bluuebunny/crossref_metadata_2025_split huggingface dataset:
A simple method for faster nonbonded force evaluations
Authors: Shen Min‐Yi , Freed Karl F. 
Published: March 2005

AbstractAccurate approximations are introduced for the evaluation of inverse interparticle distances such that square root or division operations are not required in the computation of interparticle interactions and forces. These generally applicable approximations are illustrated by incorporation into the protein simulation package TINKER (Pappu, R. V.; Hart, R. K.; Ponder, J. W. J Phys Chem B 1998, 102, 9725; Ponder, J. W.; Richards, F. M. J Comput Chem 1987, 8, 1016; Dudek, M. J.; Ramnarayan, K.; Ponder, J. W. J Comput Chem 1998, 19, 548) along with several other speed enhancement strategies. With these modifications, implicit solvent Langevin dynamics simulations of proteins are performed factors of 4.6 times faster than the modified open source distributed program. Programming speedups are obtained by extensive vectorization, simplification of the inner loop to avoid IF statements, and by using lookup tables for the distance dependent “dielectric constant” in implicit solvent models. Benchmarks are provided for the all‐atom, implicit solvent dynamics of Met‐enkephalin, the villin headpiece, the B1 domain of protein‐G, and barnase. We also discuss the more general applicability of the approximation methods to explicit solvent simulations and of look‐up tables for other implicit solvent models such as the generalized Born models. © 2005 Wiley Periodicals, Inc. J Comput Chem 26: 691–698, 2005
Relationship between renal anemia and prognostic stages of IgA nephropathy
Authors: Aruga Seiki , Horiuchi Tomohide , Shou Ichiyu , Tashiro Kyouichi , Kurusu Atsushi , Fukui Mitsumine , Horikoshi Satoshi , Tomino Yasuhiko 
Published: March 2005

AbstractIn 2002, the Joint Committee of the Special Study Group on Progressive Glomerular Diseases, Ministry of Health, Labor and Welfare of Japan newly revised the clinical guidelines for IgA nephropathy (Sakai et al.: Jpn J Nephrol 37:417–421, 1995; Tomino and Sakai: Clin Exp Nephrol, 7, 93–97, 2003). The prognostic stages were classified into four groups: the good prognosis group (Group I), relatively good prognosis group (Group II), relatively poor prognosis group (Group III), and poor prognosis group (Group IV). The relationship between the levels of Hb, Ht, and RBC in peripheral blood and the renal prognostic stages was determined in 62 patients with IgA nephropathy in the present study. The mean levels of Hb, Ht, and RBC were significantly lower in Group IV than in Group I (P<0.05). However, there were no significant changes in the levels of serum creatinine (s‐Cr) or creatinine clearance (CCr) among these four groups. It appears that the levels of Hb, Ht, and RBC in peripheral blood may be important clinical parameters for the evaluation of prognostic stages in patients with IgA nephropathy. J. Clin. Lab. Anal. 19:80–83, 2005. © 2005 Wiley‐Liss, Inc.
Effective repetitive dystrophin gene transfer into skeletal muscle of adult mdx mice using a helper‐dependent adenovirus vector expressing the coxsackievirus and adenovirus receptor (CAR) and dystrophin
Authors: Uchida Yuji , Maeda Yasushi , Kimura En , Yamashita Satoshi , Nishida Yasuto , Arima Toshiyuki , Hirano Teruyuki , Uyama Eiichiro , Mita Shuji , Uchino Makoto 
Published: March 2005

AbstractBackgroundThe helper‐dependent adenovirus (HDAd) vector is less immunogenic and has a larger cloning capacity of up to 37 kb enough to carry the full‐length dystrophin cDNA. However, high and long‐term expression of dystrophin transduced to mature muscle still remains difficult. One of the main reasons for this is that the expression of the coxsackievirus and adenovirus receptor (CAR) is very low in mature muscle.MethodsWe have constructed two different HDAd vectors. One contains the LacZ and the murine full‐length dystrophin expression cassette (HDAdLacZ‐dys), and the other is a new, improved vector containing the CAR and the dystrophin expression cassette (HDAdCAR‐dys).ResultsWe initially demonstrated high dystrophin expression and prevention of the dystrophic pathology in mdx muscle injected during the neonatal phase with HDAdLacZ‐dys. Furthermore, we demonstrated that repeated injections of HDAdCAR‐dys into mature muscle led to approximately nine times greater dystrophin‐positive fibers in number than a single injection, thereby recovering the expression of dystrophin‐associated proteins. This data has also shown that HDAdCAR‐dys enabled administration of adenovirus (Ad) vector to the host with pre‐existing immunity to the same serotype of Ad.ConclusionsRepetitive injections of the HDAd vector containing the CAR and the dystrophin expression cassette could improve the efficiency of subsequent dystrophin gene transfer to mature mdx muscle. This result suggests that our new HDAd vector will provide a novel gene therapy strategy for Duchenne muscular dystrophy, raising the prospects for gene therapy of other hereditary myopathies. Copyright © 2005 John Wiley & Sons, Ltd.
A branch‐and‐price algorithm for the capacitated p‐median problem
Authors: Ceselli Alberto , Righini Giovanni 
Published: March 2005

AbstractThe capacitated p‐median problem is the variation of the well‐known p‐median problem in which a demand is associated to each user, a capacity is associated to each candidate median, and the total demand of the users associated to the same median must not exceed its capacity. We present a branch‐and‐price algorithm, that exploits column generation, heuristics and branch‐and‐bound to compute optimal solutions. We compare our branch‐and‐price algorithm with other methods proposed so far, and we present computational results both on test instances taken from the literature and on random instances with different values of the ratio between the number of medians and the number of users. © 2004 Wiley Periodicals, Inc. NETWORKS, Vol. 45(3), 125–142 2005
Late effect of prenatal irradiation on the hippocampal histology and brain weight in adult mice
Authors: Hossain M. , Chetana M. , Devi P. Uma 
Published: March 2005

AbstractWe studied the changes in the brain weight and hippocampal histology in adult offspring exposed to 0.25–1.5 Gy of 60Co gamma radiations during day 14 or 17 of gestation. Irradiation with 0.5–1.5 Gy produced a significant decrease in brain weight of the offspring at 6 and 12 months of age. Exposure to 1 Gy at day 14 or 17 of gestation resulted in significant decrease in the number of neurons in the CA3 and CA4 regions of hippocampus of 200 μm length, while 1.5 Gy significantly affected CA1 region also. The fetal period (13–18 days of gestation) of mouse development is an active phase of brain development involving proliferation, migration and differentiation of cerebral cortex and associated structures. The present results show that exposure at this period of mouse development to moderate doses of gamma radiation can induce permanent deficits in the brain histology, which can adversely affect the learning and memory in adults.
Genetic Engineering of Polysaccharide Structure: Production of Variants of Xanthan Gum in Xanthomonas campestris
Authors: Hassler Randal A. , Doherty Daniel H. 
Published: March 2005

AbstractXanthan gum is an extracellular heteropolysaccharide produced by the bacterium Xanthomonas campestris. Xanthan has wide commercial application as a viscosifier of aqueous solutions. Previously, through genetic engineering, a set of mutants defective in the xanthan biosynthetic pathway has been obtained. Certain mutants were shown to synthesize and polymerize structural variants of the xanthan repeating unit and thus produce “variant xanthans”. Initial studies of solution viscosities of these polymers, presented here, indicate that the variants have rheological properties similar to, but not identical with, xanthan. These results indicate that acetylation and pyruvylation can affect the viscometric properties of xanthan. Specifically, the presence of pyruvate increases viscosity, whereas acetate decreases viscosity. In addition, the elimination of sugar residues from xanthan side chains also has a major effect on viscosity. Compared to wild‐type xanthan, polymer lacking the terminal mannose (polytetramer) is a poor viscosifier. In contrast, polymer lacking both the terminal mannose and glucuronic acid (polytrimer) is a superior viscosifier, on a weight basis. There is a negative effect of acetylation on the viscosity of polytetramer xanthan, but there is seemingly no effect of acetylation on polytrimer xanthan viscosity. The further study of these materials should provide insight into the relationship between xanthan structure and rheological behavior.
Experimental and Theoretical Evidence for Convective Nutrient Transport in an Immobilized Cell Support
Authors: Bringi V. , Dale B. E. 
Published: March 2005

AbstractEven though immobilized‐cell reactors possess several engineering advantages over free‐cell reactors, their full potential has not been realized because mass transfer often limits the rate of nutrient supply and product removal from immobilized cell supports. We studied the interaction between mass transfer and reaction kinetics in the anaerobic conversion of glucose to CO2 and ethanol by yeast immobilized in a porous rotating disk on the agitator shaft of a conventional CSTR. A Sherwood number correlation was used to show that external mass‐transfer resistances were negligible under typical operating conditions. The modulus of Weisz based on observable reaction parameters was used to gauge the importance of pore diffusion limitations. Under conditions for which significant pore diffusion effects and hence low effectiveness factors (η =ca. 0.1) would be predicted, the observed reaction rates were much higher than expected (η=ca. 1), suggesting that pore diffusion limitations were at least partially relieved by convective transport of glucose into the support. Two possible mechanisms of convective transport are discussed. We hypothesize that gas evolution was responsible for the convective enhancement of glucose supply.
Recovery of Clostridium thermosulfurogenes Produced β‐Amylase by (Hydroxypropyl)methylcellulose Partition
Authors: Miranda Everson A. , Berglund Kris A. 
Published: March 2005

AbstractA procedure for recovering Clostridium thermosulfurogenes produced β‐amylase from fermentation broth by partition was developed. The partition was achieved by addition of ammonium sulfate to an aqueous solution of the enzyme with (hydroxypropyl)methylcellulose. The β‐amylase‐containing pellet formed upon centrifugation could be redissolved and the polymer recovered by a second salt addition. The process was not dependent on polymer/enzyme solution pH, but it was affected by temperature, polymer nominal molecular weight and loading, and fermentation carbon source. Unlike more traditional aqueous‐phase partitions, such as poly(ethylene glycol)/dextran, the current approach appeared to be biospecific.
Representation of Phase Equilibrium Behavior of Antibiotics
Authors: Zhu Yizu , Evans Lawrence B. , Chen Chau‐Chyun 
Published: March 2005

AbstractThe phase equilibrium behavior of biomolecules is important both in understanding the partition mechanisms and in the design and optimization of downstream recovery processes. Chen et al. (1989) proposed a molecular thermodynamic framework that successfully represents the liquid‐solid equilibrium behavior of amino acids and small peptides as functions of temperature, ionic strength, solvent compositions, and pH. Based on this theoretical framework, this paper presents recent results in representing the liquid‐solid equilibrium behavior (solubilities) and the liquid‐liquid equilibrium behavior (phase partitioning) of β‐lactam antibiotics, which are amino acid derivatives and important chemotherapeutic agents.
Defining an Optimal Carbon Source/Methionine Feed Strategy for Growth and Cephalosporin C Formation by Cephalosporium acremonium
Authors: Vicik Steven M. , Fedor Anthony J. , Swartz Randall W. 
Published: March 2005

AbstractThe effect of the method of methionine addition, growth‐limiting carbon source (glucose vs sucrose), and culture growth rate on cephalosporin C production was investigated in a Cephalosporium acremonium defined medium fed batch fermentation. Batch addition of methionine, at a concentration of 3 g/L, prior to the start of a fed sucrose fermentation was found to interfere with the ability of the culture to utilize this sugar, thus limiting growth and decreasing cephalosporin C production. Batch methionine addition had no effect on glucose‐limited cultures. Concurrent exponential feeding of methionine with sucrose improved both culture growth and productivity. Under the control of identical carbon source limiting feed profiles, sucrose was observed to support greater cephalosporin C production than glucose. Optimal cephalosporin C production in a C. acremonium defined medium fed batch fermentation was obtained through controlling culture growth during the rapid growth phase at a relatively low level with respect to μmax (μ∼0.036 h−1) until achieving a desired cell mass with a concurrent sucrose and methionine feed, followed by maintaining relatively vigorous growth (μ∼0.01 h−1) with sucrose for the duration of the fermentation.
Intrinsic Growth and Fermentation Rates of Alginate‐Entrapped Saccharomyces cerevisiae
Authors: Hannoun Betty J. M. , Stephanopoulos Gregory 
Published: March 2005

AbstractExperiments were conducted under anaerobic conditions to determine the intrinsic specific rates of growth, glucose uptake, and ethanol production for Saccharomyces cerevisiae immobilized in calcium alginate. The simultaneous processes of diffusion and reaction in an alginate membrane were analyzed to determine the intrinsic specific growth and reaction rates from glucose and ethanol concentration measurements made outside the alginate phase. Under anaerobic conditions, the specific growth rate of immobilized S. cerevisiae decreased by 20% compared to the growth rate for suspended cells. The specific glucose uptake rate and specific ethanol production rate increased by a factor of 4 compared to those for suspended cells. The ethanol yield remained the same, and the biomass yield decreased to one‐fifth the yield for suspended cells. Further experiments were conducted under aerobic conditions to investigate the effects of dissolved oxygen concentration on the specific rates of growth, glucose uptake, and ethanol production of immobilized S. cerevisiae. Although the obtained results cannot be interpreted unambiguously, oxygen appears to affect immobilized cells in a way similar to the way it affects suspended cells, while the observed differences between immobilized and suspended cells under anaerobic conditions remain the same in the presence of oxygen. Due to rate variability with oxygen, the obtained results are representative of average rate values. Experimental data and simulations indicate that glucose mitigates oxygen effects, yielding relatively small rate variations with aeration rates and relatively constant ethanol yields.
Fluidized Bed Adsorption for Whole Broth Extraction
Authors: Gailliot F. P. , Gleason C. , Wilson J. J. , Zwarick J. 
Published: March 2005

AbstractFluidized bed adsorption using a high‐density synthetic resin has proven to be an invaluable technique for separating novel compounds from unfiltered fermentation broths during the very early stages of fermentation development, where product concentrations are typically in the parts per million range. Previous initial downstream processing strategies consisted of cell separation from whole broth or direct extraction with water‐immiscible solvents, both of which resulted in lengthy time cycles, conflicts with existing operations requiring the use of high‐cost centrifugal separators, and environmental/solvent recovery concerns. Laboratory and subsequent pilot plant process development work along with concomitant improvements in yield, quality, and time cycles are presented for one of several fluidized bed processes piloted in Merck's Natural Product Isolation facility.
Practical Considerations in the Measurement of Culture Fluorescence
Authors: Coppella Steven J. , Rao Govind 
Published: March 2005

AbstractWe have examined practical considerations associated with the use of a commercially available fluorescence probe for in situ measurements in bioreactors. The optical path length of the measurement was first determined and a flow cell subsequently designed. The environment (agitation/aeration rates) of the probe was found to have a significant influence on the measurement. These effects were eliminated by placing the probe in a recycle loop using the flow cell. Fluorescence measurement in the recycle loop was verified to be representative of the cell sample and to not affect cell metabolism.
Microstructure of Mixed Gelatin‐Egg White Gels: Impact on Rheology and Application to Microparticulation
Authors: Ziegler G. R. 
Published: March 2005

AbstractThe microstructure of mixed gelatin‐egg white gels was examined by using both light and electron microscopy. Interpenetrating polymer network morphology was observed in mixed gels that were macroscopically single‐phase systems. For two‐phase gels, phase volumes were determined by optical image analysis and used to predict the composite shear modulus. Rheological properties were related to observable changes in the gel microstructure. For systems containing 5.6% egg white protein and greater than 5% gelatin, the dispersed egg white phase formed capsules of roughly 1–2 μm in diameter, with a dense outer coat and a less dense interior containing voids. From this, a method for the microparticulation of proteins based on aqueous phase partitioning was developed.
Growth and Anthocyanin Accumulation in Carrot Cell Suspension Cultures Growing on Fructose, Glucose, or Their Mixtures
Authors: Zwayyed S. K. , Frazier G. C. , Dougall D. K. 
Published: March 2005

AbstractCarrot suspension cultures have been grown on glucose, fructose, and mixtures of these two sugars and the effects of these sugars on growth and anthocyanin accumulation measured. Several parameters of growth decrease with increasing glucose in the medium. The anthocyanin accumulated remains relatively low and constant until the glucose exceeds 50% of the sugar, when the anthocyanin accumulation increases with increased glucose. The data suggest that glucose and fructose are metabolized differently in these carrot cultures despite the interconversion of their 6‐phosphates in glycolysis. Ways in which the metabolism of these sugars might differ are discussed, as is the possibility of increasing the accumulation of anthocyanin by alterations in the way these sugars are made available to the cultures.
Manipulation of Heterogeneous Hybridoma Cultures for Overproduction of Monoclonal Antibodies
Authors: Mckinney Katherine L , Dilwith Robert , Belfort Georges 
Published: March 2005

AbstractIn searching for ways to manipulate heterogeneous hybridoma cell cultures (ATCC HB124) to obtain increased production of monoclonal antibodies (IgG2a), we have selected for a higher secreting but slower growing subpopulation using the level of fluorescent surface‐associated antibodies and a fluorescence‐activated cell sorter. Cell surface fluorescence was found to be correlated with specific antibody secretion rate over the short term but not with intracellular antibody content. Also, the specific secretion rate of a heterogeneous population of hybridoma cells grown in batch culture has been shown to be inversely correlated with an increase in either the initial cell concentration or the medium antibody concentration. Several experiments suggest that an upper limit exists for medium antibody concentration, above which antibody is degraded at the same rate at which it is produced. Should other cell lines behave similarly, strategies for overproduction of monoclonal antibodies suggested herein could be profitably used in industry.
Application of Immobilized Yeast Cells to Sparkling Wine Fermentation
Authors: Gòdia Francesc , Casas Carles , Solàg Carles 
Published: March 2005

AbstractThe production of sparkling wine with yeast immobilized in natural gels was investigated. Cell release from the beads to the wine was studied by using two different techniques: simple gel beads and beads with an external layer free of cells around them. In the first technique, 2% calcium alginate beads with 109 cells/g of bead and a bead dosage of 12 g/bottle were the optimal conditions to completely avoid cell leakage. When externally coated beads were employed, the dosage could be reduced to 6 g/bottle and the wine remained absolutely free of cells at the end of the fermentation. In both cases, the organoleptical properties of the sparkling wine produced with immobilized cells were found to be improved with respect to the conventional product.
Intracellular Ice Formation during the Freezing of Hepatocytes Cultured in a Double Collagen Gel
Authors: Hubel A , Toner M , Cravalho E. G , Yarmush M. L , Tompkins R. G 
Published: March 2005

AbstractDuring freezing, intracellular ice formation (IIF) has been correlated with loss in viability for a wide variety of biological systems. Hence, determination of IIF characteristics is essential in the development of an efficient methodology for cryopreservation. In this study, IIF characteristics of hepatocytes cultured in a collagen matrix were determined using cryomicroscopy. Four factors influenced the IIF behavior of the hepatocytes in the matrix: cooling rate, final cooling temperature, concentration of Me2SO, and time in culture prior to freezing. The maximum cumulative fraction of cells with IIF increased with increasing cooling rate. For cultured cells frozen in Dulbecco's modified Eagle's medium (DMEM), the cooling rate for which 50% of the cells formed ice (B50) was 70°C/min for cells frozen after 1 day in culture and decreased to 15°C/min for cells frozen after 7 days in culture. When cells were frozen in a 0.5 M Me2SO + DMEM solution, the value of B50 decreased from 70 to 50°C/min for cells in culture for 1 day and from 15 to 10°C/min for cells in culture for 7 days. The value of the average temperature for IIF (Tuf) for cultured cells was only slightly depressed by the addition of Me2SO when compared to the IIF behavior of other cell types. The results of this study indicate that the presence of the collagen matrix alters significantly the IIF characteristics of hepatocytes. Thus freezing studies using hepatocytes in suspension are not useful in predicting the freezing behavior of hepatocytes cultured in a collagen matrix. Furthermore, the weak effect of Me2SO on IIF characteristics implies that lower concentrations of Me2SO (0.5 M) may be just as effective in preserving viability. Finally, the value of B50 measured in this study indicates that cooling rates nearly an order of magnitude faster than those previously investigated could be used for cryopreservation of the hepatocytes in a collagen gel.
Use of Various Measurements for Biomass Estimation
Authors: Chattaway T. , Demain A. L. , Stephanopoulos Gregory 
Published: March 2005

AbstractElectron, carbon, and nitrogen balances can be thought of as relationships among the time rates of change of the various compounds participating in a fermentation process. As such, they define the minimum number of necessary measurements from which the remaining rates can be determined through the use of the balances. All possibilities, however, are not equivalent, and some of them lead to singularities and solutions of high sensitivity. These possibilities are reviewed in this paper, and suggestions are offered in regard to the combination of rate measurements from which robust biomass estimates can be produced.