bluuebunny/crossref_metadata_2025_split huggingface dataset:
Action inquiry and performance appraisals
Authors: Walsh Kate , Fisher Dalmar 
Published: January 2005

PurposeIntroduces the primary concepts behind the practice of action inquiry. Then, examines what current literature suggests about components of the performance appraisal process and identifies areas where applying action inquiry concepts can add a new dimension to our current understanding.Design/methodology/approachApplies action inquiry, a concept from the organizational learning and change literatures, to suggest ways to infuse meaning and mutuality into appraisal discussions to help organizational leaders and members learn and develop. Ways to do so are demonstrated through a review and discussion of seven principal research streams in the current appraisal literature.FindingsAn action inquiry approach can address many of the limitations inherent in the appraisal process and refocus appraisals as developmental tools. Potentially, appraisals can act as forums to open dialogue, invite participation and build relationships around re‐visioning one's work and career. The process can become instrumental to continual quality improvement and organizational growth suggests that a rich opportunity exists to make the performance appraisal process developmentally meaningful for individuals and potentially transformative for organizations.Originality/valueDiscusses seven themes addressed in performance appraisal research and poses new possibilities that emerge when these themes are examined through an action inquiry lens.
Spectral magnitude effects on the analyses of secondary structure from circular dichroism spectroscopic data
Authors: Miles Andrew J. , Whitmore Lee , Wallace B.A. 
Published: January 2005

AbstractThe effects of spectral magnitude on the calculated secondary structures derived from circular dichroism (CD) spectra were examined for a number of the most commonly used algorithms and reference databases. Proteins with different secondary structures, ranging from mostly helical to mostly β‐sheet, but which were not components of existing reference databases, were used as test systems. These proteins had known crystal structures, so it was possible to ascertain the effects of magnitude on both the accuracy of determining the secondary structure and the goodness‐of‐fit of the calculated structures to the experimental data. It was found that most algorithms are highly sensitive to spectral magnitude, and that the goodness‐of‐fit parameter may be a useful tool in assessing the correct scaling of the data. This means that parameters that affect magnitude, including calibration of the instrument, the spectral cell pathlength, and the protein concentration, must be accurately determined to obtain correct secondary structural analyses of proteins from CD data using empirical methods.
Assessing predictions of protein–protein interaction: The CAPRI experiment
Authors: Janin Joël 
Published: January 2005

AbstractThe Critical Assessment of PRedicted Interactions (CAPRI) experiment was designed in 2000 to test protein docking algorithms in blind predictions of the structure of protein–protein complexes. In four years, 17 complexes offered by crystallographers as targets prior to publication, have been subjected to structure prediction by docking their two components. Models of these complexes were submitted by predictor groups and assessed by comparing their geometry to the X‐ray structure and by evaluating the quality of the prediction of the regions of interaction and of the pair wise residue contacts. Prediction was successful on 12 of the 17 targets, most of the failures being due to large conformation changes that the algorithms could not cope with. Progress in the prediction quality observed in four years indicates that the experiment is a powerful incentive to develop new procedures that allow for flexibility during docking and incorporate nonstructural information. We therefore call upon structural biologists who study protein–protein complexes to provide targets for further rounds of CAPRI predictions.
Helical structure determined by NMR of the HIV‐1 (345–392)Gag sequence, surrounding p2: Implications for particle assembly and RNA packaging
Authors: Morellet Nelly , Druillennec Sabine , Lenoir Christine , Bouaziz Serge , Roques Bernard P. 
Published: January 2005

AbstractGag protein oligomerization, an essential step during virus assembly, results in budding of spherical virus particles. This process is critically dependent on the spacer p2, located between the capsid and the nucleocapsid proteins. P2 contributes also, in association with NCp7, to specific recognition of the HIV‐1 packaging signal resulting in viral genome encapsidation. There is no structural information about the 20 last amino acids of the C‐terminal part of capsid (CA[CTD]) and p2, in the molecular mechanism of Gag assembly. In this study the structure of a peptide encompassing the 14 residues of p2 with the upstream 21 residues and the downstream 13 residues was determined by 1H NMR in 30% trifluoroethanol (TFE). The main structural motif is a well‐defined amphipathic α‐helix including p2, the seven last residues of the CA(CTD), and the two first residues of NCp7. Peptides containing the p2 domain have a strong tendency to aggregate in solution, as shown by gel filtration analyses in pure H2O. To take into account the aggregation phenomena, models of dimer and trimer formed through hydrophobic or hydrophilic interfaces were constructed by molecular dynamic simulations. Gel shift experiments demonstrate that the presence of at least p2 and the 13 first residues of NCp7 is required for RNA binding. A computer‐generated model of the Gag polyprotein segment (282–434)Gag interacting with the packaging element SL3 is proposed, illustrating the importance of p2 and NCp7 in genomic encapsidation.
Crystal structure of the complex formed between a group I Phospholipase A2 and a naturally occurring fatty acid at 2.7 Å resolution
Authors: Singh Garima , Jasti Jayasankar , Saravanan K. , Sharma Sujata , Kaur Punit , Srinivasan A. , Singh Tej P. 
Published: January 2005

AbstractThis is the first evidence of a naturally bound fatty acid to a group I Phospholipase A2 (PLA2) and also to a PLA2 with Asp 49. The fatty acid identified as n‐tridecanoic acid is observed at the substrate recognition site of PLA2 hydrophobic channel. The complex was isolated from the venom of Bungarus caeruleus (Common Indian Krait). The primary sequence of the PLA2 was determined using the cDNA method. Three‐dimensional structure has been solved by the molecular replacement method and refined using the CNS package to a final R factor of 19.8% for the data in the resolution range from 20.0 to 2.7 Å. The final refined model is comprised of 912 protein atoms, one sodium ion, one molecule of n‐tridecanoic acid, and 60 water molecules. The sodium ion is located in the calcium‐binding loop with a sevenfold coordination. A characteristic extra electron density was observed in the hydrophobic channel of the enzyme, into which a molecule of n‐tridecanoic acid was clearly fitted. The MALDI–TOF measurements of the crystals had earlier indicated an increase in the molecular mass of PLA2 by 212 Da over the native PLA2. A major part of the ligand fits well in the binding pocket and interacts directly with His 48 and Asp 49. Although the overall structure of PLA2 in the present complex is similar to the native structure reported earlier, it differs significantly in the folding of its calcium‐binding loop.
Intramolecular disulphide bond arrangements in nonhomologous proteins
Authors: Hartig Gerald R.S. , Tran Tran T. , Smythe Mark L. 
Published: January 2005

AbstractThe presence and location of intramolecular disulphide bonds are a key determinant of the structure and function of proteins. Intramolecular disulphide bonds in proteins have previously been analyzed under the assumption that there is no clear relationship between disulphide arrangement and disulphide concentration. To investigate this, a set of sequence nonhomologous protein chains containing one or more intramolecular disulphide bonds was extracted from the Protein Data Bank, and the arrangements of the bonds, Protein Data Bank header, and Structural Characterization of Proteins fold were analyzed as a function of intramolecular disulphide bond concentration. Two populations of intramolecular disulphide bond‐containing proteins were identified, with a naturally occurring partition at 25 residues per bond. These populations were named intramolecular disulphide bond‐rich and ‐poor. Benefits of partitioning were illustrated by three results: (1) rich chains most frequently contained three disulphides, explaining the plateaux in extant disulphide frequency distributions; (2) a positive relationship between median chain length and the number of disulphides, only seen when the data were partitioned; and (3) the most common bonding pattern for chains with three disulphide bonds was based on the most common for two, only when the data were partitioned. The two populations had different headers, folds, bond arrangements, and chain lengths. Associations between IDSB concentration, IDSB bonding pattern, loop sizes, SCOP fold, and PDB header were also found. From this, we found that intramolecular disulphide bond‐rich and ‐poor proteins follow different bonding rules, and must be considered separately to generate meaningful models of bond formation.
The crystal structure of an eukaryotic iron superoxide dismutase suggests intersubunit cooperation during catalysis
Authors: Muñoz Inés G. , Moran Jose F. , Becana Manuel , Montoya Guillermo 
Published: January 2005

AbstractSuperoxide dismutases (SODs) are a family of metalloenzymes that catalyze the dismutation of superoxide anion radicals into molecular oxygen and hydrogen peroxide. Iron superoxide dismutases (FeSODs) are only expressed in some prokaryotes and plants. A new and highly active FeSOD with an unusual subcellular localization has recently been isolated from the plant Vigna unguiculata (cowpea). This protein functions as a homodimer and, in contrast to the other members of the SOD family, is localized to the cytosol. The crystal structure of the recombinant enzyme has been solved and the model refined to 1.97 Å resolution. The superoxide anion binding site is located in a cleft close to the dimer interface. The coordination geometry of the Fe site is a distorted trigonal bipyramidal arrangement, whose axial ligands are His43 and a solvent molecule, and whose in‐plane ligands are His95, Asp195, and His199. A comparison of the structural features of cowpea FeSOD with those of homologous SODs reveals subtle differences in regard to the metal–protein interactions, and confirms the existence of two regions that may control the traffic of substrate and product: one located near the Fe binding site, and another in the dimer interface. The evolutionary conservation of reciprocal interactions of both monomers in neighboring active sites suggests possible subunit cooperation during catalysis.
Artificial neural networks for estimating soil hydraulic parameters from dynamic flow experiments
Authors: Schmitz G. H. , Puhlmann H. , Dröge W. , Lennartz F. 
Published: January 2005

SummaryInverse methods are often used for estimating soil hydraulic parameters from experiments on flow of water through soil. We propose here an alternative method using neural networks. We teach a problem‐adapted network of radial basis functions (RBF) the relationship between soil parameters and transient flow patterns using a numerical flow model. The trained RBF network accurately identifies soil parameters from flow patterns not contained in the training scenarios. A comparison with the inverse method (Annealing‐Simplex) reveals a similarly good prediction by both approaches for randomly perturbed data and data from the real world. Nonetheless, the inverse method showed dependency on initial parameter estimates not required by the RBF network. Training demands moderately more computation and manpower than the inverse technique, but the absolutely stable and simple network application requires negligible resources. Thus, for individual applications, the network approach is slightly surpassed by the Annealing‐Simplex method. However, the RBF network has to be trained only once and, subsequently, it can be applied easily and without effort upon any number of laboratory experiments with standardized experimental setups.
Redistribution of particulate organic matter during ultrasonic dispersion of highly weathered soils
Authors: Oorts K. , Vanlauwe B. , Recous S. , Merckx R. 
Published: January 2005

SummaryThe use of ultrasonic energy for the dispersion of aggregates in studies of soil organic matter (SOM) fractionation entails a risk of redistribution of particulate organic matter (POM) to smaller particle‐size fractions. As the mechanical strength of straw also decreases with increasing state of decomposition, it can be expected that not all POM will be redistributed to the same extent during such dispersion. Therefore, we studied the redistribution of POM during ultrasonic dispersion and fractionation as a function of (i) dispersion energy applied and (ii) its state of decomposition. Three soils were dispersed at different ultrasonic energies (750, 1500 and 2250 J g−1 soil) or with sodium carbonate and were fractionated by particle size. Fraction yields were compared with those obtained with a standard particle‐size analysis. Undecomposed or incubated (for 2, 4 or 6 months) 13C‐enriched wheat straw was added to the POM fraction (0.25–2 mm) of one of the soils before dispersion and fractionation. Dispersion with sodium carbonate resulted in the weakest dispersion and affected the chemical properties of the fractions obtained through its high pH and the introduction of carbonate. The mildest ultrasonic dispersion treatment (750 J g−1) did not result in adequate soil dispersion as too much clay was still recovered in the larger fractions. Ultrasonic dispersion at 1500 J g−1 soil obtained a nearly complete dispersion down to the clay level (0.002 mm), and it did not have a significant effect on the total amount of carbon and nitrogen in the POM fractions. The 2250 J g−1 treatment was too destructive for the POM fractions since it redistributed up to 31 and 37%, respectively, of the total amount of carbon and nitrogen in these POM fractions to smaller particle‐size fractions. The amount of 13C‐enriched wheat straw that was redistributed to smaller particle‐size fractions during ultrasonic dispersion at 1500 J g−1 increased with increasing incubation time of this straw. Straw particles incubated for 6 months were completely transferred to smaller particle‐size fractions. Therefore, ultrasonic dispersion resulted in fractionation of POM, leaving only the less decomposed particles in this fraction. The amounts of carbon and nitrogen transferred to the silt and clay fractions were, however, negligible compared with the total amounts of carbon and nitrogen in these fractions. It is concluded that ultrasonic dispersion seriously affects the amount and properties of POM fractions. However, it is still considered as an acceptable and appropriate method for the isolation and study of SOM associated with silt and clay fractions.
Measurement of the size distribution of water‐filled pores at different matric potentials by stray field nuclear magnetic resonance
Authors: Bird N. R. A. , Preston A. R. , Randall E. W. , Whalley W. R. , Whitmore A. P. 
Published: January 2005

SummaryThe water retention characteristic provides the traditional data set for the derivation of a soil's pore‐size distribution. However, the technique employed to achieve this requires that assumptions be made about the way pores interconnect. We explore an alternative approach based on stray field nuclear magnetic resonance (STRAFI‐NMR) to probe the water‐filled pores of both saturated and unsaturated soils, which does not require information relating to pore connectivity. We report the relative size distributions of water‐occupied pores in saturated and unsaturated samples of two sets of glass beads of known particle size, two sands, and three soils (a silty loam, a sandy loam and a loamy sand), using measurements of the NMRT1proton relaxation time of water. TheT1values are linearly related to pore size and consequently measuredT1distributions provide a measure of the pore‐size distribution. For both the sands and the glass beads at saturation theT1distributions are unimodal, and the samples with small particle sizes show a shift to smallT1values indicating smaller voids relative to the samples with larger particles. Different matric potentials were used to reveal how the water‐occupied pore‐size distribution changes during drainage. These changes are inconsistent with, and demonstrate the inadequacies of, the commonly employed parallel‐capillary tube model of a soil pore space. We find that not all pores of the same size drain at the same matric potential. Further, we observe that theT1distribution is shifted to smaller values beyond the distribution at saturation. This shift is explained by a change in the weighted average of the relaxation rates as the proportion of water in the centre of water‐filled pores decreases. This is evidence for the presence of pendular structures resulting from incomplete drainage of pores. For the soils the results are similar except that at saturation theT1distributions are bimodal or asymmetrical, indicative of inter‐aggregate and intra‐aggregate pore spaces. We conclude that the NMR method provides a characterization of the water‐filled pore space which complements that derived from the water retention characteristic and which can provide insight into the way pore connectivity impacts on drainage.
Changes in the microbial community of an arable soil caused by long‐term metal contamination
Authors: Abaye D. A. , Lawlor K. , Hirsch P. R. , Brookes P. C. 
Published: January 2005

SummaryThe effects of past applications of farmyard manure (FYM, applied from 1942 to 1967), metal‐contaminated sewage sludge (applied from 1942 to 1961) and mineral fertilizer (NPK, applied from 1942 until now) on the microbial biomass and community structure in a sandy loam, arable soil from the Woburn Market Garden Experiment, UK, were investigated in 1998. Concentrations of Cu, Ni and Zn in soils which previously received sewage sludge were less than current European Union (EU) limits, but the soil Cd concentration was more than twice the permitted limit. Organic‐C concentration in the FYM‐treated soil and contaminated soils was about twice that of NPK‐treated soil. The initial microbial biomass‐C and estimates of total bacterial numbers by acridine orange direct count were significantly (P < 0.05) greater in the FYM‐treated soil compared with the NPK‐treated and the most contaminated soils. Total phospholipid fatty acid (PLFA) concentration (another measure of biomass) was significantly greater in the FYM‐treated soil compared with either the low or high metal‐contaminated soils, both of which contained similar PLFA concentrations. In the metal‐contaminated soils, in contrast, fluorescent Pseudomonas counts, as a percentage of total plate counts, were at least 1.5 times greater than in the uncontaminated soils. The concentrations of these microbial parameters were significantly (P < 0.05) less in the NPK soil than in all the other treatments. Biomass‐C as a percentage of organic‐C was also significantly (P < 0.05) greater in the uncontaminated soils compared with the metal‐contaminated soils. Biomass specific respiration rates in the metal‐contaminated soils were c. 1.5 times those in the FYM‐treated soil. In the metal‐contaminated soils, the concentration of mono‐unsaturated and hydroxy‐fatty acids (derived from phospholipids), and lipopolysaccharide hydroxy‐fatty acids (all indicative of Gram‐negative bacteria) were significantly (P < 0.05) greater than branched fatty acids (indicative of Gram‐positive bacteria). Furthermore, Gram‐negative counts were 62–68% greater than Gram‐positive counts in the metal‐contaminated soils. Branched fatty acid concentration was significantly (P < 0.05) greater in the FYM‐treated soil than in the metal‐contaminated soils. Gram‐positive counts were also 63% greater than Gram‐negative counts in the FYM‐treated soil. We found that effects of the relatively small heavy metal concentration caused measurable decreases in soil microbial biomass‐C concentrations, acridine orange direct counts and Gram‐positive counts. There were also increases in biomass specific respiration rates, and the microbial community had changed substantially, nearly 40 years after the metal inputs ceased. We conclude that, at the very least, the current EU permitted limits for heavy metals in agricultural soils should not be relaxed.
Wavelet analysis of the scale‐ and location‐dependent correlation of modelled and measured nitrous oxide emissions from soil
Authors: Milne A. E. , Lark R. M. , Addiscott T. M. , Goulding K. W. T. , Webster C. P. , O'Flaherty S. 
Published: January 2005

SummaryWe used the wavelet transform to quantify the performance of models that predict the rate of emission of nitrous oxide (N2O) from soil. Emissions of N2O and other soil variables that influence emissions were measured on soil cores collected at 256 locations across arable land in Bedfordshire, England. Rate‐limiting models of N2O emissions were constructed and fitted to the data by functional analysis. These models were then evaluated by wavelet variance and wavelet correlations, estimated from coefficients of the adapted maximal overlap discrete wavelet transform (AMODWT), of the fitted and measured emission rates.We estimated wavelet variances to assess whether the partition of the variance of modelled rates of N2O emission between scales reflected that of the data. Where the relative distribution of variance in the model is more skewed to coarser scales than is the case for the observation, for example, this indicates that the model predictions are too smooth spatially, and fail adequately to represent some of the variation at finer scales. Scale‐dependent wavelet correlations between model and data were used to quantify the model performance at each scale, and in several cases to determine the scale at which the model description of the data broke down. We detected significant changes in correlation between modelled and predicted emissions at each spatial scale, showing that, at some scales, model performance was not uniform in space. This suggested that the influence of a soil variable on N2O emissions, important in one region but not in another, had been omitted from the model or modelled poorly. Change points usually occurred at field boundaries or where soil textural class changed.We show that wavelet analysis can be used to quantify aspects of model performance that other methods cannot. By evaluating model behaviour at several scales and positions wavelet analysis helps us to determine whether a model is suitable for a particular purpose.