bluuebunny/crossref_metadata_2025_split huggingface dataset:
Restrained point‐charge models for disaccharides
Authors: Sigfridsson Emma , Ryde Ulf , Bush Bruce L. 
Published: August 2002

AbstractVarious methods for deriving atomic partial charges from the quantum chemical electrostatic potential and moments have been tested for the sucrose molecule. We show that if no further information is used, the charges on some carbon atoms become large and charge patterns involving these atoms are badly determined and poorly transferable. Adding lone‐pairs on the ether oxygen atoms or dividing the molecule into smaller fragments did not cure the instabilities. We develop a method, CHELP‐BOW0, that restrains charges toward zero with different weights for different atoms. These harmonic restraints preserve the linear form of the least‐squares equations, which are solved in a single step using singular‐value decomposition. CHELP‐BOW0 improves the chemical transferability of the charges compared to unrestrained methods, and slightly improves their conformational transferability. It introduces a modest degradation of the fit compared to unrestrained CHELP‐BOW (mean average deviation of the potential 0.00016 vs. 0.00010 a.u.). A second new method, CHELP‐BOWC, avoids the need for restraints by including several conformations in the fit, weighting each according to its estimated energy in solution. CHELP‐BOWC charges are more transferable than CHELP‐BOW or CHELP‐BOW0 charges to conformations not included in the training set. Restraints to zero charge do not further improve transferability of the CHELP‐BOWC charges. We, therefore, recommend CHELP‐BOW charges for rigid molecules and CHELP‐BOWC charges for flexible molecules. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 351–364, 2002
Massive docking of flexible ligands using environmental niches in parallelized genetic algorithms
Authors: Thormann Michael , Pons Miquel 
Published: August 2002

AbstractVirtual screening of large libraries of small compounds requires fast and reliable automatic docking methods. In this article we present a parallel implementation of a genetic algorithm (GA) and the implementation of an enhanced genetic algorithm (EGA) with niching that lead to remarkable speedups compared to the original version AutoDock 3.0. The niching concept is introduced naturally by sharing genetic information between evolutions of subpopulations that run independently, each on one CPU. A unique set of additionally introduced search parameters that control this information flow has been obtained for drug‐like molecules based on the detailed study of three test cases of different complexity. The average docking time for one compound is of 8.6 s using eight R10,000 processors running at 200 MHz in an Origin 2000 computer. Different genetic algorithms with and without local search (LS) have been compared on an equal workload basis showing EGA/LS to be superior over all alternatives because it finds lower energy solutions faster and more often, particularly for high dimensionality problems. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1971–1982, 2001
Involvement of transcriptional repressor ATF3 in acceleration of caspase protease activation during DNA damaging agent‐induced apoptosis
Authors: Mashima Tetsuo , Udagawa Sachiko , Tsuruo Takashi 
Published: August 2002

AbstractDNA topoisomerase inhibitors are effective chemotherapeutic agents on several solid tumor cells. They induce a specific signaling cascade that executes an active cell death process (apoptosis), including caspase activation, and the blockage of the signaling is associated with drug‐resistance of tumor cells. However, little is known about the initial signal transduction induced by the agents. In the present study, we screened genes that are initially upregulated in caspase‐independent manner. We found that the activating transcription factor 3 (ATF3) protein, a repressor of cyclic‐AMP responsive element (CRE)‐dependent transcription, was strongly induced among CRE‐BP/ATF members and subsequently accumulated in nuclei following camptothecin or etoposide treatment. During induction of apoptosis, the accumulation and the nuclear translocation of ATF3 coincided with the activation of caspase protease and were not inhibited by the broad caspase inhibitor Z‐VAD‐fmk, indicating that ATF3 induction is not a downstream event of caspase activation. When stably or transiently overexpressed, ATF3 markedly accelerated the drug‐induced apoptosis and enhanced caspase protease activation. ATF3 strongly downregulated CRE‐dependent transcription, while ATF3 did not affect the expression levels of Bcl‐2, Bcl‐x, or Bax. Our present results indicate that ATF3 plays a critical role in accelerating caspase protease activation and apoptosis. Since CRE‐dependent transcription functions as cell survival signaling, ATF3 could control the upstream signaling of apoptosis by repressing CRE‐dependent gene expression of cell survival factors. © 2001 Wiley‐Liss, Inc.
Effect of the aeration rate on pullulan production and fermentation broth rheological properties in an airlift reactor
Authors: Roukas T , Mantzouridou F 
Published: August 2002

AbstractThe effect of aeration rate on pullulan production and the rheological properties of the fermentation broth in an airlift reactor was investigated. An airlift fermenter was shown to be an appropriate fermentation system for the production of pullulan. A maximum pullulan concentration (30 kg m−3), biomass concentration (6.0 kg m−3), pullulan yield (60%, w/w) and sugar utilization (100%, w/w) was obtained at an aeration rate of 2 vvm. The mycelium and the yeast‐like cells were the morphological forms responsible for pullulan production. The highest polysaccharide concentration was obtained when the mycelial forms and the yeast‐like cells were 60% and 40% (w/w) of the total biomass, respectively. The apparent viscosity of the broth was increased with the increase of the aeration rate from 1 to 2 vvm and then decreased at higher vvms. On the other hand, the dissolved oxygen concentration and the volumetric mass transfer coefficient continually increased with the increase of the aeration rate. The mycelial forms and the production of extracellular polysaccharide were responsible for the non‐Newtonian flow behaviour of the fermentation broth. The rheological behaviour can be characterized by a power law type of equation. The relationship between shear rate/shear stress and shear rate/apparent viscosity showed a non‐Newtonian behaviour of the fermentation broth.© 2001 Society of Chemical Industry
Color Doppler sonography of hepatic artery reconstruction in liver transplantation
Authors: De Candia Alessandro , Como Giuseppe , Tedeschi Luigi , Zanardi Romeo , Vergendo Maurizio , Rositani Pasquale , Bazzocchi Massimo 
Published: August 2002

AbstractPurposeThe purpose of this study was to evaluate the Doppler spectral waveforms in the hepatic artery after liver transplantation and hepatic artery reconstruction by end‐to‐end anastomosis or aortohepatic bypass. The peak systolic velocities (PSVs), end‐diastolic velocities (EDVs), and resistance indices (RIs) between the 2 reconstruction groups were compared to establish normal post‐transplantation values.MethodsWe retrospectively reviewed the Doppler sonograms and the sonographic reports from 48 patients who had undergone liver transplantation, 30 with end‐to‐end arterial anastomoses and 18 with aortohepatic bypasses. All aortohepatic bypasses had been performed using the infrarenal technique. All sonographic examinations had been performed 3–6 months after transplantation in patients with no clinical sign of transplant failure and whose liver function test results more normal. We compared the mean hepatic artery PSVs, EDVs, and RIs of the 2 groups.ResultsDoppler spectral analysis allowed the detection of 2 types of arterial flow, a low‐resistance pattern in the end‐to‐end anastomosis group and a high‐resistance pattern with low diastolic flow in the infrarenal bypass group. The mean PSV ± standard deviation (SD) was 57 ± 16 seconds in the end‐to‐end anastomosis group and 62 ± 16 cm/second in the infrarenal bypass group. The mean EDV ± SD was 25 ± 14 cm/second in the end‐to‐end anastomosis group and 12 ± 4 cm/second in the infrarenal bypass group. The RIs ranged from 0.33 to 0.71 (mean ± SD, 0.58 ± 0.13) in the patients with end‐to‐end anastomoses and from 0.70 to 0.87 (mean ± SD, 0.77 ± 0.06) in those with infrarenal bypasses. The difference in the mean RIs between the 2 groups was statistically significant (p < 0.05).ConclusionsSpectral waveform and RI are associated with the length and caliber of the type of hepatic artery anastomosis used. End‐to‐end anastomoses are short and have a uniform small caliber; aortohepatic bypasses are longer and have a progressively by smaller caliber. We must be cognizant of the method of anastomosis used when examining patients for complications after liver transplantation because the method used affects the resulting spectral waveform and RI. © 2002 John Wiley & Sons, Inc. J Clin Ultrasound 30:12–17, 2002.
Single molecule studies by means of the two‐photon fluorescence distribution
Authors: Chirico Giuseppe , Cannone Fabio , Beretta Sabrina , Baldini Giancarlo , Diaspro Alberto 
Published: August 2002

AbstractWe have characterized a commercial confocal scanning head for the detection of single molecule fluorescence by two‐photon excitation. We have verified that the distribution of the fluorescence emitted by dyes and labeled proteins on glass substrates is discrete with quanta proportional to a common reference signal. We describe and test a simple and quantitative tool to discriminate between single molecules and molecular aggregates on single snapshots based on the analysis of the intensity distribution. We have verified the square dependence of the fluorescence intensity vs. the excitation power, suggesting that no appreciable saturation and fast photo‐damage of the chromophores takes place at the excitation power employed here. Microsc. Res. Tech. 55:359–364, 2001. © 2001 Wiley‐Liss, Inc.
Magnocellular vasopressin system in ontogenesis: Development and regulation
Authors: Ugrumov Michael V. 
Published: August 2002

AbstractThis review is devoted to the development, functional activity, and regulation of the magnocellular vasopressin (VP) system in ontogenesis. Magnocellular VP neurons originate in embryos from the neuroepithelium of the third ventricle and migrate first to the supraoptic nucleus and then to the paraventricular nucleus and accessory nuclei. The preproVP gene and synthesis are expressed simultaneously in the newly formed neurons either during migration or just after arrival in magnocellular nuclei. Still, a number of VP‐immunoreactive neurons increase in immature mammals to prepuberty, which is explained by VP expression in the initially “silent” neurons, or by an increase of VP synthesis that makes a cell distinguishable by immunocytochemistry. An enzymatic processing of preproVP is slightly delayed compared to the onset of preproVP synthesis. Axons of magnocellular neurons reach the pituitary posterior lobe before or just after the neuron arrival in magnocellular nuclei. The mechanisms of VP release from the axon terminals are developed in immature animals over the perinatal period. The VP neurons begin to react to functional (osmotic) stimulation by increased synthesis of VP mRNA and VP in immature animals from the end of fetal life. A functional maturation of the VP system is under control by neural afferents, neuropeptides, and some hormones of endocrine glands. Namely, glucocorticoids, VP, catecholamines, glutamate, and opioids provide short‐term or long‐lasting effects on differentiating VP neurons. Most of the intercellular signals inhibit the specific phenotype expression of differentiating VP neurons: VP gene and synthesis in normal conditions, as well as TH gene and synthesis under functional stimulation. Microsc. Res. Tech. 56:164–171, 2002. © 2002 Wiley‐Liss, Inc.
FMRFamide in the amphibian brain: A comprehensive survey
Authors: Rastogi Rakesh K. , D'Aniello Biagio , Pinelli Claudia , Fiorentino Maria , Di Fiore Maria M. , Di Meglio Maria , Iela Luisa 
Published: August 2002

AbstractMapping of FMRFamidergic neural circuitry in the amphibian brain has been done by immunohistochemical methods. Comparative evidence suggests that there are similarities and differences in the overall pattern of distribution of FMRFamide‐ir elements in the brain among the three amphibian orders and within each order. FMRFamide is expressed in neurons in some circumscribed areas of the brain. A part of these neurons is concentrated in classical neurosecretory areas of the hypothalamus in a bilaterally symmetrical fashion. Similar neurons occur occasionally in the midbrain, but are virtually absent from the hindbrain. Anurans are unique among amphibians to show FMRFamide neurons in the medial septum and diagonal band of Broca. A viviparous gymnophione is known to possess a small population of such neurons in the dorsal thalamus. Together, the FMRFamide neurons contribute to an extensive fiber network throughout the amphibian brain. Descriptive developmental studies suggest that the rostral forebrain‐located FMRFamide neurons originate in the olfactory placode and then migrate into the brain along the route of the vomeronasal‐olfactory‐terminal nerve complex. Olfactory placodal ablation in an anuran and a urodele provide experimental support to this contention. Other FMRFamide neuronal cell groups, in the hypothalamus and dorsal thalamus, are supposed to arise from non‐placodal precursors. The neuroanatomical distribution (projection of immunoreactive processes to areas of the fore‐, mid‐, and hindbrain as well as to cerebrospinal fluid, co‐localization with other neuropeptides, and presence in the median eminence) has furnished morphological correlates of possible functions of FMRFamide in the amphibian CNS. While amphibian FMRFamide‐like or structurally related peptides remain to be isolated and characterized, the sum of the distribution pattern of FMRFamide‐like immunoreactivity suggests that it may act as a neurotransmitter or a neuromodulator, and also may have endocrine regulatory functions. Microsc. Res. Tech. 54:158–172, 2001. © 2001 Wiley‐Liss, Inc.
Distribution patterns and morphology of sensilla on the apical segment of the antennae and palpi of Hydradephaga (Coleoptera: adephaga)
Authors: Baker Gerald T. 
Published: August 2002

AbstractThe sensilla on the terminal antennomere of selected Hydradephagans (Coleoptera) are modified in several distinct ways as compared to the sensilla on the terminal antennomere of Geadephagans (Coleoptera). There are no long sensilla of any type on antennae of Hydradephagans, the sensilla are either short, peg‐like sensilla that may be recessed in the antennal surface or they are multiporous plate‐like sensilla. Multiporous plate‐like sensilla have not been found on the antennae of Geadephagans. A pit sensillum occurs on the antennae of one family, Gyrinidae, in the Hydradephaga whereas it is found on the antennae of several species from the families of Geadephaga. The sensilla on the terminal antennomere of Hydradephaga are often grouped into sensory fields that could be located on a particular area of the antennomere. Sensory fields are also located on the apices of the maxillary and labial palps and the most unique sensory fields occur in the Noteridae. The maxillary palpal apex of Hydrocanthus oblongus (Noteridae) is bifurcate and a sensory field with several types of sensilla is at the apex of each branch. The terminal labial palpomere is greatly enlarged and has a long, slender sensory field at the apex and a secondary sensory field on a thumb‐like projection. The sensilla on the palpal apices are more diverse and complex in form as compared to the sensilla on the palps of Geadephaga. The most complex sensillum has a cuticular collar and a dome that is divided into six or seven triangular sections. The dome maybe opened or closed and a peg‐like sensillum with a very wide apical pore is situated beneath the dome. Microsc. Res. Tech. 55:330–338, 2001. © 2001 Wiley‐Liss, Inc.
Ped gene deletion polymorphism frequency in wild mice
Authors: Newmark Judith A. , Sacher Frank , Jones Gwilym S. , Warner Carol M. 
Published: August 2002

AbstractThe Ped gene influences the rate of cleavage of preimplantation embryos and their subsequent survival. Embryos that express the product of the Ped gene, Qa‐2 protein, cleave at a faster rate than embryos with an absence of Qa‐2 protein. In addition, the Ped gene has pleiotropic effects on reproduction. Thus, there is a reproductive advantage to those mouse strains that are Qa‐2 positive. The presence or absence of Qa‐2 is reflected at the DNA level by the presence or absence (deletion polymorphism) of the gene(s) encoding Qa‐2 protein. Many inbred and wild‐derived mouse strains have been characterized as Qa‐2 positive or negative, but no previous studies have looked at the distribution of the Ped gene in a population of free‐living wild mice. The purpose of this study was to determine the Ped gene deletion polymorphism frequency in a sample of free‐living wild mice. Twenty‐nine mice were collected and identified as Mus musculus. Genomic DNA extraction was performed on tail tips, and PCR was used to amplify a region from the Ped gene. Known Qa‐2 positive and negative mice were used as controls. Results showed that all 29 wild mice were positive for the Ped gene. Since the Ped gene is dominant and provides a reproductive advantage, it is not surprising that all of the wild mice were Qa‐2 positive. However, our assay could not distinguish homozygous from heterozygous mice. It is possible that the Qa‐2 deletion polymorphism is segregating in the population, and a larger sample size would identify some Qa‐2 negative mice. © 2002 Wiley‐Liss, Inc.
Phenotype plasticity in postural muscles of the crayfish Orconectes limosus Raf.: Correlation of myofibrillar ATPase‐based fiber typing with electrophysiological fiber properties and the effect of chronic nerve stimulation
Authors: Gruhn Matthias , Rathmayer Werner 
Published: August 2002

AbstractThe characteristics of the medial and lateral superficial extensor muscles (sem and sel) in the crayfish Orconectes limosus abdomen and their developmental and activity‐dependent plasticity were studied. It was shown that both muscles are innervated by at least five excitatory and one inhibitory motor neuron in a nonuniform pattern. The muscles are composed of at least three different mATPase histochemistry‐based fiber types that are all different from a fourth type in the uniform deep extensor muscles. sem and sel are composed of different ratios of these fiber types but do not show a constant fiber type pattern between segments and even between hemisegments. The three histochemically defined superficial extensor‐fiber types have characteristic electrophysiological properties. The fiber types were shown to develop successively during the first postembryonic stages of development without a change in the number of muscle fibers. Based on histochemical ATPase staining after 21 days of chronic stimulation by means of an implantable, double‐hook electrode, we show preliminary evidence that the fiber composition in the sem can switch from the presumably fast fiber type III to an intermediate type II. Repeated axotomy up to 53 days had no effect on the fiber type composition of the muscles. © 2002 Wiley‐Liss, Inc.
Phylogenetic distribution of apolipoproteins A‐I and E in vertebrates as determined by Western blot analysis
Authors: Duggan Annemarie E. , Callard Ian P. 
Published: August 2002

AbstractA putative apolipoprotein E (apoE) has been identified in the HDL and VHDL fractions of the turtle. This observation is of particular interest considering apoE has been reported absent in the domestic hen (Hermier et al., ’95; Biochim Biophys Acta: 105–118, 1995) and thus presumed absent in nonmammalian vertebrates altogether. As a result, partial amino acid sequencing of this protein was performed and revealed that one fragment shared 41% sequence identity to human apoE. Western blot analysis using antisera to apoE demonstrated cross‐reactivity to a 34‐kDa protein (putative apoE) in turtle plasma. Further investigation using anti‐apoE antibody in Western blot analysis detected immunoreactive apoE in the plasma of lamprey, spiny dogfish, skate, and alligator, but not in flounder, newt or python; its absence in several species of birds was confirmed. Using anti‐apoA‐I antibody, apoA‐I was detected in all vertebrate groups except a representative teleost (flounder). Apo‐A‐I antibody cross‐reacted weakly with some putative apoE proteins (chicken, spiny dogfish and skate) and the reverse was true for anti‐apoE, which cross‐reacted with putative apoA‐I in birds, reptiles, and elasmobranchs, confirming the molecular similarity and phylogenetic relatedness of these two proteins. J. Exp. Zool. 290:255–264, 2001. © 2001 Wiley‐Liss, Inc.
Highly efficient gene transfer into antigen‐specific primary mouse lymphocytes with replication‐deficient retrovirus expressing the 10A1 envelope protein
Authors: Annenkov Alexander E. , Daly Gordon M. , Chernajovsky Yuti 
Published: August 2002

AbstractBackgroundIntroduction of recombinant genes in the genome of primary lymphocytes by virtue of a replication‐deficient retrovirus can be used in immunological studies and for cell‐based gene therapy.MethodsPackaging cells GP+E86 producing replication‐deficient retrovirus incorporating the genes of enhanced green fluorescent protein (eGFP), C2γ or C2ξ, were generated by calcium phosphate‐mediated transfection. Clones with the highest titres of retrovirus vector were isolated from them and their supernatants were used for transduction of PT67 cells. Primary mouse lymphocytes and T‐cell hybridoma MD.45 were transduced by centrifugation with retroviral stock. The retroviral content of packaging cell supernatants was determined by dot blotting and hybridization with a DNA probe.ResultsPT67 cells produced ∼50 times more retrovirus vector than the original GP+E86 clones. When retroviral stocks of PT67 and GP+E86 cells were used at 1/50 dilution and undiluted, respectively (to normalize them forretroviral RNA content), the transduction efficiency of mouse T‐cell hybridoma was 40% and 5%, respectively. Centrifugation of target cells with retroviral stock at 2000 g for 60 min increased the percentage of transduced cells two‐ to three‐fold. Within a population of cells isolated from the draining lymph nodes of an immunized mouse and reactivated with an antigen, up to 60% of CD4+ T cells and up to 80% of B cells could be transduced with a transgene in replication‐deficient retrovirus packaged by PT67 cells using the optimized gene transfer protocol.ConclusionsThis protocol allows for the generation of packaging cells producing high titres of retrovirus vector. The 10A1 envelope protein is superior to the ecotropic one for the transduction of mouse lymphocytes. Copyright © 2002 John Wiley & Sons, Ltd.
Packing trees into planar graphs
Authors: García A. , Hernando C. , Hurtado F. , Noy M. , Tejel J. 
Published: August 2002

AbstractIn this study, we provide methods for drawing a tree with n vertices on a convex polygon, without crossings and using the minimum number of edges of the polygon. We apply the results to obtain planar packings of two trees in some specific cases. © 2002 Wiley Periodicals, Inc. J Graph Theory 40: 172–181, 2002
Hamiltonian cycles in n‐extendable graphs
Authors: Kawarabayashi Ken‐ichi , Ota Katsuhiro , Saito Akira 
Published: August 2002

AbstractA graph G of order at least 2n+2 is said to be n‐extendable if G has a perfect matching and every set of n independent edges extends to a perfect matching in G. We prove that every pair of nonadjacent vertices x and y in a connected n‐extendable graph of order p satisfy degG x+degG y ≥ p − n − 1, then either G is hamiltonian or G is isomorphic to one of two exceptional graphs. © 2002 Wiley Periodicals, Inc. J Graph Theory 40: 75–82, 2002