bluuebunny/crossref_metadata_2025_split huggingface dataset:
A practical and cost‐effective mutation scanning‐based approach for investigating genetic variation in Cryptosporidium
Authors: Jex Aaron R. , Whipp Margaret , Campbell Bronwyn E. , Cacciò Simone M. , Stevens Melita , Hogg Geoff , Gasser Robin B. 
Published: October 2007

AbstractIn the present study, we used a mutation scanning‐targeted sequencing approach to assess variation in part (pgp60) of the 60 kDa glycoprotein (gp60) gene among Cryptosporidium samples from humans in Victoria, Australia. Two nuclear ribosomal loci (the small subunit rRNA gene and the second internal transcribed spacer) were used to identify the samples as Cryptosporidium hominis (n = 74), Cryptosporidium parvum (n = 23) or Cryptosporidium meleagridis (n = 1). In total, nine distinct pgp60 sequences were identified (three C. hominis, five C. parvum and one C. meleagridis). Phylogenetic analyses of the pgp60 sequence data, employing well‐defined reference sequences for comparison, allowed the genotypic and subgenotypic classification of samples. The C. hominis samples were classified as Ib A10G2R2, Id A15G1R2, and a new genotype, designated Ib2, was identified subgenotypically as A18G1R4. The C. parvum samples were classified as IIa A18G3R1, IIa A20G3R1, IIa A22G3R1, IIa A23G3R1 and IIc A5G3R2. These findings suggested that the C. hominis metapopulation is largely homogeneous, consisting of a single dominant genotype, Ib A10G2R2, whereas the C. parvum metapopulation is considerably more heterogeneous, with no single dominant genotype. The greater level of genetic heterogeneity found among the C. parvum samples, despite the smaller sample size, may relate to the zoonotic infection pattern of this species, which would be reflective of a greater number of possible infection sources. The present mutation scanning approach, coupled with targeted sequencing of genetically distinct representatives, is a practical, cost‐effective tool for large‐scale population genetic and epidemiological studies of Cryptosporidium and other eukaryotic organisms.Nucleotide sequence data reported in this paper are available in GenBank accession nos. EU164805–EU164813
Large‐volume sample stacking for the analysis of seven β‐lactam antibiotics in milk samples of different origins by CZE
Authors: Bailón‐Pérez M. Isabel , García‐Campaña Ana M. , Cruces‐Blanco Carmen , del Olmo Iruela Monsalud 
Published: October 2007

AbstractA method for the simultaneous determination of eight β‐lactam antibiotics (nafcillin, cloxacillin, oxacillin, dicloxacillin, ampicillin, amoxicillin, and penicillin G) in fortified milk samples of different origins has been proposed by using CZE with diode‐array detection (CZE‐DAD). Optimum separation was obtained on a 64.5 cm×75 μm bubble cell capillary using 175 mM Tris buffer with 20% ethanol at pH 8.0. Methylparaben has been used as an internal standard (IS). Taking into account the lack of sensitivity of the UV–Vis detection, a solvent extraction/SPE method was applied for off‐line preconcentration and sample cleanup, and also an on‐line preconcentration methodology, such as large‐volume sample stacking (LVSS) with polarity switching, was developed, providing LODs ranging from 2 to 10 μg/L. The method permits the quantification of these residues below the levels established in milk by the EU Regulation. Satisfactory recoveries ranging from 86 to 93% were also obtained in milk samples of different origins.
CE‐MS of zein proteins from conventional and transgenic maize
Authors: Erny Guillaume L. , Marina Maria Luisa , Cifuentes Alejandro 
Published: October 2007

AbstractIn this work, an original CE‐MS method has been developed to analyze the complex zein protein fractions from maize. A thorough optimization of: (i) zein protein extraction, (ii) CE separation, and (iii) electrospray‐MS (ESI‐MS) detection is carried out in order to obtain highly informative CE‐MS profiles of this fraction. The developed CE‐MS method provides good separation of multiple zein proteins based on their electrophoretic mobilities as well as adequate characterization of these proteins based on their Mr. Zein proteins with small Mr differences (below 100 Da) were easily separated and successfully analyzed by CE‐MS. Thus, apart of the so‐called 15‐kDa‐β‐zein and 16‐kDa‐γ‐zein, which are demonstrated to be formed by a heterogeneous group of proteins, numerous α‐zeins belonging to the 19‐ and 22‐kDa fraction were also identified for the first time in this work. The usefulness of this CE‐MS method was corroborated by comparing the zein‐protein fingerprints of various maize lines including transgenic and their corresponding nontransgenic isogenic lines cultivated under the same conditions.
Analysis of opioid peptides by on‐line SPE‐CE‐ESI‐MS
Authors: Hernández Elena , Benavente Fernando , Sanz‐Nebot Victoria , Barbosa José 
Published: October 2007

AbstractIn this study, SPE‐CE‐ESI‐MS is explored for the preconcentration and separation of dilute solutions of six opioid peptides. First, a CE‐ESI‐MS methodology was developed and validated. LODs of around 1 μg/mL were obtained for all the studied peptides. For SPE‐CE‐ESI‐MS experiments, a home‐made SPE microcartridge containing a C18 sorbent was constructed near the inlet of the separation capillary. After optimizing the on‐line preconcentration methodology, LODs between 10 and 0.1 ng/mL were achieved. Repeatability, reproducibility, durability of the microcartridges and linearity of the SPE‐CE‐ESI‐MS methodology were also investigated and compared to the values obtained by CE‐ESI‐MS. Finally, human plasma samples fortified with opioid peptides were analyzed by SPE‐CE‐ESI‐MS in order to show the potential of the methodology for the analysis of biological fluids.
Gene profile analysis implicates Klotho as an important contributor to aging changes in brain white matter of the rhesus monkey
Authors: Duce James A. , Podvin Sonia , Hollander William , Kipling David , Rosene Douglas L. , Abraham Carmela R. 
Published: October 2007

AbstractConventional studies of brain changes in normal aging have concentrated on gray matter as the locus for cognitive dysfunction. However, there is accumulating evidence from studies of normal aging in the rhesus monkey that changes in white matter may be a more critical factor in cognitive decline. Such changes include ultrastructural and biochemical evidence of myelin breakdown with age, as well as more recent magnetic resonance imaging of global loss of forebrain white matter volume and magnetic resonance diffusion tension imaging evidence of increased diffusivity in white matter. Moreover, many of these white matter changes correlate with age‐related cognitive dysfunction. Based on these diverse white matter findings, the present work utilized high‐density oligonucleotide microarrays to assess gene profile changes associated with age in the white matter of the corpus callosum. This approach identified several classes of genes that were differentially expressed in aging. Broadly characterized, these genes were predominantly related to an increase in stress factors and a decrease in cell function. The cell function changes included increased cell cycle inhibition and proteolysis, as well as decreased mitochondrial function, signal transduction, and protein translation. While most of these categories have previously been reported in functional brain aging, this is the first time they have been associated directly with white matter. Microarray analysis has also enabled the identification of neuroprotective response pathways activated by age in white matter, as well as several genes implicated in lifespan. Of particular interest was the identification of Klotho, a multifunctional protein that regulates phosphate and calcium metabolism, as well as insulin resistance, and is known to defend against oxidative stress and apoptosis. Combining the findings from the microarray study enabled us to formulate a model of white matter aging where specific genes are suggested as primary factors in disrupting white matter function. In conclusion, the overall changes described in this study could provide an explanation for aging changes in white matter that might be initiated or enhanced by an altered expression of life span associated genes such as Klotho. © 2007 Wiley‐Liss, Inc.
Age‐dependent accumulation of ubiquitinated 2′,3′‐cyclic nucleotide 3′‐phosphodiesterase in myelin lipid rafts
Authors: Hinman Jason D. , Chen Ci‐Di , Oh Sun‐Young , Hollander William , Abraham Carmela R. 
Published: October 2007

AbstractChanges in brain white matter are prominent features of the aging brain and include glial cell activation, disruption of myelin membranes with resultant reorganization of the molecular components of the node of Ranvier, and loss of myelinated fibers associated with inflammation and oxidative stress. In previous studies, overexpression of CNP, a key myelin protein, was implicated in age‐related changes in myelin and axons. Here we examine the extent of CNP accumulation in brain white matter and isolated myelin of aged rhesus monkeys and its relationship to CNP degradation and partitioning in myelin. With age, excess CNP is found in myelin and throughout brain white matter accompanied by proteolytic fragments of CNP. These increases occur in the absence of changes in CNP mRNA levels. Using a combination of 2D electrophoresis, immunoprecipitation, and mass spectrometry analysis, ubiquitinated CNP was demonstrable in the Triton X‐100 insoluble lipid raft associated fractions of myelin isolated from rhesus monkeys. Further, using ubiquitin‐mediated fluorescence complementation (UbFC), ubiquitinated CNP was visualized by microscopy in both COS‐7 and MO3.13 cells and by immunoblot in MO3.13 cells and appears to at least partially localize within lipid rafts. The findings suggest that incomplete degradation of CNP due to failure of the proteasomal system and aberrant degradation by calpain‐1 leads to age‐related CNP accumulation and proteolysis. In sum, we suspect these phenomena result in age‐related dysfunction of CNP in the lipid raft, which may lead to myelin and axonal pathology. © 2007 Wiley‐Liss, Inc.
Protective effects of cysteine, methionine and vitamin C on the stomach in chronically alcohol treated rats
Authors: Amanvermez Ramazan , Tunçel Özgür K. , Demir Şerif , Kefeli Mehmet , Bek Yüksel , Çelik Cemil 
Published: October 2007

AbstractA chronic intake of high dose alcohol may cause oxidative stress and inflammation in the stomach. It is hypothesized that cysteine‐methionine and vitamin C may neutralize harmful compounds while potentiating the antioxidant capacity of the cell or tissue. The experimental animals were fed regular diets and were maintained for 90 days in the control group, the alcoholic group, which was given 2.5 g of 50% ethanol kg−1body wt. administered intragastrically every other day, or the alcoholic with antioxidant supplement group, to whom 2.5 g of 50% ethanol kg−1body wt. + a solution that contained 200 mg vitamin C, 100 mg cysteine and 100 mg methionine was administered intragastrically every other day. After the treatments, the stomach was taken for pathological and biochemical analysis. The stomach of the alcoholic group rats had higher scores of pathological findings compared with the control group, whereas the scores of the antioxidant‐supplemented group were lower than the alcoholic group. In addition, the oxidized protein and lipid content in the stomachs of the alcoholic group were significantly higher than the control, but antioxidant supplementation lowered the amount of oxidation in the antioxidant supplemented group. The amount of stomach glutathione in the alcoholic group was higher than that of the control and antioxidant‐supplemented groups. Interestingly, the level of total thiol in the stomach tissue of rats with antioxidant supplement was statistically higher than that of the control and alcoholic groups. In conclusion, the scores of the pathological findings in the stomach of rats with the antioxidant supplement were lower than the chronic alcohol‐treated rats, albeit the amount of total thiol was increased in this group. Moreover, chronic alcohol treatment led to an increase in the level of lipid and protein oxidation in the stomach tissue of rats. A simultaneous intake of ascorbate/l‐cys/l‐met along with ethanol attenuated the amount of oxidation which suggested that cysteine‐methionine and vitamin C could play a protective role in the stomach against oxidative damage resulting from chronic alcohol ingestion. Copyright © 2007 John Wiley & Sons, Ltd.
Inhibition of jet fuel aliphatic hydrocarbon induced toxicity in human epidermal keratinocytes
Authors: Inman A. O. , Monteiro‐Riviere N. A. , Riviere J. E. 
Published: October 2007

AbstractJet propellant (JP)‐8, the primary jet fuel used by the U.S. military, consists of hydrocarbon‐rich kerosene base commercial jet fuel (Jet‐A) plus additives DC1‐4A, Stadis 450 and diethylene glycol monomethyl ether. Human epidermal keratinocytes (HEK) were exposed to JP‐8, aliphatic hydrocarbon (HC) fuel S‐8 and aliphatic HC pentadecane (penta), tetradecane (tetra), tridecane (tri) and undecane (un) for 5 min. Additional studies were conducted with signal transduction pathway blockers parthenolide (P; 3.0 µm), isohelenin (I; 3.0 µm), SB 203580 (SB; 13.3 µm), substance P (SP; 3.0 µm) and recombinant human IL‐10 (rHIL‐10; 10 ng ml−1). In the absence of inhibitors, JP‐8 and to a lesser extent un and S‐8, had the greatest toxic effect on cell viability and inflammation suggesting, as least in vitro, that synthetic S‐8 fuel is less irritating than the currently used JP‐8. Each inhibitor significantly (P < 0.05) decreased HEK viability. DMSO, the vehicle for P, I and SB, had a minimal effect on viability. Overall, IL‐8 production was suppressed at least 30% after treatment with each inhibitor. Normalizing data relative to control indicate which inhibitors suppress HC‐mediated IL‐8 to control levels. P was the most effective inhibitor of IL‐8 release; IL‐8 was significantly decreased after exposure to un, tri, tetra and penta but significantly increased after JP‐8 exposure compared with controls. Inhibitors were not effective in suppressing IL‐8 release in JP‐8 exposures to control levels. This study shows that inhibiting NF‐κB, which appears to play a role in cytokine production in HC‐exposed HEK in vitro, may reduce the inflammatory effect of HC in vivo. Copyright © 2007 John Wiley & Sons, Ltd.
Beneficial drugs for liver diseases
Authors: Muriel Pablo , Rivera‐Espinoza Yadira 
Published: October 2007

AbstractLiver diseases are a major problem of worldwide proportions. However, the number of drugs actually used successfully in humans is very small. In this review some of the most promising/studied drugs utilized for liver diseases were chosen and analysed critically from the basic to the clinical point of view. Antiviral agents are not discussed because excellent reviews have appeared on this topic. The compounds/preparations described herein are, alphabetically: colchicine, corticosteroids, curcumin, glycyrrhizin, interferons (for their antifibrotic properties), Liv 52, nitric oxide, resveratrol, silymarin, sulfoadenosylmethionine, and thalidomide. Colchicine and corticosteroids have been studied extensively in animals and humans; most clinical studies suggest that these compounds are not useful in the treatment of liver diseases. Glycyrrhizin is an herbal medicine with several components that has interesting hepatoprotective properties in patients with subacute liver failure but deserves more prospective controlled trials. Interferon has shown interesting antifibrotic properties in animals and humans; prospective studies on their antifibrotic/fibrolytic activity are required. Curcumin, resveratrol and thalidomide are very attractive newly discovered protective and curative compounds on experimental hepatic diseases. Their mechanism of action is associated with the ability to down‐regulate NF‐κB and to decrease pronecrotic and profibrotic cytokines. Unfortunately, clinical studies are lacking. Sulfoadenosylmethionine and silymarin are also promising drugs utilized mainly in cholestasis but the benefits can be expanded if more controlled trials are performed. The future is to carry out controlled prospective double‐blind multicenter studies with the newly discovered drugs with proven beneficial effects on animals. Fundamental hepatobiology should also be encouraged. Copyright © 2007 John Wiley & Sons, Ltd.
Photochemistry studied with ab initio orbital‐correlation and state‐correlation plots: Classic cyclobutene ring opening, and the reaction of N2 with photoexcited O2
Authors: Shi Huancong , Roettger David C. , East Allan L. L. 
Published: October 2007

AbstractPericyclic reaction theory arose from ideas presented in 1965, based on orbital‐energy correlation diagrams (Woodward and Hoffmann) and state‐energy correlation diagrams (Longuet‐Higgins and Abrahamson). Here we have used ab initio complete‐active‐space self‐consistent field (CASSCF) calculations to generate such diagrams. First we present diagrams for the classic case of cyclobutene ring opening, to demonstrate agreement between the CASSCF results and the classic diagrams of both Woodward/Hoffmann and Longuet‐Higgins/Abrahamson. Then we present diagrams for the more difficult cases of N2 + photoexcited O2, to produce either 2 NO or NNO + O. These N2 + O2 cases feature significant electron reorganization, for which elementary pencil‐and‐paper diagrams are less accurate. Finally, the benefits and limitations of such diagrams for predicting photochemistry are briefly discussed. © 2007 Wiley Periodicals, Inc. J Comput Chem 2008
Combination of molecular dynamics method and 3D‐RISM theory for conformational sampling of large flexible molecules in solution
Authors: Miyata Tatsuhiko , Hirata Fumio 
Published: October 2007

AbstractWe have developed an algorithm for sampling the conformational space of large flexible molecules in solution, which combines the molecular dynamics (MD) method and the three‐dimensional reference interaction site model (3D‐RISM) theory. The solvent‐induced force acting on solute atoms was evaluated as the gradient of the solvation free energy with respect to the solute‐atom coordinates. To enhance the computation speed, we have applied a multiple timestep algorithm based on the RESPA (Reversible System Propagator Algorithm) to the combined MD/3D‐RISM method. By virtue of the algorithm, one can choose a longer timestep for renewing the solvent‐induced force compared with that of the conformational update. To illustrate the present MD/3D‐RISM simulation, we applied the method to a model of acetylacetone in aqueous solution. The multiple timestep algorithm succeeded in enhancing the computation speed by 3.4 times for this model case. Acetylacetone possesses an intramolecular hydrogen‐bonding capability between the hydroxyl group and the carbonyl oxygen atom, and the molecule is significantly stabilized due to this hydrogen bond, especially in gas phase. The intramolecular hydrogen bond was kept intact during almost entire course of the MD simulation in gas phase, while in the aqueous solutions the bond is disrupted in a significant number of conformations. This result qualitatively agrees with the behavior on a free energy barrier lying upon the process for rotating a torsional degree of freedom of the hydroxyl group, where it is significantly reduced in aqueous solution by a cancellation between the electrostatic interaction and the solvation free energy. © 2007 Wiley Periodicals, Inc. J Comput Chem 2008
Determination of spin‐orbit coupling contributions in the framework of density functional theory
Authors: Chiodo Sandro , Russo Nino 
Published: October 2007

AbstractWe present a noniterative method to calculate spin‐orbit coupling by means of a theoretical approach that provides the use of the full Breit–Pauli operator. This method was applied to compute one and two‐electron spin‐orbit coupling contributions between singlet and triplet, and doublet and doublet states, respectively. These states have been represented by monodeterminantal wave functions and optimized using the PW91 gradient‐corrected exchange‐correlation functional and the hybrid B3LYP one. They have been supplied by the conventional density functional theory packages, and thus coupled by our spin‐orbit coupling code. Different size basis sets have been employed and the obtained results have been compared with the corresponding ones provided by some of the already existing methods and with the experimental data. They have been found to be in good quantitative agreement. © 2007 Wiley Periodicals, Inc. J Comput Chem 2008
Improved efficiency of focal point conformational analysis with truncated correlation consistent basis sets
Authors: Kahn Kalju , Kahn Iiris 
Published: October 2007

AbstractIt has been suggested that the computational cost of correlated ab initio calculations could be reduced efficiently by using truncated basis sets on hydrogen atoms (Mintz et al., J Chem Phys 2004, 121, 5629). We now explore this proposal in the context of conformational analysis of small molecules, such as hydrogen peroxide, dimethyl ether, ethyl methyl ether, formic acid, methyl formate, and several small alcohols. It is found that truncated correlation consistent basis sets that lack certain higher angular momentum functions on hydrogen atoms offer accuracy similar to traditional Dunning's basis sets for conformational analysis. Combination of such basis sets with the basis set extrapolation technique to estimate Hartree–Fock and Møller–Plesset second order energies provides composite extrapolation model chemistries that are significantly more accurate and faster than analogous single point calculations with traditional correlation consistent basis sets. Root mean square errors of best composite extrapolation model chemistries on the used set of molecules are within 0.03 kcal/mol of traditional focal point conformational energies. The applicability of composite extrapolation methods is illustrated by performing conformational analysis of tert‐butanol and cyclohexanol. For comparison, conformational energies calculated with popular molecular mechanics force fields are also given. © 2007 Wiley Periodicals, Inc. J Comput Chem 2008