bluuebunny/crossref_metadata_2025_split huggingface dataset:
iGibbs: Improving Gibbs motif sampler for proteins by sequence clustering and iterative pattern sampling
Authors: Kim Sun , Wang Zhiping , Dalkilic Mehmet 
Published: November 2006

AbstractThe motif prediction problem is to predict short, conserved subsequences that are part of a family of sequences, and it is a very important biological problem. Gibbs is one of the first successful motif algorithms and it runs very fast compared with other algorithms, and its search behavior is based on the well‐studied Gibbs random sampling. However, motif prediction is a very difficult problem and Gibbs may not predict true motifs in some cases. Thus, the authors explored a possibility of improving the prediction accuracy of Gibbs while retaining its fast runtime performance. In this paper, the authors considered Gibbs only for proteins, not for DNA binding sites. The authors have developed iGibbs, an integrated motif search framework for proteins that employs two previous techniques of their own: one for guiding motif search by clustering sequences and another by pattern refinement. These two techniques are combined to a new double clustering approach to guiding motif search. The unique feature of their framework is that users do not have to specify the number of motifs to be predicted when motifs occur in different subsets of the input sequences since it automatically clusters input sequences into clusters and predict motifs from the clusters. Tests on the PROSITE database show that their framework improved the prediction accuracy of Gibbs significantly. Compared with more exhaustive search methods like MEME, iGibbs predicted motifs more accurately and runs one order of magnitude faster. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Serendipitous discovery of novel bacterial methionine aminopeptidase inhibitors
Authors: Evdokimov Artem G. , Pokross Matthew , Walter Richard L. , Mekel Marlene , Barnett Bobby L. , Amburgey Jack , Seibel William L. , Soper Shari J. , Djung Jane F. , Fairweather Neil , Diven Conrad , Rastogi Vinit , Grinius Leo , Klanke Charles , Siehnel Richard , Twinem Tracy , Andrews Ryan , Curnow Alan 
Published: November 2006

AbstractIn this article we describe the application of structural biology methods to the discovery of novel potent inhibitors of methionine aminopeptidases. These enzymes are employed by the cells to cleave the N‐terminal methionine from nascent peptides and proteins. As this is one of the critical steps in protein maturation, it is very likely that inhibitors of these enzymes may prove useful as novel antibacterial agents. Involvement of crystallography at the very early stages of the inhibitor design process resulted in serendipitous discovery of a new inhibitor class, the pyrazole‐diamines. Atomic‐resolution structures of several inhibitors bound to the enzyme illuminate a new mode of inhibitor binding. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Enhanced sampling of peptide and protein conformations using replica exchange simulations with a peptide backbone biasing‐potential
Authors: Kannan Srinivasaraghavan , Zacharias Martin 
Published: November 2006

AbstractDuring replica exchange molecular dynamics (RexMD) simulations, several replicas of a system are simulated at different temperatures in parallel allowing for exchange between replicas at frequent intervals. This technique allows significantly improved sampling of conformational space and is increasingly being used for structure prediction of peptides and proteins. A drawback of the standard temperature RexMD is the rapid increase of the replica number with increasing system size to cover a desired temperature range. In an effort to limit the number of replicas, a new Hamiltonian‐RexMD method has been developed that is specifically designed to enhance the sampling of peptide and protein conformations by applying various levels of a backbone biasing potential for each replica run. The biasing potential lowers the barrier for backbone dihedral transitions and promotes enhanced peptide backbone transitions along the replica coordinate. The application on several peptide cases including in all cases explicit solvent indicates significantly improved conformational sampling when compared with standard MD simulations. This was achieved with a very modest number of 5–7 replicas for each simulation system making it ideally suited for peptide and protein folding simulations as well as refinement of protein model structures in the presence of explicit solvent. Proteins 2007. © 2006 Wiley‐Liss, Inc.
Semiconductor quantum dots devices: Recent advances and application prospects
Authors: Reithmaier J. P. , Somers A. , Kaiser W. , Deubert S. , Gerschütz F. , Forchel A. , Parillaud O. , Krakowski M. , Alizon R. , Hadass D. , Bilenca A. , Dery H. , Mikhelashvili V. , Eisenstein G. , Gioannini M. , Montrosset I. , Berg T. W. , van der Poel M. , Mørk J. , Tromborg B. 
Published: November 2006

AbstractIn this paper, a brief review will be given on recent advances in semiconductor quantum dots based optoelectronic devices. The focus will be on two major application areas, i.e., telecom devices and high power light sources, where some device examples will be discussed on the current status and for the future prospects. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Anisotropic exchange interaction induced by a few photons in semiconductor microcavities
Authors: Chiappe G. , Louis E. , Anda E. V. 
Published: November 2006

AbstractWe investigate coupling of localized spins in a semiconductor quantum dot embedded in a microcavity. The cavity mode and the quantum dot exciton are coupled forming a polariton, whereas excitons interact with localized spins via exchange. The Hamiltonian, which treats all degrees of freedom quantum mechanically, is solved exactly. Main results, for up to three photons and cavities with a finite quality factor, are: a) at sufficiently low temperatures a finite anisotropic exchange interaction between spins is induced for small exciton occupation numbers, b) a finite quality factor induces an abrupt change to and fro between ferromagnetic and antiferromagnetic exchange interaction, and, c) the spin–spin correlation undergoes non‐trivial changes upon increasing the number of photons from one to three. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Resonance impurity scattering in superconductivity in PrOs4Sb12
Authors: Parker D. , Haas S. , Maki K. 
Published: November 2006

AbstractThe cover picture depicts the phase diagram of the heavy‐fermion superconductor PrOs4Sb12 (T c = 1.85 K) from measurements of magnetothermal conductivity data by K. Izawa et al. [1]. This superconductor is believed to have two phases with distinct order parameter symmetries. The high‐temperature, high‐field A‐phase contains four order parameter point nodes in the ab ‐plane and two additional nodes (not shown) along the c‐axis, while the lower‐temperature B‐phase contains just two point nodes in the ab ‐plane. This material is believed to be a spin‐triplet superconductor and exhibits two distinct superconducting transitions, as shown in the diagram. The picture relates to the Editor's Choice by David Parker et al. which proposes order parameters consistent with these data and works out the consequences of resonant impurity scattering in this material [2]. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Effects of phytoestrogenic isoflavones from red clover (Trifolium pratense L.) on experimental osteoporosis
Authors: Occhiuto F. , Pasquale R. De , Guglielmo G. , Palumbo D.R. , Zangla G. , Samperi S. , Renzo A. , Circosta C. 
Published: November 2006

AbstractThe most common type of osteoporosis is bone loss associated with ovarian hormone deficiency at menopause. There is evidence that diets which contain high levels of phytoestrogenic isoflavones are associated with a low incidence of osteoporosis and menopausal symptoms. Plant extracts, which contain high levels of isoflavones, such as Red clover (Trifolium pratense L.), have been used to reduce menopausal symptoms.The objective of this study was to evaluate the preventive effects of Red clover total isoflavones on the progression of bone loss induced by estrogens deficiency (ovariectomy) in rats. Bilateral ovariectomy was performed on female Wistar rats. One week after the operation the rats were treated with an oral dose of 20 and 40 mg of total isoflavones daily for 14 weeks. The results from this study showed that the ovariectomy reduced bone mineral content, femoral weight, femoral density, mechanical strength of the tibia and increased the levels of bone specific alkaline phosphatase in the serum and the number of osteoclasts in the femur sections compared with sham operated controls. Treatment with isoflavones significantly increased bone mineral content, mechanical strength of the tibia, femoral weight, femoral density and prevented the rise of serum alkaline phosphatase levels. In addition, the treatment with isoflavones significantly reduced the number of osteoclasts compared with the ovariectomized control rats. These findings suggest that Red clover isoflavones are effective in reducing bone loss induced by ovariectomy, probably by reducing of the bone turnover via inhibition of bone resorption. Copyright © 2006 John Wiley & Sons, Ltd.
Quantification of trandolapril and its metabolite trandolaprilat in human plasma by liquid chromatography/tandem mass spectrometry using solid‐phase extraction
Authors: Nirogi Ramakrishna V. S. , Kandikere Vishwottam N. , Shrivastava Wishu , Mudigonda Koteshwara 
Published: November 2006

AbstractA sensitive high‐performance liquid chromatography/electrospray ionization tandem mass spectrometry (MS/MS) method was developed and validated for the simultaneous quantification of trandolapril and its metabolite trandolaprilat in human plasma using ramipril as an internal standard. Following solid‐phase extraction, the analytes were separated using an isocratic mobile phase on a reversed‐phase column and analyzed by MS/MS in the multiple reaction monitoring mode using the respective [M–H]− ions, m/z 429/168 for trandolapril, m/z 401/168 for trandolaprilat and m/z 415/166 for the internal standard. The method exhibited a linear dynamic range of 20–10 000 pg/mL for both trandolapril and trandolaprilat in human plasma. The lower limit of quantification was 20 pg/mL for both trandolapril and its metabolite. Acceptable precision and accuracy were obtained for concentrations over the standard curve range. A run time of 2.0 min for each sample made it possible to analyze more than 400 human plasma samples per day. The validated method has been successfully used to analyze human plasma samples for application in pharmacokinetic, bioavailability or bioequivalence studies. Copyright © 2006 John Wiley & Sons, Ltd.
Atmospheric pressure desorption/ionization on silicon ion trap mass spectrometry applied to the quantitation of midazolam in rat plasma and determination of midazolam 1′‐hydroxylation kinetics in human liver microsomes
Authors: Steenwyk Rick C. , Hutzler J. Matthew , Sams Jim , Shen Zhouxin , Siuzdak Gary 
Published: November 2006

AbstractThe application of atmospheric pressure desorption/ionization on silicon (AP‐DIOS) coupled with ion trap mass spectrometry (ITMS) was investigated for the quantification of midazolam in rat plasma, and determination of midazolam 1′‐hydroxylation kinetics in pooled human liver microsomes. Results indicate good sensitivity with absolute detection limits for midazolam in rat plasma of approximately 300 femtograms. A linear dynamic range from approximately 10–5000 ng/mL was obtained in rat plasma with analysis times of 1 min per sample. Kinetic constants for midazolam 1′‐hydroxylation in human liver microsomes yielded an apparent Kmof 10.0 µM and Vmaxof 6.4 nmol/min/mg. Studies investigating the inhibition of 1′‐hydroxymidazolam formation by the cytochrome P450 3A4 model inhibitor ketoconazole yielded an IC50of 0.03 µM. Quantitative precision for replicate analysis of rat plasma and human liver microsomal samples was variable with relative standard deviation (RSD) values ranging from a low of approximately 3% to over 50%, with the highest variability observed in data from human liver microsomal incubations. While preliminary studies investigating the application of AP‐DIOS‐ITMS suggested feasibility of this technique to typical pharmacokinetic applications, further work is required to understand the underlying causes for the high variability observed in these investigations. Copyright © 2006 John Wiley & Sons, Ltd.
Acute and repeated administration of fluoxetine, citalopram, and paroxetine significantly alters the activity of midbrain dopamine neurons in rats: An in vivo electrophysiological study
Authors: Sekine Yoshimoto , Suzuki Katsuaki , Ramachandran P. Veeraraghavan , Blackburn Thomas P. , Ashby Charles R. 
Published: November 2006

AbstractWe examined the effect of the administration of the selective serotonin reuptake inhibitors (SSRIs) fluoxetine, citalopram, and paroxetine on the activity of spontaneously active dopamine (DA) neurons in the substantia nigra pars compacta (SNC) and ventral tegmental area (VTA) in anesthetized adult male Sprague–Dawley rats. This was accomplished using the technique of in vivo extracellular recording. A single injection of 2.5 mg/kg (i.p.) of fluoxetine significantly increased the number of spontaneously active SNC and VTA DA neurons. In contrast, a single injection of either 1 mg/kg (i.p.) of paroxetine or 5 mg/kg of fluoxetine significantly increased the number of spontaneously active VTA DA neurons. The repeated administration (one injection per day for 21 days) of all of the SSRIs produced a significant increase in the number of spontaneously active VTA DA neurons. Overall, our results indicate that the systemic administration of SSRI alters the activity of midbrain DA neurons with differential effects on VTA compared with SNC DA neurons. Synapse 61:72–77, 2007. © 2006 Wiley‐Liss, Inc.
Population studies of Cavelerius saccharivorus Okajima (Heteroptera: Lygaeidae): Adult dispersal in relation to the density
Authors: Murai Minoru 
Published: November 2006

SummaryTwo adjacent stations (H and L) were set up to study movement of C. saccharivorus adults in sugarcane fields. At the beginning of the study the density of C. saccharivorus including all stages of development was quite different between the two. The density of the first generation adult on Station H was about 5 times that on Station L. The number of C. saccharivorus on both the stations became almost the same one month after the beginning of the study. At the beginning of the study macropterous adults were more numerous in Station H than in Station L. However percentage of macropterous adults on Station L increased after one month whereas that on Station H declined.About 2,000 marked adults were released on each station during the early period of the emergence of the first generation adult. Marked insects were recaptured on both the stations one month after the release. The adults released on the dense population (H) tended to disperse more actively than those on the scarce population (L). Marked macropterous adults moved more actively than brachypterous ones. The density related dispersal of adults was considered to be an important factor to regulate the population density.
A further note on Kiritani and Nakasuji's model for stage‐frequency data including comments on the use of Tukey's jackknife technique for estimating variances
Authors: Manly B. F. J. 
Published: November 2006

SummarySome general equations for stage‐frequency estimation are presented and their applications discussed.Tukey's (1958) jackknife technique is suggested for the calculation of the approximate variances associated with estimators of population parameters.
Maternal age as a source of variation in the ability of an aphid to produce dispersing forms
Authors: MacKay A. , Wellington W. G. 
Published: November 2006

SummaryApterous parthenogentic females of the pea aphid, Acyrthosiphon pisum (Harris), begin to produce alate offspring soon after they have been subjected to crowding.Females which were born early in their own parent's reproductive period respond most strongly to crowding, producing much larger numbers of alatae than their late‐born sisters.In contrast, the early‐born daughters of most alate females do not produce winged offspring after being crowded. Some of their later‐born sisters may produce a few winged individuals, resembling in this respect the late‐born daughters of the apterous females.Control of the production of alatae thus begins in the grandparental generation. Risk‐spreading by means of differential dispersal becomes a less uncertain venture when local populations can modify their responses to environmental changes by utilizing past as well as present signals from their surroundings.
Generation carryover of a fraction of population members as an animal adaptation to unstable environmental conditions
Authors: Takahashi Fumiki 
Published: November 2006

SummaryA heterogeneous life cycle of individuals in a population was examined on its adaptive significance to an unstable environmental condition. The trend of population growth was simulated by a simple mathematical model in which a part of population in a certain generation was carried over to the next generation without participating in the reproduction.With the increase of the rate of carryover of individuals to the next generation the population fluctuation tended to be stabilized. A minute fraction of population is carried over, the effect is very large to prevent the population decline at a sequence of adverse environmental conditions. The population level increased greatly depending upon the extent of environmental change as far as the rate of carryover took an intermediate value. The optimum proportion of members to be carried over to the next generation was determined by the extent of environmental change and its frequency of occurrence.
The influence of pheromones produced by freely growing laboratory populations on the reproductive maturation of prairie deermice following prenatal and postnatal exposure
Authors: Kipps Patricia L. , Terman C. Richard 
Published: November 2006

SummarySignificantly more females reared on bedding soiled by different populations reproduced by 100 days of age than those reared on bedding soiled by the same populations (P<.1) or on clean bedding (P<.025) whereas the latter two groups did not differ significantly. Significantly greater percentages of females reproduced in both treatments maintained on soiled bedding than was true in the populations from which the bedding came. There were no significant differences between treatments in the weights of the reproductive organs (testes, seminal vesicles, ovaries, uteri) or in the numbers of corpora lutea or mature follicles in the ovaries of nulliparous females. The data suggest that if there were reproductively inhibiting pheromones influencing the population animals, they were altered or dissipated immediately after removal of the bedding from the population enclosures or that they were nonfunctional in the absence of the population animals. These data further suggest that the reproductive inhibition of population young is due to the presence of the populaton animals and that sociobiological factors within the populations act to prevent the reproductively stimulating influence of materials which may be present.
Population dynamics of Malacosoma neustria testacea (Lepidoptera: Lasiocampidae): Stabilizing process in a field population
Authors: Shiga Masakazu 
Published: November 2006

SummaryStabilizing mechanism in population of Malacosoma neustria testacea was investigated in a central part of Japan based on eight year survey.Population fluctuation in each developmental stage in the experimental field was rather small, i.e., 5.9 times in egg and 85.0 times in female adult. Pupal weight negatively correlated with the densities of 5th instar larvae and prepupae (cocoons) and correlation coefficient was highly significant in females. Population density was stabilized by density‐dependent dispersal of female moths in preovipositional period. Comparison between fecundity of emerged moths and that of actually oviposited ones in the experimental field suggested that density‐dependent dispersal took place as the result of density‐dependent size variation, i.e., small‐sized female months have higher flying ability. This hypothesis was supported by the experiment in which flying ability of newly emerged female moth was measured. Similar stabilizing mechanism is expected to occur in semelparous or pro‐ovigenic insects.
Studies on the basic components of the predation of Phytoseiulus persimilis Athias‐Henriot (Acarina: Phytoseiidae)
Authors: Ryoo Mun Il 
Published: November 2006

SummaryThe basic components of the predation of Phytoseiulus persimilisAthias‐Henriot feeding upon eggs of Tetranychus urticaeKoch were studied in an open system where the predator could disperse freely.The type of the functional response of the predator to the density of its prey was the same as that studied so far in a closed system, i.e.,Holling's Type 2. The search rate of the predator, however, was much lower in comparison with the result from a closed system. The oviposition of the predator per day was only weakly related to prey densities higher than 10 per leaf disc. But the emigration rate was inversely dependent upon the initial prey density up to 60 per leaf disc. The searching behaviour of the predator was influenced by both the web density spun by T. urticae and the density of the prey: the predator searched for its prey intensively only after it had contact with web. Mutual interference was observed in prey consumption, but not in the emigration rate. The emigration rate was largely dependent upon the prey density available per predator.
Impact of developmental variance on behavior of models for insect populations II. Models for populations with density dependent restrictions on growth
Authors: Bellows T. S. 
Published: November 2006

SummaryThe impact of variation in developmental times on behavior of models for insect populations is investigated with special reference to models which include various types of intraspecific competition. At low densities, increases in developmental variation led to decreases in reproductive rate. At high densities, increases in developmental variation led to increases in reproductive rate. There was little change in the relationship between developmental variance and generation time as density increased.
Comparison of male adult population densities of the oriental and artocarpus fruit flies, Dacus spp. (Diptera: Tephritidae), in two nearby villages in Penang, Malaysia
Authors: Hong Tan Keng , Jaal Zairi 
Published: November 2006

SummaryThe populations of native male adult oriental fruit fly Dacus dorsalis (Hendel) and artocarpus fruit fly D. umbrosus (F.) in two selected site (BU and SD) were estimated weekly by the capture‐recapture technique using live traps baited with methyl eugenol. In BU where many varieties of fruit trees were grown, the estimated population densities of D. dorsalis were between 980 and 3100 male flies per ha between May and July, 1984. During the same period, in SD where there were fewer number and varieties of fruit trees, the estimated population densities were between 300 and 1000 flies per ha. The estimated population densities of D. umbrosus over the same period were between 570 and 1290 flies per ha in BU; and between 5 and 95 flies per ha in SD.Of a total 6828 marked D. dorsalis flies released only one fly (released 6 weeks earlier in BU) was caught in a different site.