bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence and structural determinants of Cu, Zn superoxide dismutase aggregation
Authors: Khare Sagar D. , Wilcox Kyle C. , Gong Peng , Dokholyan Nikolay V. 
Published: September 2005

AbstractDiverse point mutations in the enzyme Cu, Zn superoxide dismutase (SOD1) are linked to its aggregation in the familial form of the disease amyotrophic lateral sclerosis. The disease‐associated mutations are known to destabilize the protein, but the structural basis of the aggregation of the destabilized protein and the structure of aggregates are not well understood. Here, we investigate in silico the sequence and structural determinants of SOD1 aggregation: (1) We identify sequence fragments in SOD1 that have a high aggregation propensity, using only the sequence of SOD1, and (2) we perform molecular dynamics simulations of the SOD1 dimer folding and misfolding. In both cases, we identify identical regions of the protein as having high propensity to form intermolecular interactions. These regions correspond to the N‐ and C‐termini, and two crossover loops and two β‐strands in the Greek‐key native fold of SOD1. Our results suggest that the high aggregation propensity of mutant SOD1 may result from a synergy of two factors: the presence of highly amyloidogenic sequence fragments (“hot spots”), and the presence of these fragments in regions of the protein that are structurally most likely to form intermolecular contacts under destabilizing conditions. Therefore, we postulate that the balance between the self‐association of aggregation‐prone sequences and the specific structural context of these sequences in the native state determines the aggregation propensity of proteins. Proteins 2005. © 2005 Wiley‐Liss, Inc.
How do side chains orient globally in protein structures?
Authors: Yan Aimin , Jernigan Robert L. 
Published: September 2005

AbstractAn angle Ω is defined to serve as a metric for global side‐chain orientations, which reflects the orientation of the side chain relative to the radial vector from the center of the protein to an amino acid. The side‐chain orientations of buried residues exhibit characteristically different orientations than do exposed residues, in both monomeric and dimeric structures. Overall, buried side chains point mostly inward, whereas surface side chains tend to point outward from the surface. This difference in behavior also correlates well with the residue hydrophobicity; so a global side‐chain orientation can be viewed as a direct structural manifestation of hydrophobicity. When various solvent‐accessible layers are considered, the behavior is relatively continuous between centrally located and exposed residues. In the case of interfacial residues between subunits, there are statistically significant differences between exposed residues and interface residues for ALA, ARG, ASN, ASP, GLU, HIS, LYS, THR, VAL, MET, PRO, and overall the interface residues have an increased tendency to point inward. Presumably, these substantial differences in orientations of side chains may be a manifestation of hydrophobic forces. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Predicting protein secondary structure and solvent accessibility with an improved multiple linear regression method
Authors: Qin Sanbo , He Yun , Pan Xian‐Ming 
Published: September 2005

AbstractWe have improved the multiple linear regression (MLR) algorithm for protein secondary structure prediction by combining it with the evolutionary information provided by multiple sequence alignment of PSI‐BLAST. On the CB513 dataset, the three states average overall per‐residue accuracy, Q3, reached 76.4%, while segment overlap accuracy, SOV99, reached 73.2%, using a rigorous jackknife procedure and the strictest reduction of eight states DSSP definition to three states. This represents an improvement of approximately 5% on overall per‐residue accuracy compared with previous work. The relative solvent accessibility prediction also benefited from this combination of methods. The system achieved 77.7% average jackknifed accuracy for two states prediction based on a 25% relative solvent accessibility mode, with a Mathews' correlation coefficient of 0.548. The improved MLR secondary structure and relative solvent accessibility prediction server is available at http://spg.biosci.tsinghua.edu.cn/. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Adhesion mechanism of salmon to polymer‐coated can walls
Authors: Dommershuijzen Hans , Hviid Lene , den Hartog Hans , Vereijken Johan 
Published: September 2005

AbstractMinimization of the amount of salmon adhering to the can wall after emptying is one of the convenience requirements of consumers of canned salmon. In order to achieve this, the mechanism by which salmon adheres to cans needs to be understood. The aim of this study was to provide such knowledge for polymer‐coated cans. The results indicate that gelatin, derived from salmon collagen, and myofibrillar proteins are the major proteins involved in sticking of salmon to the polymer‐coated can wall. Furthermore, it was shown that mainly hydrogen bonds are formed between the salmon proteins and the polymer surface. Therefore, making the surface more apolar can prevent sticking of salmon to polymer‐coated cans. Copyright © 2005 John Wiley & Sons, Ltd.
Identifiability, stratification and minimum variance estimation of causal effects
Authors: Tong Xingwei , Zheng Zhongguo , Geng Zhi 
Published: September 2005

AbstractThe weakest sufficient condition for the identifiability of causal effects is the weakly ignorable treatment assignment, which implies that potential responses are independent of treatment assignment in each fine subpopulation stratified by a covariate. In this paper, we expand the independence that holds in fine subpopulations to the case that the independence may also hold in several coarse subpopulations, each of which consists of several fine subpopulations and may have overlaps with other coarse subpopulations. We first show that the identifiability of causal effects occurs if and only if the coarse subpopulations partition the whole population. We then propose a principle, called minimum variance principle, which says that the estimator possessing the minimum variance is preferred, in dealing with the stratification and the estimation of the causal effects. The simulation results with the detail programming and a practical example demonstrate that it is a feasible and reasonable way to achieve our goals. Copyright © 2005 John Wiley & Sons, Ltd.
Repeated split sample validation to assess logistic regression and recursive partitioning: an application to the prediction of cognitive impairment
Authors: James Kenneth E. , White Roberta F. , Kraemer Helena C. 
Published: September 2005

AbstractScreening strategies play an important part in the identification and diagnosis of illness. Testing of such strategies in a clinical trial can have important implications for the treatment of such illnesses. Before the clinical trial, however, it is important to develop a practical screening/classification procedure that accurately predicts the presence of the illness in question. Recent published studies have shown a growing preference for classification tree/recursive partitioning procedures.This paper compares the application of logistic regression and recursive partitioning to a neuropsychological data set of 252 patients recruited from four Veterans Affairs Medical Centers. Logistic regression and recursive partitioning was used to predict cognitive impairment in 12 randomly selected exploratory/validation samples. We assessed the effect of sampling on variable selection and predictive accuracy.Predictive accuracy of the logistic regression and recursive partitioning procedures was comparable across the exploratory data samples but varied across the validation samples. Based on shrinkage, both classification procedures performed equally well for the prediction of cognitive impairment across the twelve samples. While logistic regression provided an estimated probability of outcome for each patient, it required several mathematical calculations to do so. However, logistic regression selected one or two less predictors than recursive partitioning with comparable predictive accuracy. Recursive partitioning, on the other hand, readily identified patient characteristics and variable interactions, was easy to interpret clinically and required no mathematical calculations. There was a high degree of overlap of the predictor variables between the two procedures.In the context of neuropsychological screening, logistic regression and recursive partitioning performed equally well and were quite stable in the selection of predictors for the identification of patients with cognitive impairment, although recursive partitioning may be easier to use in a clinical setting because it is based on a simple decision tree. Copyright © 2005 John Wiley & Sons, Ltd.
Estimation of attributable risk for case‐control studies with multiple matching
Authors: Lui Kung‐Jong 
Published: September 2005

AbstractKuritz and Landis considered case‐control studies with multiple matching and proposed an asymptotic interval estimator of the attributable risk based on Wald's statistic. Using Monte Carlo simulation, Kuritz and Landis demonstrated that their interval estimator could perform well when the number of matched sets was large (⩾100). However, the number of matched sets may often be moderate or small in practice. In this paper, we evaluate the performance of Kuritz and Landis' interval estimator in small or moderate number of matched sets and compare it with four other interval estimators. We note that the coverage probability of Kuritz and Landis' interval estimator tends to be less than the desired confidence level when the probability of exposure among cases is large. In these cases, the interval estimator using the logarithmic transformation and the two interval estimators derived from the quadratic equations developed here can generally improve the coverage probability of Kuritz and Landis' interval estimator, especially for the case of a small number of matched sets. Furthermore, we find that an interval estimator derived from a quadratic equation is consistently more efficient than Kuritz and Landis' interval estimator. The interval estimator using the logit transformation, although which performs poorly when the underlying odds ratio (OR) is close to 1, can be useful when both the probability of exposure among cases and the underlying OR are moderate or large. Copyright © 2005 John Wiley & Sons, Ltd.
Influence diagnostics for two‐component Poisson mixture regression models: applications in public health
Authors: Xiang Liming , Yau Kelvin K. W. , Lee Andy H. , Fung Wing K. 
Published: September 2005

AbstractIn many medical and health applications, Poisson mixture regression models are commonly used to analyse heterogeneous count data. Motivated by two data sets drawn from public health studies, influence diagnostics are proposed for assessing the sensitivity of the fitted two‐component Poisson mixture regression models. Under various perturbations of the observed data or model assumptions, influence assessments based on the local influence approach are developed for detecting clusters and/or individual observations that impact on the estimation of model parameters. Results from studies on recurrent urinary tract infections and maternity length of stay illustrate the usefulness of the influence diagnostics. Copyright © 2005 John Wiley & Sons, Ltd.
Sample‐size calculations for studies with correlated ordinal outcomes
Authors: Kim Hae‐Young , Williamson John M. , Lyles Cynthia M. 
Published: September 2005

AbstractCorrelated ordinal response data often arise in public health studies. Sample‐size (power) calculations are a crucial step in designing such studies to ensure an adequate sample to detect a significant effect. Here we extend Rochon's method of sample‐size estimation with a repeated binary response to the ordinal case. The proposed sample‐size calculations are based on an analysis with generalized estimating equations (GEE) and inference with the Wald test. Simulation results demonstrate the merit of the proposed power calculations. Analysis of an arthritis clinical trial is used for illustration. Published in 2005 by John Wiley & Sons, Ltd.
Adjusting for treatment effects in studies of quantitative traits: antihypertensive therapy and systolic blood pressure
Authors: Tobin Martin D. , Sheehan Nuala A. , Scurrah Katrina J. , Burton Paul R. 
Published: September 2005

AbstractA population‐based study of a quantitative trait may be seriously compromised when the trait is subject to the effects of a treatment. For example, in a typical study of quantitative blood pressure (BP) 15 per cent or more of middle‐aged subjects may take antihypertensive treatment. Without appropriate correction, this can lead to substantial shrinkage in the estimated effect of aetiological determinants of scientific interest and a marked reduction in statistical power. Correction relies upon imputation, in treated subjects, of the underlying BP from the observed BP having invoked one or more assumptions about the bioclinical setting. There is a range of different assumptions that may be made, and a number of different analytical models that may be used. In this paper, we motivate an approach based on a censored normal regression model and compare it with a range of other methods that are currently used or advocated. We compare these methods in simulated data sets and assess the estimation bias and the loss of power that ensue when treatment effects are not appropriately addressed. We also apply the same methods to real data and demonstrate a pattern of behaviour that is consistent with that in the simulation studies. Although all approaches to analysis are necessarily approximations, we conclude that two of the adjustment methods appear to perform well across a range of realistic settings. These are: (1) the addition of a sensible constant to the observed BP in treated subjects; and (2) the censored normal regression model. A third, non‐parametric, method based on averaging ordered residuals may also be advocated in some settings. On the other hand, three approaches that are used relatively commonly are fundamentally flawed and should not be used at all. These are: (i) ignoring the problem altogether and analysing observed BP in treated subjects as if it was underlying BP; (ii) fitting a conventional regression model with treatment as a binary covariate; and (iii) excluding treated subjects from the analysis. Given that the more effective methods are straightforward to implement, there is no argument for undertaking a flawed analysis that wastes power and results in excessive bias. Copyright © 2005 John Wiley & Sons, Ltd.
Reshaping their views: Science as liberal arts
Authors: Bramble Judith 
Published: September 2005

AbstractGeneral‐education science courses should provide students with a foundation of knowledge about how the natural world works, a clear understanding of the nature of science and scientific inquiry, and an appreciation for the relationship between science and society. This chapter suggests a variety of approaches to engage students in their own learning and, with appropriate reflection, help them construct more scientific worldviews.
Ultrasound dating at 12–14 weeks of gestation. A prospective cross‐validation of established dating formulae in in‐vitro fertilized pregnancies
Authors: Sladkevicius P. , Saltvedt S. , Almström H. , Kublickas M. , Grunewald C. , Valentin L. 
Published: September 2005

AbstractObjectivesTo determine the accuracy of established ultrasound dating formulae when used at 12–14 weeks of gestation.MethodsOne‐hundred and sixty‐seven singleton pregnancies conceived after in‐vitro fertilization (IVF) underwent a dating scan at 12–14 weeks of gestation. Gestational age at the dating scan was calculated by adding 14 days to the number of days between the date of oocyte retrieval and the date of the ultrasound scan. Gestational age according to oocyte retrieval was regarded as the true gestational age. True gestational age was compared to gestational age calculated on the basis of 21 dating formulae based on fetal crown–rump length (CRL) measurements and to three dating formulae based on fetal biparietal diameter (BPD) measurements. In a previous study the three BPD formulae tested here had been shown to be superior to four other BPD formulae when used at 12–14 weeks of gestation. The mean of the differences between estimated and true gestational age and their standard deviation (SD) were calculated for each formula. The SD of the differences was assumed to reflect random measurement error. Systematic measurement error was assumed to exist if zero lay outside the mean difference ± 2SE (SE: standard error of the mean).ResultsThe three best CRL formulae were associated with mean (non‐systematic) measurement errors of −0.0, −0.1 and −0.3 days, and the SD of the measurement errors of these formulae varied from 2.37 to 2.45. All but two of the remaining CRL formulae were associated with systematic over‐ or under‐estimation of gestational age, and the SDs of their measurement error varied between 2.25 and 4.86 days. Dating formulae using BPD systematically underestimated gestational age by −0.4 to −0.7 days, and the SDs of their measurement errors varied from 1.86 to 2.09.ConclusionsWe have identified three BPD formulae that are suitable for dating at 12–14 weeks of gestation. They are superior to all 21 CRL formulae tested here, because their random measurement errors were much smaller than those of the three best CRL formulae. The small systematic negative measurement errors associated with the BPD formulae are likely to be clinically unimportant. Copyright © 2005 ISUOG. Published by John Wiley & Sons, Ltd.
Roles of dispersal, stochasticity, and nonlinear dynamics in the spatial structuring of seasonal natural enemy–victim populations
Authors: Tobin Patrick C. , Bjørnstad Ottar N. 
Published: September 2005

AbstractNatural enemy–victim systems may exhibit a range of dynamic space–time patterns. We used a theoretical framework to study spatiotemporal structuring in a transient natural enemy–victim system subject to differential rates of dispersal, stochastic forcing, and nonlinear dynamics. Highly mobile natural enemies that attacked less mobile victims were locally spatially segregated from each other when governed by approximate linear dynamics. In contrast, in nonlinear dynamical systems, such as cyclic populations, interacting species achieved local aggregation with each other regardless of dispersal rates, and aggregation was enhanced specifically when highly mobile enemies attacked less mobile victims. These patterns of spatial aggregation held under varying levels of stochastic forcing. This work thus shows a range of dynamic spatial patterns in interacting‐species models, and how spatial aggregation between natural enemies and victims can be achieved in locally unstable populations that are linked through dispersal.
Chirality in the RNA world and beyond
Authors: Sandars P.G.H. 
Published: September 2005

Homochirality is an essential feature of biology, but how it developed in early life remains unclear. Our aim in this paper is to add to the discussion by taking a somewhat arbitrary but definite sequence of events and examining carefully the chirality at each stage. Our scenario for the development of life starts with the prebiotic, continues through a pre-RNA stage to the RNA world. This leads to the development of proteins and then to the incorporation of DNA in RNA–DNA–protein biochemistry.We argue that homochirality probably did not develop prebiotically. We see the likely chiral bifurcation point to be during the development of RNA from an achiral pre-RNA. Surprisingly, we find the driving force for this to be enantiomeric cross-inhibition in which the addition of a ‘wrong-handed’ enantiomer to a growing polymer brings the polymerization to a halt. This, it is often argued, is a serious impediment to the development of chiral purity. We suggest that the sign of handedness at this stage was probably determined by chance. We then point out that homochiral RNA was unlikely by itself to lead to homochiral proteins. We identify the additional nonlinear feature required for bifurcation to be the rapid increase in enzymic power available when the amino acids in proteins approach single handedness and structural features such as α-helices and β-sheets become viable. If this is correct, then the handedness of the protein sector is indeed linked to that of RNA. However, the relative sign of the two handednesses will have depended on the precise stereo-sensitive interaction between the RNA and protein systems. We suggest that the most plausible scenario is via the recently discovered RNA binding sites for amino acids, which are both stereo-selective and have contact with the developing genetic code. The detailed steps that determine the handedness are not yet clear and may be specific to the precise development path.It follows that if biochemistry similar to that on Earth developed extraterrestrially, we would surely have homochirality but at this stage we cannot be sure about the handedness of either the nucleic acid or the protein components.
Are grazing increaser species better tolerators than decreasers? An experimental assessment of defoliation tolerance in eight British grassland species
Authors: DEL‐VAL EK , CRAWLEY MICHAEL J. 
Published: September 2005

Summary

The importance of tolerance to herbivory for plant survival has long been recognized, but capacity for regrowth following recurrent defoliation has rarely been studied.
A glasshouse experiment was conducted with eight grassland species. We chose both species favoured under herbivory (increasers) and those that become scarce (decreasers) and manipulated the ontogeny of the plant when first clipped, as well as frequency (up to eight times) and intensity of clipping.
Plant survival was high (88%) but both frequency and intensity of clipping increased plant mortality in all species investigated (P < 0.05). Immature plants showed the highest mortality (15.9%).
Plant biomass mirrored mortality with immature plants again the most affected. As expected, control plants were largest and plants experiencing 100% biomass removal smallest. Clipping frequency was also significant, but the effect was not linear and plants that were clipped more than twice were more dramatically affected.
Biomass compensation showed species‐specific responses that were significantly related to an a priori definition of species status in the grassland: increaser species had significantly higher compensation ability after recurrent defoliation than decreaser species.
Tolerance to herbivory has been viewed as a marginal strategy for plant survival, but our results suggest that it plays an important role in explaining abundance and distribution of plant species in environments with recurrent defoliation.
Plants do not always respond linearly to environmental pressures (such as repeated defoliation) and cannot therefore be predicted by studies considering only the lower end of the possible intensities. Understanding the effects of environmental pressures on plant fitness requires the study of a broader range of intensities, at different ontogenic stages and consideration of possible response thresholds.