bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic and gene expression changes related to transgenerational carcinogenesis
Authors: Cheng Robert Y‐S. , Hockman Tyler , Crawford Erik , Anderson Lucy M. , Shiao Yih‐Horng 
Published: April 2004

AbstractTransgenerational carcinogenesis refers to transmission of cancer risk to the untreated progeny of parents exposed to carcinogens before mating. Accumulated evidence suggests that the mechanism of this process is epigenetic, and might involve hormonal and gene expression changes in offspring. To begin to test this hypothesis, we utilized a mouse model (NIH Swiss) in which exposure of fathers to Cr(III) chloride 2 wk before mating can alter incidence of neoplastic and nonneoplastic changes in offspring tissues. Utilizing a MS‐RDA approach, we found that the sperm of these fathers had a significantly higher percentage of undermethylated copies of the 45S ribosomal RNA gene (rRNA); this finding was confirmed by bisulfite sequencing. Because gene methylation is a known mechanism of expression control in germ cells, and ribosomal RNA levels have been linked to cancer, these findings are consistent with the hypothesis. Secondly, we observed that offspring of Cr(III)‐treated fathers were significantly heavier than controls, and had higher levels of serum T3. Possible effects of T3 levels on gene expression in the offspring were examined by microarray analysis of cDNAs from liver. A total of 58 genes, including 25 named genes, had expression ratios that correlated significantly with serum T3 ratios at P ≤ 0.001. Some of these genes have potential roles in growth and/or tumor suppression. These results also support the hypothesis of an epigenetic and/or gene expression–based mechanism for transgenerational carcinogenesis. Published 2004 Wiley‐Liss, Inc.
Highly informative proteome analysis by combining improved N‐terminal sulfonation for de novo peptide sequencing and online capillary reverse‐phase liquid chromatography/tandem mass spectrometry
Authors: Lee Yong Ho , Kim Min‐Sik , Choie Woo‐Suk , Min Hye‐Ki , Lee Sang‐Won 
Published: April 2004

AbstractRecently, various chemical modifications of peptides have been incorporated into mass spectrometric analyses of proteome samples, predominantly in conjunction with matrix‐assisted laser desorption/ionization mass spectrometry (MALDI MS), to facilitate de novo sequencing of peptides. In this work, we investigate systematically the utility of N‐terminal sulfonation of tryptic peptides by 4‐sulfophenyl isothiocyanate (SPITC) for proteome analysis by capillary reverse‐phase liquid chromatography/tandem mass spectrometry (cRPLC/MS/MS). The experimental conditions for the sulfonation were carefully adjusted so that SPITC reacts selectively with the N‐terminal amino groups, even in the presence of the ϵ‐amino groups of lysine residues. Mass spectrometric analyses of the modified peptides by cRPLC/MS/MS indicated that SPITC derivatization proceeded toward near completion under the experimental conditions employed here. The SPITC‐derivatized peptides underwent facile fragmentation, predominantly resulting in y‐series ions in the MS/MS spectra. Combining SPITC derivatization and cRPLC/MS/MS analyses facilitated the acquisition of sequence information for lysine‐terminated tryptic peptides as well as arginine‐terminated peptides without the need for additional peptide pretreatment, such as guanidination of lysine amino group. This process alleviated the biased detection of arginine‐terminated peptides that is often observed in MALDI MS experiments. We will discuss the utility of the technique as a viable method for proteome analyses and present examples of its application in analyzing samples having different levels of complexity.
The Phosphorylation Site Database: A guide to the serine‐, threonine‐, and/or tyrosine‐phosphorylated proteins in prokaryotic organisms
Authors: Wurgler‐Murphy Susannah M. , King Douglas M. , Kennelly Peter J. 
Published: April 2004

AbstractThe Phosphorylation Site Database [http://vigen.biochem.vt.edu/xpd/xpd.htm] provides ready access to information from the primary scientific literature concerning those proteins from prokaryotic organisms, i.e., the members of the domains Archaea and Bacteria, that have been reported to undergo covalent phosphorylation on the hydroxyl side chains of serine, threonine, and/or tyrosine residues. Where known, the sequence of the site(s) of phosphorylation and the functional consequences of phosphorylation also are included. Active links enable users to quickly access further information concerning the phosphoprotein of interest from PubMed, GenBank, SWISS‐PROT, and PIR.
On the hyperfine and magnetic properties of the alloy system Fe3−xMnxSi
Authors: Mahmood S. H. , Lehlooh A.‐F. , Saleh A. S. , Wagner F. E. 
Published: April 2004

AbstractThe results of a comprehensive Mössbauer study of the alloy system Fe3−xMnxSi are reported. The study covers a wide range of temperatures (4.2 K to 300 K), and a wide range of concentrations between x = 0 and x = 2.5. Alloys with x < 0.75 show ferromagnetic behavior up to RT, and the spectra were fitted with several sextets indicating several configurations around the Fe atoms at B and A, C sites. Alloys with x > 1.5 show antiferromagnetic ordering, and those with x > 2.0 develop new non‐cubic phases. In the concentration region 1.0 < x < 1.5 the alloys exhibit a complex magnetic behavior. Thus, the alloys were studied over a wide temperature range where transition from ferromagnetic ordering to paramagnetic phase is observed. The Curie Temperature (Tc) for the alloys in this concentration range is found to drop down sharply as x increases. The subspectrum characteristic of the B site disappears at x ∼ 1.3, indicating that the B site is completely filled with Mn at this concentration. (© 2004 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Numerical computation of cross‐coupled algebraic Riccati equations related toH2/H∞control problem for singularly perturbed systems
Authors: Mukaidani Hiroaki , Shimomura Tetsu , Xu Hua 
Published: April 2004

AbstractIn this paper, we present a numerical algorithm to the cross‐coupled algebraic Riccati equations(CARE) related toH2/H∞control problems for singularly perturbed systems (SPS) by means of Newton's method. The resulting algorithm can be widely used to solve Nash game problems and robust control problems because the CARE is solvable even if the quadratic term has an indefinite sign. We prove that the resulting iterative algorithm has the property of the quadratic convergence. Using the solution of the CARE, we construct the high‐order approximateH2/H∞controller. Copyright © 2004 John Wiley & Sons, Ltd.
On‐line estimation and path planning for multiple vehicles in an uncertain environment
Authors: Ousingsawat Jarurat , Campbell Mark E. 
Published: April 2004

AbstractA unified approach to cooperative target tracking and path planning for multiple vehicles is presented. All vehicles, friendly and adversarial, are assumed to be aircraft. Unlike the typical target tracking problem that uses the linear state and nonlinear output dynamics, a set of aircraft nonlinear dynamics is used in this work. Target state information is estimated in order to integrate into a path planning framework. The objective is to fly from a start point to a goal in a highly dynamic, uncertain environment with multiple friendly and adversarial vehicles, without collision. The estimation architecture proposed is consistent with most path planning methods. Here, the path planning approach is based on evolutionary computation technique which is then combined with a nonlinear extended set membership filter in order to demonstrate a unified approach. A cooperative estimation approach among friendly vehicles is shown to improve speed and routing of the path. Copyright © 2004 John Wiley & Sons, Ltd.
Synthese und Eigenschaften von Sr3Mo1.5Zn0.5O7‐δ, einer Phase mit perowskitverwandter Schichtstruktur
Authors: Steiner Udo , Reichelt Werner , Schmidt Marcus , Schnelle Walter 
Published: April 2004

AbstractDie neue Schicht‐Perowskit‐Phase Sr3Mo1.5Zn0.5O7‐δ wurde durch Festkörperreaktion unter Verwendung eines Zn/ZnO‐Sauerstoffpuffers dargestellt. Die Verfeinerung der Kristallstruktur erfolgte an Pulver‐Röntgenbeugungsdaten mit der Rietveld‐Methode. Die Verbindung kristallisiert tetragonal in der Raumgruppe I4/mmm (Nr. 139) mit den Gitterkonstanten a = 3.9631(3) Å, c = 20.583(1) Å. Das gemessene Sauerstoffdefizit δ ≈ 0.25 weist auf Vorliegen von gemischtvalentem Molybdän (Mo4+, Mo6+) hin.
Enteric P2X receptors as potential targets for drug treatment of the irritable bowel syndrome
Authors: Galligan James J 
Published: April 2004

The irritable bowel syndrome (IBS) is a gastrointestinal motility disorder affecting millions of patients. IBS symptoms include diarrhea, constipation and pain. The etiology of IBS is due partly to changes in the function of nerves supplying the gastrointestinal tract, immune system activation and to psychological factors. P2X receptors are multimeric ATP‐gated cation channels expressed by neuronal and non‐neuronal cells. Sensory nerve endings in the gastrointestinal tract express P2X receptors. ATP released from gastrointestinal cells activates P2X receptors on sensory nerve endings to stimulate motor reflexes and to transmit nociceptive signals. Antagonists acting at P2X receptors on sensory nerves could attenuate abdominal pain in IBS patients. Primary afferent neurons intrinsic to the gut, and enteric motor‐ and interneurons express P2X receptors. These neurons participate in motor reflexes. Agonists acting at enteric P2X receptors may enhance gastrointestinal propulsion and secretion, and these drugs could be useful for treating constipation‐predominant IBS. Antagonists acting at enteric P2X receptors would decrease propulsion and secretion and they might be useful for treating diarrhea‐predominant IBS. Current knowledge of P2X receptor distribution and function in the gut of laboratory animals provides a rational basis for further exploration of the therapeutic potential for drugs acting at P2X receptors in IBS patients. However, more information about P2X receptor distribution and function in the human gastrointestinal tract is needed. Data on the distribution and function of P2X receptors on gastrointestinal immune cells would also provide insights into the therapeutic potential of P2X receptor agents in IBS.British Journal of Pharmacology (2004) 141, 1294–1302. doi:10.1038/sj.bjp.0705761
An online database for the detection of novel archaeal sequences in human ESTs
Authors: Saunders Neil F. W. , Curmi Paul M. G. , Cavicchioli Ricardo 
Published: April 2004

Abstract
Summary: We have developed a rapid, automated screening system and online database to detect foreign sequences of archaeal origin in human expressed sequence tags. The aim of the screening is to detect transcripts that may be derived from novel, putative archaeal pathogens or symbionts.
Availability: http://psychro.bioinformatics.unsw.edu.au/pathogen/index.php
Supplementary information: http://psychro.bioinformatics.unsw.edu.au/pathogen/about.php
Metabolite fingerprinting: detecting biological features by independent component analysis
Authors: Scholz M. , Gatzek S. , Sterling A. , Fiehn O. , Selbig J. 
Published: April 2004

Abstract
Motivation: Metabolite fingerprinting is a technology for providing information from spectra of total compositions of metabolites. Here, spectra acquisitions by microchip-based nanoflow-direct-infusion QTOF mass spectrometry, a simple and high throughput technique, is tested for its informative power. As a simple test case we are using Arabidopsis thaliana crosses. The question is how metabolite fingerprinting reflects the biological background. In many applications the classical principal component analysis (PCA) is used for detecting relevant information. Here a modern alternative is introduced—the independent component analysis (ICA). Due to its independence condition, ICA is more suitable for our questions than PCA. However, ICA has not been developed for a small number of high-dimensional samples, therefore a strategy is needed to overcome this limitation.
Results: To apply ICA successfully it is essential first to reduce the high dimension of the dataset, by using PCA. The number of principal components determines the quality of ICA significantly, therefore we propose a criterion for estimating the optimal dimension automatically. The kurtosis measure is used to order the extracted components to our interest. Applied to our A. thaliana data, ICA detects three relevant factors, two biological and one technical, and clearly outperforms the PCA.
Stabilization of discordant helices in amyloid fibril‐forming proteins
Authors: Päiviö Anna , Nordling Erik , Kallberg Yvonne , Thyberg Johan , Johansson Jan 
Published: April 2004

AbstractSeveral proteins and peptides that can convert from α‐helical to β‐sheet conformation and form amyloid fibrils, including the amyloid β‐peptide (Aβ) and the prion protein, contain a discordant α‐helix that is composed of residues that strongly favor β‐strand formation. In their native states, 37 of 38 discordant helices are now found to interact with other protein segments or with lipid membranes, but Aβ apparently lacks such interactions. The helical propensity of the Aβ discordant region (K16LVFFAED23) is increased by introducing V18A/F19A/F20A replacements, and this is associated with reduced fibril formation. Addition of the tripeptide KAD or phospho‐L‐serine likewise increases the α‐helical content of Aβ(12–28) and reduces aggregation and fibril formation of Aβ(1–40), Aβ(12–28), Aβ(12–24), and Aβ(14–23). In contrast, tripeptides with all‐neutral, all‐acidic or all‐basic side chains, as well as phosphoethanolamine, phosphocholine, and phosphoglycerol have no significant effects on Aβ secondary structure or fibril formation. These data suggest that in free Aβ, the discordant α‐helix lacks stabilizing interactions (likely as a consequence of proteolytic removal from a membrane‐associated precursor protein) and that stabilization of this helix can reduce fibril formation.
Proteins can convert to β‐sheet in single crystals
Authors: Zheng Run , Zheng Xiaojing , Dong Jian , Carey Paul R. 
Published: April 2004

AbstractRaman microscopy was used to follow conformational changes in single protein crystals. Crystals of native insulin and of the 5S and 12S subunits of the enzyme transcarboxylase showed a mixture of Raman marker bands signifying α‐helix, β‐sheet and nonordered secondary structure. However, by reducing the S–S bonds in the insulin crystal, or by lowering the pH for the 5S crystal, or by soaking substrates into the 12S crystal, the secondary structure in each crystal became predominantly β‐sheet. The β‐form crystals could be dissolved only with difficulty and yielded high–molecular weight protein aggregates, indicating that the β‐sheet formation involves intermolecular contacts. Although their morphology appeared unchanged, the crystals no longer diffracted X‐rays. Using crystals that had not been exposed to laser light, the dye thioflavin T formed highly fluorescent complexes with the “β‐transformed” crystals but not with the native crystals.
Capital Income Taxes and Growth in a Stochastic Economy: A Numerical Analysis of the Role of Risk Aversion and Intertemporal Substitution
Authors: Chatterjee Santanu , Giuliano Paola , Turnovsky Stephen J. 
Published: April 2004

AbstractThis paper undertakes a numerical analysis of the effects of changes in the tax rates on domestic and foreign capital income in a stochastically growing open economy under recursive preferences, in which the rate of time preference, ɛ, and the coefficient of risk aversion, R, can be set independently. The responses of the equilibrium growth rate, its volatility, and welfare to changes in the tax changes considered are highly sensitive to the independent variations in both ɛ and R. Consequently, the errors committed by using the conventional constant elasticity utility function, even for small violations of the compatibility condition (R= 1/ɛ) can be significant, suggesting that this functional form should be employed with caution.
Hepatocellular carcinomas <2 cm in diameter complicating cirrhosis: ultrasound and clinical features in 153 consecutive patients
Authors: Rapaccini Gian Ludovico , Pompili Maurizio , Caturelli Eugenio , Covino Marcello , Lippi Maria Enrichetta , Beccaria Samuela , Cedrone Augusto , Riccardi Laura , Siena Domenico Angelo , Gasbarrini Giovanni 
Published: April 2004

Abstract: Purpose: To determine the frequencies of various echogenicity patterns in 153 consecutive unifocal hepatocellular carcinomas (HCCs) <2 cm detected in cirrhotic livers and to identify their relationships with clinical, laboratory, and microscopic features.Patients and methods: The tumors were classified as hypoechoic, hyperechoic, isoechoic, or nodule‐in‐nodule. Correlation was evaluated between hypoechoic and hyperechoic patterns and the following variables: age, gender, serum alphafetoprotein (AFP), tumor size, ultrasound features of liver parenchyma, cirrhosis etiology, and cyto/histological tumor grading.Results: One hundred and seventeen tumors (76.4%) were hypoechoic, 26 (17.0%) were hyperechoic, 5 (3.3%) were isoechoic, and 5 (3.3%) had nodule‐in‐nodule patterns. The hyperechoic pattern was more common in patients under 69 years (25.0% vs. 11.3% in those under 69 years or older, P=0.033). Patients with a hyperechoic pattern displayed a trend towards lower AFP levels and higher prevalence of hepatitis C‐related cirrhosis. The prevalence of well‐differentiated tumors was identical (56.6% and 56.5%) in the hypoechoic and hyperechoic subgroups. AFP was higher than 400 ng/ml in only 11/153 cases (7.2%).Conclusions: The hyperechoic pattern of HCC is by no means uncommon, particularly in patients under 70. Hyperechogenicity is not related to an increased frequency of well‐differentiated tumors. AFP shows limited value as a confirmatory test of small HCC.
Predictive Ability of Social Cognitive Theory in Exercise Research: An Integrated Literature Review
Authors: Keller Colleen , Fleury Julie , Gregor‐Holt Nansi , Thompson Terris 
Published: April 2004

Abstract(1) The mechanisms that underlie successful initiation and adherence to physical activity regimens are not well understood. Few theoretical models have used consistent explanatory variables that are theory‐driven and many findings that use extant models are equivocal. Social Cognitive Theory (SCT) as presented by Bandura (1986 [4], 1997 [5]) appears to have strong promise as a guide to understanding physical activity behaviors and developing clinically relevant interventions to promote the initiation and maintenance of physical activity. This critical systematic review of research using SCT was completed to determine the predictive ability of model constructs in explaining physical activity behavior and in identifying key intervention components found to enhance physical activity initiation and maintenance. Following review for quality and adequacy, published research during the years 1990‐1998 contained 27 studies that examined the relationship between the construct of SCT, self‐efficacy, and physical activity. All of the descriptive studies found a statistically significant relationship between self‐efficacy and exercise behavior. Intervention studies demonstrated that participation in an exercise program promoted self‐efficacy, and that programs designed to increase outcome expectations and self‐efficacy significantly increased exercise behavior.(2) Due to the centrality of self‐efficacy in many of the social psychological theories that help explain the attitude‐intention‐behavior triad, a strong need remains to design interventions to maximize its usefulness. Clear, generalizable, systematic and theoretically comprehensive, randomized, controlled studies are needed to understand the usefulness of the construct.
Exercise in Heart Failure: A Synthesis of Current Research
Authors: Adams Cynthia D. , Bennett Susan 
Published: April 2004

Abstract(1) Exercise intolerance, as a hallmark symptom in patients with heart failure, has been the focus of numerous research initiatives in recent years. The purpose of this review is to synthesize the current literature in order to provide the clinician with an understanding of the state of knowledge regarding the role of exercise in treatment of heart failure. Many studies speak to the effect of exercise training in this population. While sample sizes have been small and restricted predominantly to male subjects with ischemic cardiomyopathies, strong support has been documented in favor of beneficial effects of exercise in heart failure. Future research should target more representative subject pools (i.e., females, non‐ischemic cardiomyopathies, cultural minorities, frail elderly, and NYHA class IV), evaluation of impact on quality of life outcomes, exploration of different types and intensity of exercise, and formulation of specific activity prescription tools which can guide practitioners in making activity and/or exercise recommendations to those patients who have no access, or limited access, to cardiac rehabilitation programs.
Breast Cancer Risk Perception and Surveillance: An Integrative Review
Authors: Martin Wanda , Lobchuk Michelle 
Published: April 2004

AbstractPurposeA family history of breast cancer has taken on new meaning with the advancement of genetic technology and the discovery of genes related to breast cancer risk. The purpose of this review is to summarize and synthesize current literature on breast cancer risk perception and mammography screening practices as related to women who have a first‐degree relative with breast cancer.ConclusionsResearch has shown that women tend to overestimate their breast cancer risk and that risk counseling fails to have a significant effect. Inconsistent findings exist in relation to the effect of family history on screening behaviors and conflicting evidence in the relationship between risk perception and mammography use.Implications(3) Inaccurate risk perceptions for high‐risk women may be because of the inconsistent messages women are hearing in the media or from health care providers in regard to the efficacy of mammography. Practitioners need to be careful not to assume that a strong family history of breast cancer leads to increased perceived risk, which in turn promotes increased mammography use.
A Biomechanical Comparison of Initial Soft Tissue Tibial Fixation Devices
Authors: Caborn David N. M. , Brand Jeff C. , Nyland John , Kocabey Yavuz 
Published: April 2004

Background Biomechanical testing of the Intrafix device has not been performed using human tibiae. Hypothesis The Intrafix device would provide comparable or superior tibial fixation of a quadrupled hamstring tendon graft to a 35-mm-long bioabsorbable interference screw. Study Design In vitro, biomechanical study. Methods Eight paired human tibiae and 16 quadrupled hamstring tendon grafts were divided into 2 groups. Each quadrupled hamstring tendon graft was fixed in a tunnel sized to 0.5 mm graft diameter with either an Intrafix device or a screw. Results Displacement at failure was greater in the Intrafix group (17.3 ± 4.6 mm versus 10.9 ± 4.4 mm, P = .002). Load at failure (796 ± 193 N versus 647 ± 269 N), stiffness (49.2 ± 21.9 N/mm versus 64.5 ± 22 N/mm), and bone mineral density (0.74 ±0.15 gm/cm3 versus 0.74 ± 0.14 gm/cm3) did not display significant differences for the Intrafix device and the screw, respectively (P > .05). Conclusions Displacement at failure was greater for the Intrafix device. Clinical Relevance Increased displacement at failure for the Intrafix group suggests slippage from sheath channel deployment. Concentric fixation may not occur when less than optimal tibial bone mineral density increases the difficulty of attaining precise sheath deployment and quadrupled hamstring tendon graft strand alignment.