bluuebunny/crossref_metadata_2025_split huggingface dataset:
Protein simple sequence conservation
Authors: Sim Kim Lan , Creamer Trevor P. 
Published: February 2004

AbstractProtein simple sequences, a subset of low‐complexity sequences, are regions of sequence highly enriched in one or a few residue types. Simple sequences are exceedingly common, the average being more than one per protein sequence. Despite being so common, such sequences are not well‐studied. The simple sequences that have been subjected to detailed study are often found to possess important functions. Here we present a survey of protein simple sequences, generally enriched in a single residue type, with the aim of studying their conservation. We find that the majority of such simple sequences are not conserved. However, conserved protein simple sequences are relatively common, with ∼11% of the surveyed protein families possessing a conserved simple sequence. The data obtained in this study support the idea that simple sequences are conserved for functional reasons. Such functions can range from substrate binding, to mediating protein‐protein interactions, to structural integrity. A perhaps surprising finding is that the residue enriching a conserved simple sequence is itself not necessarily conserved. Neither is the length of many of the highly conserved simple sequences. In the few cases where structural and functional data is available it is found that the conserved simple sequences are consistent with both local structure and function. The data presented support the idea that protein simple sequences can be conserved and have important roles in protein structure and function. Proteins 2004;54:000–000. © 2004 Wiley‐Liss, Inc.
What is the protein design alphabet?
Authors: Dokholyan Nikolay V. 
Published: February 2004

AbstractSelecting a protein sequence that corresponds to a specific three‐dimensional protein structure is known as the protein design problem. One principal bottleneck in solving this problem is our lack of knowledge of precise atomic interactions. Using a simple model of amino acid interactions, we determine three crucial factors that are important for solving the protein design problem. Among these factors is the protein alphabet—a set of sequence elements that encodes protein structure. Our model predicts that alphabet size is independent of protein length, suggesting the possibility of designing a protein of arbitrary length with the natural protein alphabet. We also find that protein alphabet size is governed by protein structural properties and the energetic properties of the protein alphabet units. We discover that the usage of average types of amino acid in proteins is less than expected if amino acids were chosen randomly with naturally occurring frequencies. We propose three possible scenarios that account for amino acid underusage in proteins. These scenarios suggest the possibility that amino acids themselves might not constitute the alphabet of natural proteins. Proteins 2004;54:000–000. © 2004 Wiley‐Liss, Inc.
A novel method for protein secondary structure prediction using dual‐layer SVM and profiles
Authors: Guo Jian , Chen Hu , Sun Zhirong , Lin Yuanlie 
Published: February 2004

AbstractA high‐performance method was developed for protein secondary structure prediction based on the dual‐layer support vector machine (SVM) and position‐specific scoring matrices (PSSMs). SVM is a new machine learning technology that has been successfully applied in solving problems in the field of bioinformatics. The SVM's performance is usually better than that of traditional machine learning approaches. The performance was further improved by combining PSSM profiles with the SVM analysis. The PSSMs were generated from PSI‐BLAST profiles, which contain important evolution information. The final prediction results were generated from the second SVM layer output. On the CB513 data set, the three‐state overall per‐residue accuracy, Q3, reached 75.2%, while segment overlap (SOV) accuracy increased to 80.0%. On the CB396 data set, the Q3 of our method reached 74.0% and the SOV reached 78.1%. A web server utilizing the method has been constructed and is available athttp://www.bioinfo.tsinghua.edu.cn/pmsvm. Proteins 2004;00:000–000. © 2004 Wiley‐Liss, Inc.
The role of pH on instability and aggregation of sickle hemoglobin solutions
Authors: Manno M. , San Biagio P. L. , Palma M. U. 
Published: February 2004

AbstractUnderstanding the physical basis of protein aggregation covers strong physical and biomedical interests. Sickle hemoglobin (HbS) is a point‐mutant form of normal human adult hemoglobin (HbA). It is responsible for the first identified “molecular disease,” as its propensity to aggregation is responsible for sickle cell disease. At moderately higher than physiological pH value, this propensity is inhibited: The rate of aggregate nucleation becomes exceedingly small and solubility after polymerization increases. These order‐of‐magnitude effects on polymer nucleation rates and concurrent relatively modest changes of solubility after polymerization are here shown to be related to both pH‐induced changes of location and shape of the liquid–liquid demixing (LLD) region. This allows establishment of a self‐consistent contact between the thermodynamics of the solution as such (i.e., the LLD region), the kinetics of fiber nucleation, the theory of percolation, and the thermodynamics of gelation. The observed pH‐induced changes are largely attributable to strong perturbations of hydrophobic hydration configurations and related free energy by electric charges. Similar mechanisms of effective control of aggregate nucleation rates by means of agents such as cosolutes, pH, salts, and additives, shifting the LLD and associated regions of anomalous fluctuations, promise to be relevant to the whole field of protein aggregation pathologies. Proteins 2004;00:000–000. © 2004 Wiley‐Liss, Inc.
Conformational subspace in simulation of early‐stage protein folding
Authors: Jurkowski Wiktor , Brylinski Michał , Konieczny Leszek , Wiíniowski Zdzisław , Roterman Irena 
Published: February 2004

AbstractA probability calculus was used to simulate the early stages of protein folding in ab initio structure prediction. The probabilities of particular ϕ and ψ angles for each of 20 amino acids as they occur in crystal forms of proteins were used to calculate the amount of information necessary for the occurrence of given ϕ and ψ angles to be predicted. It was found that the amount of information needed to predict ϕ and ψ angles with 5° precision is much higher than the amount of information actually carried by individual amino acids in the polypeptide chain. To handle this problem, a limited conformational space for the preliminary search for optimal polypeptide structure is proposed based on a simplified geometrical model of the polypeptide chain and on the probability calculus. These two models, geometric and probabilistic, based on different sources, yield a common conclusion concerning how a limited conformational space can represent an early stage of polypeptide chain‐folding simulation. The ribonuclease molecule was used to test the limited conformational space as a tool for modeling early‐stage folding. Proteins 2004. © 2004 Wiley‐Liss, Inc.
Evaluation of the Quality of a Car Braking System by a Dynamic Simulator
Authors: Celentano G. , Iervolino R. , Fontana V. , Porreca S. 
Published: February 2004

AbstractQuality has become one of the more important factors in the purchasing decisions of the consumer. At the moment, the tools available for variability analysis in the production process, which is the main cause of quality degradation, are mostly based on statistical approaches that neglect the physical relationships that exist in a man‐made system. In this paper a new general methodology is proposed, which gives evidence of how the development of a mathematical model could be more suitable if set by a relatively limited amount of data and a number of experimental tests. The implementation of the model in a dynamic simulator allows one to evaluate the effects of the variability of the most critical elements on the quality of the whole system numerically. The effectiveness of the procedure is demonstrated by the evaluation of some quality indexes of a car braking system. Copyright © 2004 John Wiley & Sons, Ltd.
Experimental ‘Reliability Growth’ or ‘Reliability Verification’ Related with the Amount of Innovation in a New Car Model
Authors: Parigi P. , Vianello M. 
Published: February 2004

AbstractReliability growth testing, i.e. the ‘growth’ of reliability, is a consolidated systematic method used by Fiat Auto to increase and ‘demonstrate’ reliability while testing vehicles. If a new car model is not very different from the previous one (being used as reference), a single ‘verification’ experimental phase on the vehicles which is consistent with the end product may be sufficient for a reliability statistical demonstration. In this case, the resultant confidence interval may be very large, especially when we want to predict the in field failure frequency after applying corrective actions. Conversely, if the new product shows too many problems, we could obviously define, at any moment, a specific (and more demanding) reliability growth plan and restart the experiments. This paper suggests the cases in which we should choose a reliability growth test or a reliability verification test, whilst considering the total amount of design variations with respect to the reference model: completely new model, restyling, face lifting, etc. Copyright © 2004 John Wiley & Sons, Ltd.
Rules of electron correlation energies of van der Waals' complexes RgX (Rg = Ar, Kr, X = F, Cl, Br)
Authors: Wei Jichong , Zhuo Shuping , Ju Guanzhi 
Published: February 2004

AbstractFirst, the intrapair and interpair correlation energies of the Rg atom, X atom, and the optimized RgX (Rg = Ar, Kr, X = F, Cl, Br) complexes are calculated by the MELD program at the 6‐311++g(d), 6‐311++g(3df, 3pd), and cc‐pvqz basis sets (denoted by basis sets a, b, and c, respectively). It is found that the relationship Ecorr(RgX) ≈ Ecorr(Rg) + Ecorr(X) is correct for all the above systems but introducing an unsound absolute error for some RgX systems. Second, the same calculations are selectively carried out for ArF (the smallest system) and KrBr (the largest system) at their increasing interatomic distance. It was found that both the correlation energies of ArF and those of KrBr will decrease whenever the interatomic distance of them become larger. On the basis of our results, we provided an approach to quickly estimate the correlation energies of RgX complexes by which not only the absolute error becomes smaller but more computation work is saved than the direct calculation. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Model for phase coexistence in phase transitions
Authors: Wang Y. , Ahuja R. , Johansson B. 
Published: February 2004

AbstractWe propose a general model for describing the phenomena of phase coexistence in relation to pressure induced phase transformations by means of the T–P distribution in statistical thermodynamics. Using the well‐known B1–B2 transition in NaCl as a prototype, we demonstrate how phase coexistence gives rise to the changes in the bulk modulus and the equation‐of‐state across the transition. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004
Application of physical habitat simulation (PHABSIM) modelling to modified urban river channels
Authors: Booker D. J. , Dunbar M. J. 
Published: February 2004

AbstractPrediction of changes to in‐stream ecology are highly desirable if decisions on river management, such as those relating to water abstractions, effluent discharges or modifications to the river channel, are to be justified to stakeholders. The physical habitat simulation (PHABSIM) system is a well‐established hydro‐ecological model that provides a suite of tools for the numerical modelling of hydraulic habitat suitability for fish and invertebrate species. In the UK, the most high‐profile PHABSIM studies have focused on rural, groundwater‐dominated rivers and have related to low flow issues. Conversely, there have been few studies of urban rivers. This paper focuses on the application of PHABSIM to urban rivers and demonstrates how sensitivity analyses can be used to assess uncertainty in PHABSIM applications. Results show that physical habitat predictions are sensitive to changes in habitat suitability indices, hydraulic model calibration and the temporal resolution of flow time‐series. Results show that there is greater suitable physical habitat over a wider range of flows in a less engineered river channel when compared to a more engineered channel. The work emphasizes the need for accurate information relating to the response of fish and other organisms to high velocities. Copyright © 2004 John Wiley & Sons, Ltd.
Simulating effects of hydro‐dam alteration on thermal regime and wild steelhead recruitment in a stable‐flow Lake Michigan tributary
Authors: Horne Brad D. , Rutherford Edward. S. , Wehrly Kevin E. 
Published: February 2004

AbstractHydroelectric dams may affect anadromous fish survival and recruitment by limiting access to upstream habitats and adversely affecting quality of downstream habitats. In the Manistee River, a tributary to Lake Michigan, two hydroelectric dams potentially limit recruitment of anadromous rainbow trout (steelhead) by increasing tailrace water temperatures to levels that significantly reduce survival of young‐of‐year (YOY) fish. The objectives of this study were to determine whether proposed restoration scenarios (dam removals or a bottom withdrawal retrofit) would alter the Manistee River thermal regime and, consequently, improve wild steelhead survival and recruitment. Physical process models were used to predict Manistee River thermal regimes following each dam alteration scenario. Empirical relationships were derived from historical field surveys to quantify the effect of temperature on YOY production and potential recruitment of Manistee River steelhead. Both dam alteration scenarios lowered summer temperatures and increased steelhead recruitment by between 59% and 129%, but total recruitments were still low compared to other Great Lakes tributaries. Considering only temperature effects, bottom withdrawal provides the greatest promise for increasing natural steelhead recruitment by decreasing the likelihood of year‐class failures in the warmest summers. Results of this study may allow managers to evaluate mitigation alternatives for Manistee River dams during future relicensing negotiations, and illustrate the utility of physical process temperature models in groundwater‐fed rivers. Copyright © 2004 John Wiley & Sons, Ltd.
Application of a 2D hydrodynamic model to design of reach‐scale spawning gravel replenishment on the Mokelumne River, California
Authors: Pasternack Gregory B. , Wang C. Lau , Merz Joseph E. 
Published: February 2004

AbstractIn‐stream chinook salmon (Oncorhynchus tschawytscha) spawning habitat in California's Central Valley has been degraded by minimal gravel recruitment due to river impoundment and historic gravel extraction. In a recent project marking a new direction for spawning habitat rehabilitation, 2450 m3 of gravel and several boulders were used to craft bars and chutes. To improve the design of future projects, a test was carried out in which a commercial modelling package was used to design and evaluate alternative gravel configurations in relation to the actual pre‐ and post‐project configurations. Tested scenarios included alternate bars, central braid, a combination of alternate bars and a braid, and a flat riffle with uniformly spaced boulders. All runs were compared for their spawning habitat value and for susceptibility to erosion. The flat riffle scenario produced the most total, high, and medium quality habitat, but would yield little habitat under flows deviating from the design discharge. Bar and braid scenarios were highly gravel efficient, with nearly 1 m2 of habitat per 1 m3 of gravel added, and yielded large contiguous high quality habitat patches that were superior to the actual design. At near bankfull flow, negligible sediment entrainment was predicted for any scenario. Copyright © 2004 John Wiley & Sons, Ltd.
Lend me your wallets: the effect of charismatic leadership on external support for an organization
Authors: Flynn Francis J. , Staw Barry M. 
Published: February 2004

AbstractWe argue that charismatic leadership can influence external support for the organization, particularly in making the company more attractive to outside investors. Two studies were conducted to test this general hypothesis. First, an archival study demonstrated that the stock of companies headed by charismatic leaders appreciated more than the stock of comparable companies, even after differences in corporate performance were controlled. It was also found that the effect of charismatic leadership was heightened under more difficult economic conditions. Second, an experiment was conducted in which the salience of charismatic leadership was manipulated, along with information about the prospects for an organization's turnaround. Results showed that appeals from a charismatic leader led to increased investment in the firm, and the leader's influence was greater when the prospects for an organizational turnaround were more difficult. It was also found that an endowment of stock enhanced the influence of charismatic appeals and that charismatic leadership may have affected the general risk propensities of followers. These findings were interpreted in terms of an external perspective on leadership, illustrating how leaders can manage the firm's economic and social environment. Copyright © 2004 John Wiley & Sons, Ltd.
Corruption and change: the impact of foreign direct investment
Authors: Robertson Christopher J. , Watson Andrew 
Published: February 2004

AbstractThis study examines influences on the level of corruption in countries from a strategic perspective. Corruption is one of the country‐level influences on market entry, investment, and other decisions fundamental to strategic management at the international level. The study examines the impact on corruption of change in levels of foreign direct investment (FDI). It uses the Corruption Perceptions Index (CPI) scores computed by Transparency International for 1999 and 2000. Results indicate that the more rapid the rate of change in FDI, the higher the level of corruption. Higher levels of perceived corruption are associated with each of two dimensions of national culture: uncertainty avoidance and masculinity. Research and managerial implications are also discussed. Copyright © 2004 John Wiley & Sons, Ltd.
Fast, accurate call graph profiling
Authors: Spivey J. M. 
Published: February 2004

AbstractExisting methods for call graph profiling, such as that used by gprof, deal badly with programs that have shared subroutines, mutual recursion, higher‐order functions, or dynamic method binding. This article discusses a way of improving the accuracy of a call graph profile by collecting more information during execution, without significantly increasing the overhead of profiling. The method is based on keeping track of a context, consisting of the set of subroutines that are active at a particular moment during execution, together with the calling arcs between these subroutines. The profiler records the time spent in each context during execution of the program, and thus obtains an accurate measurement of the total time during which each subroutine was active. By recording arc information for only the most recent activation of each subroutine, it is possible to arrange that even recursive programs give rise to a finite number of these contexts, and in typical real programs, the number of distinct contexts remains manageably small. The data can be collected efficiently during execution by constructing a finite‐state machine whose states correspond to contexts, so that when a context is entered for a second or subsequent time, only a single access of a hash table is needed to update the state of the profiling monitor. Copyright © 2003 John Wiley & Sons, Ltd.
A ReScUE XML/EDI model
Authors: Lu Eric Jui‐Lin , Wu Chang‐Chuan 
Published: February 2004

AbstractSince electronic data interchange (EDI) is one of the most important components in electronic commerce and since Extensible Markup Language (XML) provides Internet developers with a powerful vehicle for exchanging messages, XML/EDI has received much attention from almost all well‐known international enterprises and is believed to be the next generation EDI. However, since XML allows developers to design their own elements and attributes, it is almost certain businesses will receive XML documents with unknown elements. Generally, human intervention is required to solve the problem. Therefore, it is indispensable to design an efficient scheme to resolve the unknown elements. In this paper, we propose a ReScUE XML/EDI model such that transformation templates will be generated automatically for documents with unknown elements, and the documents will be converted into expected format. This model increases the flexibility of XML/EDI systems and reduces human intervention. Copyright © 2003 John Wiley & Sons, Ltd.
Silica‐supported biomimetic membranes
Authors: Ariga Katsuhiko 
Published: February 2004

AbstractThe hybridization of lipid membranes with inorganic silica‐based framework results in mechanically stable biomembrane mimics. This account describes three types of silica‐based biomimetic membranes. As the first example, a Langmuir monolayer of dialkylalkoxysilane was polymerized and immobilized onto a porous glass plate. Permeability through the monolayer‐immobilized glass was regulated by phase transition of the immobilized monolayer. In the second example, spherical vesicles covalently attached to a silica cover layer (Cerasome) were prepared. The Cerasome was stable enough to be assembled into layer‐by‐layer films without destruction of its vesicular structure. This material could be an example of the multicellular assembly. Mesoporous silica films densely filling peptide assemblies (Proteosilica) are introduced as the third example. The Proteosilica was synthesized as a transparent film through template sol‐gel reaction using amphiphilic peptides. © 2004 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 3: 297–307; 2004: Published online in Wiley InterScience (www.interscience.wiley.com) DOI 10.1002/tcr.10071
Synthesis of tumor‐associated glycopeptide antigens for the development of tumor‐selective vaccines
Authors: Dziadek Sebastian , Kunz Horst 
Published: February 2004

AbstractIn contrast to normal cells, the glycoprotein profile on epithelial tumor cells is distinctly altered. Due to an incomplete
formation of the glycan side‐chains resulting from a premature sialylation, additional peptide epitopes become accessible
to the immune system in mucin‐type glycoproteins on tumor cells. These tumor‐associated structure alterations
constitute the basis for a selective immunological attack on cancer cells. For the construction of immunostimulating antigens,
glycopeptide partial structures from the mucins MUC1 and MUC4 carrying the tumor‐associated sialyl‐TN,
α2,6‐sialyl‐T and α2,3‐sialyl‐T antigens have been synthesized. Employing different
linkers such as the allylic HYCRON or the fluoride‐sensitive PTMSEL anchor, the antigenic glycopeptide structures
were constructed on the solid phase utilizing pre‐assembled glycosyl amino acid building blocks prepared in
solution by convergent chemical or chemoenzymatic strategies. The proliferation of cytotoxic T cells has been induced
applying a construct composed of a sialyl‐TN MUC1‐glycopeptide conjugated with a tetanus toxin
T cell peptide epitope. © 2004 The Japan Chemical Journal Forum and Wiley Periodicals, Inc. Chem Rec 3: 308–321,
2004: Published online in Wiley InterScience (www.interscience.wiley.com)
DOI 10.1002/tcr10074