bluuebunny/crossref_metadata_2025_split huggingface dataset:
A new tetradentate ligand for atom transfer radical polymerization
Authors: Ding Shijie , Shen Youqing , Radosz Maciej 
Published: June 2004

AbstractThe properties of a ligand, including molecular structure and substituents, strongly affect the catalyst activity and control of the polymerization in atom transfer radical polymerization (ATRP). A new tetradentate ligand, N,N′‐bis(pyridin‐2‐ylmethyl‐3‐hexoxo‐3‐oxopropyl)ethane‐1,2‐diamine (BPED) was synthesized and examined as the ligand of copper halide for ATRP of styrene (St), methyl acrylate (MA), and methyl methacrylate (MMA), and compared with other analogous linear tetrdendate ligands. The BPED ligand was found to significantly promote the activation reaction: the CuBr/BPED complex reacted with the initiators so fast that a large amount of Cu(II)Br2/BPED was produced and thus the polymerizations were slow for all the monomers. The reaction of CuCl/BPED with the initiator was also fast, but by reducing the catalyst concentration or adding CuCl2, the activation reaction could be slowed to establish the equilibrium of ATRP for a well‐controlled living polymerization of MA. CuCl/BPED was found very active for the polymerization of MA. For example, 10 mol% of the catalyst relatively to the initiator was sufficient to mediate a living polymerization of MA. The CuCl/BPED, however, could not catalyze a living polymerization of MMA because the resulting CuCl2/BPED could not deactivate the growing radicals. The effects of the ligand structures on the catalysis of ATRP are also discussed. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 3553–3562, 2004
Accuracy of absence of fetal breathing movements in predicting preterm birth: a systematic review
Authors: Honest H. , Bachmann L. M. , Sengupta R. , Gupta J. K. , Kleijnen J. , Khan K. S. 
Published: June 2004

AbstractObjectiveTo determine the accuracy with which the absence of fetal breathing movements on ultrasound examination predicts spontaneous preterm birth in women with threatened preterm labor.MethodsData sources included Medline, Embase, Pascal, Biosis, Cochrane Library, Medion, National Research Register, SciSearch, conference papers, and manual searching of bibliographies of known primary and review articles. A study was selected if it used absence of fetal breathing movements on ultrasound to predict spontaneous preterm birth in women with threatened preterm labor but before advanced cervical dilatation. Two reviewers independently selected studies and extracted data on their characteristics, quality and accuracy. Accuracy data were used to form 2 × 2 contingency tables with birth within 48 h and within 7 days of testing as the reference standards. Likelihood ratios for a positive test (LR+) and negative test (LR−) were calculated as a measure of accuracy.ResultsThere were eight studies, which included a total of 328 women, evaluating the accuracy of absence of fetal breathing movements in predicting spontaneous preterm birth in women with threatened preterm labor. There were differences in the methodological quality among the included studies. All were lacking in one or more item that make up an ideal test accuracy study. For women presenting with threatened preterm labor, meta‐analysis showed a summary LR+ of 14.80 (95% CI, 6.30–34.79) with a corresponding summary LR− of 0.46 (95% CI, 0.36–0.58) for predicting preterm birth within 7 days, and summary LR+ of 7.84 (95% CI, 1.12–54.99) and summary LR− of 0.25 (95% CI, 0.13–0.48) for predicting preterm birth within 48 h of testing.ConclusionAbsence of fetal breathing movements has the potential to be a useful test in predicting preterm birth both within 7 days and within 48 h of testing. However, the available studies were deficient in their sample size and quality of methodology. Future research should be undertaken to evaluate this technology and to address the methodological deficiencies. Copyright © 2004 ISUOG. Published by John Wiley & Sons, Ltd.
Impaired endothelium‐dependent and ‐independent vasodilation in elderly patients with chronic heart failure
Authors: Morgan David R. , Dixon Lana J. , Hanratty Colm G. , Hughes Sinead M.T. , Leahey William J. , Rooney Keith P. , Johnston G. Dennis , McVeigh Gary E. 
Published: June 2004

AbstractBackground:Impaired endothelium‐dependent and independent vasodilator responses in chronic heart failure (CHF) have been well described. Previous studies involved younger patients and omitted medications prior to study.Aims:We explored if new therapeutic interventions would restore vasodilator responses in typical patients with chronic heart failure.Methods and results:24 patients and 15 controls were recruited, patients were maintained on their usual medications. Forearm blood flow responses were measured by venous occlusion plethysmography in response to incremental doses of sodium nitroprusside (SNP) (6, 9 and 12 nmol/min), acetylcholine (ACH) (120, 180 and 240 nmol/min), angiotensin II (AII) (1, 10 and 100 nmol/min) and Ng‐Nitro‐l‐arginine methyl ester (l‐NAME) (1, 2 and 4 nmol/min) infused into the non‐dominant brachial artery. FBF responses to SNP were impaired in patients compared with controls (13.7(9.9,17.4) vs. 24.8(18.6,30.9)) arbitrary units, P<0.001). Similarly FBF responses to ACH were reduced in patients compared with controls (7.5(4.2,10.9) vs. 24.8(16.4,33.2)) arbitrary units, P<0.001. Decreased FBF was noted in response to AII and l‐NAME but was significant only for AII and did not differ between groups.Conclusions:In elderly patients with CHF, endothelium‐dependent and independent vasodilator responses were blunted compared with controls. Defects in nitric oxide bioavailability and smooth muscle responsiveness are not reversed by modern medical management of the heart failure syndrome.
Effects of bisoprolol treatment for chronic heart failure initiated and followed up by primary care physicians
Authors: Schuchert A. ,   On behalf of the BISEX Investigators (Appendix A)
Published: June 2004

Primary care physicians prescribe beta‐blockers for chronic heart failure infrequently. The aims of the study were to assess the effects of beta‐blocker treatment in out‐clinic patients with regard to NYHA class and frequency of adverse events. Beta‐blocker treatment was initiated and followed up by primary care physicians.Methods:Chronic heart failure patients already treated with ACE‐inhibitors and diuretics were included. The 24‐week follow‐up consisted of a titration phase followed by a maintenance phase. The patients received the beta‐blocker bisoprolol with an initial dose of 1.25 mg and a maximal dose of 10 mg.Results:NYHA class II, III and IV had 174, 146, and one patient, respectively. Treatment duration lasted 189±73 days with a maximal bisoprolol dose of 7.2±3.2 mg. Sixty‐one percent of the patients tolerated at least 7.5 mg bisoprolol. The NYHA class improved from 2.4±0.5 at baseline to 1.8±0.6 at week 24 (P<0.001). At final assessment, 74% of the patients showed an improvement. The number of permanent treatment withdrawals was 57 (17%). Death occurred in six patients and hospitalisation in 38 patients.Conclusions:Bisoprolol treatment in patients with chronic heart failure was effectively and safely carried out by primary care physicians.
Hyaline cartilage degenerates after autologous osteochondral transplantation
Authors: Tibesku C. O. , Szuwart T. , Kleffner T. O. , Schlegel P. M. , Jahn U. R. , Van Aken H. , Fuchs S. 
Published: June 2004

AbstractObjectives: Autologous osteochondral grafting is a well‐established clinical procedure to treat focal cartilage defects in patients, although basic research on this topic remains sparse. The aim of the current study was to evaluate (1) histological changes of transplanted hyaline cartilage of osteochondral grafts and (2) the tissue that connects the transplanted cartilage with the adjacent cartilage in a sheep model.Method: Both knee joints of four sheep were opened surgically and osteochondral grafts were harvested and simultaneously transplanted to the contralateral femoral condyle. The animals were sacrificed after three months and the received knee joints were evaluated histologically.Results: Histological evaluation showed a complete ingrowth of the osseous part of the osteochondral grafts. A healing or ingrowth at the level of the cartilage could not be observed. Histological evaluation of the transplanted grafts according to Mankin revealed significantly more and more severe signs of degeneration than the adjacent cartilage, such as cloning of chondrocytes and irregularities of the articular surface.Conclusion: We found no connecting tissue between the transplanted and the adjacent cartilage and histological signs of degeneration of the transplanted hyaline cartilage. In the light of these findings, long‐term results of autologous osteochondral grafts in human beings have to be followed critically. © 2004 Orthopaedic Research Society. Published by Elsevier Ltd. All rights reserved.
A statistical framework for the design of microarray experiments and effective detection of differential gene expression
Authors: Zhang Shu-Dong , Gant Timothy W. 
Published: June 2004

Abstract
Motivation: Microarray experiments generate a high data volume. However, often due to financial or experimental considerations, e.g. lack of sample, there is little or no replication of the experiments or hybridizations. These factors combined with the intrinsic variability associated with the measurement of gene expression can result in an unsatisfactory detection rate of differential gene expression (DGE). Our motivation was to provide an easy to use measure of the success rate of DGE detection that could find routine use in the design of microarray experiments or in post-experiment assessment.
Results: In this study, we address the problem of both random errors and systematic biases in microarray experimentation. We propose a mathematical model for the measured data in microarray experiments and on the basis of this model present a t-based statistical procedure to determine DGE. We have derived a formula to determine the success rate of DGE detection that takes into account the number of microarrays, the number of genes, the magnitude of DGE, and the variance from biological and technical sources. The formula and look-up tables based on the formula, can be used to assist in the design of microarray experiments. We also propose an ad hoc method for estimating the fraction of non-differentially expressed genes within a set of genes being tested. This will help to increase the power of DGE detection.
Availability: The functions to calculate the success rate of DGE detection have been implemented as a Java application, which is accessible at http://www.le.ac.uk/mrctox/microarray_lab/Microarray_Softwares/Microarray_Softwares.htm
Supplementary information at ftp://alcyone.mrc.le.ac.uk/Pub/twg1/BioInf03-0661suppl.pdf
Reconstruction of gene networks using Bayesian learning and manipulation experiments
Authors: Pournara Iosifina , Wernisch Lorenz 
Published: June 2004

Abstract
Motivation: The analysis of high-throughput experimental data, for example from microarray experiments, is currently seen as a promising way of finding regulatory relationships between genes. Bayesian networks have been suggested for learning gene regulatory networks from observational data. Not all causal relationships can be inferred from correlation data alone. Often several equivalent but different directed graphs explain the data equally well. Intervention experiments where genes are manipulated can help to narrow down the range of possible networks.
Results: We describe an active learning algorithm that suggests an optimized sequence of intervention experiments. Simulation experiments show that our selection scheme is better than an unguided choice of interventions in learning the correct network and compares favorably in running time and results with methods based on value of information calculations.
Availability: Algorithms are available from the authors on request.
Bayesian integrated functional analysis of microarray data
Authors: Bhattacharjee Madhuchhanda , Pritchard Colin C. , Nelson Peter S. , Arjas Elja 
Published: June 2004

Abstract
Motivation: The statistical analysis of microarray data usually proceeds in a sequential manner, with the output of the previous step always serving as the input of the next one. However, the methods currently used in such analyses do not properly account for the fact that the intermediate results may not always be correct, then leading to cumulating error in the inferences drawn based on such steps.
Results: Here we show that, by an application of hierarchical Bayesian methodology, this sequential procedure can be replaced by a single joint analysis, while systematically accounting for the uncertainties in this process. Moreover, we can also integrate relevant functional information available from databases into such an analysis, thereby increasing the reliability of the biological conclusions that are drawn. We illustrate these points by analysing real data and by showing that the genes can be divided into categories of interest, with the defining characteristic depending on the biological question that is considered. We contend that the proposed method has advantages at two levels. First, there are gains in the statistical and biological results from the analysis of this particular dataset. Second, it opens up new possibilities in analysing microarray data in general.
Supplementary information: http://www.rni.helsinki.fi/~mab/
Java Treeview—extensible visualization of microarray data
Authors: Saldanha Alok J. 
Published: June 2004

Abstract
Summary: Open source software encourages innovation by allowing users to extend the functionality of existing applications. Treeview is a popular application for the visualization of microarray data, but is closed-source and platform-specific, which limits both its current utility and suitability as a platform for further development. Java Treeview is an open-source, cross-platform rewrite that handles very large datasets well, and supports extensions to the file format that allow the results of additional analysis to be visualized and compared. The combination of a general file format and open source makes Java Treeview an attractive choice for solving a class of visualization problems. An applet version is also available that can be used on any website with no special server-side setup.
Availability: http://jtreeview.sourceforge.net under GPL.
An entity tagger for recognizing acquired genomic variations in cancer literature
Authors: McDonald Ryan T. , Winters R. Scott , Mandel Mark , Jin Yang , White Peter S. , Pereira Fernando 
Published: June 2004

Abstract
Summary: VTag is an application for identifying the type, genomic location and genomic state-change of acquired genomic aberrations described in text. The application uses a machine learning technique called conditional random fields. VTag was tested with 345 training and 200 evaluation documents pertaining to cancer genetics. Our experiments resulted in 0.8541 precision, 0.7870 recall and 0.8192 F-measure on the evaluation set.
Availability: The software is available at http://www.cis.upenn.edu/group/datamining/software_dist/biosfier/.
Protein complex prediction via cost-based clustering
Authors: King A. D. , Pržulj N. , Jurisica I. 
Published: June 2004

Abstract
Motivation: Understanding principles of cellular organization and function can be enhanced if we detect known and predict still undiscovered protein complexes within the cell's protein–protein interaction (PPI) network. Such predictions may be used as an inexpensive tool to direct biological experiments. The increasing amount of available PPI data necessitates an accurate and scalable approach to protein complex identification.
Results: We have developed the Restricted Neighborhood Search Clustering Algorithm (RNSC) to efficiently partition networks into clusters using a cost function. We applied this cost-based clustering algorithm to PPI networks of Saccharomyces cerevisiae, Drosophila melanogaster and Caenorhabditis elegans to identify and predict protein complexes. We have determined functional and graph-theoretic properties of true protein complexes from the MIPS database. Based on these properties, we defined filters to distinguish between identified network clusters and true protein complexes.
Conclusions: Our application of the cost-based clustering algorithm provides an accurate and scalable method of detecting and predicting protein complexes within a PPI network.
Availability: The RNSC algorithm and data processing code are available upon request from the authors.
Supplementary Information: Supplementary data are available at http://www.cs.utoronto.ca/~juris/data/ppi04/
Automatic annotation of organellar genomes with DOGMA
Authors: Wyman Stacia K. , Jansen Robert K. , Boore Jeffrey L. 
Published: June 2004

Abstract
Summary: The Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of organellar (plant chloroplast and animal mitochondrial) genomes. It is a Web-based package that allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes. DOGMA provides a graphical user interface for viewing and editing annotations. Annotations are stored on our password-protected server to enable repeated sessions of working on the same genome. Finished annotations can be extracted for direct submission to GenBank.
Availability: http://phylocluster.biosci.utexas.edu/dogma/
Supplementary information: Detailed documentation and tutorials for annotating both animal mitochondrial and plant chloroplast genomes can be found on the DOGMA home page.
A New Biology for a New Century
Authors: Woese Carl R. 
Published: June 2004

SUMMARYBiology today is at a crossroads. The molecular paradigm, which so successfully guided the discipline throughout most of the 20th century, is no longer a reliable guide. Its vision of biology now realized, the molecular paradigm has run its course. Biology, therefore, has a choice to make, between the comfortable path of continuing to follow molecular biology's lead or the more invigorating one of seeking a new and inspiring vision of the living world, one that addresses the major problems in biology that 20th century biology, molecular biology, could not handle and, so, avoided. The former course, though highly productive, is certain to turn biology into an engineering discipline. The latter holds the promise of making biology an even more fundamental science, one that, along with physics, probes and defines the nature of reality. This is a choice between a biology that solely does society's bidding and a biology that is society's teacher.
Compartmentalization of Gene Expression duringBacillus subtilisSpore Formation
Authors: Hilbert David W. , Piggot Patrick J. 
Published: June 2004

SUMMARYGene expression in members of the familyBacillaceaebecomes compartmentalized after the distinctive, asymmetrically located sporulation division. It involves complete compartmentalization of the activities of sporulation-specific sigma factors, σFin the prespore and then σEin the mother cell, and then later, following engulfment, σGin the prespore and then σKin the mother cell. The coupling of the activation of σFto septation and σGto engulfment is clear; the mechanisms are not. The σ factors provide the bare framework of compartment-specific gene expression. Within each σ regulon are several temporal classes of genes, and for key regulators, timing is critical. There are also complex intercompartmental regulatory signals. The determinants for σFregulation are assembled before septation, but activation follows septation. Reversal of the anti-σFactivity of SpoIIAB is critical. Only the origin-proximal 30% of a chromosome is present in the prespore when first formed; it takes ≈15 min for the rest to be transferred. This transient genetic asymmetry is important for prespore-specific σFactivation. Activation of σErequires σFactivity and occurs by cleavage of a prosequence. It must occur rapidly to prevent the formation of a second septum. σGis formed only in the prespore. SpoIIAB can blockσGactivity, but SpoIIAB control does not explain why σGis activated only after engulfment. There is mother cell-specific excision of an insertion element insigKand σE-directed transcription ofsigK, which encodes pro-σK. Activation requires removal of the prosequence following aσG-directed signal from the prespore.
ERK and p38 MAPK-Activated Protein Kinases: a Family of Protein Kinases with Diverse Biological Functions
Authors: Roux Philippe P. , Blenis John 
Published: June 2004

SUMMARY
Conserved signaling pathways that activate the mitogen-activated
protein kinases (MAPKs) are involved in relaying extracellular
stimulations to intracellular responses. The MAPKs
coordinately regulate cell proliferation, differentiation, motility,
and survival, which are functions also known to be mediated by members
of a growing family of MAPK-activated protein kinases (MKs;
formerly known as MAPKAP kinases). The MKs are related
serine/threonine kinases that respond to mitogenic and stress stimuli
through proline-directed
phosphorylation and activation of
the kinase domain by extracellular signal-regulated kinases 1 and 2 and
p38 MAPKs. There are currently 11 vertebrate MKs in five
subfamilies based on primary sequence homology: the ribosomal S6
kinases, the mitogen- and stress-activated kinases, the
MAPK-interacting kinases, MAPK-activated protein
kinases 2 and 3, and MK5. In the last 5 years, several MK substrates
have been identified, which has helped tremendously to identify the
biological role of the members of this family. Together with data from
the study of MK-knockout mice, the identities of the MK substrates
indicate that they play important roles in diverse biological
processes, including mRNA translation, cell proliferation and
survival, and the nuclear genomic response to mitogens and cellular
stresses. In this article, we review the existing data on the MKs and
discuss their physiological functions based on recent
discoveries.
Microbial Responses to Microgravity and Other Low-Shear Environments
Authors: Nickerson Cheryl A. , Ott C. Mark , Wilson James W. , Ramamurthy Rajee , Pierson Duane L. 
Published: June 2004

SUMMARY
Microbial adaptation to environmental stimuli is essential for survival. While several of these stimuli have been studied in detail, recent studies have demonstrated an important role for a novel environmental parameter in which microgravity and the low fluid shear dynamics associated with microgravity globally regulate microbial gene expression, physiology, and pathogenesis. In addition to analyzing fundamental questions about microbial responses to spaceflight, these studies have demonstrated important applications for microbial responses to a ground-based, low-shear stress environment similar to that encountered during spaceflight. Moreover, the low-shear growth environment sensed by microbes during microgravity of spaceflight and during ground-based microgravity analogue culture is relevant to those encountered during their natural life cycles on Earth. While no mechanism has been clearly defined to explain how the mechanical force of fluid shear transmits intracellular signals to microbial cells at the molecular level, the fact that cross talk exists between microbial signal transduction systems holds intriguing possibilities that future studies might reveal common mechanotransduction themes between these systems and those used to sense and respond to low-shear stress and changes in gravitation forces. The study of microbial mechanotransduction may identify common conserved mechanisms used by cells to perceive changes in mechanical and/or physical forces, and it has the potential to provide valuable insight for understanding mechanosensing mechanisms in higher organisms. This review summarizes recent and future research trends aimed at understanding the dynamic effects of changes in the mechanical forces that occur in microgravity and other low-shear environments on a wide variety of important microbial parameters.