bluuebunny/crossref_metadata_2025_split huggingface dataset:
Concentration‐dependent effects on the rapid and efficient activation of the MAP kinase signaling cascade
Authors: Schwacke John H. , Voit Eberhard O. 
Published: March 2007

AbstractModern proteomic techniques are making it possible to identify and quantitate increasingly complex mixtures of cellular proteins. Translating the relative expression measurements collected in these experiments into an understanding of the associated physiological phenomena continues to be a challenge for the field of systems biology. We demonstrate how methods of mathematical and computational systems biology permit us to proffer explanations for the observed concentration ranges of signaling components found in the highly conserved mitogen‐activated protein kinase (MAPK) cascade. The analysis demonstrates that alterations in the naturally occurring MAPK and MAPK kinase (MAPKK) concentrations would negatively affect the efficiency of short‐term responses of the cascade. Thus, while there seems to be no a priori rationale for particular features of the involved kinases, the observed ranges of their characteristic parameters appear to be far from coincidental. This result is deduced from the first principles of mass action kinetics and holds for wide variations in MAPKK kinase (MAPKKK) concentrations, differential preference for unphosphorylated and monophosphorylated forms of kinase substrates, and for cases where the monophosphorylated MAPKK exhibits kinase activity. The results demonstrate how theoretical systems biology complements molecular biology by providing specific rationale for observed natural designs in a fashion hardly achievable with experimentation alone.
Proteome informatics for cancer research: From molecules to clinic
Authors: Brusic Vladimir , Marina Ovidiu , Wu Catherine J. , Reinherz Ellis L. 
Published: March 2007

AbstractProteomics offers the most direct approach to understand disease and its molecular biomarkers. Biomarkers denote the biological states of tissues, cells, or body fluids that are useful for disease detection and classification. Clinical proteomics is used for early disease detection, molecular diagnosis of disease, identification and formulation of therapies, and disease monitoring and prognostics. Bioinformatics tools are essential for converting raw proteomics data into knowledge and subsequently into useful applications. These tools are used for the collection, processing, analysis, and interpretation of the vast amounts of proteomics data. Management, analysis, and interpretation of large quantities of raw and processed data require a combination of various informatics technologies such as databases, sequence comparison, predictive models, and statistical tools. We have demonstrated the utility of bioinformatics in clinical proteomics through the analysis of the cancer antigen survivin and its suitability as a target for cancer immunotherapy.
Surrogacy theory and models of convoluted organic systems
Authors: Konopka Andrzej K. 
Published: March 2007

AbstractThe theory of surrogacy is briefly outlined as one of the conceptual foundations of systems biology that has been developed for the last 30 years in the context of Hertz‐Rosen modeling relationship. Conceptual foundations of modeling convoluted (biologically complex) systems are briefly reviewed and discussed in terms of current and future research in systems biology. New as well as older results that pertain to the concepts of modeling relationship, sequence of surrogacies, cascade of representations, complementarity, analogy, metaphor, and epistemic time are presented together with a classification of models in a cascade. Examples of anticipated future applications of surrogacy theory in life sciences are briefly discussed.
Electrostatic potential–density relationships in molecules
Authors: Jalbout Abraham F. 
Published: March 2007

AbstractIn this work, we present Hartree–Fock and density functional theory nuclear electrostatic potential–density relationships for several homonuclear diatomic molecules. The results of our calculations are encouraging with relatively low errors in the energies. Implications for the application of this work to novel molecular energy equations as well as the need for further improvement of these newly proposed relationships in molecules have been addressed. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Theoretical evidence of d‐orbital aromaticity in anionic metal X (X = Sc, Y, La) clusters
Authors: Chi Xian X. , Liu Yong 
Published: March 2007

AbstractThe equilibrium geometries, total electronic energies, and vibrational frequencies for singlet, triplet, and quinted states of three all‐metal X (X = Sc, Y, and La) anions and nine relevant neutral singlet MX3 (M = Li, Na, K, X = Sc, Y, La) clusters are investigated with four density functional theory (DFT) and correlated ab initio methods B3LYP, B3PW91, MP2, and CCSD(T). To our knowledge, the theoretical study on these clusters composed of the transition metal Sc, Y, La is first reported here. The calculated results show that for the X clusters the singlet states with trigonal D3h structures are the lowest energetically, while the neutral singlet MX3 clusters each have two stable isomers: one trigonal pyramidal C3v and one bidentate C2v structures with the pyramidal C3v isomer being ground state. In addition, we calculate the resonance energies (RE) and nucleus‐independent chemical shift (NICS) for the singlet trigonal X rings and show that these singlet trigonal X rings exhibit higher degree of aromaticity. The detailed molecular orbital (MO) analyses reveal that the singlet trigonal X anions have one delocalized σ‐type and one delocalized π‐type MOs, which follow the 4n + 2 electron counting rule, respectively and play an important role in rendering these species two‐fold aromaticity. Here, an explicit theoretical evidence is given to prove that the contribution to the two‐fold aromaticity of the singlet trigonal X (X = Sc, Y, and La) rings originates primarily from the d‐orbital bonding interactions of these component transition metal X atoms. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Theoretical study on the Diels–Alder reaction of cyclopentadiene with methacrolein catalyzed by diethylimidazolium cation
Authors: Sun Hui , Zhang Dongju , Ma Chen , Liu Chengbu 
Published: March 2007

AbstractThe theoretical studies of how room temperature ionic liquids control desired reactions are very scarce in contrast with their increasing applications in many fields as recyclable solvents, catalysts, and reaction mediums. The present work considers the Diels–Alder (D‐A) reaction of cyclopentadiene with methacrolein in the presence of diethylimidazolium salts as the first prototype of our systemic studies about important organic synthesis reactions catalyzed by room temperature ionic liquids. We show the mechanism details of the D‐A reactions with and without the dialkylimidazolium cation and rationalize the experimental findings based on the results from the quantum chemistry calculations at the AM1, HF/6‐31G(d), and B3PW91/6‐31G(d,p) levels of theory, respectively. It is found that the diethylimidazolium cation acts as a Lewis acid center to catalyze the D‐A reaction, which decreases the barrier and increases the asynchronicity of the D‐A reaction, but does not change the potential energy surface profile of the reaction compared to the noncatalyzed process. The present results rationalize the early experimental findings well and provide the first prototype for theoretically understanding the D‐A reaction in the presence of dialkylimidazolium salts. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Net information measures for modified Yukawa and Hulthén potentials
Authors: Patil S. H. , Sen K. D. 
Published: March 2007

AbstractThe dimensional analyses of the position and momentum variances‐based quantum mechanical Heisenberg uncertainty measure, as well as the entropic information measures given by the Shannon information entropy sum and the product of Fisher information measures are carried out for two widely used nonrelativistic isotropic exponential‐cosine screened Coulomb potentials generated by multiplying the superpositions of (i) Yukawa‐like, −Z(e−μr/r), and (ii) Hulthén‐like, −Zμ(1/(eμr − 1)), potentials by cos(bμr) followed by addition of the term a/r2, where a and b ≥ 0, μ are the screening parameters and Z, in case of atoms, denotes the nuclear charge. Under the spherical symmetry, all the information measures considered are shown to be independent of the scaling of the set [μ, Z] at a fixed value of μ/Z, a, and b and the other parameters defining the superpositions of the potentials. Numerical results are presented, which support the validity of the scaling properties. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Computer aid molecular design based on meta‐heuristics techniques
Authors: Rusu T. , Bulacovschi V. 
Published: March 2007

AbstractOne of the challenges in modern chemistry is the problem of designing new molecules with desired properties. The traditional approach to this problem are usually expensive and time‐consuming iterative process with the scientist or engineer hypothesizing a compound, synthesizing the material, testing for desired properties, and redesigning the candidate if the desired properties are not met. In the last years, a lot of scientists have reached to the conclusion that the artificial intelligence methods can improve/facilitate the design of new macromolecules with desired properties. One of the challenges in computer aid macromolecular design is to avoid local minima. Our paper present the use of meta‐heuristics techniques that can solve this problem. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007
Electron ionization mass spectral study of selected N‐amide and N‐alkyl derivatives of cytisine
Authors: Przybył Anna K. , Prukała Wiesław , Kikut‐Ligaj Dariusz 
Published: March 2007

Abstract(–)‐Cytisine and its derivatives are promising alkaloids in the development of new drugs for the treatment of disorders of the central nervous system (CNS). Electron ionization (EI) mass spectral fragmentations of cytisine (1), N‐methylcytisine (2), N‐ethylcytisine (3), N‐acetylcytisine (4), N‐propionylcytisine (5) and N‐benzoylcytisine (6) have been investigated. Detailed fragmentation pathways have been identified for all significant ions, including a few characteristic fragment ions. The principal fragmentation routes of compounds 1–6 have been determined on the basis of EI low‐resolution, high‐resolution and B2/E linked scans as well as linked scans at constant B/E. Copyright © 2007 John Wiley & Sons, Ltd.
Differentiation of three pairs of positional isomers of hybrid peptides with repeats of phenylalanine‐β3‐h‐valine/β3‐h‐valine‐phenylalanine by electrospray ionization tandem mass spectrometry
Authors: Ramesh V. , Reddy P. Nagi , Srinivas R. , Srinivasulu G. , Kunwar A. C. 
Published: March 2007

AbstractElectrospray ionization ion trap mass spectrometry has been used to distinguish three pairs of positional isomers of a new series of N‐blocked hybrid peptides derived from repeats of phenylalanine(D)‐β3‐h‐valine/β3‐h‐valine‐phenylalanine(D) (FβV/βVF) non‐natural amino acids. MSn of protonated isomeric peptides produces characteristic fragmentation involving the peptide backbone, the Boc group and the side chain. FβV‐peptides can be distinguished from βVF‐peptides by the loss of R‐OH from [M+H−Boc+H]+, which is either of relatively low abundance or totally absent for the latter peptides. In contrast, βVF‐peptides show abundant Mannich base characteristic ions by the elimination of ammonia, and imine due to a retro‐Mannich cleavage. This fragmentation is absent for FβV‐peptides. When β‐valine is at the C‐terminus, abundant b ions are produced. This is ascribed to the probable formation of a stable diketopiperazine structure, and this has been supported by the loss of H2O and CO in the CID spectra of b ions. The hybrid dipeptide acids have also been distinguished in negative ion mass spectrometry. Copyright © 2007 John Wiley & Sons, Ltd.
The persistence of abnormal returns at industry and firm levels: Evidence from Spain
Authors: Bou Juan Carlos , Satorra Albert 
Published: March 2007

AbstractWe apply structural equation models to longitudinal data on profits of firms within industries to study the persistence of abnormal returns. We obtain a two‐way variance decomposition for abnormal returns: at firm vs. industry levels, and at permanent vs. transitory components. This decomposition enables us to assess the relative importance of the fundamental components of abnormal returns discussed in the literature. The method is applied to a panel of 5,000 Spanish firms observed over the period 1995–2000. We conclude that: (a) there are significant and permanent differences between profit rates at both industry and firm levels; (b) variation of abnormal returns at firm level is greater than at industry level; and (c) firm and industry levels do not differ significantly regarding rates of convergence of abnormal returns. Copyright © 2007 John Wiley & Sons, Ltd.
Performance consequences of new CEO ‘Outsiderness’: Moderating effects of pre‐ and post‐succession contexts
Authors: Karaevli Ayse 
Published: March 2007

AbstractThis study seeks to reconcile inconsistent findings on the performance consequences of new CEO origin. Drawing on five decades of empirical research on CEO succession outcomes, I develop a more refined theoretical conceptualization and a finer‐grained measurement of the underlying construct of the insider vs. outsider CEO, and build and test a more comprehensive and nuanced framework of the succession context. A longitudinal investigation of the U.S. airline and chemical industries (1972–2002) indicates that new CEO ‘Outsiderness’, conceptualized as a continuum raging from new CEOs who have a greater combination of firm and industry tenure to those who have no experience in the firm and the industry, has no main effect on post‐succession firm performance. However, significant moderating effects are found when environmental munificence, pre‐succession firm performance, and concomitant strategic and senior executive team changes are considered. Together, these findings highlight the need to consider both pre‐ and post‐succession contextual factors for evaluating the performance effects of new CEO outsiderness. Copyright © 2007 John Wiley & Sons, Ltd.
Does peripheral knowledge complement control? An empirical test in technology outsourcing alliances
Authors: Tiwana Amrit , Keil Mark 
Published: March 2007

AbstractWhile the normative logic for forming technology outsourcing alliances is that such alliances allow outsourcing firms to specialize deeper in their domain of core competence without being distracted by noncore activities, recent empirical studies have reported the puzzling phenomenon of some firms continuing to invest in R&D in domains that are fully outsourced to specialized alliance partners. An underlying—and widely made—assertion that can potentially reconcile this contradiction is that ‘peripheral’ knowledge (specialized knowledge in the domain of outsourced activities) complements control in technology outsourcing alliances. However, this assertion is untested; and empirically testing it is the objective of this research study. Using data from 59 software services outsourcing alliances, we show that such peripheral knowledge and alliance control are imperfect complements: peripheral knowledge complements outcomes‐based formal control but not process‐based control. Thus, outsourcing firms might sometimes need knowledge outside their core domain because such knowledge facilitates effective alliance governance. Our theoretical elaboration and empirical testing of the assumed complementarities between peripheral knowledge and control in technology outsourcing alliances has significant implications for strategy theory and practice, which are also discussed. Copyright © 2007 John Wiley & Sons, Ltd.
Genomotyping of Pseudomonas putida strains using P. putida KT2440-based high-density DNA microarrays: implications for transcriptomics studies
Authors: Ballerstedt Hendrik , Volkers Rita J. M. , Mars Astrid E. , Hallsworth John E. , Santos Vitor A. Martins dos , Puchalka Jaçek , van Duuren Joost , Eggink Gerrit , Timmis Ken N. , de Bont Jan A. M. , Wery Jan 
Published: March 2007

Abstract

Pseudomonas putida KT2440 is the only fully sequenced P. putida strain. Thus, for transcriptomics and proteomics studies with other P. putida strains, the P. putida KT2440 genomic database serves as standard reference. The utility of KT2440 whole-genome, high-density oligonucleotide microarrays for transcriptomics studies of other Pseudomonas strains was investigated. To this end, microarray hybridizations were performed with genomic DNAs of subcultures of P. putida KT2440 (DSM6125), the type strain (DSM291T), plasmid pWW0-containing KT2440-derivative strain mt-2 (DSM3931), the solvent-tolerant P. putida S12, and several other Pseudomonas strains. Depending on the strain tested, 22 to 99% of all genetic elements were identified in the genomic DNAs. The efficacy of these microarrays to study cellular function was determined for all strains included in the study. The vast majority of DSM6125 genes encoding proteins of primary metabolism and genes involved in the catabolism of aromatic compounds were identified in the genomic DNA of strain S12: a prerequisite for reliable transcriptomics analyses. The genomotypic comparisons between Pseudomonas strains were used to construct highly discriminative phylogenetic relationships. DSM6125 and DSM3931 were indistinguishable and clustered together with strain S12 in a separate group, distinct from DSM291T. Pseudomonas monteilii (DSM14164) clustered well with P. putida strains.
Effects of fragmentation on parasite burden (nematodes) of generalist and specialist small mammal species in secondary forest fragments of the coastal Atlantic Forest, Brazil
Authors: Püttker Thomas , Meyer‐Lucht Yvonne , Sommer Simone 
Published: March 2007

AbstractParasites are considered to play an important role in the regulation of wild animal populations. We investigated parasite burden of gastrointestinal nematodes and body condition in specialist and generalist small mammal species in secondary forest fragments in the highly endangered coastal Atlantic Forest. We hypothesized that body condition decreases with increasing parasite load and that parasite burden increases with increasing fragmentation in specialist species but not in generalist species as a consequence of differing responses to fragmentation effects. Investigated species were Akodon montensis, Oligoryzomys nigripes, and Delomys sublineatus (rodents) and the marsupials Marmosops incanus and Gracilinanus microtarsus. Prevalence of parasites was high in all species except for the arboreal G. microtarsus, presumably because of decreased infection probability. No correlation was found between body condition and parasite load in any of the species. Contrary to our expectations, body condition of the specialists D. sublineatus and M. incanus increased in both species with increasing fragmentation. In D. sublineatus, parasite burden increased and body condition decreased in fragments with relatively high density probably due to increased contact rates and facilitation of infection with nematodes. In all generalist species, low or no correlation between parasite burden and fragmentation was detected, suggesting little effect of fragmentation on population health.
Proteophosphoglycan is differentially expressed in sodium stibogluconate-sensitive and resistant Indian clinical isolates ofLeishmania donovani
Authors: SAMANT M. , SAHASRABUDDHE A. A. , SINGH N. , GUPTA S. K. , SUNDAR S. , DUBE A. 
Published: March 2007

SUMMARYLeishmaniaproduce several types of mucin-like glycoproteins called proteophosphoglycans (PPGs) some of which are secreted while others are found on the surface of promastigotes and amastigotes. These proteins are thought to be important in the transmission, invasion and subsequent intracellular survival of parasites. The structure and function of PPGs are species and stage-specific in the case ofL.majorandL. mexicana, but no such information has hitherto been available forL. donovani. This study presents, for the first time, an initial characterization (localization) of PPG in sodium stibogluconate (SSG)-resistant and sensitive clinical isolates ofL. donovanifrom Bihar (India) by confocal microscopy, flow cytometry and Western blotting using antibodies toL. majorPPG. Confocal microscopy analysis revealed that both promastigotes and amastigotes possess PPG on their cell membrane and flagellar pocket membrane but its expression was variable in different isolates. The quantitative analysis by FACS and Western blotting showed that the expression and intensity of PPG bands was higher in SSG-resistant isolates. This study suggests the possibilities of involvement of PPG in drug-resistant mechanisms and of using PPG abundance as a marker for identifying drug-resistant clinical isolates in Indian kala azar.
A model to account for the consequences of host nutrition on the outcome of gastrointestinal parasitism in sheep: logic and concepts
Authors: VAGENAS D. , BISHOP S. C. , KYRIAZAKIS I. 
Published: March 2007

SUMMARYA deterministic, dynamic simulation model is developed to account for the interactions between gastrointestinal parasitism and host nutrition, and predict their consequences on performance and level of parasitism of sheep. Larval intake and established adult worms are assumed to result in nutrient loss for the host. In order to reduce this loss the host will mount an immune response, which will affect the establishment rate of incoming larvae, mortality rate of adult worms, and fecundity of female worms, as well as nutrient loss caused by larval intakeper se. Host anorexia is modelled as a function of worm mass. Parasitism is also assumed to affect the allocation of ingested nutrients to the host's bodily functions, with maintenance getting absolute priority, and protein allocated to immunity and production proportionally to their requirements. Inputs to the model include the expected growth attributes of the animal, feed quality, various parasitological parameters and daily larval intake. Outputs include feed intake, growth rate and body composition, as well as worm burden and faecal egg counts. The model allows exploration of the consequences of gastrointestinal parasitism on sheep of different growth characteristics, kept under environments that vary in the provision of nutrients and exposure to parasites.
Vapour is the principal source of water imbibed by seeds in unsaturated soils
Authors: Wuest Stewart 
Published: March 2007

AbstractThe assumption that seeds imbibe most of the water required for germination as liquid through seed-to-soil contact has been a dominant theme in germination research and seeding technology. Under most conditions, seeds are also exposed to water vapour during imbibition, but the relative contributions of liquid and vapour are difficult to assess. In water uptake models that include vapour, procedures used to estimate potential vapour imbibition have underappreciated the effect of distance on diffusion rate. At the same time, the amount of seed-to-soil contact and the liquid bridge from soil water to the seed tend to be greatly overestimated, considering the soil water contents often found in the field. Most researchers have recorded an approximately equal time to germination at soil water contents ranging from field capacity to nearly permanent wilting point, and little response to bulk density, soil type or seed–soil contact. While hydraulic conductivity decreases by several orders of magnitude as soil water content, bulk density and seed-contact decrease, relative humidity remains near 100%. There are several experiments demonstrating timely germination in water vapour alone. The combined evidence contradicts the assumption that seed–soil contact is important for imbibition of water by seeds. Water vapour should be considered the primary source of water for seeds in unsaturated soils.