followed by addition of ferrous nitrate in a two‐step oxidization. The benefits of the new process were good quality, safe operation, and less pollution. The wastewater treatment of the highly concentrated ammonium‐nitrogen of iron oxide red production was also studied. The method of chemical precipitation, which uses MgSO4 and Na2HPO4 to form guano, was applied. It was defined that the optimal conditions are as follows: the pH was about 10, and the mole ratio of Mg:N:P was 1.1:1.0:1.3. In the wastewater of iron oxide red production, the concentrated ammonium‐nitrogen was reduced from 417.5 to 1.9 mg/L, and the removal efficiency was up to 99.5%. At the same time, MgNH4PO4·6H2O can be used as compound‐fertilizer. © 2008 American Institute of Chemical Engineers Environ Prog, 2008
Model‐based linkage analysis with imprinting for quantitative traits: ignoring imprinting effects can severely jeopardize detection of linkage
Authors: Sung Yun Ju , Rao D.C. 
Published: March 2008

AbstractGenes with imprinting (parent‐of‐origin) effects express differently when inheriting from the mother or from the father. Some genes for development and behavior in mammals are known to be imprinted. We developed parametric linkage analysis that accounts for imprinting effects for continuous traits, implementing it in MORGAN. To study misspecification of imprinting on linkage analysis, we simulated eight markers over a 35 cM region with phenotypes where imprinting contributes 0, 25, 50, and 75% of the variance of a quantitative trait locus (QTL) effect and analyzed them under all four models. Multipoint lod scores were computed and maximized over the same 35 cM region. Our most important finding is the dramatic lod score improvement under the correct imprinting model over the no‐imprinting model. For data with minor QTL allele frequency 0.05, the correct model provided the highest lod scores with maximum expected lod scores over 4 in all settings. Ignoring imprinting provided the lowest lod scores with maximum expected lod scores between −9.9 and 2.4. In the extreme scenario, cases with max lod ≥3 from the correct imprinting model and max lod ≤−2 from the no‐imprinting model occurred in 86% of replications. Models with misspecified imprinting produced lod scores intermediate between those with correct imprinting and with no imprinting. The effects of model misspecification were less pronounced for singlepoint analysis. Our multipoint results illustrate that ignoring true imprinting severely impairs detection of linkage and erroneously excludes genomic regions (with max lod <−2), whereas accounting for it can substantially improve linkage detection. Genet. Epidemiol. 2008. © 2008 Wiley‐Liss, Inc.
LINE‐1 hypomethylation is inversely associated with microsatellite instability and CpG island methylator phenotype in colorectal cancer
Authors: Ogino Shuji , Kawasaki Takako , Nosho Katsuhiko , Ohnishi Mutsuko , Suemoto Yuko , Kirkner Gregory J. , Fuchs Charles S. 
Published: March 2008

AbstractThe CpG island methylator phenotype (CIMP) with widespread promoter CpG island methylation is a phenotype in colorectal cancer, associated with microsatellite instability (MSI) and BRAF mutation. Genome‐wide hypomethylation may also play an important role in genomic instability. However, the relation between global DNA methylation level and methylation in individual CpG islands remains uncertain. Utilizing 869 population‐based colorectal cancers, we measured long interspersed nucleotide element‐1 (LINE‐1) methylation level by Pyrosequencing, which correlates with global DNA methylation level. We quantified DNA methylation in 8 CIMP‐specific promoters (CACNA1G, CDKN2A (p16), CRABP1, IGF2, MLH1, NEUROG1, RUNX3 and SOCS1) by real‐time PCR (MethyLight technology). LINE‐1 methylation levels in tumors were approximately normally distributed (mean, 61.4%; median, 62.3%; standard deviation, 9.6%). Among the 869 tumors, 128 (15%) were classified as CIMP‐high (≥6/8 methylated promoters). The mean LINE‐1 methylation level was higher in CIMP‐high tumors (65.1%, p < 0.0001) than non‐CIMP‐high tumors (60.7%), and higher in MSI‐high tumors (64.7%, p < 0.0001) than non‐MSI‐high tumors (60.7%). When tumors were stratified by MSI/CIMP status, compared to non‐MSI‐high non‐CIMP‐high tumors (mean LINE‐1 methylation level, 60.4%), the mean LINE‐1 methylation level was higher in MSI‐high CIMP‐high (64.8%, p < 0.0001), MSI‐high non‐CIMP‐high (64.6%, p = 0.03) and non‐MSI‐high CIMP‐high tumors (66.1%, p = 0.0003). In addition, 18q loss of heterozygosity in non‐MSI‐high tumors was correlated with LINE‐1 hypomethylation (p = 0.004). In conclusion, both CIMP‐high and MSI‐high are inversely associated with LINE‐1 hypomethylation, suggesting that CIMP/MSI and genomic hypomethylation may represent different pathways to colorectal cancer. Our data also support a possible link between global hypomethylation and chromosomal instability. © 2008 Wiley‐Liss, Inc.
Consistency in infant sleeping arrangements and mother–infant interaction
Authors: Taylor Nicole , Donovan Wilberta , Leavitt Lewis 
Published: March 2008

AbstractThis study examined the association between infant sleeping arrangements (i.e., habitual co‐sleeping, inconsistent co‐sleeping, and non‐co‐sleeping) and quality of mother–infant interaction during play in a sample of mothers, each with a typically developing infant (N=70). Mother–infant dyads who experienced consistency in infant sleeping arrangements in a typical week at 6 months (i.e., habitual co‐sleeping or non‐co‐sleeping) were characterized by more positive maternal and infant behavior and dyadic quality of interaction at 9 months compared with dyads who experienced inconsistency in sleeping arrangements. Additionally, a greater amount of co‐sleeping per week was associated with an increased duration of breastfeeding, mothers working fewer hours, less infant temperamental intensity, and less maternal depression. This study underscores the advantages of empirically based studies that consider consistency in infant sleep experience as a factor that is associated with more positive mother–child interaction.
Theoretical investigation of anthracene‐9,10‐endoperoxide vertical singlet and triplet excitation spectra
Authors: Corral Inés , González Leticia 
Published: March 2008

AbstractThe electronic absorption spectrum of anthracene‐9,10‐endoperoxide (APO) has been investigated by means of multiconfigurational multi‐state second order perturbation theory on complete active space self‐consistent field wavefunctions (MS‐CASPT2/CASSCF) and two single reference methods: time‐dependent density functional theory (TD‐DFT) and coupled cluster of second order (CC2). After testing several active spaces and basis sets, a CAS (14,12) active space together with an ANO‐S basis set was found an appropriate choice to describe the vertical singlet and triplet electronic states of APO. Unfortunately, TD‐DFT and CC2 methods cannot reproduce the MS‐CASPT2 and experimental spectrum. Our MS‐CASPT2//CASSCF(14,12)/ANO‐S calculations predict a predominant π*OOσ*OO character for the lowest singlet excited state S1 at 3.85 eV. Accordingly, the lowest singlet state of APO should be responsible for homolysis of the endoperoxide group. The next two absorbing excited states, experimentally proposed to be responsible for singlet oxygen production and therefore connected to the biological interest of APO, have been computed vertically at 4.34 and 4.59 eV and assigned to πCCπ*CC and π*OOπ*CC transitions, respectively. The vertical triplet electronic spectrum follows the singlet vertical spectrum ordering. The high density of triplet and singlet excited states of different nature within few eV points to the possibility of intersystem crossings between potential energy surfaces of different multiplicity. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008
Simulations of proteins with inhomogeneous degrees of freedom: The effect of thermostats
Authors: Mor Amit , Ziv Guy , Levy Yaakov 
Published: March 2008

AbstractProteins with a long flexible polymeric tail attached at their N‐ or C‐terminus are studied using molecular dynamics (MD) simulations of a coarse‐grained model for protein folding where the temperature is regulated by either the Berendsen or the Langevin thermostat. These thermostats show different abilities to regulate the temperature of these systems that include flexible and more rigid regions. In the simulations with the Berendsen thermostat, the flexible tail is significantly hotter than the protein, both in its folded and unfolded states. Upon weakening the strength of the Berendsen thermostat, the temperature gradient between the fast and the slow degrees of freedom is significantly decreased, yet linkage between the temperatures of the flexible tail and the protein remains. The Langevin thermostat is proven to regulate the temperature of these inhomogenous systems reliably, without discriminating between the slow and fast degrees of freedom. The Langevin thermostat is less sensitive than is the Berendsen thermostat to the strength of the coupling between the protein system and the thermal bath. Our study calls for special care in choosing the thermostat for MD simulations of systems with inhomogenous degrees of freedom. Using the Berendsen thermostat with strong coupling would result in mistaken thermodynamic descriptions of such systems. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008
Theoretical studies on pyridoxal 5′‐phosphate‐dependent transamination of α‐amino acids
Authors: Liao Rong‐Zhen , Ding Wan‐Jian , Yu Jian‐Guo , Fang Wei‐Hai , Liu Ruo‐Zhuang 
Published: March 2008

AbstractDensity functional methods have been applied to investigate the irreversible transamination between glyoxylic acid and pyridoxamine analog and the catalytic mechanism for the critical [1,3] proton transfer step in aspartate aminotransferase (AATase). The results indicate that the catalytic effect of pyridoxal 5′‐phosphate (PLP) may be attributed to its ability to stabilize related transition states through structural resonance. Additionally, the PLP hydroxyl group and the carboxylic group of the amino acid can shuttle proton, thereby lowering the barrier. The rate‐limiting step is the tautomeric conversion of the aldimine to ketimine by [1,3] proton transfer, with a barrier of 36.3 kcal/mol in water solvent. A quantum chemical model consisting 142 atoms was constructed based on the crystal structure of the native AATase complex with the product L‐glutamate. The electron‐withdrawing stabilization by various residues, involving Arg386, Tyr225, Asp222, Asn194, and peptide backbone, enhances the carbon acidity of 4′‐C of PLP and Cα of amino acid. The calculations support the proposed proton transfer mechanism in which Lys258 acts as a base to shuttle a proton from the 4′‐C of PLP to Cα of amino acid. The first step (proton transfer from 4′‐C to lysine) is shown to be the rate‐limiting step. Furthermore, we provided an explanation for the reversibility and specificity of the transamination in AATase. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008
Development of glycyl radical parameters for the OPLS‐AA/L force field
Authors: Komáromi István , Owen Michael C. , Murphy Richard F. , Lovas Sándor 
Published: March 2008

AbstractOn the basis of quantum chemical calculations Cα‐glycyl radical parameters have been developed for the OPLS‐AA/L force field. The molecular mechanics hypersurface was fitted to the calculated quantum chemical surface by minimizing their molecular mechanics parameter dependent sum‐of‐squares deviations. To do this, a computer program in which the molecular mechanics energy derivatives with respect to the parameters were calculated analytically was developed, implementing the general method of Lifson and Warshel (J Chem Phys 1968, 49, 5116) for force field parameter optimization. This program, in principle, can determine the optimal parameter set in one calculation if enough representative value points on the quantum chemical potential energy surface are available and there is no linear dependency between the parameters. Some of the parameters in quantum calculations, including several new torsion types around a bond as well as angle parameters at a new central atom type, are not completely separable. Consequently, some restrictions and/or presumptions were necessary during parameter optimization. The relative OPLS‐AA energies reproduced those calculated quantum chemically almost perfectly. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008
Ab initio protein structure prediction with force field parameters derived from water‐phase quantum chemical calculation
Authors: Katagiri Daisuke , Fuji Hideyoshi , Neya Saburo , Hoshino Tyuji 
Published: March 2008

AbstractMolecular dynamics (MD) simulations are extensively used in the study of the structures and functions of proteins. Ab initio protein structure prediction is one of the most important subjects in computational biology, and many trials have been performed using MD simulation so far. Since the results of MD simulations largely depend on the force field, reliable force field parameters are indispensable for the success of MD simulation. In this work, we have modified atom charges in a standard force field on the basis of water‐phase quantum chemical calculations. The modified force field turned out appropriate for ab initio protein structure prediction by the MD simulation with the generalized Born method. Detailed analysis was performed in terms of the conformational stability of amino acid residues, the stability of secondary structure of proteins, and the accuracy for prediction of protein tertiary structure, comparing the modified force field with a standard one. The energy balance between α‐helix and β‐sheet structures was significantly improved by the modification of charge parameters. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008
Identification of DPPA4 and other genes as putative Sox2:Oct‐3/4 target genes using a combination of in silico analysis and transcription‐based assays
Authors: Chakravarthy Harini , Boer Brian , Desler Michelle , Mallanna Sunil Kumar , McKeithan Timothy W. , Rizzino Angie 
Published: March 2008

AbstractSox2 and Oct‐3/4 function as master regulators during mammalian embryogenesis, where they are believed to regulate a critical gene regulatory network by cooperatively binding to DNA regulatory regions composed of adjacent HMG and POU motifs (HMG/POU cassettes). Previous studies have identified seven genes that contain highly active HMG/POU cassettes (referred to as Sox2:Oct‐3/4 target genes). Importantly, nearly all known Sox2:Oct‐3/4 target genes appear to be essential for embryogenesis. Recent genome‐wide ChIP‐chip studies identified over 300 genes that are co‐occupied by Sox2 and Oct‐3/4, which suggests that most Sox2:Oct‐3/4 target genes remain to be identified. The work described here used a 3‐step strategy for identifying additional Sox2:Oct‐3/4 target genes. First, we employed in silico analysis to search for putative HMG/POU cassettes in 50 genes reported to be co‐occupied by Sox2 and Oct‐3/4 in embryonic stem cells. We identified 39 genes that contain putative HMG/POU cassettes. Next, we tested the activity of seven of the putative HMG/POU cassettes in a transcription‐based assay and determined that nearly all are functional. Finally, as a proof‐of‐principle, we tested one of the seven cassettes (DPPA4) in the context of its endogenous promoter using a promoter/reporter gene construct. DPPA4 was tested in part because it was shown recently to play an important role in ES cell self‐renewal. We determined that the 5′ flanking region of the DPPA4 gene contains a functional HMG/POU cassette and behaves as a Sox2:Oct‐3/4 target gene. Finally, we used a transcription‐based assay to help develop a refined consensus sequence for HMG/POU cassettes. J. Cell. Physiol. 216: 651–662, 2008, © 2008 Wiley‐Liss, Inc.
Treponema denticola lipooligosaccharide activates gingival fibroblasts and upregulates inflammatory mediator production
Authors: Tanabe Shin‐ichi , Bodet Charles , Grenier Daniel 
Published: March 2008

AbstractIn response to bacterial challenges, fibroblasts, a major constituent of gingival connective tissue, can produce immunoregulatory cytokines and proteolytic enzymes that may contribute to tissue destruction and the progression of periodontitis, a chronic inflammatory disease affecting tooth‐supporting tissues, including alveolar bone. The spirochete Treponema denticola is a major etiological agent of periodontitis and can invade oral tissues. The aim of the present study was to investigate the inflammatory response of gingival fibroblasts to T. denticola lipooligosaccharide (LOS). T. denticola LOS induced significant production of various inflammatory mediators by fibroblasts, including interleukin‐6, interleukin‐8, monocyte chemoattractant protein 1, nitric oxide, and prostaglandin E2. In addition, the secretion of matrix metalloproteinase 3, an enzyme active on basement membrane components, was also significantly increased. The response of fibroblasts was dose‐dependent and much stronger following a 24 h stimulation period. The expression and/or phosphorylation state of several signaling proteins, including Fos, MKK1, MKK2, MKK3/6, NF‐κB p50, and NF‐κB p65, was enhanced following stimulation of fibroblasts with T. denticola LOS. In summary, T. denticola LOS induced an inflammatory response in gingival fibroblasts and may thus contribute to the immunopathogenesis of periodontitis and the progression of the disease. J. Cell. Physiol. 216: 727–731, 2008, © 2008 Wiley‐Liss, Inc.
Metastases to intramammary lymph nodes in patients with breast cancer: Sonographic findings
Authors: Edeiken‐Monroe Beth S. , Monroe Douglas P. , Monroe Brett J. , Arnljot Kristine , Giaccomazza Maria , Sneige Nour , Fornage Bruno D. 
Published: March 2008

AbstractPurpose.To describe the sonographic characteristics of intramammary lymph node metastasis (ILNM) in patients with breast cancer and to assess the value of sonography and sonographically guided fine needle aspiration biopsy (FNAB) in their diagnosis.Methods.We retrospectively reviewed the charts and films of 19 women with biopsy‐documented ILNM who were seen in our breast diagnostic center between December 1999 and July 2003. The sonographic appearance of the nodes was analyzed and correlated with clinical and mammographic findings and with biopsy results.Results.The ILNMs were clinically and mammographically occult in 7 (37%) of the 19 women. The diameter of the ILNMs was less than 1 cm in 15 (79%) cases. The volume of the central echogenic hilum was less than 50% of the total volume of the node in each of the patients. There was marked decrease in cortical echogenicity of the ILN in all cases. Metastatic involvement was established via sonographically guided FNAB in each of the 19 suspicious intramammary lymph nodes.Conclusion.Sonography and sonographically guided FNAB are valuable methods of assessment for ILNM in patients with known or suspected breast cancer. The most consistent sonographic features associated with ILNM were reduction in the volume of the central echogenic hilum and marked hypoechogenicity of the node's cortex. © 2008 Wiley Periodicals, Inc. J Clin Ultrasound, 2008.