bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of spacing between the exfoliated clay platelets on the crystallization behavior of polyamide‐6 in polyamide‐6/clay nanocomposites
Authors: Li Yongjin , Shimizu Hiroshi 
Published: November 2005

AbstractExfoliated polyamide‐6 (PA6)/organoclay nanocomposite films with planar‐oriented clay platelets were prepared by the simple hot pressing of melt‐extruded nanocomposite pellets. The average distance between the neighboring clay platelets was controlled by changes in the clay loading content in the nanocomposites. The effects of the clay platelet spacing on the crystallization behavior of PA6 were investigated with transmission electron microscopy and wide‐angle X‐ray diffraction. The crystal lamellae were found to be mainly perpendicular to the clay surface for the nanocomposites with large spacing between the clay sheets at low clay loading contents. This perpendicular orientation morphology was attributed to the strong interactions between the PA6 molecular chain and the clay surface. In contrast, the crystal lamellae were found to be parallel to the clay surface when the spacing between the neighboring clay platelets was less than 30 nm. It was concluded that the confinement crystallization of PA6 within the nanoscale channels formed by clay sheets resulted in this parallel orientation texture. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 284–290, 2006
Signals, receptors, and cytokines involved in the immunomodulatory and anti‐inflammatory properties of apoptotic cells
Authors: Fürnrohr Barbara G. , Sheriff Ahmed , Munoz Luis , von Briesen Hagen , Urbonaviciute Vilma , Neubert Kirsten , Kalden Joachim R. , Herrmann Martin , Voll Reinhard E. 
Published: November 2005

AbstractCell death can occur controlled by apoptosis or rather uncontrolled by necrosis. The decision to initiate an inflammatory response has to be made for dying cells, which arise by hundreds of billions each day. They carry valuable information with respect to the possible influence of pathogens. Apoptosis and the swift phagocytosis of dying cells by macrophages and neighboring tissue cells act together to remove supernumerary, dangerous, or damaged cells. Apoptosis, in contrast to necrosis, normally does not induce inflammation or organ damage. Apoptotic cells maintain their membrane integrity for a relatively long time, thereby preventing the release of tissue damaging contents and proinflammatory mediators. In addition, early recognition and efficient, non‐inflammatory removal of the apoptotic cells essentially contribute to preventing an inflammatory response and organ damage. Furthermore, apoptotic cells can even actively suppress inflammation and modulate immune responses by inhibiting the release of proinflammatory cytokines but augmenting the secretion of anti‐inflammatory and immunomodulatory cytokines from monocytes/macrophages (MoMa) and dendritic cells. The anti‐inflammatory effect of apoptotic cells is mediated by the thrombospondin receptor (CD36) on MoMa and, most likely, other surface receptors, which are not yet molecularly identified. Elevation of intracellular cAMP levels seems to be critically involved in the induction of the anti‐inflammatory state in MoMa.These findings have important implications for clinical medicine. On the one hand side, exposure to high amounts of apoptotic cells in conditions such as cancer or certain viral infections may result in clinically relevant immunosuppression. On the other hand side, therapeutic induction of apoptosis can ameliorate inflammatory diseases. Furthermore, pathogens can misuse apoptotic cells as ‘Trojan horses’ to silently infect and paralyze macrophages. We point out that several pathogens such as HIV, Plasmodium falciparum, Trypanosoma cruzi and Leishmania major mimic apoptotic cells for silent entry and immune escape.Albeit apoptotic cells exert immunosuppressive effects, the impaired clearance of dead cells causes the release of potential autoantigens and, thereby, fosters autoimmunity. At least in a subgroup of patients with systemic lupus erythematosus impaired phagocytosis of dead cells by macrophages has been observed and may contribute to the etiopathogenesis of this autoimmune disorder.
Cloning and Characterization of an Agglutinin Gene from Arisaema lobatum
Authors: Lin Juan , Zhou Xuanwei , Pang Yongzhen , Gao Han , Fei Jiong , Shen Guo-an , Wang Jin , Li Xinsheng , Sun Xiaofen , Tang Kexuan 
Published: November 2005

A novel agglutinin gene was cloned from Arisaema lobatum using SMART RACE-PCR technology. The full-length cDNA of Arisaema lobatum agglutinin (ala) was 1078 bp and contained a 774 bp open reading frame encoding a lectin precursor (proproprotein) of 258 amino acid residues with a 23 aa signal peptide. ALA contained three mannose-binding sites (QXDXNXVXY) with two-conserved domains of 45% identity, ALA-DOM1 and ALA-DOM2. The three-dimensional structure of ALA was very similar to that of GNA (Galanthus nivalis agglutinin). ALA shared varying identities, ranging from 40% to 85%, with mannose-binding lectins from other species of plant families, such as Araceae, Alliaceae, Iridaceae, Lillaceae, Amaryllidaceae and Bromeliaceae. Genomic sequence of ala was also cloned using genomic walker technology, and it was found to contain three putative TATA boxes and eight possible CAAT boxes in the 5′-flanking region. No intron was found within the region of genomic sequence. Southern blot analysis indicated that the ala belonged to a multi-copy gene family. Expression pattern analysis revealed that the ala preferentially expressed in the tissues with the higher expression being found in spadix, bud, leaf, spathe and tuber. The cloning of the ala gene not only provides a basis for further investigation of its structure, expression and regulation mechanism, but also enables us to test its potential role in controlling pests and fungal diseases by transferring the gene into plants in the future.
Relationship between cytokines and tumour markers in patients with chronic heart failure
Authors: Kosar Feridun , Aksoy Yuksel , Ozguntekin Gulacan , Ozerol Ibrahim , Varol Ercan 
Published: November 2005

AbstractAims:Serum levels of some cytokines and tumour markers are elevated in patients with chronic heart failure (HF). We aimed to investigate the relationship between circulating levels of cytokines and tumour markers in patients with HF.Methods:We included 35 HF patients and 33 normal controls. HF patients were divided into two groups: mild HF (NYHA class I/II) (n=10) and severe HF (NYHA class III/IV) (n=25). Serum cytokine levels (TNF‐α, IL‐1 ß, IL‐6, and IL‐10) were measured by ELISA and tumour markers (CA 125, CA 19–9, CA 15–3, CEA and AFP) by chemiluminescent enzyme immunoassay.Results:Serum levels of TNF‐α, IL‐6, and IL‐10 as cytokines, and CA 125 and CA 19–9 as tumour markers were significantly higher in HF patients than in normal controls (p<0.0001 for all). Serum levels of TNF‐α, IL‐6 and IL‐10 and CA 125 in the severe HF patients were significantly higher than in the mild HF patients (p<0.001 for all). Correlation analysis showed that CA 125 was positively related to TNF‐α (r=0.624, p<0.001), IL‐6 (r=0.671, p<0.001), and IL‐10 (r=0.545, p<0.001) in HF.Conclusion:These findings show that CA 125 is markedly elevated in patients with HF, and correlates with serum TNF‐α, IL‐6 and IL‐10 levels. Therefore, we speculate that among the tumour markers studied, only CA 125 is closely related to the cytokine system.
Psychotic-like experiences in the general community: the correlates of CIDI psychosis screen items in an Australian sample
Authors: SCOTT JAMES , CHANT DAVID , ANDREWS GAVIN , McGRATH JOHN 
Published: November 2005

Background. Apart from individuals with clinical psychosis, community surveys have shown that many otherwise well individuals endorse items designed to identify psychosis. The aim of this study was to characterize the demographic correlates of individuals who endorse psychosis screening items in a large general community sample.Method. The National Survey of Mental Health and Wellbeing interviewed 10641 individuals living in private dwellings in Australia. As part of a diagnostic interview (the CIDI), respondents were asked between three and six items originally designed to screen for potential psychosis. We examined the impact of selected demographic variables on endorsement of these items including sex, age, marital status, migrant status, urban/rural status, employment, education, and socio-economic status.Results. An estimated 11·7% of the Australian population endorsed at least one psychosis-screening item. Significantly higher endorsement was associated with younger age, migrants from non-English-speaking backgrounds, those who had never married or who were divorced/separated or unemployed, those living in urban regions and those from the lowest socio-economic levels.Conclusions. Many of the correlates of endorsement of psychosis-screen items are also associated with psychosis. Unravelling the factors that contribute to this broader non-clinical phenotype will aid our understanding of psychosis.
AN INTERVIEW WITH ROBERT AUMANN
Authors: Hart Sergiu 
Published: November 2005

Who is Robert Aumann? Is he an economist or a mathematician? A rational scientist or a deeply religious man? A deep thinker or an easygoing person?These seemingly disparate qualities can all be found in Aumann; all are essential facets of his personality. A pure mathematician who is a renowned economist, he has been a central figure in developing game theory and establishing its key role in modern economics. He has shaped the field through his fundamental and pioneering work, work that is conceptually profound, and much of it also mathematically deep. He has greatly influenced and inspired many people: his students, collaborators, colleagues, and anyone who has been excited by reading his papers or listening to his talks.Aumann promotes a unified view of rational behavior, in many different disciplines: chiefly economics, but also political science, biology, computer science, and more. He has broken new ground in many areas, the most notable being perfect competition, repeated games, correlated equilibrium, interactive knowledge and rationality, and coalitions and cooperation.But Aumann is not just a theoretical scholar, closed in his ivory tower. He is interested in real-life phenomena and issues, to which he applies insights from his research. He is a devoutly religious man; and he is one of the founding fathers—and a central and most active member—of the multidisciplinary Center for the Study of Rationality at the Hebrew University in Jerusalem.Aumann enjoys skiing, mountain climbing, and cooking—no less than working out a complex economic question or proving a deep theorem. He is a family man, a very warm and gracious person—of an extremely subtle and sharp mind.This interview catches a few glimpses of Robert Aumann's fascinating world. It was held in Jerusalem on three consecutive days in September 2004. I hope the reader will learn from it and enjoy it as much as we two did.
Within-host evolution of CD8+-TL epitopes encoded by overlapping and non-overlapping reading frames of simian immunodeficiency virus
Authors: Hughes Austin L. , Piontkivska Helen , Krebs Kendall C. , O'Connor David H. , Watkins David I. 
Published: November 2005

Abstract
Summary: In order to understand the impact of overlapping reading frames on natural selection by host CD8+ T lymphocytes (CD8+-TL), we analyzed the pattern of nucleotide substitution in simian immunodeficiency virus (SIV) genomes sampled from populations at time of death in 35 rhesus monkeys. Both the mean number of nonsynonymous nucleotide substitutions per nonsynonymous site (dN) and the mean number of synonymous nucleotide substitutions per synonymous site (dS) were elevated in overlap regions in comparison to non-overlap regions. Mean dN exceeded mean dS in CD8+-TL epitopes restricted by the host's class I major histocompatibility complex molecules. This pattern, which is indicative of positive Darwinian selection favoring amino acid changes in these epitopes, was seen in both overlap and non-overlap regions; but mean dN was particularly elevated in restricted CD8+-TL epitopes encoded in overlap regions. Amino acid changes from the inoculum were defined as parallel if the same amino acid change occurred at the same site independently in two or more monkeys, and a surprisingly high proportion (71.9%) of observed amino acid changes throughout the SIV genome occurred in parallel in different monkeys. The proportion of parallel changes in restricted epitopes encoded by overlapping reading frames was still higher (80%), supporting the hypothesis that the interaction of positive selection and overlapping reading frames enhances the probability of convergent or parallel amino acid change.
Contact: austin@biol.sc.edu
Four-helix bundle: a ubiquitous sensory module in prokaryotic signal transduction
Authors: Ulrich Luke E. , Zhulin Igor B. 
Published: November 2005

Abstract
Motivation: Transmembrane chemoreceptors in Escherichia coli utilize ligand-binding domains for detecting various external signals. The structure of this domain in the E.coli aspartate receptor, Tar, is known and its signal transduction mechanism is under investigation. Current domain models for this important sensory module are inaccurate and, therefore, cannot reveal the distribution of this domain within the current genomic landscape.
Results: We carried out sensitive and exhaustive PSI-BLAST searches initiated with the sequence corresponding to a known structure of the four-helix, ligand-binding domain of the aspartate chemoreceptor. From the resulting sequences, we built a multiple sequence alignment for this domain family, which confirmed that the current TarH model is erroneous and fails to detect most of the domain homologs. In the process, we developed a technique that visualizes the secondary structure prediction of each protein sequence in order to improve the multiple sequence alignment. We found that the four-helix up-and-down bundle represents a large domain family and includes representatives of all major classes of prokaryotic signal transduction, namely histidine kinases, di-guanylate cyclases and chemotaxis receptors.
Contact: gtg209d@mail.gatech.edu
Supplementary Information: Supplementary data are available on Bioinformatics online.
Incorporation of splice site probability models for non-canonical introns improves gene structure prediction in plants
Authors: Sparks Michael E. , Brendel Volker 
Published: November 2005

Abstract
Motivation: The vast majority of introns in protein-coding genes of higher eukaryotes have a GT dinucleotide at their 5′-terminus and an AG dinucleotide at their 3′ end. About 1–2% of introns are non-canonical, with the most abundant subtype of non-canonical introns being characterized by GC and AG dinucleotides at their 5′- and 3′-termini, respectively. Most current gene prediction software, whether based on ab initio or spliced alignment approaches, does not include explicit models for non-canonical introns or may exclude their prediction altogether. With present amounts of genome and transcript data, it is now possible to apply statistical methodology to non-canonical splice site prediction. We pursued one such approach and describe the training and implementation of GC-donor splice site models for Arabidopsis and rice, with the goal of exploring whether specific modeling of non-canonical introns can enhance gene structure prediction accuracy.
Results: Our results indicate that the incorporation of non-canonical splice site models yields dramatic improvements in annotating genes containing GC–AG and AT–AC non-canonical introns. Comparison of models shows differences between monocot and dicot species, but also suggests GC intron-specific biases independent of taxonomic clade. We also present evidence that GC–AG introns occur preferentially in genes with atypically high exon counts.
Availability: Source code for the updated versions of GeneSeqer and SplicePredictor (distributed with the GeneSeqer code) isavailable at . Web servers for Arabidopsis, rice and other plant species are accessible at , and , respectively. A SplicePredictor web server is available at . Software to generate training data and parameterizations for Bayesian splice site models is available at
Contact: vbrendel@iastate.edu
Supporting information:
Maximum significance clustering of oligonucleotide microarrays
Authors: de Ridder Dick , Staal Frank J. T. , van Dongen Jacques J. M. , Reinders Marcel J. T. 
Published: November 2005

Abstract
Motivation: Affymetrix high-density oligonucleotide microarrays measure the expression of DNA transcripts using probesets, i.e. multiple probes per transcript. Usually, these multiple measurements are transformed into a single probeset expression level before data analysis proceeds; any information on variability is lost. In this paper we demonstrate how individual probe measurements can be used in a statistic for differential expression. Furthermore, we show how this statistic can serve as a criterion for clustering microarrays.
Results: A novel clustering algorithm using this maximum significance criterion is demonstrated to be more efficient with the measured data than competing techniques for dealing with repeated measurements, especially when the sample size is small.
Availability: MATLAb source code can be found at
Contact: D.deRidder@ewi.tudelft.nl
Detecting periodic patterns in unevenly spaced gene expression time series using Lomb–Scargle periodograms
Authors: Glynn Earl F. , Chen Jie , Mushegian Arcady R. 
Published: November 2005

AbstractMotivation: Periodic patterns in time series resulting from biological experiments are of great interest. The commonly used Fast Fourier Transform (FFT) algorithm is applicable only when data are evenly spaced and when no values are missing, which is not always the case in high-throughput measurements. The choice of statistic to evaluate the significance of the periodic patterns for unevenly spaced gene expression time series has not been well substantiated.Methods: The Lomb–Scargle periodogram approach is used to search time series of gene expression to quantify the periodic behavior of every gene represented on the DNA array. The Lomb–Scargle periodogram analysis provides a direct method to treat missing values and unevenly spaced time points. We propose the combination of a Lomb–Scargle test statistic for periodicity and a multiple hypothesis testing procedure with controlled false discovery rate to detect significant periodic gene expression patterns.Results: We analyzed the Plasmodium falciparum gene expression dataset. In the Quality Control Dataset of 5080 expression patterns, we found 4112 periodic probes. In addition, we identified 243 probes with periodic expression in the Complete Dataset, which could not be examined in the original study by the FFT analysis due to an excessive number of missing values. While most periodic genes had a period of 48 h, some had a period close to 24 h. Our approach should be applicable for detection and quantification of periodic patterns in any unevenly spaced gene expression time-series data.Availability: The computations were performed in R. The R code is available fromContact: chenj@umkc.eduSupplementary information: The online supplement is available at
Statistical estimation of gene expression using multiple laser scans of microarrays
Authors: Khondoker Mizanur R. , Glasbey Chris A. , Worton Bruce J. 
Published: November 2005

Abstract
Summary: We propose a statistical model for estimating gene expression using data from multiple laser scans at different settings of hybridized microarrays. A functional regression model is used, based on a non-linear relationship with both additive and multiplicative error terms. The function is derived as the expected value of a pixel, given that values are censored at 65 535, the maximum detectable intensity for double precision scanning software. Maximum likelihood estimation based on a Cauchy distribution is used to fit the model, which is able to estimate gene expressions taking account of outliers and the systematic bias caused by signal censoring of highly expressed genes. We have applied the method to experimental data. Simulation studies suggest that the model can estimate the true gene expression with negligible bias.
Availability: FORTRAN 90 code for implementing the method can be obtained from the authors.
Contact: mizanur@bioss.ac.uk
A bi-dimensional regression tree approach to the modeling of gene expression regulation
Authors: Ruan Jianhua , Zhang Weixiong 
Published: November 2005

Abstract
Motivation: The transcriptional regulation of a gene depends on the binding of cis-regulatory elements on its promoter to some transcription factors and the expression levels of the transcription factors. Most existing approaches to studying transcriptional regulation model these dependencies separately, i.e. either from promoters to gene expression or from the expression levels of transcription factors to the expression levels of genes. Little effort has been devoted to a single model for integrating both dependencies.
Results: We propose a novel method to model gene expression using both promoter sequences and the expression levels of putative regulators. The proposed method, called bi-dimensional regression tree (BDTree), extends a multivariate regression tree approach by applying it simultaneously to both genes and conditions of an expression matrix. The method produces hypotheses about the condition-specific binding motifs and regulators for each gene. As a side-product, the method also partitions the expression matrix into small submatrices in a way similar to bi-clustering. We propose and compare several splitting functions for building the tree. When applied to two microarray datasets of the yeast Saccharomyces cerevisiae, BDTree successfully identifies most motifs and regulators that are known to regulate the biological processes underlying the datasets. Comparing with an existing algorithm, BDTree provides a higher prediction accuracy in cross-validations.
Availability: The software is available upon request from the authors.
Contact: zhang@cse.wustl.edu
Supplementary information:
REDfly: a Regulatory Element Database for Drosophila
Authors: Gallo Steven M. , Li Long , Hu Zihua , Halfon Marc S. 
Published: November 2005

Abstract
Summary: Bioinformatics studies of transcriptional regulation in the metazoa are significantly hindered by the absence of readily available data on large numbers of transcriptional cis-regulatory modules (CRMs). Even the richly annotated Drosophila melanogaster genome lacks extensive CRM information. We therefore present here a database of Drosophila CRMs curated from the literature complete with both DNA sequence and a searchable description of the gene expression pattern regulated by each CRM. This resource should greatly facilitate the development of computational approaches to CRM discovery as well as bioinformatics analyses of regulatory sequence properties and evolution.
Availability:
Contact: mshalfon@buffalo.edu