bluuebunny/crossref_metadata_2025 huggingface dataset:
Within Case Designs: Distribution Free Methods
Authors: Lix Lisa M. , Keselman H. J.
Published: September 2005

In within‐case designs, subjects are measured repeatedly over time or across multiple experimental conditions. Univariate and multivariate parametric procedures for testing within‐case effects may lose statistical power under departures from a multivariate normal distribution. Nonparametric procedures based on rank scores or bootstrapping are useful alternatives for testing within‐case effects when the data are skewed or have heavy tails.
Yates' Correction
Authors: Stefanescu Catalina , Berger Vance W. , Hershberger Scott L.
Published: September 2005

Yates' correction for continuity adjusts the formula for Pearson's chi‐square test by subtracting 0.5 from each observed value in a 2 × 2 contingency table. This formula is used when at least one cell of the table has an expected frequency less than 5, although some sources say that this correction should be used when the expected frequency is less than 10.
Social Networks
Authors: Wasserman Stanley , Pattison Philippa , Steinley Douglas
Published: September 2005

Network analysis is the interdisciplinary study of social relations and has roots in anthropology, sociology, psychology, and applied mathematics. It conceives of social structure in relational terms, and its most fundamental construct is that of a
social network,
comprising at the most basic level a set of
social actors
and a set of
relational ties
connecting pairs of these actors. The
nodes
or
members
of the network can be groups or organizations as well as people. Network analysis involves a combination of theorizing, model building, and empirical research, including (possibly) sophisticated data analysis. The goal is to study network structure, often analyzed using such concepts as density, centrality, prestige, mutuality, and role.
Correlation Studies
Authors: Busk Patricia L.
Published: September 2005

Correlational study is a specific type of descriptive research in which the researcher is interested in relationships between two or more variables. Researchers collect data for these variables on a single sample of adequate size.
Sequential Decision Making
Authors: Vos Hans J.
Published: September 2005

The purpose of this entry is to describe optimal rules for sequential mastery tests in the context of education. In a sequential mastery test, the decision is to classify a student as a master, a nonmaster, or to continue testing and administering another random item. The framework of Bayesian sequential decision theory is used; that is, optimal rules are obtained by minimizing the posterior expected losses associated with all possible decision rules at each stage of testing. The main advantage of this approach is that costs of testing can be taken explicitly into account. For given maximum number of items to be administered, it is shown how the appropriate action can be computed at each stage of testing for different number‐correct score.
Hierarchical Item Response Theory Modeling
Authors: Bolt Daniel , Kim Jee‐Seon
Published: September 2005

The synthesis of hierarchical modeling with item response theory (IRT) has led to psychometric models for item response datasets that possess hierarchical structure. In this entry, an overview is provided of hierarchical IRT methodology and its usefulness as a general framework both for traditional IRT models and new extensions. Models for both random person and random item effects are discussed.
Factor Score Estimation
Authors: Hershberger Scott L.
Published: September 2005

Factors scores are measures of principal components or common factors. Under the principal components model, the factor scores are uniquely determined; under the common factor model, they are not. In the latter situation, the factor scores are indeterminate, potentially having an infinite number of solution sets, and thus their true values can only be estimated. Three methods of factor score estimation are discussed: (a) regression, (b) Bartlett's method, and (c) Anderson and Rubin's method. Although the properties and values of the factor score estimates produced by the three methods differ, the estimates are in general highly correlated.
New Item Types and Scoring
Authors: Drasgow Fritz , Mattern Krista
Published: September 2005

The advent of the computer has broadened the concept of testing and assessment. Previously, tests were mainly restricted to a paper‐and‐pencil medium and a multiple‐choice format; however, the computer coupled with recent advancements in its technological sophistication has afforded test developers much more freedom in the types of tests they create. Much research in this area has been devoted to the development of
innovative item types
, which utilize the computer's capabilities to improve assessment or assess characteristics that traditional items cannot. Innovative items allow for a more extensive assessment of individual differences; however, the benefits of these new items do not come without a cost. Scoring innovative items is usually not as simplistic as employing a multiple‐choice key, and, often, the items require extremely complicated scoring algorithms. In this chapter, we provide a review of innovative item types and their accompanying scoring issues. Owing to limited space and a rapidly changing field, it is impossible to provide an exhaustive review; therefore, we focus on the most recent and influential research in the field.
Heuristics
Authors: Hoffrage Ulrich
Published: September 2005

A heuristic is a means for finding something – information, an insight, or a solution to a given problem. Examples range from inspecting the problem, through vaguely defined rules of thumb, to precisely defined procedures that can be implemented in computer programs.
Randomized Response Technique
Authors: Everitt Brian S.
Published: September 2005

A technique that can be used in surveys to collect honest answers to sensitive questions.
M
artingales
Authors: Laming Donald
Published: September 2005

The concept of a martingale is explained and illustrated with several examples from the psychological literature. Martingales are also compared with the related notion of a random walk. It is shown that the variance of successive sums in a martingale is monotonically increasing and the theorem is quoted that, if the variance is bounded, the distribution of the sum tends asymptotically to a limit.
Probability: Foundations of
Authors: Macdonald Ranald R.
Published: September 2005

Probability and probability models are mathematical representations of uncertainties. They can be seen either as analogies with urn models or as a logical system which conforms to a set of probability laws or axioms. It is argued that if uncertainties conform to an urn model or to the probability axioms and the probability space is dense enough then there is a correct probability associated with every uncertainty. Because probability laws place constraints on uncertainties there are disputes over where probabilities apply. One view is that probabilities are relative frequencies. This means that probabilities do not apply to unique events as it might be necessary to break down any relative frequency further before it can be applied to a particular event. Nevertheless some conformity between people's judgments and the frequency view of probability are reported. An alternative subjective approach takes probabilities to be measures of belief but it is unclear then why they should conform to probability laws. A partial answer is that if a person X bets in accordance with subjective probabilities which violate these laws then X can be made to lose regardless of the state of the world. Problems with taking probabilities to be measures of belief are discussed and it is concluded that neither the frequency nor the subjective approaches provide absolute standards against which people's uncertainty judgments should be compared. Theorists have attempted to identify objective probabilities but it is unclear how their existence could ever be established. Nevertheless the search for objective probabilities is defended.
Social Interaction Models
Authors: Hewitt John K.
Published: September 2005

Social interaction is modeled in behavior genetics as the influence of one individual's phenotype on another. The consequences of this for phenotypic variances and covariances among relatives of different degrees of relationship can be predicted from an extension to the usual path models. Social cooperation (or imitation) and social competition (or contrast) result in different patterns of variation and resemblance that depend on the prior similarity of the interacting pair. Although of considerable theoretical interest, the behavior genetics literature does not offer many convincing examples of the empirical effects of such social interactions.
Conditional Independence
Authors: Longford Nicholas T.
Published: September 2005

In principle, all independence is conditional, qualified by the context and assumptions under which it applies. In practice, conditional independence represents the first step away from (unconditional) independence toward models that account for, describe, or explain the dependence among variables.
Outlier Detection
Authors: Wilcox Rand R.
Published: September 2005

Outliers are a serious concern because modern outlier detection methods suggest that they are relatively common, can distort commonly used summaries of data, and can result in relatively low efficiency and low power when using methods based on means or least squares regression. Methods for dealing with outliers, in the context of estimation and hypothesis testing, are outlined.
Binomial Test
Authors: Wagner‐Menghin Michaela M.
Published: September 2005

This entry illustrates the binomial distribution and uses a common coin toss experiment as an example for calculating the probabilities of the binomial distribution. The binomial test is then introduced as a valuable test when dealing with dichotomous variables. Using the introduced coin toss experiment, the statistical hypothesis of this test and the calculation of an exact binomial test with and without software are illustrated.
Clustered Data
Authors: Fitzmaurice Garrett M.
Published: September 2005

Clustered data commonly arise in studies in the behavioral sciences. For example, clustered data arise when observations are obtained on children nested within schools. From a statistical standpoint, the main feature of clustered data that needs to be accounted for in any analysis is the fact that units from the same cluster are likely to respond in a more similar manner than units from different clusters. As a consequence, clustered data may not contain quite as much information as investigators might otherwise like to believe it does.
Survival Analysis
Authors: Landau Sabine
Published: September 2005

Survival analysis is the study of the distribution of event times (death, relapse, completion of an experimental task). A distinguishing feature of survival or time to event data is the presence of censoring, that is, all that is known sometimes is that an event occurred later than a given point in time. This article provides a brief description of the classical methods for nonparametric, semiparametric and fully parametric analysis of survival times.
Item Bias Detection: Modern Approaches
Authors: Mellenbergh Gideon J.
Published: September 2005

A general definition of differential item functioning (DIF) is presented. The definition is specified for DIF between two groups and a test (questionnaire) that measures one latent trait. Methods for DIF detection are described for dichotomous, ordinal‐polytomous, and continuous item responses under unidimensional item response theory (IRT) models.
Classical Statistical Inference Extended: Split‐Tailed Tests
Authors: Harris Richard J.
Published: September 2005

Two‐tailed tests of statistical significance do not take into account the strength of the evidence that existed before the study under investigation was conducted with respect to the sign of the population effect being tested. The split‐tailed test incorporates this prior evidence by assigning a greater proportion of alpha to the rejection region corresponding to the direction of effect most strongly supported by the prior evidence. In addition to providing greater power than a two‐tailed test when the researcher's assessment of the prior evidence is correct (but much lower power to detect the correct direction of effect when the prior evidence has led to the wrong expectation), split‐tailed tests also make clear that one‐tailed tests represent the extreme case of infinite bias in favor of one's prior hypothesis about the sign of the population effect and, thus, violate the principle that scientific hypotheses must be disconfirmable.
Nonparametric Correlation (tau)
Authors: Howell David C.
Published: September 2005

Kendall's correlation coefficient (τ) for ranked data, often known as Kendall's tau, is based on the number of inversions in a set of ranks. Data on
X
and
Y
are replaced by their ranks, and the correlation (τ) between the ranks is computed.
Nonparametric Correlation (

r

s

)
Authors: Howell David C.
Published: September 2005

Spearman's correlation coefficient (
r

S

) for ranked data, often known as Spearman's rho, actually represents the standard Pearson product‐moment correlation applied to ranked data. Data on
X
and
Y
are replaced by their ranks, and then the correlation between the ranks is computed.
Classification and Regression Trees
Authors: Everitt Brian S.
Published: September 2005

Multiple regression, logistic regression and other members of the generalized linear model family are widely used but may not always give a faithful description of the data when the assumptions on which they are based are not met, or in the presence of higher‐order interactions among some of the explanatory variables. An entirely different approach to explaining the relationship between a response variable and a set of explanatory variables that has been developed to overcome some of these possible problems is the classification and regression (CART) procedure, which extracts subgroups of observations within which the explanatory variables are relatively homogeneous, and between which the response variable is relatively distinct. Creation of subgroups takes place according to a tree structure, in essence a series of binary splits. Often the resulting tree is readily interpretable and offers insight into the structure and pattern in the data.
Heritability: Overview
Authors: Rose Richard J.
Published: September 2005

Heritability, a statistical measure originating in quantitative genetics, is an estimate of the contribution of genetic differences to the differences observed in a measured variable (e.g., some dimension of behavior) in a given population at a given time. Heritability is a population concept. It is an estimate, typically made from the resemblance observed among relatives. It does not describe individuals; it refers only to the underlying differences between people.
Measurement of Xenobiotic Carbonyl Reduction in Human Liver Fractions
Authors: Rosemond M. Jane Cox
Published: September 2005

Carbonyl reducing enzymes are involved in the metabolism of endogenous as well as xenobiotic molecules. Enzymes that catalyze the reversible oxidoreduction of aldehyde and ketone moieties include alcohol dehydrogenases, aldo‐keto reductases, quinone reductases, and short‐chain dehydrogenases/reductases. These enzymes differ with respect to subcellular location, cofactor dependence, and susceptibility to chemical inhibitors. Thus, it is possible to assess the relative contributions of these enzyme systems in the hepatic metabolism of a particular xenobiotic through simple in vitro experiments with commercially available reagents. The approaches described in this unit assume the availability of analytical procedures for measuring the parent compound and metabolites, such as HPLC with radiochemical, UV, or MS detection. Thus, the purpose of this unit is to outline methods for the study of the enzymatic carbonyl reduction of a drug development candidate or other xenobiotic molecule of interest.
Overview of Behavioral Teratology
Authors: Branchi Igor , Bignami Giorgio , Alleva Enrico
Published: September 2005

The discipline of behavioral teratology is based on the study of behavior as a powerful tool to identify and disentangle noxious effects of compounds known or suspected to be potentially neurotoxic early during development. Indeed, because behavior is the ultimate output of the brain, behavioral assessments can provide critical information on the noxious actions exerted by selected chemicals—information which is different from, and complementary to, the information provided by neurochemical, cellular, and histological evaluations. In particular, behavioral assessments allow one to investigate the integrity of a number of brain processes, helping to identify selected structural and/or functional alterations. A large number of behavioral protocols are available which are rapid, simple, quantitative, easily replicable, and reliable as indices of brain dysfunction. This unit provides an overview of the field of behavioral teratology.
Statistical Analysis of Behavioral Data
Authors: Chiarotti Flavia
Published: September 2005

The statistical analysis of behavioral data follows the collection and checking of the data, and is aimed at assessing the effect of treatments on the observed behaviors. In this unit, different behavioral tests and the response variables collected in each test are briefly described, to introduce a detailed description of the strategies for the analysis of such data. The main purpose of this unit is to enable the reader to choose the appropriate procedure for the statistical analysis, based on the type of data and experimental design adopted. Moreover, conditions for the application of the most common parametric and nonparametric tests for the comparison among groups in regard to the measures of location are also presented. Finally, some suggestions on the presentation of results coming from the different statistical analyses are given.
Protein Charge Determination
Authors: Winzor Donald J.
Published: September 2005

The most popular current method of determining protein valence entails the calculation of net charge from amino acid sequence/composition. However, the inaccuracy of that approach was recognized long before the advent of the protein data banks and computer programs to facilitate its adoption. Capillary zone electrophoresis affords the simplest and most economical procedure for obtaining a reliable estimate of the net charge of a protein in the buffer system of interest. This unit explains the major pitfalls in the calculation of net charge from protein sequence data.
Preparation of Soluble Proteins fromEscherichia coli
Authors: Wingfield Paul T.
Published: September 2005

Purification of human IL‐1β is used in this unit as an example of the preparation of soluble proteins fromE. coli. Bacteria containing IL‐1β are lysed, and IL‐1 β in the resulting supernatant is purified by anion‐exchange chromatography, salt precipitation and cation‐exchange chromatography, and then concentrated. Finally, the IL‐1 β protein is applied to a gel‐filtration column to separate it from remaining higher‐ and lower‐molecular‐weight contaminants, the purified protein is stored frozen or is lyophilized. The purification protocol described is typical for a protein that is expressed in fairly high abundance (i.e., >5% total protein) and accumulates in a soluble state.
Two‐Dimensional Gel Electrophoresis
Authors: Adams Lonnie D. , Gallagher Sean R.
Published: September 2005

Two‐dimensional gel electrophoresis is the combination of two high‐resolution electrophoretic procedures (isoelectric focusing and SDS‐polyacrylamide gel electrophoresis) to provide much greater resolution than either procedure alone. In the first‐dimension gel, solubilized proteins are separated according to their isoelectric point (pI) by isoelectric focusing. This gel is then applied to the top of an SDS‐slab gel and electrophoresed. The proteins in the first‐dimension gel migrate into the second‐dimension gel where they are separated on the basis of their molecular weight. The basic protocols in this unit are based on the type of equipment originally described by O'Farrell in 1975. For very basic or very acidic proteins, two alternate protocols are provided. A third alternate protocol describes how two‐dimensional electrophoresis can be performed using a minigel system. Protein sample preparation is presented in the support protocol.
Human Complement Components C4A and C4B Genetic Diversities: Complex Genotypes and Phenotypes
Authors: Chung Erwin K. , Wu Yee Ling , Yang Yan , Zhou Bi , Yu C. Yung
Published: September 2005

This unit describes methods that can accurately determine the genotypes and phenotypes of human complement components C4A and C4B. Specifically, they allow investigators to determine how many C4 genes are present in a diploid genome of a human subject and to quantify how many of them encode C4A proteins and how many of them encode C4B proteins. In addition, methods to determine how many long and short C4 genes are present in a diploid genome of a subject are described together with experimental strategies to determine haplotypes and order or configuration of these genes in the MHC. Finally, methods to assess the degree of polymorphism in C4A and C4B proteins and whether low protein levels of plasma C4 may be caused by low C4 gene dosages and/or by mutant C4 genes.
One‐Pot Conversion of Cephalosporin C to 7‐Aminocephalosporanic Acid in the Absence of Hydrogen Peroxide
Authors: Lopez‐Gallego Fernando , Batencor Lorena , Hidalgo Aurelio , Mateo Cesar , Fernandez‐Lafuente Roberto , Guisan Jose M.
Published: September 2005

The main drawback in the production of 7‐aminocephalosporanic acid (7‐ACA) at the industrial level is the inactivation of the enzymes implicated in the process due to the presence of hydrogen peroxide during the reaction. As an alternative, we have developed the conversion of cephalosporin C to 7‐ACA in a single reactor without the presence of hydrogen peroxide during the reaction, achieving more than 80% yield. In order to develop this process, D‐amino acid oxidase (DAAO) was co‐immobilized with catalase (CAT), which is able to fully eliminate in situ the hydrogen peroxide formed by the neighbouring DAAO molecules. Thus, the product of the reaction is only α‐ketoadipyl‐7‐ACA. This system prevents the inactivation of the oxidase by hydrogen peroxide, solving the main problem of the enzymatic process. Moreover, we have found that α‐ketoadipyl‐7‐ACA is recognized as a substrate by glutaryl acylase (GAC) and hydrolyzed as long as glutaric acid is absent from the reaction medium (because it is able to inhibit the hydrolysis). The low stability of α‐ketoadipyl‐7‐ACA justifies the use of a single reactor, in which glutaryl acylase is already present when this substrate is generated. Thus, the whole process may (and must) be performed in a single step, and in the absence of hydrogen peroxide that could affect the stabilities of the involved enzymes.
Synthesis of N‐Heteroaryl(trifluoromethyl)hydroxyalkanoic Acid Esters by Highly Efficient Solid Acid‐Catalyzed Hydroxyalkylation of Indoles and Pyrroles with Activated Trifluoromethyl Ketones
Authors: Abid Mohammed , Török Béla
Published: September 2005

The synthesis of N‐heteroaryl(trifluoromethyl)hydroxyalkanoic acid esters by solid acid‐catalyzed Friedel–Crafts hydroxyalkylation of indoles and pyrroles with ethyl 3,3,3‐trifluoropyruvate and ethyl 4,4,4‐trifluoroacetoacetate is described. The inexpensive and readily available K‐10 montmorillonite is found to be an efficient catalyst for the synthesis of a wide variety of trifluoromethylated indol‐3‐yl‐ and pyrrol‐2‐yl‐hydroxypropionic and ‐butanoic acid esters. Using a series of substituted indoles and pyrroles the corresponding products were isolated in excellent yield (up to 98%) and 100% selectivity under mild experimental conditions, during very short reaction times. Beyond these, the ease of product isolation, catalyst stability and handling make this process an attractive, environmentally benign alternative for the synthesis of the target compounds.
Ionic Liquid as Catalyst and Reaction Medium: A Simple, Convenient and Green Procedure for the Synthesis of Thioethers, Thioesters and Dithianes using an Inexpensive Ionic Liquid, [pmIm]Br
Authors: Ranu Brindaban C. , Jana Ranjan
Published: September 2005

An easily accessible and inexpensive room temperature ionic liquid, 1‐pentyl‐3‐methylimidazolium bromide, [pmIm]Br efficiently catalyzes the reaction of alkyl halides or acyl halides with thiols without any solvent at room temperature leading to the synthesis of thioethers and thioesters in high yields. This reaction has also been extended for the preparation of dithianes and transthioetherification. The ionic liquid is recovered and recycled for subsequent runs.
Runx2: A master organizer of gene transcription in developing and maturing osteoblasts
Authors: Schroeder Tania M. , Jensen Eric D. , Westendorf Jennifer J.
Published: September 2005

Runx2 is essential for osteoblast development and proper bone formation. A member of the Runt domain family of transcription factors, Runx2 binds specific DNA sequences to regulate transcription of numerous genes and thereby control osteoblast development from mesenchymal stem cells and maturation into osteocytes. Although necessary for gene transcription and osteoblast development, Runx2 is not sufficient for optimal gene expression or bone formation. Runx2 cooperates with numerous proteins, including transcription factors and cofactors, is posttranslationally modified, and associates with the nuclear matrix to integrate a variety of signals and organize crucial events during osteoblast development and maturation. Consistent with its role as a master organizer, alterations in Runx2 expression levels are associated with skeletal diseases. Runx2 haploinsufficiency causes cleidocranial dysplasia, while Runx2 overexpression is common in many bone‐metastatic cancers. In this review, we summarize the molecular mechanisms by which Runx2 integrates signals through coregulatory interactions, and discuss how its role as a master organizer may shift depending on promoter structure, developmental cues, and cellular context. Birth Defects Research (Part C) 75:213–225, 2005. © 2005 Wiley‐Liss, Inc.
Muscle function and dysfunction in health and disease
Authors: Huh Michael S. , Smid Johnathan K. , Rudnicki Michael A.
Published: September 2005

Skeletal muscles of the trunk and limbs developmentally originate from the cells of the dermomyotomal compartment of the somite. A wealth of knowledge has been accumulated with regard to understanding the molecular regulation of embryonic skeletal myogenesis. Myogenic induction is controlled through a complex series of spatiotemporal dependent signaling cascades. Secreted signaling molecules from surrounding structures not only initiate the myogenic program, but also influence proliferation and differentiation decisions. The proper coordination of these molecular events is thus critical for the formation of physiologically functional skeletal muscles. Hereditary congenital skeletal muscle defects arise due to genetics lesions in myogenic specific components. Understanding the mechanistic routes of congenital skeletal muscle disease therefore requires a comprehensive knowledge of the developmental system. Ultimately, the application of this knowledge will improve the diagnostic and therapeutic methodologies for such diseases. The aim of this review is to overview our current understanding of skeletal muscle development and associated human congenital diseases. Birth Defects Research (Part C) 75:180–192, 2005. © 2005 Wiley‐Liss, Inc.
Dlx genes, p63, and ectodermal dysplasias
Authors: Morasso Maria I. , Radoja Nadezda
Published: September 2005

Many events in vertebrate morphogenesis and organogenesis develop from epithelial/mesenchymal interactions. These processes involve a series of sequential and reciprocal interactions between the thickened epithelial sheets and underlying mesenchymal cells. Much has been learned from in vitro assays and knockout experiments in mice on the early signaling molecules that regulate the initial stages of the epithelial/mesenchymal interactions. In this review, we discuss effectors of these initial signals, specifically the p63 and Dlx families of transcription factors, that play central roles in embryonic patterning and regulation of different developmental processes, and provide a review of some of the mutations in these genes that have been associated with ectodermal dysplasias (EDs). Birth Defects Research (Part C) 75:163–171, 2005. Published 2005 Wiley‐Liss, Inc.
Tendon and ligament: Development, repair and disease
Authors: Tozer Samuel , Duprez Delphine
Published: September 2005

Tendons and ligaments (T/L) are very similar fibrous tissues that respectively connect muscle to bone and bone to bone. They are comprised of fibroblasts that produce large amounts of extra‐cellular matrix, resulting in a dense and hypocellular structure. The complex molecular organization of T/L, together with high water content, are responsible for their viscoelastic properties, hence insuring their mechanical function. We will first review recent work on tendon embryology and discuss ligament formation, which has been less documented. We will next summarize our current knowledge of T/L molecular architecture, alterations of which are a major cause for disease. We will finally focus on T/L repair after injury and on genetic diseases responsible for T/L defects. Birth Defects Research (Part C) 75:226–236, 2005. © 2005 Wiley‐Liss, Inc.
Mechanisms of synovial joint and articular cartilage formation: Recent advances, but many lingering mysteries
Authors: Pacifici Maurizio , Koyama Eiki , Iwamoto Masahiro
Published: September 2005

Synovial joints are elegant, critically important, and deceptively simple biomechanical structures. They are comprised of articular cartilage that covers each end of the opposing skeletal elements, synovial fluid that lubricates and nourishes the tissues, ligaments that hold the skeletal elements in check, and a fibrous capsule that insulates the joints from surrounding tissues. Joints also exhibit an exquisite arrays of shapes and sizes, best exemplified by the nearly spherical convex femoral head articulating into a nearly spherical concave hip acetabulum, or a phalangeal joint with two condyles on the distal side articulating in reciprocally‐shaped sockets on the opposing proximal side. Though few in number, joint tissues are highly specialized in structure and function. This is illustrated by articular cartilage with its unique extracellular matrix, unique biomechanical resilience, its largely avascular nature, and its ability to persist through life with minimal turnover of its cells and components. The fact that interest in synovial joints has remained unabated for decades is a reflection of their fundamental importance for organism function and quality of life, and for their susceptibility to a variety of acquired and congenital conditions, most importantly arthritis. This has led to many advances in this field that encompass molecular genetics to biomechanics to medicine. Regrettably, what continues to be poorly understood are the mechanisms by which synovial joints actually form in the developing embryo. If available, this information would be not only of indisputable biological interest, but would also have significant biomedical ramifications, particularly in terms of designing novel tissue regeneration or reconstruction therapies. This review focuses on recent advances in understanding the mechanisms of synovial joint formation in the limbs, and places and discusses the information within the context of classic studies and the many mysteries and questions that remain unanswered. Birth Defects Research (Part C) 75:237–248, 2005. © 2005 Wiley‐Liss, Inc.
Prediction of atomic structure from sequence for double helical DNA oligomers
Authors: Farwer Jochen , Packer Martin J. , Hunter Christopher A.
Published: September 2005

DNA can adopt different conformations depending on the base sequence, solvent, electrolyte composition and concentration, pH, temperature, and interaction with proteins. Here we present a model for calculating the three‐dimensional atomic structure of double‐stranded DNA oligomers. A theoretical energy function is used for calculating the interactions within the base steps and an empirical backbone function is used to restrict the conformational space accessible to the bases and to account for the conformational coupling of neighboring steps in a sequence. Conformational searching on large structures or a large number of structures is possible, because each base step can be described by just two primary degrees of freedom (slide and shift). A genetic algorithm is used to search for low‐energy structures in slide–shift space, and this allows very rapid optimization of DNA oligomers. The other base step parameters have been previously optimized for all possible slide–shift sequence combinations, and a heuristic algorithm is used to add the atomic details of the backbone conformation in the final step of the calculation. The structures obtained by this method are very similar to the corresponding X‐ray crystal structures observed experimentally. The average RMSD is 2.24 Åfor a set of 20 oligomer structures. For 15 of these sequences, theX‐ray crystal structure is the global energy minimum. The other 5 are bistable sequences that have B‐form global energy minima but crystallize as A‐DNA. © 2005 Wiley Periodicals, Inc. Biopolymers 81: 51–61, 2006

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Dielectric characterization of neutralized and nonneutralized chitosan upon drying
Authors: Viciosa M. T. , Dionísio M. , Mano J. F.
Published: September 2005

Isothermal dielectric loss spectra of neutralized and nonneutralized chitosan were acquired in successive runs from –130°C up to increasing final temperatures, in a frequency range between 20 Hz and 1 MHz. Essentially, three relaxation processes were detected in the temperature range covered: (i) a β‐wet process, detected when the sample has a higher water content that vanishes after heating to 150°C; (ii) a β process, which is located at temperatures below 0°C, becoming better defined and maintaining its location after annealing at 150°C independently of the protonation state of the amino side group; and (iii) a σ process that deviates to higher temperatures with drying, being more mobile in the nonneutralized form. Moreover, in dried neutralized chitosan, a fourth process was detected in the low frequency side of the secondary β process that diminishes after annealing. Whether this process is a distinct relaxation of the dried polymer or a deviated β‐wet process due to the loss of water residues achieved by annealing is not straightforward. Only β and σ processes persist after annealing at 150°C. The changes in molecular mobility upon drying of these two relaxation processes were evaluated. © 2005 Wiley Periodicals, Inc. Biopolymers 81: 149–159, 2006

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Prospective study of the effect of rectopexy on colonic motility in patients with rectal prolapse
Authors: Brown A J , Nicol L , Anderson J H , McKee R F , Finlay I G
Published: September 2005

Background

Patients with rectal prolapse have abnormal hindgut motility. This study examined the effect of rectal prolapse surgery on colonic motility.

Methods

Twelve patients undergoing sutured rectopexy were studied before and 6 months after surgery by colonic manometry, colonic transit study and clinical assessment of bowel function. The results were compared with those from seven control subjects.

Results

Before surgery colonic pressure was greater in patients than controls (P < 0·050). Controls responded to a meal stimulus by increasing colonic pressure; this increase was absent in patients. After rectopexy, colonic pressure reduced towards control values and patients' colonic pressure response to a meal returned. High-amplitude propagated contractions (HAPCs) were seen in all controls but in only three patients before and two patients after surgery. Three patients had prolonged colonic transit before and eight after rectopexy.

Conclusion

Patients with rectal prolapse have abnormal colonic motility associated with reduced HAPC activity. Rectopexy reduces colonic pressure but fails to restore HAPCs, reduce constipation or improve colonic transit. These observations help explain the pathophysiology of constipation associated with rectal prolapse.
Feasibility of autonomic nerve-preserving surgery for advanced rectal cancer based on analysis of micrometastases
Authors: Matsumoto T , Ohue M , Sekimoto M , Yamamoto H , Ikeda M , Monden M
Published: September 2005

Background

Autonomic nerve preservation has been advocated as a means of preserving urinary and sexual function after surgery for rectal cancer, but may compromise tumour clearance. The aim of this study was to determine the incidence of micrometastasis in the connective tissues surrounding the pelvic plexus.

Methods

The study included 20 consecutive patients who underwent rectal surgery with bilateral lymph node dissection for advanced cancer. A total of 78 connective tissues medial and lateral to the pelvic plexus and 387 lymph nodes were sampled during surgery. All connective tissue samples and 260 lymph nodes were examined for micrometastases by reverse transcriptase–polymerase chain reaction (RT–PCR) after operation. All patients were followed prospectively for a median of 36·0 months.

Results

Of 245 histologically negative lymph nodes, 38 (15·5 per cent) were shown by RT–PCR to harbour micrometastases. However, micrometastases to tissues surrounding the pelvic plexus were detected in only two (3 per cent) of 78 tissues, that is in two of 20 patients. Clinical follow-up showed that the two patients had a poor prognosis owing to distant metastases.

Conclusion

Autonomic nerve-preserving surgery may be feasible for advanced rectal cancer, but study of more patients positive for micrometastases is required.
Endothelin-1 levels predict 3-year survival in patients who have amputation for critical leg ischaemia
Authors: Newton D J , Khan F , McLaren M , Kennedy G , Belch J J F
Published: September 2005

Background

Most patients with critical leg ischaemia (CLI) have co-existing coronary heart disease, which is the main cause of their increased mortality rate. The aim of this study was to investigate whether any markers of endothelial function could predict death in these patients.

Methods

In a cohort of 39 patients with CLI who were scheduled for lower-limb amputation, blood levels of vascular endothelial growth factor, homocysteine, endothelin (ET) 1, von Willebrand factor and vascular cell adhesion molecule 1 were measured, as well as forearm vascular responses to the endothelium-dependent vasodilator acetylcholine.

Results

Levels of ET-1 were significantly higher in patients who subsequently died within 3 years than in those who were still alive (P = 0·002) and Cox proportional hazards regression analysis demonstrated that ET-1 was an independent predictor of all-cause mortality : hazard ratio 3·53 (95 per cent confidence interval (c.i.) 1·29 to 9·70; P = 0·007) and cardiovascular mortality : hazard ratio 4·15 (95 per cent c.i. 1·30 to 13·23); P = 0·014.

Conclusion

ET-1 was an independent predictor of death in these patients with CLI.
Selective use of ultrasonographic vascular mapping in the assessment of patients before haemodialysis access surgery
Authors: Wells A C , Fernando B , Butler A , Huguet E , Bradley J A , Pettigrew G J
Published: September 2005

Background

Use of routine preoperative ultrasonography to determine the optimum site for haemodialysis access surgery increases the number of distal arteriovenous fistulas formed and improves overall patency rates. Nevertheless its use in all patients is time consuming and costly. This study examined whether clinical parameters could be used to determine the requirement for preoperative ultrasonography.

Methods

Between March 2002 and October 2003, 145 consecutive patients were reviewed in the vascular access clinic. Patients were first assessed clinically, a site for vascular access surgery was proposed, and the need for radiological mapping studies recorded. A second, blinded, clinician determined the site for vascular access surgery using ultrasonography. The correlation between clinical and ultrasonographic findings was then examined.

Results

Ultrasonography was considered unnecessary using clinical criteria in 106 patients. Subsequent ultrasonographic mapping altered the management of only one patient. In contrast, the management of 18 of the 39 patients in whom ultrasonography was thought necessary was influenced by radiological imaging. A 1-year primary patency rate of 77·0 per cent was achieved following vascular access surgery on the study population.

Conclusion

Clinical parameters could be used to determine the need for preoperative vascular ultrasonographic mapping; imaging was not required in the majority of patients.
Experimental cooling-induced preconditioning attenuates skin flap failure
Authors: Kubulus D , Amon M , Roesken F , Rücker M , Bauer I , Menger M D
Published: September 2005

Background

Microvascular perfusion failure is a leading cause of tissue necrosis in reconstructive surgery. In the present experimental study the effect of local hypothermia was investigated as a possible preconditioning procedure that could induce stress proteins such as heat-shock protein (HSP) 70 and HSP-32 (haem oxygenase (HO) 1). The effect on flap microcirculation and survival was also studied.

Methods

Ears of hairless mice were subjected to local hypothermia (30 min, 4°C) 24 h before flap creation. A pedicled flap was elevated by incision of four-fifths of the base of the ear. Microcirculatory dysfunction and tissue necrosis were analysed quantitatively over 5 days by means of intravital fluorescence microscopy. HO-1 and HSP-70 protein expression were determined by western blot analysis. HO-1 distribution within the flap tissue was also analysed by immunohistochemistry. Animals with unconditioned flaps served as controls.

Results

Cooling induced a marked expression of HO-1 without induction of HSP-70 protein. This was paralleled by a significant improvement in microvascular perfusion (P < 0·050) that was predominantly regulated by the dilatation of nutritive capillaries. The cooling-mediated improvement in microcirculation resulted in a significant reduction in final flap necrosis (P < 0·050).

Conclusion

In this experimental study preoperative cooling was associated with the expression of HO-1 and was an effective conditioning procedure.
Prospective evaluation of 6895 groin hernia repairs in women
Authors: Koch A , Edwards A , Haapaniemi S , Nordin P , Kald A
Published: September 2005

Background

Although 8 per cent of groin hernia repairs are performed in women, there is little published literature relating specifically to women. This study compared differences in outcome between women and men after groin hernia repair.

Methods

Data collected prospectively in the Swedish Hernia Register between 1992 and 2003 were analysed, including 6895 groin hernia repairs in women and 83 753 in men.

Results

A higher proportion of emergency operations was carried out in women (16·9 per cent) than men (5·0 per cent), leading to bowel resection in 16·6 and 5·6 per cent respectively. During reoperation femoral hernias were found in 41·6 per cent of the women who were diagnosed with a direct or indirect inguinal hernia at the primary operation. The corresponding proportion for men was 4·6 per cent. The hernia repair was not classified as a standard operation (e.g. Shouldice, Lichtenstein, Plug/Mesh, TAPP/TEP) in 38·2 per cent of women and 11·2 per cent of men. Women had a significantly higher risk of reoperation for recurrence than men, and techniques associated with the lowest risk for reoperation in men had the highest risk in women.

Conclusion

A greater proportion of women than men require emergency groin hernia repair, with consequently higher rates of bowel resection, complications and death. Surgical techniques developed for use in men may put women at unnecessary risk.
Development of instructional, interactive, multimedia anatomy dissection software: A student‐led initiative
Authors: Inwood Matthew J. , Ahmad Jamil
Published: September 2005

Although dissection provides an unparalleled means of teaching gross anatomy, it constitutes a significant logistical and financial investment for educational institutions. The increasing availability and waning cost of computer equipment has enabled many institutions to supplement their anatomy curriculum with Computer Aided Learning (CAL) software. At the Royal College of Surgeons in Ireland, two undergraduate medical students designed and produced instructional anatomy dissection software for use by first and second year medical students. The software consists of full‐motion, narrated, QuickTime MPG movies presented in a Macromedia environment. Forty‐four movies, between 1–11 min in duration, were produced. Each movie corresponds to a dissection class and precisely demonstrates the dissection and educational objectives for that class. The software is distributed to students free of charge and they are encouraged to install it on their Apple iBook computers. Results of a student evaluation indicated that the software was useful, easy to use, and improved the students' experience in the dissection classes. The evaluation also indicated that only a minority of students regularly used the software or had it installed on their laptop computers. Accordingly, effort should also be directed toward making the software more accessible and increasing students' comfort and familiarity with novel instructional media. The successful design and implementation of this software demonstrates that CAL software can be employed to augment, enhance and improve anatomy instruction. In addition, effective, high quality, instructional multimedia software can be tailored to an educational institution's requirements and produced by novice programmers at minimal cost. Clin. Anat. 18:613–617, 2005. © 2005 Wiley‐Liss, Inc.
Unique origin of the inferior alveolar artery
Authors: Jergenson Margaret A. , Norton Neil S. , Opack Joseph M. , Barritt Laura C.
Published: September 2005

The inferior alveolar artery is the major blood supply to the mandible and mandibular teeth. This artery has a very consistent path, originating from the maxillary artery and passing inferiorly until it enters the mandibular foramen, accompanied by the inferior alveolar nerve and vein. During routine dissection of a 90‐year‐old female cadaver, a unique origin of the inferior alveolar artery was observed on the left side. The artery branched off the external carotid artery, just superior to the stylohyoid and posterior belly of the digastric muscle in the posterior region of the submandibular triangle. From its starting point the artery passed superiorly in the stylomandibular fascia and made a curving arch into the pterygomandibular space to enter the mandibular foramen with the inferior alveolar nerve. The position and branching pattern of the maxillary artery were otherwise typical. The inferior alveolar artery on the right side displayed a normal branching pattern within the infratemporal fossa. Results of surgical procedures in this area, such as sliding osteotomy of the mandible, could be impacted by this anomaly. Clin. Anat. 18:597–601, 2005. © 2005 Wiley‐Liss, Inc.