bluuebunny/crossref_metadata_2025 huggingface dataset:
Family management of child waiting for a organ transplant / Manejo familiar da criança que espera por um transplante de órgãos
Authors: Ruiz Hellen Angélica , Castillo Ana Márcia Chiaradia Mendes , Silva Lucía , Dos Santos Alves Daniela Fernanda
Published: March 2024

Objetivo: conhecer a experiência de manejo familiar da criança à espera de um transplante de órgãos sólidos de acordo com o Modelo de estilos de manejo familiar. Método: foi realizado um estudo qualitativo que utilizou o modelo supracitado como referencial teórico. Foram aplicadas entrevistas, de forma remota, a nove familiares de crianças que aguardavam por um transplante de órgãos. Os dados foram analisados através do modelo híbrido de análise temática. Resultados: as famílias definem que essa fase oscila entre o medo do transplante, da rejeição do órgão e possibilidade de morte em fila de espera, e a esperança na melhora do quadro clínico. Considerações finais: identificar as necessidades da família que aguarda por um transplante possibilita ao profissional de saúde implementar intervenções.
Beamlets and Multiscale Modeling
Authors: Huo Xiaoming
Published: October 2006

Beamlets is a data structure to be used to analyze linear or curvilinear features in two dimensional space. Beamlets are a collection of dyadically organized line segments, taking a range of positions, orientations, and having various lengths. The key advantage of such a data structure is that it forms a multiscale framework for linear and curvilinear features. This data structure enables new methods in statistical modeling, statistic estimation, denoising, data reduction, and compression. The new methods are both computationally efficient and theoretically optimal. The derived methods are particularly suitable for large size data.
Computer Vision, Statistics in
Authors: Chellappa Rama , Chowdhury Amit K. Roy
Published: October 2006

Computer Vision (CV) broadly refers to the discipline where extraction of useful 2D and/or 3D information from one or more images is of interest. Useful information could consist of features such as edges, lines, curves and textures, or information about depth, motion, object descriptions, etc. CV problems are usually ill‐posed inverse problems. Since the image data is usually obtained from sensors such as video cameras, infrared, radar, etc., the information extraction processes often have to deal with data that is corrupted by noise from the sensors and the environment. Statistics can help in obtaining robust and accurate solutions to these inverse problems by modeling the noise processes. We present here a broad overview of the applications of statistics to different computer vision problems and explain in detail two particular applications, tracking and motion analysis, where statistical approaches have been used very successfully.
C
opula Process,
A
rchimedean
Authors: Malov S. V.
Published: October 2006

Archimedean copulas have a wide field of applications in probability theory and in mathematical statistics. The copula arose first in the work of Sklar [14]. It is the function which characterizes principal connection of components in a random vector independently of marginal distributions. Archimedean copula process was introduced as a generalization of the scheme of independent random variables. The most of interesting applications of this object was in the order statistics theory and in the extreme values theory. The extreme type theorems and some characterizations of classes of sequences via properties of order statistics and record values can be improved from the class of independent random variables to the class of Archimedean copula processes. In this way the proportional Archimedean copula process appeared as the generalization of the
F
α
‐scheme for independent random variables. Some representations of the Archimedean copula process via independent random variables will be also given.
Agricultural Surveys
Authors: Vogel (Retired) Frederic A.
Published: October 2006

In this entry, an overview of the history of the development of various statistical procedures used to forecase and measure agricultural production is provided. Though the examples mostly apply to the United States (with the agricultural statistics as developed by the United States Department of Agriculture), some methods used in other countries are also mentioned at appropriate places.
Continuum Regression
Authors: Sundberg Rolf
Published: October 2006

When, in a multiple regression, regressors are near‐collinear, so‐called regularized or shrinkage regression methods can be highly preferable to ordinary least squares, by trading bias for variance. Continuum regression, introduced by Stone and Brooks in 1990, ties together several more classical regularized regression methods, such as principal components regression, partial least squares regression, and ridge regression.
Spacings, Linear Combinations of
Authors: Huffer Fred W. , Lin Chien‐Tai
Published: October 2006

Problems involving the distribution of linear combinations of spacings occur in many areas of statistics. This article gives expressions for the density and distribution function of an arbitrary linear combination of spacings. General methods are also presented for computing the distribution of the maximum or minimum of any finite collection of linear combinations of spacings. When the coefficients of the linear combinations are rational, these methods can be implemented on computer algebra systems to produce exact symbolic expressions for the distributions. These expressions can be used to compute numerical answers accurate to any required degree of precision.
Spearman Correlation Coefficients, Differences between
Authors: Myers Leann , Sirois Maria J.
Published: October 2006

Testing the equality of two population correlation coefficients when the data are bivariate normal and Pearson correlation coefficients are used as estimates of the population parameters is a straightforward procedure covered in many introductory statistics courses. The coefficients are converted using Fisher's
z
‐transformation with standard errors (
N
 − 3)
−1/2
. The two transformed values are then compared using a standard normal procedure. When data are not bivariate normal, Spearman's correlation coefficient rho is often used as the index of correlation. Comparison of two Spearman rhos is not as well documented. Three approaches were investigated using Monte Carlo simulations. Treating the Spearman coefficients as though they were Pearson coefficients and using the standard Fisher's
z
‐transformation and subsequent comparison was more robust with respect to Type I error than either ignoring the nonnormality and computing Pearson coefficients or converting the Spearman coefficients to Pearson equivalents prior to transformation.
Kurtosis
Authors: Zenga Michele
Published: October 2006

The interpretation of the kurtosis index β2proposed by Karl Pearson is first examined. The Moors' indexTbased on quantiles and some partial orderings of kurtosis (by Van Zwet, Laurence, and Loh) are presented. Zenga's new approach to kurtosis, working for symmetrical as well as for asymmetrical distribution, is introduced. This latter approach is based on the definition of a particular transformation increasing kurtosis; a kurtosis curve, for the left and the right side of a distribution, can thus be obtained.
Partial Least Squares Regression
Authors: Helland Inge
Published: October 2006

Partial least squares regression was introduced as an algorithm in the early 1980s, and it has gained much popularity in chemometrics. PLSR—or PLSR1—is a regression method for collinear data, and can be seen as a competitor to principal component regression. The method makes it possible to combine prediction with a study of a joint latent structure in thex,y‐variables. PLSR2 is a generalization to several dependent variables. PLSR1 can be understood from a statistical point of view via its parameter algorithm and the corresponding population model.
Central Limit Theorems, Convergence Rates for
Authors: Nadarajah S. , Kotz S.
Published: October 2006

In this short entry, rates of convergence associated with central limit theorems are discussed. Specifically, the Liapunov bounds and the Berry‐Esseen bounds for the absolute value of the difference of the distribution of the standardized sums ofnrandom variables and the standard normal distribution are briefly described.
Income Inequality Measures
Authors: Dagum Camilo
Published: October 2006

This study purports to present, analyze, and evaluate the following:

The income inequality measures (IIMs) proposed since Pareto and Gini and to derive their corresponding utility and disutility functions from the specification of a fundamental equation of income. Furthermore, a dual relationship between utility and disutility functions and between IIMs and social welfare functions are established.

The decomposition approach of the generalized entropy measure (GEM) and the Gini ratio showing the extreme limitations of GEM to meaningful account for the contribution of the between‐group inequalities.

The directional distance ratio (DDR) between binary combinations of income distributions showing that it is a better alternative to the decomposition approach, and unlike the latter, DDR offers sound policy implications.

The distance function between income distributions.
Generalized Order Statistics
Authors: Kamps Udo
Published: October 2006

Order statistics and record values appear in many statistical applications and are widely used in statistical modeling and inference. Both models describe random variables arranged in ascending order of magnitude. Generalized order statistics provide a unified approach to a variety of models of ordered random variables with different interpretations, such as ordinary order statistics, sequential order statistics, progressively type II censored order statistics, record values,kth record values, and Pfeifer's records. These models can be effectively applied, for example, in reliability theory. Here, an order statistic represents the life length of somek‐out‐of‐nsystem, which is an important technical structure. For this application, sequential order statistics serve to describe influences of failures on the life‐length distributions of the remaining components. Record values are used in shock models, and they are closely connected with the occurrence times of some corresponding nonhomogeneous Poisson process, with some minimal repair scheme, and with the relevation transform. The distribution theory of generalized order statistics is established along the lines of ordinary order statistics. By this, we find that many well‐known properties of order statistics and record values are also valid for generalized order statistics. The results on generalized order statistics concern their distribution theory, relations and bounds for moments, characterizations of distributions, preservation of aging properties and stochastic ordering, extreme‐value theory, and statistical inference with respect to model and distribution parameters.
Antieigenvalues and Antieigenvectors
Authors: Khattree Ravindra
Published: October 2006

In this entry, the concepts of antieigenvalues and antieigenvectors are first introduced. Then, various statistical situations wherein these entities arise naturally are explained.
Surrogate Markers
Authors: Molenberghs Geert
Published: October 2006

The validation of surrogate endpoints has been studied by Prentice. He presented a definition as well as a set of criteria that are equivalent if the surrogate and true endpoints are binary. Freedman and colleagues supplemented these criteria with the so‐called
proportion explained
. Buyse and Molenberghs proposed to replace the proportion explained by two quantities:
(i)
the
relative effect
linking the effect of treatment on both endpoints and
(ii)
the
adjusted association
, an individual‐level measure of agreement between both endpoints. Later, a number of proposals have been made to replace the single‐unit validation measures by multiunit (e.g., meta‐analytic) counterparts.
Musicology, Statistics in
Authors: Beran Jan
Published: October 2006

Quantitative musicology is a relatively new field of statistical applications that is increasingly important due to the availability of digitized data. In principle, all fields of statistical theory are potentially useful. In contrast to genuinely quantitative sciences, many questions in musicology have no unique ‘correct’ answer, and often no strictly objective optimality criterion exists to find an optimal solution to a problem. In this paper, some typical examples illustrate the role of statistics in musicology
Stirling Family of Distributions
Authors: Sibuya Masaaki
Published: October 2006

A family of pmf's that have Stirling numbers as a factor, including record number distributions and classical occupancy distributions, is treated. An extended family and related distributions are mentioned.
What's Right with You: Helping Students Find and Use Their Personal Strengths
Authors: Shushok Frank , Hulme Eileen
Published: September 2006

Fixing what's wrong—with students, institutions, and cultures—is the most prevalent approach to change. Frank Shushok and Eileen Hulme offer the discovery and exploitation of what's right as a powerful alternative.
6: Principles of Undergraduate Learning: The Not-So-Easy Road to Writing and Committing to Them
Authors: Hamilton Sharon J. , Banta Trudy W. , Evenbeck Scott E.
Published: September 2006

Indiana University–Purdue University Indianapolis has joined campuses across the nation in identifying and assessing student learning outcomes. With its twenty schools, diverse populations, and multiple goals, how this urban institution managed to organize much of its work around six learning principles is a tale of both caution and triumph.
The Best of Both Worlds: Coupling Research and Assessment
Authors: Yousey Kimberly M.
Published: September 2006

Practical inquiry combines the formal research techniques of formulating questions and conducting literature reviews with site-based data collection and use of findings to improve practice. Rochester Institute of Technology has used this approach to improve support for their residential students.
MODEL—molecular descriptor lab: A web‐based server for computing structural and physicochemical features of compounds
Authors: Li Z.R. , Han L.Y. , Xue Y. , Yap C.W. , Li H. , Jiang L. , Chen Y.Z.
Published: September 2006

Molecular descriptors represent structural and physicochemical features of compounds. They have been extensively used for developing statistical models, such as quantitative structure activity relationship (QSAR) and artificial neural networks (NN), for computer prediction of the pharmacodynamic, pharmacokinetic, or toxicological properties of compounds from their structure. While computer programs have been developed for computing molecular descriptors, there is a lack of a freely accessible one. We have developed a web‐based server, MODEL (Molecular Descriptor Lab), for computing a comprehensive set of 3,778 molecular descriptors, which is significantly more than the ∼1,600 molecular descriptors computed by other software. Our computational algorithms have been extensively tested and the computed molecular descriptors have been used in a number of published works of statistical models for predicting variety of pharmacodynamic, pharmacokinetic, and toxicological properties of compounds. Several testing studies on the computed molecular descriptors are discussed. MODEL is accessible at http://jing.cz3.nus.edu.sg/cgi‐bin/model/model.cgi free of charge for academic use. Biotechnol. Bioeng. 2007;97: 389–396. © 2006 Wiley Periodicals, Inc.
Modeling of local dynamic behavior of phenol degradation in an internal loop airlift bioreactor by yeast Candida tropicalis
Authors: Feng Wei , Wen Jianping , Liu Cuiyun , Yuan Qing , Jia Xiaoqiang , Sun Yan
Published: September 2006

A coupled computational fluid dynamic (CFD) model, combining hydrodynamics with biochemical reactions, was developed to simulate the local transient flow patterns and the dynamic behaviors of cell growth and phenol biodegradation by yeast Candida tropicalis in an internal loop airlift reactor (ILALR). To validate this proposed model effectively, the simulated local hydrodynamic characteristics of the gas‐mineral salt medium solution (gas‐liquid) two‐phase system, at a phenol concentration of 1,200 mg L−1 and no presence of cells, was experimentally investigated in the ILALR using laser Doppler anemometer (LDA) measurements and conductivity probe. Furthermore, the validation of the simulated phenol biodegradation behavior by C. tropicalis at different initial concentrations of phenol and cell was also carried out in the ILALR. The time‐averaged and transient results of the model simulations illustrated a satisfactory agreement with the experimental data. Finally, the local instantaneous flow and phenol biodegradation features, including gas holdup, gas velocity, liquid velocity, cell concentration, and phenol concentration inside the ILALR were successfully predicted by the proposed model. Biotechnol. Bioeng. 2007;97: 251–264. © 2006 Wiley Periodicals, Inc.
Metabolic engineering of sesquiterpene metabolism in yeast
Authors: Takahashi Shunji , Yeo Yunsoo , Greenhagen Bryan T. , McMullin Tom , Song Linsheng , Maurina‐Brunker Julie , Rosson Reinhardt , Noel Joseph P. , Chappell Joe
Published: September 2006

Terpenes are structurally diverse compounds that are of interest because of their biological activities and industrial value. These compounds consist of chirally rich hydrocarbon backbones derived from terpene synthases, which are subsequently decorated with hydroxyl substituents catalyzed by terpene hydroxylases. Availability of these compounds is, however, limited by intractable synthetic means and because they are produced in low amounts and as complex mixtures by natural sources. We engineered yeast for sesquiterpene accumulation by introducing genetic modifications that enable the yeast to accumulate high levels of the key intermediate farnesyl diphosphate (FPP). Co‐expression of terpene synthase genes diverted the enlarged FPP pool to greater than 80 mg/L of sesquiterpene. Efficient coupling of terpene production with hydroxylation was also demonstrated by coordinate expression of terpene hydroxylase activity, yielding 50 mg/L each of hydrocarbon and hydroxylated products. These yeast now provide a convenient format for investigating catalytic coupling between terpene synthases and hydroxylases, as well as a platform for the industrial production of high value, single‐entity and stereochemically unique terpenes. Biotechnol. Bioeng. 2007;97: 170–181. © 2006 Wiley Periodicals, Inc.
Responses of the photosynthetic machinery of Spirulina maxima to induced reactive oxygen species
Authors: Ganesh Aparna B. , Manoharan Periakaruppan T. , Suraishkumar G.K.
Published: September 2006

The photosynthetic machinery of Spirulina maxima was studied when subjected to induced reactive oxygen species (ROS) to examine the organism's responses to stress. Significant decreases in both photosynthetic efficiency and growth rate were observed. Exposure to 0.01 mmol H2O2/(g cell), which induced the lowest specific intracellular ROS level (siROS) led to a 15% decrease in specific growth rate; an increase in siROS by 70‐fold led to a 25% decrease in specific growth rate. Similarly, siROS induced by 0.01 mmol H2O2/(g cell) led to 15% inhibition in photosynthetic efficiency, while an increase in siROS by 40‐ or 70‐fold led to about 60% inhibition in photosynthetic efficiency. To further understand the effects of induced ROS on photosynthetic machinery, we performed a detailed pigmentation analysis as well as analyzed Phycobilisomes (PBS), Photosystem II (PSII), and Photosystem I (PSI), the three important components of cyanobacterial photosynthetic apparatus. We found carotenoids (beta‐carotene and lutein) to be most sensitive to siROS. Also, specific levels of phycocyanin and allophycocyanin, which are important PBS pigments, decreased significantly in response to H2O2. Further, electron transport assays revealed that ROS cause damage primarily to PSII, whereas they do not significantly affect PSI in comparison; siROS induced by 0.01 mmol H2O2/(g cell) led to a 15% inhibition of PSII, and increase in siROS by 9‐, 40‐, and 70‐fold led to 22%, 36%, and 46% inhibition, respectively. Biotechnol. Bioeng. 2007;96:1191–1198. © 2006 Wiley Periodicals, Inc.
The conformational quality of insoluble recombinant proteins is enhanced at low growth temperatures
Authors: Vera Andrea , González‐Montalbán Nuria , Arís Anna , Villaverde Antonio
Published: September 2006

Protein aggregation is a major bottleneck during the bacterial production of recombinant proteins. In general, the induction of gene expression at sub‐optimal growth temperatures improves the solubility of aggregation‐prone polypeptides and minimizes inclusion body (IB) formation. However, the effect of low temperatures on the quality of the recombinant protein, especially within the insoluble cell fraction, has been hardly ever explored. In this work, we have examined the conformational status of a recombinant GFP protein when produced in Escherichia coli below 37°C. As expected, the fraction of aggregated protein largely decreased at lower temperatures, while the conformational quality of both soluble and aggregated GFP, as reflected by its specific fluorescence emission, progressively improved. This observation indicates that physicochemical conditions governing protein folding affect concurrently the quality of the soluble and the aggregated forms of a misfolding‐prone protein, and that protein misfolding and aggregation are clearly not coincident events. Biotechnol. Bioeng. 2007;96:1101–1106. © 2006 Wiley Periodicals, Inc.
The YfiD protein contributes to the pyruvate formate‐lyase flux in an Escherichia coli arcA mutant strain
Authors: Zhu Jiangfeng , Shalel‐Levanon Sagit , Bennett George , San Ka‐Yiu
Published: September 2006

The product of yfiD gene is similar to pyruvate formate‐lyase (PFL) activase and it has been reported to activate PFL by replacing the glycyl radical domain. To quantitate the effect of YfiD on the cell metabolism in microaerobic cultures, glucose‐limited chemostat cultures were conducted with Escherichia coli yfiD mutant and yfiDarcA mutant strains. The microaerobic condition was controlled by purging the culture media with 2.5% O2 in N2. The intracellular metabolic flux distributions in these cultures were estimated based on C‐13 labeling experiments. By comparing with the flux distributions in wild‐type E. coli and the arcA mutant, it was shown that YfiD contributes to about 18% of the PFL flux in the arcA mutant, but it did not contribute to the PFL flux in wild‐type E. coli. It was also shown that the cell used both PFL and pyruvate dehydrogenase (PDH) to supplement the acetyl‐coenzyme A (AcCoA) pool under microaerobic conditions. The flux through PDH was about 22–30% of the total flux toward AcCoA in the wild‐type, the yfiD mutant and yfiDarcA mutant strains. Relatively higher lactate production was seen in the yfiDarcA mutant than the other strains, which was due to the lower total flux through PFL and PDH toward AcCoA in this strain. Biotechnol. Bioeng. 2007;97:138–143. © 2006 Wiley Periodicals, Inc.
Production of bio‐hydrogen by mesophilic anaerobic fermentation in an acid‐phase sequencing batch reactor
Authors: Cheong Dae‐Yeol , Hansen Conly L. , Stevens David K.
Published: September 2006

The pH and hydraulic retention time (HRT) of an anaerobic sequencing batch reactor (ASBR) were varied to optimize the conversion of carbohydrate‐rich synthetic wastewater into bio‐hydrogen. A full factorial design using evolutionary operation (EVOP) was used to determine the effect of the factors and to find the optimum condition of each factor required for high hydrogen production rate. Experimental results from 20 runs indicate that a maximum hydrogen production rate of 4,460–5,540 mL/L/day under the volumetric organic loading rate (VOLR) of 75 g‐COD/L/day obtained at an observed design point of HRT = 8 h and pH = 5.7. The hydrogen production rate was strongly dependent on the HRT, and the effect was statistically significant (P < 0.05). However, no significant effect (P > 0.05) was found for the pH on the hydrogen production rate. When the ASBR conditions were set for a maximum hydrogen production rate, the hydrogen production yield and specific hydrogen production rate were 60–74 mL/g‐COD and 330–360 mL/g‐VSS/day, respectively. The hydrogen composition was 43–51%, and no methanogenesis was observed. Acetate, propionate, butyrate, valerate, caproate, and ethanol were major liquid intermediate metabolites during runs of this ASBR. The dominant fermentative types were butyrate‐acetate or ethanol‐acetate, representing the typical anaerobic pathway of Clostridium species. This hydrogen‐producing ASBR had a higher hydrogen production rate, compared with that produced using continuous‐flow stirred tank reactors (CSTRs). This study suggests that the hydrogen‐producing ASBR is a promising bio‐system for prolonged and stable hydrogen production. Biotechnol. Bioeng. 2007;96: 421–432. © 2006 Wiley Periodicals, Inc.
Gastroesophageal reflux symptoms in patients with adenocarcinoma of the esophagus or cardia
Authors: Chak Amitabh , Faulx Ashley , Eng Charis , Grady William , Kinnard Margaret , Ochs‐Balcom Heather , Falk Gary
Published: October 2006

BACKGROUND.

The efficacy of endoscopic screening for chronic gastroesophageal reflux symptoms of heartburn and regurgitation in adult subjects depends on the sensitivity of this strategy for detecting Barrett esophagus in subjects before the development of adenocarcinoma of the esophagus or cardia. The aim of the current study was to determine what proportion of patients with cancer of the esophagus or cardia would have been candidates for a screening endoscopy before their cancer diagnosis based on the presence and duration of preceding reflux symptoms.

METHODS.

All patients with adenocarcinoma of the esophagus, adenocarcinoma of the cardia, or long‐segment Barrett esophagus presenting for endoscopy at 4 tertiary care and 2 Veterans Affairs (VA) hospitals were given a previously validated questionnaire to determine their recall of common gastroesophageal reflux symptoms.

RESULTS.

The study population of 375 subjects consisted primarily of 294 (78%) white men. Only 67 of 110 patients (61%) with adenocarcinoma of the esophagus and 8 of 21 patients (38%) with adenocarcinoma of the cardia recalled symptoms of heartburn or regurgitation being present for >5 years before their diagnosis of cancer. Only 40 of 110 patients (36%) with adenocarcinoma of the esophagus and 5 of 21 patients (24%) with adenocarcinoma of the cardia recalled weekly symptoms being present for >5 years before their cancer diagnosis. Of the 244 patients with Barrett esophagus, 170 (70%) recalled heartburn or regurgitation for >5 years and 89 patients (37%) recalled weekly symptoms for >5 years.

CONCLUSIONS.

Current practice, which uses a screening strategy of performing endoscopy in patients with >5 years of heartburn or regurgitation, can detect Barrett epithelium in only a limited proportion of those patients at risk for developing adenocarcinoma of the esophagus or adenocarcinoma of the cardia. Cancer 2006. © 2006 American Cancer Society.
The use of multivariate statistics to elucidate patterns of floodplain sedimentation at different spatial scales
Authors: Thoms Martin C. , Parsons Melissa E. , Foster John M.
Published: October 2006

Floodplains are depositional features of riverine landscapes that display complex sedimentation patterns that are amenable to multi‐scale approaches. We examined sedimentation in the Lower Balonne floodplain, Queensland, Australia, at three different spatial scales: the channel (103 km), floodplain process zone (10 km) and geomorphic unit (102 m) scales, and compared scale‐related patterns evident from stratigraphy with those evident from quantitative multivariate analysis. Three stratigraphic sequences were found in the Lower Balonne floodplain: generally fining upward, episodic fining upward, and mud‐dominated. Stratigraphical analysis revealed the detailed character of sedimentary sequences embedded within the scale patterns derived from multivariate analysis. Multivariate statistical analyses of a range of textural and geochemical data revealed different patterns of floodplain sedimentation at each scale. At the channel scale, sediment texture and geochemistry were more heterogeneous in the Culgoa River than in Briarie Creek. At the floodplain process zone scale clear patterns of sediment texture and geochemistry were observed along the upper, mid and lower floodplain process zones of Briarie Creek, but not along the Culgoa River. At the geomorphic unit scale, clear patterns of sediment texture and geochemistry were observed among the bank, buried channel and flat floodplain units of the Culgoa River, but were not as clear in Briarie Creek. Recognition of rivers as hierarchically organized systems is an emerging paradigm in river science. Our study supports this paradigm by demonstrating that different sedimentation patterns occur at different scales to reveal a hierarchically organized floodplain environment. Copyright © 2006 John Wiley & Sons, Ltd.
Dating young geomorphic surfaces using age of colonizing Douglas fir in southwestern Washington and northwestern Oregon, USA
Authors: Pierson Thomas C.
Published: October 2006

Dating of dynamic, young (<500 years) geomorphic landforms, particularly volcanofluvial features, requires higher precision than is possible with radiocarbon dating. Minimum ages of recently created landforms have long been obtained from tree‐ring ages of the oldest trees growing on new surfaces. But to estimate the year of landform creation requires that two time corrections be added to tree ages obtained from increment cores: (1) the time interval between stabilization of the new landform surface and germination of the sampled trees (germination lag time or GLT); and (2) the interval between seedling germination and growth to sampling height, if the trees are not cored at ground level. The sum of these two time intervals is the colonization time gap (CTG). Such time corrections have been needed for more precise dating of terraces and floodplains in lowland river valleys in the Cascade Range, where significant eruption‐induced lateral shifting and vertical aggradation of channels can occur over years to decades, and where timing of such geomorphic changes can be critical to emergency planning.

Earliest colonizing Douglas fir (Pseudotsuga menziesii) were sampled for tree‐ring dating at eight sites on lowland (<750 m a.s.l.), recently formed surfaces of known age near three Cascade volcanoes – Mount Rainier, Mount St. Helens and Mount Hood – in southwestern Washington and northwestern Oregon. Increment cores or stem sections were taken at breast height and, where possible, at ground level from the largest, oldest‐looking trees at each study site. At least ten trees were sampled at each site unless the total of early colonizers was less. Results indicate that a correction of four years should be used for GLT and 10 years for CTG if the single largest (and presumed oldest) Douglas fir growing on a surface of unknown age is sampled. This approach would have a potential error of up to 20 years. Error can be reduced by sampling the five largest Douglas fir instead of the single largest. A GLT correction of 5 years should be added to the mean ring‐count age of the five largest trees growing on the surface being dated, if the trees are cored at ground level. This correction would have an approximate error of ±5 years. If the trees are cored at about 1·4 m above the ground surface (breast height), a CTG correction of 11 years should be added to the mean age of the five sampled trees (with an error of about ±7 years). Published in 2006 by John Wiley & Sons, Ltd.
Cancer‐germline gene expression in pediatric solid tumors using quantitative real‐time PCR
Authors: Jacobs Joannes F.M. , Brasseur Francis , Hulsbergen‐van de Kaa Christina A. , van de Rakt Mandy W.M.M. , Figdor Carl G. , Adema Gosse J. , Hoogerbrugge Peter M. , Coulie Pierre G. , de Vries I. Jolanda M.
Published: October 2006

Cancer‐germline genes (CGGs) code for immunogenic antigens that are present on various human tumors but not on normal tissues. The importance of CGGs in cancer immunotherapy has led to detailed studies of their expression in a range of human tumors. We measured the levels of expression of 12 CGGs in various pediatric solid tumors to identify targets for therapeutic cancer vaccines. Quantitative real‐time PCR (qPCR) was used to measure the expression of 8 MAGE genes and of genes LAGE‐2/NY‐ESO‐1 and GAGE‐1, 2, 8 in 9 osteosarcomas, 10 neuroblastomas, 12 rhabdomyosarcomas and 18 Ewing's sarcomas. Nine tumors were also examined by immunohistochemistry with monoclonal antibodies specific for the MAGE‐A1, MAGE‐A4 and NY‐ESO‐1 proteins. All osteosarcoma and 80% of neuroblastoma samples expressed several CGGs at high levels. Six of 12 rhabdomyosarcomas and 11 of 18 Ewing's sarcomas expressed at least one CGG. Immunohistochemistry data correlated well with qPCR results and showed a homogeneous protein distribution pattern in most positive tumors. No correlation was found between the levels of CGG expression in the tumors and clinicopathological parameters of the patients. Pediatric solid tumors express several CGGs, which encode antigens that could be targeted in therapeutic vaccination trials. Several CGGs of the MAGE, GAGE and LAGE families are coexpressed in a large proportion of osteosarcoma and neuroblastoma samples. Some rhabdomyosarcomas express several of these genes at high levels. Ewing's sarcomas have an overall low CGG expression. © 2006 Wiley‐Liss, Inc.
Comparison of implicit solvent models for the simulation of protein–surface interactions
Authors: Sun Yu , Latour Robert A.
Published: October 2006

Empirical force field‐based molecular simulations can provide valuable atomistic‐level insights into protein–surface interactions in aqueous solution. While the implicit treatment of solvation effects is desired as a means of improving simulation efficiency, existing implicit solvent models were primarily developed for the simulation of peptide or protein behavior in solution alone, and thus may not be appropriate for protein interactions with synthetic material surfaces. The objective of this research was to calculate the change in free energy as a function of surface–separation distance for peptide–surface interactions using different empirical force field‐based implicit solvation models (ACE, ASP, EEF1, and RDIE with the CHARMM 19 force field), and to compare these results with the same calculations conducted using density functional theory (DFT) combined with the self‐consistent reaction field (SCRF) implicit solvation model. These comparisons show that distinctly different types of behavior are predicted with each implicit solvation method, with ACE providing the best overall agreement with DFT/SCRF calculations. These results also identify areas where ACE is in need of improvement for this application and provide a basis for subsequent parameter refinement. © 2006 Wiley Periodicals, Inc. J Comput Chem, 2006
Reflections on migration of clay and structural changes in nanocomposites
Authors: Lewin Menachem
Published: October 2006

The profound effect on flame retardancy of the blending of small amounts of clay with polymers is believed to be due to the formation of a protective clay‐rich char barrier on the surface of the pyrolyzing polymer during combustion. The mode of formation of this barrier is discussed, in view of recent results. Evidence is reviewed, showing that the organically layered silicon particles migrate to, and accumulate on the surface of the molten polymer at temperatures far below pyrolysis temperature. The causes of the migration are: temperature and viscosity gradients of the melt with regard to heat source; propelling the organically layered silicon to the surface by gas bubbles from the decomposing surfactant and polymer; and by the difference in surface free energy between the polymer and the polymer/clay aggregate. The interfacial tension of the clay/polymer aggregates is calculated for a number of polymers, and shown to be much lower than the surface tension of the low surface free energy ingredient. It is suggested that these aggregates migrate to the surface. The decomposition of the surfactant in the clay above 200°C brings about, in the case of polypropylene/nanocomposite, two simultaneous and opposing phenomena: the migration of the clay; and the conversion of the nanocomposite into a non‐colloidal microcomposite. The decomposition of the surfactant is accompanied by an increase in interlayer distance, and internal pressure in the clay particles, culminating either in a separation of the external layers (i.e. exfoliation), or in their collapse into each other, forming a microcomposite. Mechanistic considerations are presented. Copyright © 2006 John Wiley & Sons, Ltd.
Electroactive composite systems containing high conductive polymer layers on poly(ethylene) porous films
Authors: Elyashevich G. K. , Smirnov M. A. , Kuryndin I. S. , Bukošek V.
Published: October 2006

New composite electroactive materials containing conducting polymers were elaborated by oxidative polymerization of aniline and pyrrole onto porous poly(ethylene) films. The morphology of the conducting phase on the surface of the composites was investigated by scanning electron microscopy. The influence of preparation method and porous support structure on electric and mechanical properties of the composite materials was studied. The correlation between the composites electroconductivity and the absorbance of electromagnetic radiation in the IR region was observed. It was found that gas separation and ion‐exchange membrane properties of the composites strongly depend on their conductivity and content of conducting component. Copyright © 2006 John Wiley & Sons, Ltd.
Unambiguous identification of thiouracil residue in urine collected in non‐treated bovine by tandem and high‐resolution mass spectrometry
Authors: Pinel Gaud , Maume Daniel , Deceuninck Yoann , Andre François , Le Bizec Bruno
Published: October 2006

Thyrostats are banned compounds in Europe since 1981 (directive 81/602/EC) because of their carcinogenic and teratogenic properties. However, the occurrence of thiouracil (TU) in bovine urines from national monitoring plans with quantifications in the range 1–10 µg · L−1 occasionally raises the question of its origin which might either be the consequence of an illegal administration or the result of ‘endogenous’ production. In order to definitively and unambiguously identify the so‐called thiouracil signal in non‐treated bovine urines, independent mass spectrometry (MS) approaches have been used. Different reagents (3‐IBBr, 3‐BrBBr and PFBBr) were used to derivatise and to extract TU from urine samples and characterisation of the residues was performed by means of different MS approaches [LC/(ESI‐)MS/MS, GC/(EI+)MS/MS and HRMS (EI and NCI)]. These combined strategies allowed for an independent and confident identification of TU in bovine urine samples collected from animals never treated with any thyrostatic drugs. This result is of prime importance for laboratories and risk managers involved in the field of forbidden growth promoters control: detection of TU residue in bovine urine will have to be carefully considered as a non‐systematic proof of illegal administration. Copyright © 2006 John Wiley & Sons, Ltd.
An adaptive phase I design for identifying a biologically optimal dose for dual agent drug combinations
Authors: Mandrekar Sumithra J. , Cui Yue , Sargent Daniel J.
Published: October 2006

Historically, designs for dose seeking trials using chemotherapeutic drug combinations have been geared towards finding the maximum tolerated dose, with safety as the primary outcome. With target based agents whose dose–efficacy curves are unknown and dose–toxicity relationships may be minimal, alternative designs are needed. In this paper, we propose an extension to an adaptive single agent dose‐finding design previously reported. A generalization of the continuation ratio model allowing separate toxicity and efficacy curves for each agent in a dual agent combination, generating a dose success surface for the combination, is proposed. A continual reassessment approach with a straightforward dose selection criterion using the accumulated data from all patients treated to that point is employed. Our simulation studies demonstrate favourable operating characteristics in terms of experimentation and recommendation rates, and the average sample size, under a variety of scenarios. The proposed approach allowing the incorporation of both the toxicity and efficacy of each agent into the identification of an optimal dosing region for a combination is novel and warrants further consideration. Copyright © 2006 John Wiley & Sons, Ltd.
Anti-self-dual Lagrangians: Variational resolutions of non-self-adjoint equations and dissipative evolutions
Authors: Ghoussoub Nassif
Published: September 2006

We develop the concept and the calculus of
anti-self-dual
(
ASD
)
Lagrangians
and their derived vector fields which seem inherent to many partial differential equations and evolutionary systems. They are natural extensions of gradients of convex functions – hence of self-adjoint positive operators – which usually drive dissipative systems, but also provide representations for the superposition of such gradients with skew-symmetric operators which normally generate unitary flows. They yield variational formulations and resolutions for large classes of non-potential boundary value problems and initial-value parabolic equations. Solutions are minima of newly devised energy functionals, however, and just like the self (and anti-self) dual equations of quantum field theory (e.g. Yang–Mills) the equations associated to such minima are not derived from the fact they are critical points of the functional

I

, but because they are also zeroes of suitably derived Lagrangians. The approach has many advantages: it solves variationally many equations and systems that cannot be obtained as Euler–Lagrange equations of action functionals, since they can involve non-self-adjoint or other non-potential operators; it also associates variational principles to variational inequalities, and to various dissipative initial-value first order parabolic problems. These equations can therefore be analyzed with the full range of methods – computational or not – that are available for variational settings. Most remarkable are the permanence properties that ASD Lagrangians possess making their calculus relatively manageable and their domain of applications quite broad.

On introduit et développe la notion de
Lagrangien anti-autodual
qui apparait dans plusieurs problèmes de géométrie et de physique théorique. Cette classe inclut les champs de gradient de fonctions convexes qui sont à la base de systèmes dissipatifs, mais aussi la superposition de ces derniers avec les opérateurs anti-symétriques qui, par contre, engendrent des flots conservatifs. Comme pour les équations autoduales de Yang–Mills, ces Lagrangiens permettent la résolution variationnelle de plusieurs équations différentielles du premier ordre qui ne rentrent donc pas dans le cadre de la théorie de Euler–Lagrange. Les solutions proviennent de minima de certaines (nouvelles) fonctionelles d'énergie, mais les équations ne sont pas derivées du fait qu'elles sont des points critiques, mais du fait qu'elles sont des racines de Lagrangiens positifs associés obtenus par une extension d'une astuce de Bogomolnyi. Cette nouvelle approche variationelle a plusieurs avantages, surtout qu'elle est applicable dans plusieurs situations, puisque la classe des Lagrangiens anti-autoadjoints est assez riche, étant stable – entre autres – par les opérations du calcul fonctionnel de l'analyse convexe, ainsi que celui des opérateurs anti-symétriques.
Maslov index for homoclinic orbits of Hamiltonian systems
Authors: Chen Chao-Nien , Hu Xijun
Published: September 2006

A useful tool for studying nonlinear differential equations is index theory. For symplectic paths on bounded intervals, the index theory has been completely established, which revealed tremendous applications in the study of periodic orbits of Hamiltonian systems. Nevertheless, analogous questions concerning homoclinic orbits are still left open. In this paper we use a geometric approach to set up Maslov index for homoclinic orbits of Hamiltonian systems. On the other hand, a relative Morse index for homoclinic orbits will be derived through Fredholm index theory. It will be shown that these two indices coincide.
SECRET AGENT, an Arabidopsis thaliana O‐GlcNAc transferase, modifies the Plum pox virus capsid protein
Authors: Scott Cheryl L. , Hartweck Lynn M. , de Jesús Pérez José , Chen Dinghu , García Juan Antonio , Olszewski Neil E.
Published: September 2006

The capsid protein of Plum pox virus (PPV‐CP) is modified with O‐linked GlcNAc (O‐GlcNAc). While Arabidopsis has two O‐GlcNAc transferases, SECRET AGENT (SEC) and SPINDLY (SPY), previous work suggests that SEC modifies PPV‐CP and that the modification plays a role in the infection process. Here, we show that when co‐expressed in Escherichia coli SEC modifies PPV‐CP. Deletion mapping and site‐directed mutagenesis identified three threonine and a serine located near the N‐terminus of PPV‐CP that are modified by SEC. Two of these threonines have recently been shown to be modified in virus from plants suggesting that SEC has the same specificity in plants and E. coli.
Habitat suitability modelling of economically important fish species with commercial fisheries data
Authors: Morris Liz , Ball David
Published: October 2006

In this study we used catch and effort data from a commercial fishery to generate habitat suitability models for Port Phillip Bay, Victoria, Australia. Species modelled were King George whiting (Sillaginodes punctata), greenback flounder (Rhombosolea tapirina), Australian salmon (Arripis trutta and A. truttaceus), and snapper (Pagrus auratus). Locations of commercial catches were reported through a grid system of fishing blocks. Spatial analyses in a Geographic Information System (GIS) were applied to describe each fishing block by its habitat area. A multivariate approach was adopted to group each fishing block by its dominant habitats. Standardized catch per unit effort values were overlaid on these groups to identify those that returned high or low catches for each species. A simple set of rules was then devised to predict the habitat suitability for each habitat combination in a fishing block. The spatial distribution of these habitats was presented in a GIS. These habitat suitability models were consistent with existing anecdotal information and expert opinion. While the models require testing, we have shown that in the absence of adequate fishery-independent data, commercial catch and effort data can be used to produce habitat suitability models at a bay-wide scale.