bluuebunny/crossref_metadata_2025_split huggingface dataset:
Boronate affinity saccharide electrophoresis: A novel carbohydrate analysis tool
Authors: Jackson Thomas R. , Springall Jeremy S. , Rogalle Damien , Masumoto Naoko , Ching Li Hung , D'Hooge François , Perera Semali P. , Jenkins Toby A. , James Tony D. , Fossey John S. , van den Elsen Jean M. H. 
Published: October 2008

AbstractThe incorporation of specialised carbohydrate affinity ligand methacrylamido phenylboronic acid in polyacrylamide gels for fluorophore‐assisted carbohydrate electrophoresis greatly improved the effective separation of saccharides that show similar mobilities in standard electrophoresis. Polyacrylamide gel electrophoresis using methacrylamido phenylboronic acid in low loading (typically 0.5–1% dry weight) was unequivocally shown to alter retention of labelled saccharides depending on their boronate affinity. While conventional fluorophore‐assisted carbohydrate electrophoresis of 2‐aminoacridone labelled glucose oligomers showed an inverted parabolic migration, an undesired trait of small oligosaccharides labelled with this neutral fluorophore, boron affinity saccharide electrophoresis separation of these carbohydrates completely restored their predicted running order, based on their charge/mass ratio, and resulted in improved separation of the analyte saccharides. These results exemplify boron affinity saccharide electrophoresis as an important new technique for analysing carbohydrates and sugar‐containing molecules.
Collapse of a nonductile concrete frame: Evaluation of analytical models
Authors: Yavari Soheil , Elwood Kenneth J. , Wu Chiun‐lin 
Published: October 2008

AbstractThe current paper presents nonlinear dynamic analyses that simulate shaking table tests performed on a four‐column reinforced concrete frame described in a companion paper. The frame consists of two ductile and two nonductile columns interconnected by a stiff beam. In order to validate existing analytical models for nonductile concrete columns, a blind comparison of the test data and results of the analysis is performed. The analysis adequately captures the drift response and correctly detects collapse of the structure; however, strength degradation due to cover spalling is exaggerated in the analytical model. Refinement of the analysis by changing the concrete cover model results in an excellent agreement between the test data and analysis results at the initiation of shear failure and collapse of the frame. The experimental data are further compared with lumped‐plasticity nonlinear models used in engineering practice. The results suggest that the sudden strength degradation used in ASCE/SEI 41‐06 results in an exaggerated estimate of the displacement demands. It is also observed that ignoring the strength degradation, using an elastic‐perfectly‐plastic model, provides a good estimate of the displacement demands when strength degradation is not severe. Copyright © 2008 John Wiley & Sons, Ltd.
The nonconserved N‐terminus of protein phosphatase 2B confers its properties to protein phosphatase 1
Authors: Xie Xiu‐Jie , Huang Wei , Xue Cheng‐Zhe , Wei Qun 
Published: October 2008

AbstractThe protein phosphatase 1 catalytic subunit (PP1c) and the protein phosphatase 2B (PP2B or calcineurin) catalytic subunit (CNA) contain nonconserved N‐terminal regions followed by conserved phosphatase cores. To examine the role of the N‐termini of these two phosphatases, we substituted the residues 1–8 of PP1c with residues 1–42 of CNA, which is designated CNA(1‐42)‐PP1(9‐330). The activities of CNA(1‐42)‐PP1(9‐330) were similar to those of PP2B and different from those of PP1. The chimera was at least fourfold less sensitive to inhibition by okadaic acid, but was stimulated by nickel ions and chlorogenic acid, characteristics of PP2B not of PP1. These observations suggest that the N‐terminus of CNA shifts the properties of PP1 toward those of PP2B. Our findings provide evidence that the nonconserved N‐terminus of PP2B not only functions as important regulatory domain but also confers itself particular characteristics. This region may be targeted for regulation of PP2B activities in vivo. © 2008 IUBMB IUBMB Life, 61(2): 178–183, 2009
Genome‐scale modeling of Synechocystis sp. PCC 6803 and prediction of pathway insertion
Authors: Fu Pengcheng 
Published: October 2008

AbstractBACKGROUND: Cyanobacterium Synechocystis sp. PCC 6803 has been used widely as a model system for the study of photosynthetic organisms and higher plants. The aim of this work was to integrate the genomic information, biochemistry and physiological information available for Synechocystis sp. PCC 6803 to reconstruct a metabolic network for system biology investigations.RESULTS: A genome‐scale Synechocystis sp. PCC 6803 metabolic network, including 633 genes, 704 metabolites and 831 metabolic reactions, was reconstructed for the study of optimal Synechocystis growth, network capacity and functions. Heterotrophic, photoautotrophic and mixotrophic growth conditions were simulated. The Synechocystis model was used for in silico predictions for the insertion of ethanol fermentation pathway, which is a novel approach for bioenergy and biofuels production developed in the authors' laboratory. Simulations of Synechocystis cell growth and ethanol production were compared with actual metabolic measurements which showed a satisfactory agreement.CONCLUSION: The Synechocystis metabolic network developed in this study is the first genome‐scale mathematical model for photosynthetic organisms. The model may be used not only in global understanding of cellular metabolism and photosynthesis, but also in designing metabolic engineering strategies for desirable bio‐products. Copyright © 2008 Society of Chemical Industry
Human umbilical cord blood cells directly suppress ischemic oligodendrocyte cell death
Authors: Hall A.A. , Guyer A.G. , Leonardo C.C. , Ajmo C.T. , Collier L.A. , Willing A.E. , Pennypacker K.R. 
Published: October 2008

AbstractPrevious reports have shown that human umbilical cord blood cells (HUCBCs) administered intravenously 48 hr following middle cerebral artery occlusion reduce infarct area and behavioral deficits of rodents. This cellular therapy is potently neuroprotective and antiinflammatory. This study investigates the effect of HUCBC treatment on white matter injury and oligodendrocyte survival in a rat model of ischemia. Intravenous infusion of 106 HUCBCs 48 hr poststroke reduced the amount of white matter damage in vivo as seen by quantification of myelin basic protein staining in tissue sections. To determine whether HUCBC treatment was protective via direct effects on oligodendrocytes, cultured oligodendrocytes were studied in an in vitro model of oxygen glucose deprivation. Active caspase 3 immunohistochemistry and the lactate dehydrogenase assay for cytotoxicity were used to determine that HUCBCs provide protection to oligodendrocytes in vitro. Based on these results, it is likely that HUCBC administration directly protects oligodendrocytes and white matter. This effect is likely to contribute to the increased behavioral recovery observed with HUCBC therapy. © 2008 Wiley‐Liss, Inc.
Linear peak capacity of a comprehensive multi‐dimensional separation
Authors: Blumberg Leonid M. 
Published: October 2008

AbstractIn order to resolve (quantifiably and identifiably separate) the same number of peaks in the analysis of the same mixture yielding statistically uniform peak distribution, a comprehensive 2‐D separation needs a two times larger peak capacity than a 1‐D separation does. Each additional dimension further reduces the utilization of the peak capacity of comprehensive multi‐dimensional (MD) separation by a factor of two per dimension. As a result, the same peak capacity means different things for separations with different dimensionalities. This complicates the use of the peak capacity for comparison of the potential separation performance of the separations with different dimensionalities. To facilitate the comparison, a concept of a linear peak capacity has been proposed. The linear peak capacity of an MD separation is the peak capacity of a 1‐D separation that, in the analysis of the same mixture, is statistically expected to resolve the same number of peaks as the MD separation is. There are other factors that differently affect the performance of the separations that have different dimensionalities. Peak capacity of a 2‐D separation with a rectangular separation space is 27% larger than the product of the peak capacities of its first and second dimension. This advantage of a 2‐D separation is essentially nullified by the fact that the peak capacity of the first dimension of an optimized 2‐D separation cannot be higher than 80% of the peak capacity of its first dimension standing alone. All in all, the incremental peak capacity gained from addition of a second dimension will not exceed 50% of the peak capacity of the added second dimension. All results are valid for arbitrarily shaped (not necessarily Gaussian) peaks.
Learning respect: Showing and earning esteem is crucial for leaders
Authors: Glover Sarah L. , Hannum Kelly M. 
Published: October 2008

AbstractAlthough little research has been done on respect as an aspect of leadership, it's clear that being respected and respectful is increasingly important for leaders in today's global environment. What is far less clear is the meaning of respect and which behaviors people from various cultures see as respectful. Understanding the three ways in which respect is given or received can help leaders successfully gain and demonstrate respect across cultures.
Ring‐Opening Polymerization of DD‐Lactide Catalyzed by Novozyme 435
Authors: Hans Marc , Keul Helmut , Moeller Martin 
Published: October 2008

AbstractIn contrast to LLA, DLA is converted in toluene solution under mild reaction conditions (50–70 °C) using Novozyme 435 (immobilized CALB) to form the corresponding polymer. The influence of several parameters, such as enzyme concentration, temperature and monomer concentration, on the polymerization rate and the monomer conversion was studied. In contrast to the Novozyme 435 catalyzed polymerization of ε‐caprolactone, enzyme deactivation occurs. It is attributed to the deprivation of water from the enzyme. This work points out that by careful selection of the reaction conditions, it is possible to obtain poly(D‐lactide) in reasonable molecular weights and in high yields using Novozyme 435 catalysis.magnified image
Innovation and the opportunity cost of monopoly
Authors: Reksulak Michael , Shughart William F. , Tollison Robert D. 
Published: October 2008

AbstractInnovation enables monopolists to lower their costs, expand their outputs, and reduce their prices. It is conventional to conclude that social welfare unambiguously increases as a result. Assuming linear demand and marginal cost, this paper shows, however, that innovation raises the opportunity cost of monopoly: as a firm enjoying market power becomes more efficient, greater amounts of surplus are sacrificed by consumers because of the progressive monopolist's failure to produce the new, larger competitive output. Innovation, in other words, increases the social value of competition by raising the deadweight cost of monopoly. Copyright © 2008 John Wiley & Sons, Ltd.
Influence of a cocoa‐enriched diet on specific immune response in ovalbumin‐sensitized rats
Authors: Pérez‐Berezo Teresa , Ramiro‐Puig Emma , Pérez‐Cano Francisco J. , Castellote Cristina , Permanyer Joan , Franch Àngels , Castell Margarida 
Published: October 2008

AbstractPrevious studies in young rats have reported the impact of 3 weeks of high cocoa intake on healthy immune status. The present article describes the effects of a longer‐term cocoa‐enriched diet (9 weeks) on the specific immune response to ovalbumin (OVA) in adult Wistar rats. At 4 weeks after immunization, control rats produced anti‐OVA antibodies, which, according their amount and isotype, were arranged as follows: IgG1 > IgG2a > IgM > IgG2b > IgG2c. Both cocoa diets studied (4% and 10%) down‐modulated OVA‐specific antibody levels of IgG1 (main subclass associated with the Th2 immune response in rats), IgG2a, IgG2c and IgM isotypes. Conversely, cocoa‐fed rats presented equal or higher levels of anti‐OVA IgG2b antibodies (subclass linked to the Th1 response). Spleen and lymph node cells from OVA‐immunized control and cocoa‐fed animals proliferated similarly under OVA stimulation. However, spleen cells from cocoa‐fed animals showed decreased interleukin‐4 secretion (main Th2 cytokine), and lymph node cells from the same rats displayed higher interferon‐γ secretion (main Th1 cytokine). These changes were accompanied by a reduction in the number of anti‐OVA IgG‐secreting cells in spleen. In conclusion, cocoa diets induced attenuation of antibody synthesis that may be attributable to specific down‐regulation of the Th2 immune response.
Starch‐entrapped microspheres extend in vitro fecal fermentation, increase butyrate production, and influence microbiota pattern
Authors: Rose Devin J. , Keshavarzian Ali , Patterson John A. , Venkatachalam Mahesh , Gillevet Patrick , Hamaker Bruce R. 
Published: October 2008

AbstractPrevious research has revealed that waxy corn starch which has been entrapped in a matrix of electrostatically cross‐linked alginate, shows a slow digestion rate such that much of the starch may reach the colon; thus making this a new type of resistant starch. The purpose of this research was to test the fermentative properties of starch‐entrapped microspheres using a batch fecal fermentation method. Fermentation of starch‐entrapped microspheres showed significantly lower rates of gas production compared to waxy corn starch, and showed significant increases in total SCFAs during the latter stages of fermentation (24–48 h), whereas waxy corn starch did not. Cooking the starch‐entrapped microspheres increased the amount of SCFAs and the molar fraction of butyrate produced during fermentation. Bacterial fingerprinting revealed that uncooked starch‐entrapped microspheres have a unique effect on the microbiota that is different from waxy corn starch alone, but cooking causes a shift toward a pattern more closely resembling that of the starch. Starch‐entrapped microspheres may deliver slowly fermentable carbohydrate to the colon, with the ability to influence the microbiota. Further human studies are required to determine whether these characteristics occur in vivo.
Meshfree simulation of failure modes in thin cylinders subjected to combined loads of internal pressure and localized heat
Authors: Qian Dong , Eason Thomas , Li Shaofan , Liu Wing Kam 
Published: October 2008

AbstractThis paper focuses on the non‐linear responses in thin cylindrical structures subjected to combined mechanical and thermal loads. The coupling effects of mechanical deformation and temperature in the material are considered through the development of a thermo‐elasto‐viscoplastic constitutive model at finite strain. A meshfree Galerkin approach is used to discretize the weak forms of the energy and momentum equations. Due to the different time scales involved in thermal conduction and failure development, an explicit–implicit time integration scheme is developed to link the time scale differences between the two key mechanisms. We apply the developed approach to the analysis of the failure of cylindrical shell subjected to both heat sources and internal pressure. The numerical results show four different failure modes: dynamic fragmentation, single crack with branch, thermally induced cracks and cracks due to the combined effects of pressure and temperature. These results illustrate the important roles of thermal and mechanical loads with different time scales. Copyright © 2008 John Wiley & Sons, Ltd.
The stem cell niche
Authors: Walker MR , Patel KK , Stappenbeck TS 
Published: October 2008

AbstractVirtually every tissue of the adult organism maintains a population of putatively slowly‐cycling stem cells that maintain homeostasis of the tissue and respond to injury when challenged. These cells are regulated and supported by the surrounding microenvironment, referred to as the stem cell ‘niche’. The niche includes all cellular and non‐cellular components that interact in order to control the adult stem cell, and these interactions can often be broken down into one of two major mechanistic categories—physical contact and diffusible factors. The niche has been studied directly and indirectly in a number of adult stem cell systems. Herein, we will first focus on the most well‐understood niches supporting the germline stem cells in the lower organisms Caenorhabditis elegans and Drosophila melanogaster before concentrating on the more complex, less well‐understood mammalian niches supporting the neural, epidermal, haematopoietic and intestinal stem cells. Copyright © 2008 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Comparative proteomics profile of osteoblasts cultured on dissimilar hydroxyapatite biomaterials: An iTRAQ‐coupled 2‐D LC‐MS/MS analysis
Authors: Xu Jinling , Khor Khiam Aik , Sui Jianjun , Zhang Jianhua , Tan Tuan Lin , Chen Wei Ning 
Published: October 2008

AbstractHydroxyapatite (HA) and its derived bioceramic materials have been widely used for skeletal implants and/or bone repair scaffolds. It has been reported that carbon nanotube (CNT) is able to enhance the brittle ceramic matrix without detrimental to the bioactivity. However, interaction between osteoblasts and these bioceramics, as well as the underlying mechanism of osteoblast proliferation on these bioceramic surfaces remain to be determined. Using iTRAQ‐coupled 2‐D LC‐MS/MS analysis, we report the first comparative proteomics profiling of human osteoblast cells cultured on plane HA and CNT reinforced HA, respectively. Cytoskeletal proteins, metabolic enzymes, signaling, and cell growth proteins previous associated with cell adhesion and proliferation were found to be differentially expressed on these two surfaces. The level of these proteins was generally higher in cells adhered to HA surface, indicating a higher level of cellular proliferation in these cells. The significance of these findings was further assessed by Western blot analysis. The differential protein profile in HA and CNT strengthened HA established in our study should be valuable for future design of biocompatible ceramics.
Multi‐constraint computational design suggests that native sequences of germline antibody H3 loops are nearly optimal for conformational flexibility
Authors: Babor Mariana , Kortemme Tanja 
Published: October 2008

AbstractThe limited size of the germline antibody repertoire has to recognize a far larger number of potential antigens. The ability of a single antibody to bind multiple ligands due to conformational flexibility in the antigen‐binding site can significantly enlarge the repertoire. Among the six complementarity determining regions (CDRs) that generally comprise the binding site, the CDR H3 loop is particularly variable. Computational protein design studies showed that predicted low energy sequences compatible with a given backbone structure often have considerable similarity to the corresponding native sequences of naturally occurring proteins, indicating that native protein sequences are close to optimal for their structures. Here, we take a step forward to determine whether conformational flexibility, believed to play a key functional role in germline antibodies, is also central in shaping their native sequence. In particular, we use a multi‐constraint computational design strategy, along with the Rosetta scoring function, to propose that the native sequences of CDR H3 loops from germline antibodies are nearly optimal for conformational flexibility. Moreover, we find that antibody maturation may lead to sequences with a higher degree of optimization for a single conformation, while disfavoring sequences that are intrinsically flexible. In addition, this computational strategy allows us to predict mutations in the CDR H3 loop to stabilize the antigen‐bound conformation, a computational mimic of affinity maturation, that may increase antigen binding affinity by preorganizing the antigen binding loop. In vivo affinity maturation data are consistent with our predictions. The method described here can be useful to design antibodies with higher selectivity and affinity by reducing conformational diversity. Proteins 2009. © 2008 Wiley‐Liss, Inc.
Natural history of the E1‐like superfamily: Implication for adenylation, sulfur transfer, and ubiquitin conjugation
Authors: Burroughs A. Maxwell , Iyer Lakshminarayan M. , Aravind L. 
Published: October 2008

AbstractThe E1‐like superfamily is central to ubiquitin (Ub) conjugation, biosynthesis of cysteine, thiamine, and MoCo, and several secondary metabolites. Yet, its functional diversity and evolutionary history is not well understood. We develop a natural classification of this superfamily and use it to decipher the major adaptive trends occurring in the evolution of the E1‐like superfamily. Within the Rossmann fold, E1‐like proteins are closest to NAD(P)/FAD‐dependent dehydrogenases and S‐AdoMet‐dependent methyltransferases. Hence, their phosphotransfer activity is an independent catalytic “invention” with respect to such activities seen in other Rossmannoid folds. Sequence and structure analysis reveals a striking diversity of residues and structures involved in adenylation, sulfotransfer, and substrate binding between different E1‐like families, allowing us to predict previously uncharacterized functional adaptations. E1‐like proteins are fused to several previously undetected domains, such as a predicted sulfur transfer domain containing a novel superfamily of the TATA‐binding protein fold, different types of catalytic domains, a novel winged helix‐turn‐helix domain and potential adaptor domains related to Ub conjugation. On the basis of these fusions, we develop a generalized model for the linking of E1 catalyzed adenylation/thiolation with further downstream reactions. This is likely to involve a dynamic interplay between the E1 active sites and diverse fused C‐terminal domains. We also predict participation of E1‐like domains in previously uncharacterized bacterial secondary metabolism pathways, new cysteine biosynthesis systems, such as those associated with archaeal O‐phosphoseryl tRNA, metal–sulfur cluster assembly (e.g., in nitrogen fixation) and Ub‐conjugation. Evolutionary reconstructions suggest that the last universal common ancestor contained a single E1‐like domain possessing both phosphotransfer and thiolating activities and participating in multiple sulfotransfer reactions. The E1‐like superfamily subsequently expanded to include 26 families clustering into three major radiations. These are broadly involved in Ub activation, cofactor and cysteine biosynthesis, and biosynthesis of secondary metabolites. In light of this, we present evidence that in eukaryotes other E1‐like enzymes such as Urm1 were independently recruited for Ubl conjugation, probably functioning without conventional E2‐like enzymes. Proteins 2009. © 2008 Wiley‐Liss, Inc.