bluuebunny/crossref_metadata_2025 huggingface dataset:
A Fire‐Explicit Population Viability Analysis of Hypericum cumulicola in Florida Rosemary Scrub
Authors: Quintana‐Ascencio Pedro Francisco , Menges Eric S. , Weekley Carl W.
Published: August 2003

Abstract: Land managers seeking to reestablish historical fire regimes need guidance on how to apply prescribed fire to promote the population persistence of endangered species. We explored extinction risks of Hypericum cumulicola, a fire‐dependent plant endemic to the Lake Wales Ridge, Florida ( U.S.A ). Stochastic and deterministic matrix population models based on six censuses ( 1994–1999 ) and data from several germination and seedling survival experiments were used to compare H. cumulicola demography and extinction probabilities under different fire regimes. Environmental variation associated with site, year, and winter precipitation was included in these models. We estimated time to extinction of unburned populations of different sizes and the probabilities of extinction under no fire, different regular fire‐return intervals, and alternating short and long fire‐return intervals. Following an initial fire, even relatively large populations of thousands of individuals may become locally extinct within 300–400 years without additional fires. Extinction probability declined as intervals between fires decreased. Fire intervals openface>50 years resulted in an appreciable extinction probability after 200 years. Cycles of highly staggered short and long fire‐return intervals caused slightly higher chances of extinction than regular fire‐return intervals. The simulations were sensitive to estimates of survival in the seed bank. Active management will be required to restore favorable fire regimes in areas where fire has been suppressed. To maintain biodiversity, managers should consider variable fire regimes to match the requirements of a variety of species with different life histories.
Assessment of Farmer Attitudes and Behavioral Intentions toward Bird Conservation on Organic and Conventional Florida Farms
Authors: Jacobson Susan K. , Sieving Kathryn E. , Jones Gregory A. , Van Doorn Annamaria
Published: August 2003

Abstract:To enhance efforts to conserve birds, especially insectivorous species, we examined the social dimensions of conventional and organic farming in northern Florida ( U.S.A.). Using a framework for the adoption of agricultural innovations, we developed a 44‐item survey instrument to measure farmers' sociodemographic background, farm characteristics, participation in social organizations, communication and information networks, and perceived barriers and incentives to adopting bird‐friendly practices. Seventy‐six surveys were completed, with a response rate of 84% for organic farmers and 60% for conventional farmers. The population of conventional farmer was composed of more males who were older, less educated, and earned a greater income than organic farmers. Conventional farms were on average 20 times larger than organic farms and grew less than half the varieties of crops. These two factors correlated with higher agreement with statements that a considerable amount of money is spent on pest management and that leaf‐eating insects cause considerable damage. Fewer conventional than organic farmers scouted for pests daily, an important component of integrated pest management. Almost all farmers ( 95% ) reported recognizing most of the bird species on their farms. More organic farmers ( 31% ) than conventional farmers ( 12% ) reported more than 30 bird species on their farms. Farmers' overall willingness to attract birds to their farms was not correlated with economic or noneconomic incentives and barriers to adopting bird‐friendly practices, such as current costs of pest management, experience with bird damage to crops, and farmers' knowledge of insectivorous birds and birds on their farms. Innovations in current farming practices that could enhance bird populations should be disseminated through existing social networks and media channels identified in this paper.
Examining Synaptotagmin 1 Function in Dense Core Vesicle Exocytosis under Direct Control of Ca2+
Authors: Sørensen Jakob B. , Fernández-Chacón Rafael , Südhof Thomas C. , Neher Erwin
Published: August 2003

We tested the long-standing hypothesis that synaptotagmin 1 is the Ca2+ sensor for fast neurosecretion by analyzing the intracellular Ca2+ dependence of large dense-core vesicle exocytosis in a mouse strain carrying a mutated synaptotagmin C2A domain. The mutation (R233Q) causes a twofold increase in the KD of Ca2+-dependent phospholipid binding to the double C2A-C2B domain of synaptotagmin. Using photolysis of caged calcium and capacitance measurements we found that secretion from mutant cells had lower secretory rates, longer secretory delays, and a higher intracellular Ca2+-threshold for secretion due to a twofold increase in the apparent KD of the Ca2+ sensor for fast exocytosis. Single amperometric fusion events were unchanged. We conclude that Ca2+-dependent phospholipid binding to synaptotagmin 1 mirrors the intracellular Ca2+ dependence of exocytosis.
Cross-adaptation between Olfactory Responses Induced by Two Subgroups of Odorant Molecules
Authors: Takeuchi Hiroko , Imanaka Yukie , Hirono Junzo , Kurahashi Takashi
Published: August 2003

It has long been believed that vertebrate olfactory signal transduction is mediated by independent multiple pathways (using cAMP and InsP3 as second messengers). However, the dual presence of parallel pathways in the olfactory receptor cell is still controversial, mainly because of the lack of information regarding the single-cell response induced by odorants that have been shown to produce InsP3 exclusively (but not cAMP) in the olfactory cilia. In this study, we recorded activities of transduction channels of single olfactory receptor cells to InsP3-producing odorants. When the membrane potential was held at −54 mV, application of InsP3-producing odorants to the ciliary region caused an inward current. The reversal potential was 0 ± 7 mV (mean ± SD, n = 10). Actually, InsP3-producing odorants generated responses in a smaller fraction of cells (lilial, 3.4%; lyral, 1.7%) than the cAMP-producing odorant (cineole, 26%). But, fundamental properties of responses were surprisingly homologous; namely, spatial distribution of the sensitivity, waveforms, I-V relation, and reversal potential, dose dependence, time integration of stimulus period, adaptation, and recovery. By applying both types of odorants alternatively to the same cell, furthermore, we observed cells to exhibit symmetrical cross-adaptation. It seems likely that even with odorants with different modalities adaptation occurs completely depending on the amount of current flow. The data will also provide evidence showing that olfactory response generation and adaptation are regulated by a uniform mechanism for a wide variety of odorants.
Severe corrosion in a waste incinerator plant due to flue gas and steam leakage
Authors: de Weijer Ton , Huijbregts Wally
Published: August 2003

In a new build waste incinerator, the waste (refuse derived fuel) was burned on a discontinuous moving grate. Frequent furnace overpressure peaks occurred because of this firing method and as a result, flue gas and fly‐ash were pushed out of the boiler and into the building. During the plant start up period, a seal in a water‐feed pipeline broke, and a large amount of condensed steam was discharged into the boiler house. Shortly thereafter, very severe corrosion was noticed on the galvanised gangways, steel building components, the boiler aluminium sheeting and on processing lines. A theoretical study of the condensation of the flue gas indicated that sulphuric acid would condense before it reached the external aluminium sheeting and that under normal conditions, dry hydrochloric acid fumes would be removed by the boiler house ventilators. However, the steam leakage had caused the hydrochloric acid to be dissolved in the condensed water and that had resulted in the severe corrosion damage, which had become evident subsequently.
An evaluation of corrosion prevention practices in agricultural equipment manufactured and used in Nigeria
Authors: Jekayinfa S.O. , Ojediran J.O. , Okekunle P.O.
Published: August 2003

In order to evaluate the effectiveness of the corrosion prevention practices applied to agricultural equipment manufactured and used in Nigeria, it is necessary to identify the various corrosion prevention methods and specify the contribution and the efficiency of each method to corrosion protection. This paper outlines the basic corrosion prevention methods used in practice and attempts to evaluate the effectiveness of their use in relation to agricultural service in Nigeria. The results of this study indicated the use of oils, fats, waxes and lubricants on metal parts, spraying with gasoline on corrosion‐sensitive parts constituted the majority of applied corrosion protection in industries where the equipment is manufactured and/or used. The study concluded by giving practical recommendations that are essential for improving corrosion prevention in the Nigerian agricultural industry.
Commitment, trust and work behaviour
Authors: de Gilder Dick
Published: August 2003

In this study differences in trust, commitment and justice perceptions were investigated between contingent and core employees in two hotels, as well as their effects on work behaviour. Contingent workers showed lower commitment to the team and to the organisation, and displayed less favourable work‐related behaviours than core employees. Commitment to the team mediated between job status (contingent vs. core employees) and five work‐related behaviours. Furthermore, depending on job status, trust and commitment were differentially related to work‐related behaviours. The implications of these results are discussed.
Leadership style for school‐based management in Hong Kong
Authors: Wong Evia O.W.
Published: August 2003

The 1990s are an important era of the Hong Kong education system. The introduction of school‐based management arouses a number of school reforms to keep up with the changing demands of the community which synthesizes into a global and knowledge‐based economy emphasizing the development of attitudes towards life‐long learning and multiple intelligence. The school reforms arouse a number of critical impacts on the school governance and management targeting at providing students with learning opportunities in an authentic and meaningful context. This in turn raises the importance of leadership style for effective school‐based management covering the aspects of vision, mission and goals; change and strategic thinking; people as well as school culture.
Appraisal training focused on what really matters
Authors: Piggot‐Irvine Eileen
Published: August 2003

Outlines the training approach adopted to assist appraisers to develop an educative process in appraisal. Such a process results in the sort of high trust, open relationship between appraisers and appraisees which enables problems to be discussed and resolved. This educative process has considerable overlap with the values and strategies of productive reasoning. General principles of the training and the programme itself are discussed. The final part of this paper reports on appraiser and appraisee perceptions on the impact of the training.
Differential developments of Taiwanese schools in organizational learning: exploration of critical factors
Authors: Jack Lam Y.L. , Marshall Chan C.M. , Pan H.L.W. , Wei H.C.P.
Published: August 2003

Against the backgrounds of twin forces (grass‐root and government) that have governed the reform movement in Taiwan since 1995, the present paper attempts to assess school development along the path towards learning organizations. Guiding the present assessment is a newly conceived model, which resorts to organizational learning processes and outcomes to construct a two‐by‐two typology, and four possible stages of development were postulated. From the distribution of a sample of 88 elementary and secondary Taiwanese schools, a bipolar concentration of schools in the relatively unchanged conditions and advanced stages of organizational learning were found. This suggested a sharp contrast between schools that prefer status quo versus those that actively search for new directions in meeting the rising challenges. Further exploration of factors that promote organizational changes revealed that external, intra‐organizational and, to a smaller extent, the contextual factors all play some part in organizational learning. Additional interviews with principals of schools located in differential stages of development clarify how their perception and mentality shape their schools’ development.
Do networks learn?
Authors: Keka¨le Tauno , Viitala Riita
Published: August 2003

Introduces the special issue on learning in networks. Attempts to answer whether a network is capable of learning and, if so, how this learning could be described, and asks if it should be seen instead as a tool – a learning forum – for learning by individuals, groups and organizations.
Re‐conceptualising learning spaces: developing capabilities in a high‐tech small firm
Authors: Macpherson Allan , Jones Ossie , Zhang Michael , Wilson Alison
Published: August 2003

Examines the process of managerial learning in a relatively remote rural small‐sized firm. Relational competences and organisational innovation are key to the capture, employment and creation of knowledge and learning within the firm. The case study organisation has created a virtual cluster of innovation, through their supply network, that reaches well beyond the traditional regional institutional support mechanisms. Through this network of relationships, they have enhanced their own learning, facilitated the learning of supplier firms and integrated knowledge to create opportunities for product innovation and development. The paper concludes that these learning experiences indicate policy implications for the support of learning in small firms. To overcome failings in traditional support systems, policy should be directed at the development and maintenance of learning networks. This informal and organisational specific approach to learning and development overcomes some of the barriers to managerial learning in SMEs, and is a method that will address the specific business needs of small firms.
Structural characterization of transglutaminase‐catalyzed cross‐linking between glyceraldehyde 3‐phosphate dehydrogenase and polyglutamine repeats
Authors: Ruoppolo Margherita , Orrù Stefania , Francese Simona , Caputo Ivana , Esposito Carla
Published: August 2003

The accumulation of abnormal polyglutamine‐containing protein aggregates within the cytosol and nuclei of affected neurons is a hallmark of the progressive neurodegenerative disorders caused by an elongated (CAG)nrepeat in the genome. The polyglutamine domains are excellent substrates for the enzyme transglutaminase type 2 (tissue), resulting in the formation of cross‐links with polypeptides containing lysyl groups. Enzymatic activity toward the Qndomains increases greatly upon lengthening of such Qnstretches (n > 40). Among the possible amine donors, the glycolytic enzyme glyceraldehyde‐3‐phosphate‐dehydrogenase was shown to tightly bind several proteins involved in polyglutamine expansion diseases. Recently, the authors have shown that K191, K268, and K331, out of the 26 lysines present in glyceraldehyde‐3‐phosphate‐dehydrogenase, are the reactive amine‐donor sites forming cross‐links with substance P, which bears the simplest Qndomain (n = 2). The present study reports that synthetic peptides of both pathological and nonpathological length (n = 43 and 17, respectively) form cross‐links with the same K residues located in the C‐terminal region of glyceraldehyde‐3‐phosphate‐dehydrogenase. In addition, it is shown that extra K residues present in the C termini of glyceraldehyde‐3‐phosphate‐dehydrogenase are susceptible to cross‐linking in the presence of transglutaminase. The present results indicate a possible modulating effect of Qnstretches on tissue transglutaminase substrate specificity and mechanism of recognition.
The topomer search model: A simple, quantitative theory of two‐state protein folding kinetics
Authors: Makarov Dmitrii E. , Plaxco Kevin W.
Published: August 2003

Most small, single‐domain proteins fold with the uncomplicated, single‐exponential kinetics expected for diffusion on a smooth energy landscape. Despite this energetic smoothness, the folding rates of these two‐state proteins span a remarkable million‐fold range. Here, we review the evidence in favor of a simple, mechanistic description, the topomer search model, which quantitatively accounts for the broad scope of observed two‐state folding rates. The model, which stipulates that the search for those unfolded conformations with a grossly correct topology is the rate‐limiting step in folding, fits observed rates with a correlation coefficient of ∼0.9 using just two free parameters. The fitted values of these parameters, the pre‐exponential attempt frequency and a measure of the difficulty of ordering an unfolded chain, are consistent with previously reported experimental constraints. These results suggest that the topomer search process may dominate the relative barrier heights of two‐state protein‐folding reactions.
Partial NMR assignments and secondary structure mapping of the isolated α subunit of Escherichia coli tryptophan synthase, a 29‐kD TIM barrel protein
Authors: Vadrevu Ramakrishna , Falzone Christopher J. , Matthews C. Robert
Published: August 2003

The α subunit of tryptophan synthase (αTS) from S. typhimurium belongs to the triosephosphate isomerase (TIM) or the (β/α)8 barrel fold, one of the most common structures in biology. To test the conservation of the global fold in the isolated Escherichia coli homolog, we have obtained a majority of the backbone assignments for the 29‐kD αTS by using standard heteronuclear multidimensional NMR methods on uniformly 15N‐ and 15N/13C‐labeled protein and on protein selectively 15N‐labeled at key hydrophobic residues. The secondary structure mapped by chemical shift index, nuclear Overhauser enhancements (NOEs), and hydrogen‐deuterium (H‐D) exchange, and several abnormal chemical shifts are consistent with the conservation of the global TIM barrel fold of the isolated E. coli αTS. Because most of the amide protons that are slow to exchange with solvent correspond to the β‐sheet residues, the β‐barrel is likely to play an important role in stabilizing the previously detected folding intermediates for E. coli αTS. A similar combination of uniform and selective labeling can be extended to other TIM barrel proteins to obtain insight into the role of the motif in stabilizing what appear to be common partially folded forms.
Pressure‐induced unfolding of the molten globule of all‐Ala α‐lactalbumin
Authors: Lassalle Michael W. , Li Hua , Yamada Hiroaki , Akasaka Kazuyuki , Redfield Christina
Published: August 2003

Pressure‐induced unfolding of a molten globule (MG) was studied in a residue‐specific manner with 1H‐15N two‐dimensional NMR spectroscopy using a variant of human α‐lactalbumin (α‐LA), in which all eight cysteines had been replaced with alanines (all‐Ala α‐LA). The NMR spectrum underwent a series of changes from 30 to 2000 bar at 20°C and from −18°C to 36°C at 2000 bar, showing a highly heterogeneous unfolding pattern according to the secondary structural elements of the native structure. Unfolding began in the loop part of the β‐domain, and then extended to the remainder of the β‐domain, after which the α‐domain began to unfold. Within the α‐domain, the pressure stability decreased in the order: D‐helix ∼ 310‐helix > C‐helix ∼ B‐helix > A‐helix. The D‐helix, C‐terminal 310‐helix and a large part of B‐ and C‐helices did not unfold at 2000 bar, even at 36°C or at −18°C. The results verify that the MG state consists of a mixture of variously unfolded conformers from the mostly folded to the nearly totally unfolded that differ in stability and partial molar volume. Not only heat but also cold denaturation was observed, supporting the view that the MG state is stabilized by hydrophobic interactions.
Structural energetics of protein–carbohydrate interactions: Insights derived from the study of lysozyme binding to its natural saccharide inhibitors
Authors: García‐Hernández Enrique , Zubillaga Rafael A. , Chavelas‐Adame Eneas A. , Vázquez‐Contreras Edgar , Rojo‐Domínguez Arturo , Costas Miguel
Published: August 2003

High‐sensitivity isothermal titration calorimetry was used to characterize the binding of the glycohydrolitic enzyme hen egg‐white lysozyme to its natural saccharide inhibitors, chitobiose and chitrotriose. Measurements were done at a pH of 4.7, in the 15°C −45°C temperature range. Using a structural‐energetic parameterization derived previously for lectin‐carbohydrate associations, both binding enthalpies and entropies for the present systems and for the complex of chitobiose with turkey egg‐white lysozyme from the literature were correctly accounted for. These observations suggest that both lysozymes and lectins follow the same structural‐energetic behavior in the binding to their ligands. From the analysis of lysozyme data in conjunction with other binding data reported in the literature, an ad hoc parameterization of ΔCp for protein–carbohydrate complexes was derived for the first time. The novel parameters for both polar and apolar surface areas differed significantly from correlations obtained previously from model compounds and protein‐folding data. As ΔCp is extremely sensitive to changes in solvent structure, this finding indicates that protein–carbohydrate complexes have distinctive hydration properties. According to our analysis, the dehydration of polar groups is the major cause for the observed decrease in ΔCp, which implies that these groups behave hydrophobically. The contribution of apolar surface areas was found of the expected sign, but their specific weight is much smaller than those obtained in other correlations. This small contribution to ΔCp is consistent with Lemieux's hypothesis of a low degree of hydration of apolar surfaces on carbohydrates.
Homology modeling and molecular dynamics simulations of the N‐terminal domain of wheat high molecular weight glutenin subunit 10
Authors: Cazalis Roland , Aussenac Thierry , Rhazi Larbi , Marin Antoine , Gibrat Jean‐François
Published: August 2003

High molecular weight glutenin subunits (HMW‐GS) are of a particular interest because of their biomechanical properties, which are important in many food systems such as breadmaking. Using fold‐recognition techniques, we identified a fold compatible with the N‐terminal domain of HMW‐GS Dy10. This fold corresponds to the one adopted by proteins belonging to the cereal inhibitor family. Starting from three known protein structures of this family as templates, we built three models for the N‐terminal domain of HMW‐GS Dy10. We analyzed these models, and we propose a number of hypotheses regarding the N‐terminal domain properties that can be tested experimentally. In particular, we discuss two possible ways of interaction between the N‐terminal domains of the y‐type HMW glutenin subunits. The first way consists in the creation of interchain disulfide bridges. According to our models, we propose two plausible scenarios: (1) the existence of an intrachain disulfide bridge between cysteines 22 and 44, leaving the three other cysteines free of engaging in intermolecular bonds; and (2) the creation of two intrachain disulfide bridges (involving cysteines 22–44 and cysteines 10–55), leaving a single cysteine (45) for creating an intermolecular disulfide bridge. We discuss these scenarios in relation to contradictory experimental results. The second way, although less likely, is nevertheless worth considering. There might exist a possibility for the N‐terminal domain of Dy10, Nt‐Dy10, to create oligomers, because homologous cereal inhibitor proteins are known to exist as monomers, homodimers, and heterooligomers. We also discuss, in relation to the function of the cereal inhibitor proteins, the possibility that this N‐terminal domain has retained similar inhibitory functions.
Energy landscape and dynamics of the β‐hairpin G peptide and its isomers: Topology and sequences
Authors: Ma Buyong , Nussinov Ruth
Published: August 2003

We have investigated free energy landscape [MM/PBSA + normal modes entropy] of permutations in the G peptide (41–56) from the protein G B1 domain by studying six isomers corresponding to moving the hydrophobic cluster along the β‐strands (toward the turn: T1, AGEWTYDDKTFTVTET; T2, GEDTWDYATFTVTKTE; T3, GEDDWTYATFTVTKTE; toward the end: E1, WTYDDAGETKTFTVT; E2, WEYTGDDATKTETFTV; E3, WTYEGDDATKTETFTV). The free energy terms include molecular mechanics energy, Poisson‐Boltzmann electrostatic solvation energy, surface area solvation energy, and conformational entropy estimated by using normal mode analysis. From the wild type to T1, then T3, and finally T2, we see a progressively changing energy landscape, toward a less stable β‐hairpin structure. Moving the hydrophobic cluster outside toward the end region causes a greater change in the energy landscape. α‐Helical instead of a β‐hairpin structure was the most stable form for the E2 isomer. However, no matter how much the sequence changes, for all variants studied, ideal “native” β‐hairpin topologies remain as minima (regardless of whether global or local) in the energy landscape. In general, we find that the energy landscape is dependent on the hydrophobic cluster topology and on the sequence. Our present study indicates that the key is the relative conformational energies of the different conformations. Changes in the sequence strongly modulate the relative stabilities of topologically similar regions in the energy landscape, rather than redefine the topology space. This finding is consistent with a population redistribution in the process of protein folding. The limited variation of topological space, compared with the number of possible sequence changes, may relate to the observation that the number of known protein folds are far less than the sequential allowance.
Asymmetric mutation rates at enzyme–inhibitor interfaces: Implications for the protein–protein docking problem
Authors: Bradford James R. , Westhead David R.
Published: August 2003

We have carried out a thorough and systematic sequence‐structure study on how the pattern of conservation at the interface differs from the noninteracting surface in seven proteases and their inhibitors. As expected, the interface of a protease could be easily distinguished from the noninteracting surface by a concentrated area of conservation. In contrast, there was less distinction to be made between the interface and the noninteracting surface of inhibitors, and in five of the seven cases, a higher proportion of the interface area was variable compared to the rest of the surface. This is likely to cause a problem for binding‐site prediction methods that assume the largest cluster of highly conserved residues on the surface of a protein corresponds to the interface. We conclude that such methods would succeed when applied to our protease test cases, but complications could arise with the inhibitors. These results also impact on methods to solve the protein–protein docking problem that use conservation at the interface to provide the location of the two protein binding sites prior to application of the docking algorithm.
Calculating pKa values in enzyme active sites
Authors: Nielsen Jens Erik , McCammon J. Andrew
Published: August 2003

The ionization properties of the active‐site residues in enzymes are of considerable interest in the study of the catalytic mechanisms of enzymes. Knowledge of these ionization constants (pKa values) often allows the researcher to identify the proton donor and the catalytic nucleophile in the reaction mechanism of the enzyme. Estimates of protein residue pKa values can be obtained by applying pKa calculation algorithms to protein X‐ray structures. We show that pKa values accurate enough for identifying the proton donor in an enzyme active site can be calculated by considering in detail only the active‐site residues and their immediate electrostatic interaction partners, thus allowing for a large decrease in calculation time. More specifically we omit the calculation of site‐site interaction energies, and the calculation of desolvation and background interaction energies for a large number of pairs of titratable groups. The method presented here is well suited to be applied on a genomic scale, and can be implemented in most pKa calculation algorithms to give significant reductions in calculation time with little or no impact on the accuracy of the results. The work presented here has implications for the understanding of enzymes in general and for the design of novel biocatalysts.
Archaeal signal peptides—A comparative survey at the genome level
Authors: Bardy Sonia L. , Eichler Jerry , Jarrell Ken F.
Published: August 2003

The correct delivery of noncytoplasmic proteins to locations both within and outside the cell depends on the appropriate targeting signals. Protein translocation across the bacterial plasma membrane and the eukaryal endoplasmic reticulum membrane relies on cleavable N‐terminal signal peptides. Although the signal peptides of secreted proteins in Bacteria and Eukarya have been extensively studied at the sequence, structure, and functional levels, little is known of the nature of archaeal signal peptides. In this report, genome‐based analysis was performed in an attempt to define the amino acid composition, length, and cleavage sites of various signal peptide classes in a wide range of archaeal species. The results serve to present a picture of the archaeal signal peptide, revealing the incorporation of bacterial, eukaryal, and archaeal traits.
A graph‐theory algorithm for rapid protein side‐chain prediction
Authors: Canutescu Adrian A. , Shelenkov Andrew A. , Dunbrack Roland L.
Published: August 2003

Fast and accurate side‐chain conformation prediction is important for homology modeling, ab initio protein structure prediction, and protein design applications. Many methods have been presented, although only a few computer programs are publicly available. The SCWRL program is one such method and is widely used because of its speed, accuracy, and ease of use. A new algorithm for SCWRL is presented that uses results from graph theory to solve the combinatorial problem encountered in the side‐chain prediction problem. In this method, side chains are represented as vertices in an undirected graph. Any two residues that have rotamers with nonzero interaction energies are considered to have an edge in the graph. The resulting graph can be partitioned into connected subgraphs with no edges between them. These subgraphs can in turn be broken into biconnected components, which are graphs that cannot be disconnected by removal of a single vertex. The combinatorial problem is reduced to finding the minimum energy of these small biconnected components and combining the results to identify the global minimum energy conformation. This algorithm is able to complete predictions on a set of 180 proteins with 34,342 side chains in <7 min of computer time. The total χ1 and χ1 + 2 dihedral angle accuracies are 82.6% and 73.7% using a simple energy function based on the backbone‐dependent rotamer library and a linear repulsive steric energy. The new algorithm will allow for use of SCWRL in more demanding applications such as sequence design and ab initio structure prediction, as well addition of a more complex energy function and conformational flexibility, leading to increased accuracy.
Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein–nucleic acid complex crystals
Authors: Kantardjieff Katherine A. , Rupp Bernhard
Published: August 2003

Estimating the number of molecules in the crystallographic asymmetric unit is one of the first steps in a macromolecular structure determination. Based on a survey of 15,641 crystallographic Protein Data Bank (PDB) entries the distribution of VM, the crystal volume per unit of protein molecular weight, known as Matthews coefficient, has been reanalyzed. The range of values and frequencies has changed in the 30 years since Matthews first analysis of protein crystal solvent content. In the statistical analysis, complexes of proteins and nucleic acids have been treated as a separate group. In addition, the VM distribution for nucleic acid crystals has been examined for the first time. Observing that resolution is a significant discriminator of VM, an improved estimator for the probabilities of the number of molecules in the crystallographic asymmetric unit has been implemented, using resolution as additional information.
Prospects and limitations of the rational engineering of fibrillar collagens
Authors: Majsterek Ireneusz , McAdams Erin , Adachi Eijiro , Dhume Shirish T. , Fertala Andrzej
Published: August 2003

Recombinant collagens are attractive proteins for a number of biomedical applications. To date, significant progress was made in the large‐scale production of nonmodified recombinant collagens; however, engineering of novel collagen‐like proteins according to customized specifications has not been addressed. Herein we investigated the possibility of rational engineering of collagen‐like proteins with specifically assigned characteristics. We have genetically engineered two DNA constructs encoding multi‐D4 collagens defined as collagen‐like proteins, consisting primarily of a tandem of the collagen II D4 periods that correspond to the biologically active region. We have also attempted to decrease enzymatic degradation of novel collagen by mutating a matrix metalloproteinase 1 cleavage site present in the D4 period. We demonstrated that the recombinant collagen α‐chains consisting predominantly of the D4 period but lacking most of the other D periods found in native collagen fold into a typical collagen triple helix, and the novel procollagens are correctly processed by procollagen N‐proteinase and procollagen C‐proteinase. The nonmutated multi‐D4 collagen had a normal melting point of 41°C and a similar carbohydrate content as that of control. In contrast, the mutant multi‐D4 collagen had a markedly lower thermostability of 36°C and a significantly higher carbohydrate content. Both collagens were cleaved at multiple sites by matrix metalloproteinase 1, but the rate of hydrolysis of the mutant multi‐D4 collagen was lower. These results provide a basis for the rational engineering of collagenous proteins and identifying any undesirable consequences of altering the collagenous amino acid sequences.
The structure of Pseudomonas P51 Cl‐muconate lactonizing enzyme: Co‐evolution of structure and dynamics with the dehalogenation function
Authors: Kajander Tommi , Lehtiö Lari , Schlömann Michael , Goldman Adrian
Published: August 2003

Bacterial muconate lactonizing enzymes (MLEs) catalyze the conversion of cis,cis‐muconate as a part of the β‐ketoadipate pathway, and some MLEs are also able to dehalogenate chlorinated muconates (Cl‐MLEs). The basis for the Cl‐MLEs dehalogenating activity is still unclear. To further elucidate the differences between MLEs and Cl‐MLEs, we have solved the structure of Pseudomonas P51 Cl‐MLE at 1.95 Å resolution. Comparison of Pseudomonas MLE and Cl‐MLE structures reveals the presence of a large cavity in the Cl‐MLEs. The cavity may be related to conformational changes on substrate binding in Cl‐MLEs, at Gly52. Site‐directed mutagenesis on Pseudomonas MLE core positions to the equivalent Cl‐MLE residues showed that the variant Thr52Gly was rather inactive, whereas the Thr52Gly‐Phe103Ser variant had regained part of the activity. These residues form a hydrogen bond in the Cl‐MLEs. The Cl‐MLE structure, as a result of the Thr‐to‐Gly change, is more flexible than MLE: As a mobile loop closes over the active site, a conformational change at Gly52 is observed in Cl‐MLEs. The loose packing and structural motions in Cl‐MLE may be required for the rotation of the lactone ring in the active site necessary for the dehalogenating activity of Cl‐MLEs. Furthermore, we also suggest that differences in the active site mobile loop sequence between MLEs and Cl‐MLEs result in lower active site polarity in Cl‐MLEs, possibly affecting catalysis. These changes could result in slower product release from Cl‐MLEs and make it a better enzyme for dehalogenation of substrate.
Innovation and Performance: Benchmarking Australian Firms
Authors: Feeny Simon , Rogers Mark
Published: August 2003

This article empirically analyses the link between innovation and performance using a sample of large Australian firms, with a specific aim of developing benchmarking tools. Innovation is measured by firms' investment in R&D and applications for patents, trademarks and designs. An innovation index is constructed to provide one method of benchmarking. The index incorporates a firm's innovative activities into a single figure after accounting for firm size. The index provides a ranking of the most innovative firms in Australia. A second method of benchmarking uses a stochastic production frontier. This type of analysis identifies the firms which are located closest to a ‘best practice innovation frontier’.
Econom(etr)ics of crime and litigation
Authors: van Tulder F. P. , van Velthoven B. C. J.
Published: August 2003

Economists approach the behaviour of potential criminals, litigants and law enforcement agencies in terms of rational choice: the actors choose the best alternatives in terms of costs and benefits within the choices open to them. The prime focus of economists is on the general factors in society affecting the crime and litigation level and on the interaction between the crime and litigation level and the legal system. In doing so they have to study the interaction between the micro level of individual decision making and the macro level of the law enforcement system reacting on these decisions. Data are often only available at aggregate (macro) level. Econometric studies at the macro level, especially time series, have the problem that many effects have to be estimated from a limited number of data. Various types of studies and some empirical results regarding crime, litigation and the workload of judicial services are discussed.
Analysing neighbourhood influence in criminology
Authors: Elffers Henk
Published: August 2003

Neighbourhood influence in criminology can be conceptualised both as pertaining to the influence of characteristics of a neighbourhood on its inhabitants, and to the mutual influence of characteristics of adjacent neighbourhoods on each other. The first conceptualisation asks for multilevel analysis, the second one for one of several spatial dependency (spatial autocorrelation) methods. Various models in both traditions are discussed and illustrated with data on victimisation and on burglary.
Statistical aspects of interpreting DNA profiling in legal cases
Authors: Sjerps M. , Kloosterman A. D.
Published: August 2003

DNA profiling has become one of the most powerful forensic techniques that is used in criminal investigations to identify suspects. Moreover, scientific DNA evidence has become an important component in criminal trials. The interpretation of DNA evidence involves many statistical and probabilistic aspects, which have been the subject of fierce debates over past years. Many controversies are rooted in the differences between the so‐called Likelihood Ratio approach to evidence interpretation and other methods. However, though interesting for the statistician and probability theorist, these discussions are obstructive for legal proceedings. Fortunately, many issues have by now been settled, but the ever‐expanding possibilities keep on raising new discussion topics. This paper provides a brief overview of the statistical discussion, and addresses some of the most interesting issues in more detail.
A Note on the Poll Tax
Authors: Clausing Thorsten
Published: August 2003

A poll tax is usually seen as the standard example of a lump sum tax and therefore as allocationally efficient. In this paper, it is shown that in a dynamic setting with endogenous fertility, a poll tax may yield a Pareto‐inferior outcome as compared to a percentage consumption tax.
On the Popular Support for Progressive Taxation
Authors: Klor Esteban F.
Published: August 2003

The “popular support for progressive taxation theorem” (Marhuenda and Ortuño‐Ortín, 1995) provides an important formalization of the intuition that a majority of relatively poor voters over rich ones leads to progressive income taxation. Yet the theorem does not provide an equilibrium outcome. In addition, it assumes an overly restrictive domain of tax schedules and no incentive effects of income taxation. This paper shows that none of these assumptions of the theorem can be relaxed completely. Most notably, it is shown that a majority of poor voters does not imply progressive taxation in a more general policy space and that a regressive tax schedule may obtain a majority over a progressive one when individuals' income is endogenous.
Inequality in Incomes and Access to Education: A Cross‐country Analysis (1960–95)
Authors: Checchi Daniele
Published: August 2003

Abstract.  In the current debate on the relationship between inequality in income distribution and growth, one of the possible links works through access to education. Starting from an optimal demand for education where, among other things, the years of education depend on family income, we derive two testable predictions in the analysis of aggregate data on school enrolments: a negative (linear) dependence of enrolment rates on the Gini concentration index on income distribution; and a positive dependence on public resources invested in education and/or on skill premium in the labour market. These predictions are tested on a (unbalanced) panel of 108 countries for the period 1960–95. The main finding of this analysis is that, once we control for the degree of development with the (log of) per capita output, financial constraints seem mainly relevant in limiting the access to secondary education. However, when considering gender differences, there is evidence that female participation in education is more conditioned by family wealth, in some cases starting from primary education. Finally, there is weak evidence that public resources spent on education raise the enrolment rates.
Early Retirement and Economic Incentives: Evidence from a Quasi‐natural Experiment
Authors: Røed Knut , Haugen Fredrik
Published: August 2003

Abstract.  During the 1990s, a new subsidized early retirement option was assigned quasi‐randomly to two‐thirds of Norwegian elderly workers. We use this ‘natural experiment’ to evaluate how economic incentives affect retirement behaviour. The new retirement option reduced employment substantially, and this effect escalated over time. It did not substitute for disability pension or long‐term unemployment, and approximately two out of three retirees would have stayed employed without it. Subsidized retirement was primarily voluntary, but there is also some evidence that firms took advantage of the retirement programme to ‘push out’ excess workers.
Unions and the Welfare Impact of Foreign Direct Investment — A Wisdom Extension
Authors: Bughin Jacques , Vannini Stefano
Published: August 2003

Abstract.  This paper extends the recent literature, e.g. Leahy and Montagna (Economic Journal 110: 80–92, 2000), in relation to the link between unionization, inward foreign direct investment (FDI) and country welfare in an oligopoly market structure. It is shown that the common results, that unions may reduce welfare under FDI while multinational enterprises (MNEs) will strictly trade off union wages at each location, are generally driven by the assumption relating to the scope of the bargaining with the union, namely the ‘right to manage’ (RTM). In particular, our extension to efficient bargaining (EB) demonstrates that union power may increase welfare in the presence of FDI, while the MNEs’ choice between FDI and exports will include profit‐sharing arbitrage with unions, in addition to the usual wage comparison considerations.
Market Expectations in the UK Before and After the ERM Crisis
Authors: Söderlin Paul
Published: August 2003

The British pound left the ERM on 16 September 1992 after a period of turbulence. UK monetary policy soon shifted to lower short interest rates, and an inflation target was announced. This paper uses daily option prices to estimate how the market's probability distribution of the future mark–pound exchange rate and UK and German interest rates changed over the summer and autumn of 1992. The results show, among other things, how various policy decisions affected the market's assessment of the probabilities of realignments and lending rate cuts.
The Returns to the Quantity and Quality of Education: Evidence for Men in England and Wales
Authors: Harmon Colm , Walker Ian
Published: August 2003

Until the late 1960s, state schooling in England and Wales was determined by an ability test of pupils at age 11 which had an effect on both the quantity and quality of education. By estimating the relationship between earnings and earlier schooling during a period when school areas changed from selective to non‐selective education, we consider how the returns to the quantity of education are confounded by differences in the quality of schooling and whether the effects of quality are confounded by its correlation with quantity. Our results confirm recent evidence that returns to education quantity are large and quality effects are small.
Managing the future forest resource through designer trees
Authors: Todoroki C. L. , Carson S. D.
Published: August 2003

With today's tree improvement technology coupled with knowledge of the influence of forest management practices on tree growth and log quality, it is possible to manipulate tree form to engineer trees with specific characteristics. Theoretically we can create forest portfolios to optimize suitability for different end uses. We could design structural forests for optimal building materials, LongClears Forests for furniture and mouldings markets, or PulpWood Forests for pulp and paper industries. This project's goal was to explore methods for identifying tree characteristics that could be manipulated to optimize production of specific lumber products, namely LongClears. A model that works backwards from the targeted product through wood processing with linkage to forest management and genetic selection strategies is proposed. The model uses a combination of mathematical programming and operations research techniques including data envelopment analysis, log sawing optimization, and sawmill simulation to identify properties of the optimal log and designer tree.