bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nested, non‐parametric, correlative analysis of microarrays for heterogenous phenotype characterization
Authors: Kowalski Jeanne , Blackford Amanda , Feng Changyong , Mamelak Adam J. , Sauder Daniel N. 
Published: June 2006

AbstractWe present a non‐parametric approach for qualitatively selecting candidate genes to characterize several criteria that are nested among genes selected on the basis of their individual, similar effects upon an array‐wide closeness measure. In this setting, a goal is to obtain a reliable characterization of phenotypes, based on very high‐dimensional data from a few samples. As opposed to a distance‐based approach, the proposed measure defines closeness based on gene signal profiles (functionals) rather than on isolated (numerical) differences in each gene between samples. By using such a measure to characterize intensity differences, we effectively separate biological from artifactual variation in expression, due to tissue effects or signal calibration. Based on this measure, we successively examine the significance of the following: a set of similarly behaved genes relative to all arrayed genes, a set of candidate genes relative to similarly behaved genes, individual candidate genes relative to non‐candidates, and the direction, as over‐ or under‐expressed, of candidate genes. In each setting, sample pairs are the units of analysis, with U‐statistics the theoretical framework. We illustrate the method on a microarray experiment, where the goal is to select sets of genes that characterize a type of skin cancer and its histological subtypes. Copyright © 2006 John Wiley & Sons, Ltd.
Robustness of a multivariate normal approximation for imputation of incomplete binary data
Authors: Bernaards Coen A. , Belin Thomas R. , Schafer Joseph L. 
Published: June 2006

AbstractMultiple imputation has become easier to perform with the advent of several software packages that provide imputations under a multivariate normal model, but imputation of missing binary data remains an important practical problem. Here, we explore three alternative methods for converting a multivariate normal imputed value into a binary imputed value: (1) simple rounding of the imputed value to the nearer of 0 or 1, (2) a Bernoulli draw based on a ‘coin flip’ where an imputed value between 0 and 1 is treated as the probability of drawing a 1, and (3) an adaptive rounding scheme where the cut‐off value for determining whether to round to 0 or 1 is based on a normal approximation to the binomial distribution, making use of the marginal proportions of 0's and 1's on the variable. We perform simulation studies on a data set of 206 802 respondents to the California Healthy Kids Survey, where the fully observed data on 198 262 individuals defines the population, from which we repeatedly draw samples with missing data, impute, calculate statistics and confidence intervals, and compare bias and coverage against the true values. Frequently, we found satisfactory bias and coverage properties, suggesting that approaches such as these that are based on statistical approximations are preferable in applied research to either avoiding settings where missing data occur or relying on complete‐case analyses. Considering both the occurrence and extent of deficits in coverage, we found that adaptive rounding provided the best performance. Copyright © 2006 John Wiley & Sons, Ltd.
Das Verhältnis von Bautechnik und Festigkeitslehre in Gerstners “Handbuch der Mechanik” – Zum 250. Geburtstag von Franz Joseph Ritter von Gerstner
Authors: Kurrer Karl‐Eugen 
Published: June 2006

AbstractWie kein anderer vor ihm gründete Gerstner in seinem dreibändigen “Handbuch der Mechanik” die Festigkeitslehre auf das Experiment. Hierzu referierte er die klassischen Festigkeitsversuche Musschenbroek s, Rondelet s, Eytelwein s, Rennie s, Telford s, Brown s, Brunel s, Barlow s, Tredgold s, Navier s und Dufour s, die er durch eigene umfangreiche Versuchsserien ergänzte. Letztere gewann er mit von ihm entworfenen Apparaten zur Ermittlung der Zug‐ und Biegefestigkeit. Gerstner s Versuche zur Zugfestigkeit von Schmiedeeisen und Stahl beispielsweise setzten – was zahlenmäßige Genauigkeit, Methode und Anwendungen betrifft – Maßstäbe. So gab er im Rahmen des geplanten Baus einer Kettenbrücke in Prag einen Polynomansatz des Spannungs‐Dehnungs‐Diagramms von Stahl und Schmiedeeisen an, dessen Parameter er experimentell bestimmte. Dabei unterschied Gerstner klar zwischen einem linearen Bereich (“vollkommene Elastizität”) und nichtlinearen Bereich (“unvollkommene Elastizität”) und warnte vor der Überschreitung der Proportionalitätsgrenze insbesondere bei Kettenbrücken. Auch der Biegefestigkeit von Holz‐ und Eisenkonstruktionen räumte er breiten Raum ein.Mit seiner empirisch akzentuierten Festigkeitslehre schuf Gerstner die Grundlagen einer physikalisch begründeten Proportionslehre des Bau‐ und Maschineningenieurs, die historisch‐logisch den Übergang zur Baustatik und der klassischen Bemessungstheorie Navier s bildete. (© 2006 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Science teachers' attempts at integrating feminist pedagogy through collaborative action research
Authors: Capobianco Brenda M. 
Published: June 2006

AbstractThe purpose of this study was to examine the experiences of three science teachers attempting to transform their practice by conducting action research on feminist science teaching. The teachers engaged in systematic, self‐critical inquiry of their own practice and joined 8 other science teachers to engage in collaborative conversations about the nature of science, science teaching, and science education as a way of coming to a better understanding of how science can be taught for a more diverse group of students. Data were gathered via semistructured interviews, whole‐group discussions, classroom observations, and review of supporting documents. Data analysis was based on narrative inquiry, where particular attention was given to the construction and reconstruction of the teachers' stories of their practical inquiries. Results indicated that the teachers as researchers of their own practice gained new knowledge about feminist science teaching and, furthermore, generated a cluster of pedagogical possibilities for inclusive, dynamic science teaching. © 2006 Wiley Periodicals, Inc. J Res Sci Teach
Identification and characterization of calcium and manganese transporting ATPase (PMR1) gene of Pichia pastoris
Authors: Dux Michael P. , Inan Mehmet 
Published: July 2006

AbstractA gene homologous to Saccharomyces cerevisiae PMR1 has been cloned in the methylotrophic yeast Pichia pastoris. The entire P. pastoris PMR1 gene (PpPMR1) codes a protein of 924 amino acids. Sequence analysis of the PpPMR1 cDNA and the genomic DNA revealed that there is no intron in the coding region. The putative gene product contains all of the conserved regions observed in P‐type ATPases and exhibits 66.2%, 60.3% and 50.6% identity to Pichia angusta (Hansenula polymorpha), Saccharomyces cerevisiae PMR1 and human ATP2C1 gene products, respectively. A pmr1 null mutant strain of P. pastoris exhibited growth defects in media with the addition of EGTA, but with supplementation of Ca2+ to a calcium‐deficient media reversed the growth defects of the mutant strain. Manganese reversed the growth defects of the mutant strain; however, the cell growth was not as profound as the Ca2+‐supplemented media. The results demonstrated that the P. pastoris gene encodes the functional homologue of the S. cerevisiae PMR1 gene product, a P‐type Ca2+/Mn2+‐ATPase. The DNA sequence of the P. pastoris PMR1 gene has been submitted to GenBank under Accession No. DQ239958. Copyright © 2006 John Wiley & Sons, Ltd.
Genetic and biochemical characterization of 16 acute intermittent porphyria cases with a high prevalence of the R173W mutation
Authors: To‐Figueras J. , Badenas C. , Carrera C. , Muñoz C. , Milá M. , Lecha M. , Herrero C. 
Published: June 2006

SummaryAcute intermittent porphyria (AIP) is a metabolic disease with a variable prevalence among different countries. In some areas of southern Europe it remains to be fully evaluated. We undertook a genetic and biochemical study of 16 unrelated Spanish AIP patients and relatives. The genetic analyses showed they harboured the following mutations in the porphobilinogen deaminase gene: R173W, G111R, L278P, L238P, R116W, R26C, 340insT, 730delCT, 691del30bp, and IVS14+1g>a. The mutation R173W was found in 6 patients (37.5%), including the only patients of our series with >3 recurrent porphyria attacks. While in clinical remission, all AIP patients exhibited sustained increased excretion of porphyrins and precursors. PBG excretion showed a high between‐subject variation and was not related to erythrocyte PBG deaminase activity. The study of family members allowed the identification of 22 asymptomatic AIP carriers. These included 8 persons harbouring the R173W mutation belonging to four different families. Six of these latent AIP subjects showed increased PBG elimination, and in two the urinary levels were >10‐fold the normal limit. These results reinforce the hypothesis that the R173W mutation may have a high biochemical and clinical penetrance among AIP patients.
Molecular characterization of a germ-cell-specific antigen, TEX101, from mouse testis
Authors: Jin Hong , Yoshitake Hiroshi , Tsukamoto Hiroki , Takahashi Mai , Mori Miki , Takizawa Toshihiro , Takamori Kenji , Ogawa Hideoki , Kinoshita Katsuyuki , Araki Yoshihiko 
Published: July 2006

SummaryTEX101, a glycoprotein we recently identified, is primarily characterized as a unique germ-cell-specific marker protein that shows sexually dimorphic expression during mouse gonad development. Based on data obtained from molecular biological as well as immuno-morphological studies, we believe this molecule may play a role in the process underlying germ cell formation. However, many points remain unclear as the molecular characteristics and its physiological functions are far from being completely understood. To clarify the molecular basis of TEX101, we herein report a further biochemical characterization of the molecule using testicular Triton X-100 extracts from mice. Deglycosylation studies using endoglycohydrolases that deleteN-linked oligosaccharides (OS) from the molecule show that TEX101 is highly (approximately 47%)N-glycosylated. All potentialN-glycosylation sites within TEX101 are glycosylated and most of these sites are occupied by endoglycosidase F2-sensitive biantennary complex type OS units. In addition, an extremely low population among TEX101 possesses only endoglycosidase H-sensitive hybrid type OS units. In studies using phosphatidylinositol-specific phospholipase C against native testicular cells orTEX101transfectant, the enzyme treatment caused major reduction of the TEX101 expression on the cell, suggesting that TEX101, at least in part, is expressed as a glycosylphosphatidylinositol-anchored protein. Taken together, these findings will help elucidate the molecular nature of TEX101, a marker molecule that appeared on germ cells during gametogenesis.
Influence of anthropometric parameters and bone size on bone mineral density using volumetric quantitative computed tomography and dual X-ray absorptiometry at the hip
Authors: Guglielmi G. , van Kuijk C. , Li J. , Meta M. D. , Scillitani A. , Lang T. F. 
Published: June 2006

Purpose: To evaluate the influence of anthropometric parameters (age, height, and weight) and bone size on bone mineral density (BMD) using volumetric quantitative computed tomography (QCT) and dual X-ray absorptiometry (DXA) in a group of elderly women. Material and Methods: BMD values were obtained with DXA and QCT at the spine and hip in a cohort of 84 elderly women (mean age 73±6 years). QCT measures included trabecular, integral, and cortical BMD assessed at the hip and spine as well as cross-sectional areas of the mid-vertebrae and proximal femora. Spinal integral and femoral neck BMD measures were well matched to the regions of bone quantified on anteroposterior (AP) spine DXA and the femoral neck region of hip DXA. Results: When QCT parameters were linearly regressed against body height and weight, only the relationships with weight were found to be statistically significant. Except for cortical BMD at the femoral neck, all BMD and geometric parameters measured from both DXA and QCT showed statistically significant associations with body weight ( r2 = 0.4, 0.0001< P<0.02). The strongest associations with weight were found for DXA Neck (DXA_NECK) and DXA lumbar spine (DXA_LSP) ( r2 = 0.4, P<0.0001). Conclusion: The relationship of DXA BMD is stronger than QCT BMD with body weight and it encompasses the response of both bone size and density to increasing body mass.
Percutaneous vertebroplasty for patients with osteoporosis: a one-year follow-up
Authors: Chang C. -Y. , Teng M. M. -H. , Wei C. -J. , Luo C. -B. , Chang F. -C. 
Published: June 2006

Purpose: To evaluate changes in height and wedge angle of treated vertebral bodies and kyphosis angle 1 year after vertebroplasty. Material and Methods: We reviewed radiographs of 95 vertebral bodies treated with vertebroplasty in 60 patients with osteoporosis. Only vertebral bodies with imaging evidence of a new fracture or avascular necrosis received vertebroplasty. Images were obtained for evaluation before vertebroplasty (B), within 2 weeks after vertebroplasty (T), and after 1 year (T1). Results: The mean wedge angle decreased by 5.4° from B to T1. Mean of the anterior, central, and posterior heights of the fractured bodies increased by 12.6%, 9.6%, and 3.1%, respectively, from B to T1. The kyphosis angle improved by 3.2° initially from B to T, but the improvement later disappeared. In 48% of these patients, a new fracture developed after vertebroplasty, and 63% of the fractures were adjacent to a vertebroplasty-treated vertebral body. Conclusion: The increase in height and wedge angle of the vertebral bodies generally lasted at least 1 year. Improvement in kyphosis angles was lost 1 year after vertebroplasty because new fractures occurred in 48% of these patients. Prevention of new fractures after vertebroplasty remains an important task.
Eicosapentapeptide repeats (EPRs): novel repeat proteins specific to flowering plants
Authors: Archak Sunil , Nagaraju Javaregowda 
Published: June 2006

Abstract
In this report, we describe a novel tandem peptide repeat protein, Eicosapentapeptide repeat (EPR), which occurs notably only in flowering plants. The EPRs are characterized by a 25 amino acid repeat unit, X2CX4CX10CX2HGGG, repeated 10 times tandemly. Sequence search revealed that the repeat motif is highly conserved across its occurrence. EPRs are predicted to exist as quasi-globular stable structures owing to highly conserved amino acid positions and potential disulfide bridges. Proteins containing EPRs are predicted to be located in chloroplasts; non-enzymatic and peptide or DNA-binding in molecular function; and they are possibly involved in transcription regulation.
Contact: jnagaraju@cdfd.org.in
Supplementary information: Architecture, identifiers and annotations of EPRs; search parameters, distribution and sequence alignment; 2D structure prediction and disulfide connectivity are provided as pdf files S1–S8, at Bioinformatics online.
GEL: a novel genotype calling algorithm using empirical likelihood
Authors: Nicolae Dan L. , Wu Xiaolin , Miyake Kazuaki , Cox Nancy J. 
Published: June 2006

Abstract
Motivation: Preliminary results on the data produced using the Affymetrix large-scale genotyping platforms show that it is necessary to construct improved genotype calling algorithms. There is evidence that some of the existing algorithms lead to an increased error rate in heterozygous genotypes, and a disproportionately large rate of heterozygotes with missing genotypes. Non-random errors and missing data can lead to an increase in the number of false discoveries in genetic association studies. Therefore, the factors that need to be evaluated in assessing the performance of an algorithm are the missing data (call) and error rates, but also the heterozygous proportions in missing data and errors.
Results: We introduce a novel genotype calling algorithm (GEL) for the Affymetrix GeneChip arrays. The algorithm uses likelihood calculations that are based on distributions inferred from the observed data. A key ingredient in accurate genotype calling is weighting the information that comes from each probe quartet according to the quality/reliability of the data in the quartet, and prior information on the performance of the quartet.
Availability: The GEL software is implemented in R and is available by request from the corresponding author at nicolae@galton.uchicago.edu
Contact: nicolae@galton.uchicago.edu
Parallel multifactor dimensionality reduction: a tool for the large-scale analysis of gene–gene interactions
Authors: Bush William S. , Dudek Scott M. , Ritchie Marylyn D. 
Published: June 2006

Abstract
Summary: Parallel multifactor dimensionality reduction is a tool for large-scale analysis of gene–gene and gene–environment interactions. The MDR algorithm was redesigned to allow an unlimited number of study subjects, total variables and variable states, and to remove restrictions on the order of interactions being analyzed. In addition, the algorithm is markedly more efficient, with ∼150-fold decrease in runtime for equivalent analyses. To facilitate the processing of large datasets, the algorithm was made parallel.
Availability: Parallel MDR is freely available for non-commercial research institutions. For full details see . An open-source version of MDR software is available at .
Contact: ritchie@chgr.mc.vanderbilt.edu
MAGOS: multiple alignment and modelling server
Authors: Garnier N. , Friedrich A. , Bolze R. , Bettler E. , Moulinier L. , Geourjon C. , Thompson J. D. , Deléage G. , Poch O. 
Published: July 2006

Abstract
Summary: MAGOS is a web server allowing automated protein modelling coupled to the creation of a hierarchical and annotated multiple alignment of complete sequences. MAGOS is designed for an interactive approach of structural information within the framework of the evolutionary relevance of mined and predicted sequence information.
Availability: The web server is freely available at
Supplementary information: The website supplies detailed explanations and illustrations of processes and results at
Contact: e.bettler@ibcp.fr
C3H/HeJ Mouse Model for Spontaneous Chronic Otitis Media
Authors: MacArthur Carol J. , Hefeneider Steven H. , Kempton J Beth , Trune Dennis R. 
Published: July 2006

AbstractObjectives/Hypothesis: Chronic otitis media is a significant clinical problem. Understanding the mechanisms of chronic otitis media is critical for its control. However, little is known of these processes as a result of lack of animal models of spontaneous otitis media. The C3H/HeJ mouse has a single amino acid substitution in its toll‐like receptor 4 (TLR4), making it insensitive to endotoxin. As a result, these mice cannot clear Gram‐negative bacteria. The chronically inflamed middle ear in this animal provides us the opportunity to study spontaneous chronic otitis media.Study Design and Methods: Otoscopy and auditory brain response (ABR) evaluation of C3H/HeJ mice at 3, 5, 7, 9, and 11 months were carried out under sedation. At 12 months of age, mice were killed and histologic analysis of the middle ear, inner ear, and eustachian tube was carried out.Results: Tympanic membrane visualization and ABR thresholds in 7‐ to 8‐month‐old C3H/HeJ mice showed that approximately half developed middle and inner ear disease spontaneously. The significant elevation of thresholds suggested a sensorineural component in addition to the conductive loss. Middle and inner ear histology showed some degree of middle and inner ear inflammation in half the mice, paralleling the ABR data.Conclusions: The histopathologic changes reported here in the C3H/HeJ mouse model of chronic otitis media have been reported in human chronic otitis media. This spontaneous model of chronic otitis media will be valuable for the characterization of middle and inner ear inflammatory disease processes that are induced by middle ear infections.
Studying and evaluating anti‐corrosion coatings and inhibitors using the wire beam electrode method in conjunction with electrochemical noise analysis
Authors: Tan Yong‐Jun , Wang Ting , Liu Tie , Aung Naing‐Naing 
Published: June 2006

PurposeTo provide a summary of research work carried out mainly in the authors' group for evaluating various protective coatings including rustproofing oils, and also for studying corrosion inhibitors using the wire beam electrode (WBE) method.Design/methodology/approachA range of published papers published during the past 15 years was summarised and reviewed. Recent research work in the authors' group was also included, which involved the combined use of the WBE with electrochemical noise analysis and the scanning reference electrode technique.FindingsThe WBE method has been developed into a very useful tool of evaluating the performance of coatings and inhibitors. In particular, The WBE is uniquely applicable for determining the performance of coatings and inhibitors to control localised corrosion.Research limitations/implicationsFocusing mainly on recent research.Practical implicationsA useful source of information for researchers and graduate students working in the areas of organic coating and inhibitor research.Originality/valueThe first summary or review on this research topic.
Effect of modified packaging and storage time of cocoa pods on the commercial quality of cocoa beans
Authors: Aroyeun S.O. , Ogunbayo J.O. , Olaiya A.O. 
Published: June 2006

PurposeLack of good post‐harvest storage of cocoa pods has been responsible for the low commercial quality of cocoa beans. This study aims to evaluate the effect of modified packaging and storage time of cocoa pods on the corresponding commercial qualities of cocoa beans.Design/methodology/approachPreweighed cocoa pods obtained from the experimental station of the Cocoa Research Institute of Nigeria, Ibadan, Nigeria were stored under three modified packaging conditions, namely: black non transparent polythene film (BNTPEF), transparent polythene film (TPEF) and NA(normal atmosphere environment).FindingsThe study found that there was a rise in the mean temperatures of samples in all the storage environments up to the 12th day of storage, after which the mean temperature declined until the end of the storage period. Cocoa butter fat, bean weights, severity of decay and mould growths depended on the type of packaging and storage time.Originality/valueAtp<0.05 the use of modified packaging of cocoa pods significantly affects the commercial values of the beans. The best of these qualities was conserved in the TPEF.