bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of a core set of genes that signifies pathways underlying cardiac hypertrophy
Authors: Strøm Claes C. , Kruhøffer Mogens , Knudsen Steen , Stensgaard‐Hansen Frank , Jonassen Thomas E. N. , Ørntoft Torben F. , Haunsø Stig , Sheikh Søren P. 
Published: January 2005

AbstractAlthough the molecular signals underlying cardiac hypertrophy have been the subject of intense investigation, the extent of common and distinct gene regulation between different forms of cardiac hypertrophy remains unclear. We hypothesized that a general and comparative analysis of hypertrophic gene expression, using microarray technology in multiple models of cardiac hypertrophy, including aortic banding, myocardial infarction, an arteriovenous shunt and pharmacologically induced hypertrophy, would uncover networks of conserved hypertrophy‐specific genes and identify novel genes involved in hypertrophic signalling. From gene expression analyses (8740 probe sets, n = 46) of rat ventricular RNA, we identified a core set of 139 genes with consistent differential expression in all hypertrophy models as compared to their controls, including 78 genes not previously associated with hypertrophy and 61 genes whose altered expression had previously been reported. We identified a single common gene program underlying hypertrophic remodelling, regardless of how the hypertrophy was induced. These genes constitute the molecular basis for the existence of one main form of cardiac hypertrophy and may be useful for prediction of a common therapeutic approach. Supplementary material for this article can be found at: http://www.interscience.wiley.com/jpages/1531‐6912/suppmat Copyright © 2004 John Wiley & Sons, Ltd.
Meeting report: The Institute for Genomic Research/Wellcome Trust Conference: Genomes 2004 14–17 April 2004, The Wellcome Trust Conference Centre, The Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
Authors: Wixon Jo 
Published: January 2005

AbstractThis conference brought the microbial genomics community together to share their most up‐to‐the‐minute achievements, so much so that several talks cannot be covered here, as the work discussed has not yet been published. This meeting report has details of a cross‐section of the talks from the sessions on ‘Genome analysis and comparative genomics’, ‘Computational genomics’ and ‘Functional genomics’, ranging from studies on complex environmental samples, to specific pathogenic bacteria, to yeasts. Copyright © 2004 John Wiley & Sons, Ltd.
The SOFG anatomy entry list (SAEL): an annotation tool for functional genomics data
Authors: Parkinson Helen , Aitken Stuart , Baldock Richard A. , Bard Jonathan B. L. , Burger Albert , Hayamizu Terry F. , Rector Alan , Ringwald Martin , Rogers Jeremy , Rosse Cornelius , Stoeckert Christian J. , Davidson Duncan 
Published: January 2005

AbstractA great deal of data in functional genomics studies needs to be annotated with low‐resolution anatomical terms. For example, gene expression assays based on manually dissected samples (microarray, SAGE, etc.) need high‐level anatomical terms to describe sample origin. First‐pass annotation in high‐throughput assays (e.g. large‐scale in situ gene expression screens or phenotype screens) and bibliographic applications, such as selection of keywords, would also benefit from a minimum set of standard anatomical terms. Although only simple terms are required, the researcher faces serious practical problems of inconsistency and confusion, given the different aims and the range of complexity of existing anatomy ontologies. A Standards and Ontologies for Functional Genomics (SOFG) group therefore initiated discussions between several of the major anatomical ontologies for higher vertebrates. As we report here, one result of these discussions is a simple, accessible, controlled vocabulary of gross anatomical terms, the SOFG Anatomy Entry List (SAEL). The SAEL is available from http://www.sofg.org and is intended as a resource for biologists, curators, bioinformaticians and developers of software supporting functional genomics. It can be used directly for annotation in the contexts described above. Importantly, each term is linked to the corresponding term in each of the major anatomy ontologies. Where the simple list does not provide enough detail or sophistication, therefore, the researcher can use the SAEL to choose the appropriate ontology and move directly to the relevant term as an entry point. The SAEL links will also be used to support computational access to the respective ontologies. Copyright © 2004 John Wiley & Sons, Ltd.
Growth factor‐responsive progenitors in the postnatal mammalian retina
Authors: Zhao Xing , Das Ani V. , Soto‐Leon Frank , Ahmad Iqbal 
Published: January 2005

AbstractIt is thought that the adult mammalian retina lacks the regenerative capacity of fish and amphibians retina because it does not harbor a progenitor population. However, recent observations suggest that another derivative of the optic neuroepithelium, the ciliary body, contains a mitotically quiescent population of neural progenitors that proliferate in the presence of growth factors and demonstrate properties of neural stem cells. Examination of the hypothesis that similar mitotically quiescent and growth factor‐responsive progenitors may exist in the postnatal retina revealed a population of cells located in the periphery of the retina that displayed proliferative responsiveness to growth factors and possessed potential to support neurogenesis. Given their marginal position and neural properties and potential, these cells may represent a residual population of retinal progenitors, analogous to those found in the ciliary marginal zone of fish and amphibians. Their progressive decrease in proliferative potential and number in postnatal stages suggests a temporal decline in regulatory signaling that supports their maintenance during retinal neurogenesis. Developmental Dynamics 232:349–358, 2005. © 2005 Wiley‐Liss, Inc.
Accounting for haplotype uncertainty in matched association studies: A comparison of simple and flexible techniques
Authors: Kraft Peter , Cox David G. , Paynter Randi A. , Hunter David , De Vivo Immaculata 
Published: January 2005

AbstractPopulation‐based case‐control studies measuring associations between haplotypes of single nucleotide polymorphisms (SNPs) are increasingly popular, in part because haplotypes of a few “tagging” SNPs may serve as surrogates for variation in relatively large sections of the genome. Due to current technological limitations, haplotypes in cases and controls must be inferred from unphased genotypic data. Using individual‐specific inferred haplotypes as covariates in standard epidemiologic analyses (e.g., conditional logistic regression) is an attractive analysis strategy, as it allows adjustment for nongenetic covariates, provides omnibus and haplotype‐specific tests of association, and can estimate haplotype and haplotype × environment interaction effects. In principle, some adjustment for the uncertainty in inferred haplotypes should be made. Via simulation, we compare the performance (bias and mean squared error of haplotype and haplotype × environment interaction effect estimates) of several analytic strategies using inferred haplotypes in the context of matched case‐control data. These strategies include using only the most likely haplotype assignment, the expectation substitution approach described by Stram et al. ([2003b] Hum. Hered. 55:179–190) and others, and an improper version of multiple imputation. For relatively uncomplicated haplotype structures and moderate haplotype relative risks (≤2), all methods performed comparably well (small bias with appropriately‐sized confidence intervals). For larger relative risks, the most likely haplotype and multiple imputation strategies showed noticeable bias towards the null; the expectation substitution strategy still performed well. When there was more uncertainty in the inferred haplotypes, the most likely and multiple imputation strategies showed even more bias towards the null, while the expectation substitution method had slightly smaller than nominal confidence intervals for larger relative risks (≥5). An application to progesterone‐receptor haplotypes and endometrial cancer further illustrates that the performance of all these methods depends on how well the observed haplotypes “tag” the unobserved causal variant. Genet. Epidemiol. © 2005 Wiley‐Liss, Inc.
Liquid chromatographic/electrospray ionization tandem mass spectrometric analysis for the quantification of buprenorphine, norbuprenorphine, buprenorphine‐3‐β‐D‐glucuronide and norbuprenorphine‐3‐β‐D‐glucuronide in human plasma
Authors: Murphy Constance M. , Huestis Marilyn A. 
Published: January 2005

AbstractA liquid chromatographic/electrospray ionization tandem mass spectrometric method for the quantification of the synthetic opiate buprenorphine (BUP), norbuprenorphine (NBUP), buprenorphine‐3‐β‐D‐glucuronide (BUP‐3‐G) and norbuprenorphine‐3‐β‐D‐glucuronide (NBUP‐3‐G) in human plasma was developed and validated. Identification and quantification were based on the following transitions: m/z 468 to 396 and 414 for BUP, m/z 414 to 326 and 340 for NBUP, m/z 644 to 468 for BUP‐3‐G and m/z 590 to 414 for NBUP‐3‐G. Calibration by linear regression analysis utilized deuteratated internal standards and a weighting factor of 1/x. The method was accurate and precise across a linear dynamic range of 0.6–50.0 ng ml−1. Pretreatment of plasma samples using solid‐phase extraction was sufficient to limit matrix suppression to <30% for all four analytes. The method proved to be suitable for the quantification of BUP and the related metabolites in plasma samples collected from BUP‐maintained study participants. Copyright © 2004 John Wiley & Sons, Ltd.
Novel function of neuronal PAS domain protein 1 in erythropoietin expression in neuronal cells
Authors: Ohsawa Shizue , Hamada Shun , Kakinuma Yoshihiko , Yagi Takeshi , Miura Masayuki 
Published: January 2005

AbstractThe basic helix loop helix‐PAS (bHLH‐PAS) transcription factors have diverse roles in physiologic responses to the environment and in early development. One bHLH‐PAS protein, neuronal PAS domain protein 1 (NPAS1), is reported to be expressed only in the central nervous system beginning at the late embryonic stage, but its function is unknown. Using an anti‐NPAS1 antibody, we have shown that NPAS1 expression in cerebral cortex was observed first around embryonic Day 16.5 (E16.5) and was then dispersed throughout the region as cortical development progressed. From the similarity with hypoxia‐inducible factor‐1α (HIF‐1α), we investigated whether NPAS1 regulates transcription of erythropoietin (EPO), which is the target of HIF‐1α and is expressed in the brain during the early developmental stage. In the present study, we have shown that NPAS1 binds to the enhancer region of Epo in vivo. A luciferase reporter assay revealed a repressive effect of NPAS1 on hypoxia‐responsive element‐regulated gene expression. These results raise the possibility that NPAS1 plays a role in late central nervous system development by modulating EPO expression in response to cellular oxygen level. © 2005 Wiley‐Liss, Inc.
The pyrolysis of trimethylene sulfide. A unimolecular decomposition
Authors: Jeffers P. , Dasch C. , Bauer S. H. 
Published: January 2005

AbstractThe kinetics of decomposition of trimethylene sulfide to ethylene and thioformaldehyde was investigated in a single‐pulse shock tube using the «relative rate» technique. The extent of reaction was measured in the reflected shock regime from 860° to 1170°K, but experimental difficulties limited the useful data to the temperature range of 980°–1040°K. The first‐order rate constant was found to be k = 1013.0 exp (−48,200/RT) sec−1. This result sets an upper limit of 50 kcal/mole for the standard enthalpy of formation of CH2S, with 35 kcal/mole as a more likely value. The isomerization of cyclopropane to propene was used for the reference reaction; in turn, this was checked, in a relative rate experiment, against the pyrolysis of cyclohexene.
A differential technique which is independent of initial conditions for calculating the rate constant of a second‐order reaction
Authors: Wen Walter Y. 
Published: January 2005

AbstractIt has been shown that experimental errors of the initial conditions of a second‐order reaction can cause erroneous results with the rate constant calculated directly from the differential or integrated rate expression. By means of a computer method, a differential technique has been developed so that precise initial reactant conditions are not necessary for calculating a second‐order rate constant if continuous measurements of a single reaction variable are available. The technique has been successfully applied to the data of Kistiakowsky and Lacher on the condensation of acrolein and butadiene.
A classical trajectory study of the effect of reaction barrier height on the vibrational energy transfer efficiency in the Cl + HCl system
Authors: Thommarson Ronald L. , Berend George C. 
Published: January 2005

AbstractThe effects of reaction barrier height and initial rotational excitation of the reactants on the overall rate of H atom exchange between atomic chlorine and HCl (v = 0) and on the 0 → 1 vibrational excitation of HCl via reactive and nonreactive collisions have been investigated using quasiclassical trajectory techniques. Two empirical LEPS potential energy surfaces were employed in the calculations having reaction barrier heights of 9.84 and 7.05 kcal mol−1. Trajectory studies of planar collisions were carried out on each surface over a range of relative translational energies with the ground‐state HCI collision partner given initial rotational excitation corresponding J = 0, 3, and 7. Initial molecular rotation was found to be relatively inefficient in promoting the H atom exchange; the computed rate coefficient for H atom exchange between Cl + HCl (v = 0, J = 7) was only 4 times larger than that for CI + HCI (v = 0, J = 0). The vibrational excitation rate coefficient exhibited a stronger dependence on initial molecular rotational excitation. The observed increase in the vibrational excitation rate coefficient with increasing initial molecular rotational excitation was due primarily to nonreactive intermolecular R → V energy transfer. The vibrational excitation rate coefficients increase with decreasing reaction barrier height.
The thermal decomposition of azomethane. III. Kinetics of the noninhibited reaction
Authors: Paquin Y. , Forst W. 
Published: January 2005

AbstractThe thermal decomposition of azomethane (A) has been studied in a static system at temperatures between 250° and 320°C and at pressures between 5 and 402 torr, with particular attention to identification of products. Major products, in decreasing order of importance, were nitrogen, methane, ethane, methylethyldiimide, dimethylhydrazone, propane, tetramethylhydrazine, ethylene, methylpropyldiimide, and methylethylhydrazone. Carbon balance at the lowest pressure and highest temperature was 92%, but decreased with increasing pressure and decreasing temperature owing to the formation of a polymer. A fairly simple mechanism accounts reasonably well for a short chain in the decomposition, propagated by the radical CH3N2CH2 (B), and for the five most abundant products, except ethane. It turns out that there is a second source of ethane, arising by C2H5 + A → C2H6 + B; this explains an anomalously high apparent activation energy for the reaction CH3 + A → CH4 + B. Ethyl radicals are also shown to be responsible for the formation of propane, ethylene, methylethylhydrazone, and methylpropyldiimide. The radical B decomposes to CH3 + CH2 + N2, and the methylene radical (probably both singlet and triplet) is shown to yield C2H5 at low pressure and high temperature, and mostly polymer at high pressure and low temperature.
Reactions in the gas and liquid phases: Comparison of kinetic and thermodynamic data
Authors: Patrick C. R. 
Published: January 2005

AbstractAn analysis is made of relationships to be expected between the enthalpies and entropies of reactions carried out in the gas and liquid phases, assuming ideal thermodynamic behavior of the components. The results of the analysis are compared with experimental results reported in the literature. Some discrepancies are noted. These may be the consequence of experimental error or may be due to substantial deviations from thermodynamic ideality. If the latter is commonplace, there will be difficulties in making useful predictions and correlations of thermodynamic and kinetic parameters in the liquid phase.
The mechanism of cooxidation of isobutyraldehyde and octene‐2
Authors: Montorsi G. , Caprara G. , Pregaglia G. , Messina G. 
Published: January 2005

AbstractThe mechanism of isobutyraldehyde‐octene‐2 cooxidation at 20°C has been investigated. The ratio of cis to trans epoxides in the reaction products shows that, at aldehyde concentrations lower than 1.0M, the epoxide is formed mainly by a radical route. The difference in the ΔH of formation of cis and trans epoxides is around 0.8 kcal/mole at 20°. The isobutyraldehyde involved in the radical epoxidation chain has been found almost quantitatively to be isopropylhydroperoxide, which is formed through the decarboxylation of i‐PrCO2· radicals, addition of oxygen, and abstraction of hydrogen atoms from the aldehyde. A rate constant of about 14 M−1 sec−1 at 20° has been determined for the latter reaction. The chain length for the cooxdination reaction decreases from 75 to 20 as the isobutyraldehyde concentration goes from 1.0 to 0.3M. The termination step seems to involve mainly the interaction of two i‐PrO2 · radicals. The cooxidation of octene‐2 with pivalaldehyde follows a similar mechanism, but the chain length is about ten times higher under the same experimental conditions.
Addition of ethyl radicals to carbon monoxide. Kinetic and thermochemical properties of the propionyl radical
Authors: Watkins K. W. , Thompson William W. 
Published: January 2005

AbstractAzoethane was irradiated in the presence of carbon monoxide in the temperature range of 238 to 378 K. Kinetic parameters for the addition of ethyl radicals to carbon monoxide and for the decomposition of propionyl radicals were determined. The rate constants were found to be log k(cm3 mol−1 sec−1) = 11.19 ‐ 4.8/θ and log k(sec−1) = 12.77 ‐ 14.4/θ, respectively. Estimated thermochemical properties of the propionyl radical are ΔHf0 = ‐10.6 ± 1.0 kcal mol−1, S0 = 77.3 ± 1.0 cal K−1 mol−1, and D(C2H5COH) = 87.4 kcal mol−1.
Photolysis of alkyl iodides at 147.0 nm. The reaction H + CnH2n + 1I → HI + CnH2n + 1
Authors: Rebbert R. E. , Lias S. G. , Ausloos P. 
Published: January 2005

AbstractThe 147 nm (8.4 eV) photolysis of gaseous C2H5I, n‐C3H7I, and sec‐C3H7I was investigated in the presence of and absence of HI. The main overall processes are:

These dissociative processes occur mainly as a result of initial cleavage of the weak CI bond, followed by decomposition of the internally excited alkyl radicals. In all cases, approximately 5‐10% of the alkyl radicals thus formed do not undergo dissociation at pressures around 3‐7 torr. There is also evidence for the elimination of HI as well as CC cleavage in the primary dissociation. The former is indicated by deuterium labeling experiments and the formation of cyclopropane (Φ = 0.04) as a product in the photolysis of n‐C3H7I. Because the processes listed above provide a constant source of H atoms whose quantum yield can be exactly determined, it was feasible to obtain accurate values for ka/kb: magnified image For thermally equilibrated H atoms (300 K), ka/kb is 0.44 ± 0.04, 0.57 ± 0.06, 0.95 ± 0.1, and 0.024 ± 0.01 for C2H5I, n‐C3H7I, sec‐C3H7I, and C2H5Br, respectively.
Mechanism of oxidation of cyclohexanehexol (inositol) by quinquevalent vanadium
Authors: Kumar Ashok , Mehrotra Raj Narain 
Published: January 2005

AbstractThe oxidation of inositol by quinquevalent vandadium in acid medium is a first‐order reaction both in vanadium (V) and inositol. The stoichiometry of the reaction is consistent with the use of two equivalents of vanadium (V) per mole of inositol with the formation of one mole of inosose. The reaction is catalyzed both by sulfuric and perchloric acid, but the rate is faster in sulfuric acid than in perchloric acid. In 1M–6M perchloric acid solutions the reaction has shown a variable order in H+, but in solutions of 2M–5M sulfuric and perchloric acid of constant ionic strength, the rate has a linear dependence on [H+]2. There is also a linear correlation between the rate and bisulfate ions in sulfuric acid at constant hydrogen ion concentration. The energy of activation is found to be 19 kcal/mole and a negative entropy value of − 14 e.u. A suitable mechanism, consistent with the kinetics in 2M–5M acid solutions, is suggested and the values of various rate constants are evaluated.
The kinetics of the reaction between magnesium and EBT
Authors: Koren Ruth , Perlmutter‐Hayman Berta , Shinar Ruth 
Published: January 2005

AbstractThe kinetics of the reaction between Mg2+ and Eriochrome‐Black‐T (EBT) has been investigated in the pH range between 7.05 and 9.0, in the presence of 12% ethanol. The reaction is found to consist of two parallel paths, one involving the tervalent unprotonated ligand, and one its monoprotonated form. The rate constant for the unprotonated ligand has a “normal” value, whereas that for the protonated form is much lower. The numerical value of the rate constant for the unprotonated ligand obtained from results at a magnesium concentration of 10−3M and a pH up to 9.0 is, however, inconsistent with that obtained from results at [Mg2+] = (1 to 4) × 10−3M and pH up to 8.1. This can be explained, at least partially, if we assume the intermediate MgHD to lose its proton not only to H2O, but also to other bases present in the solution.
Solvation of ligandopentaamminecobalt (III) complexes in dimethyl sulfoxide–water mixtures
Authors: Reynolds Warren L. , Barber Elaine S. , Crandall Robin 
Published: January 2005

AbstractThe rate constants for the replacement of water from the inner‐coordination shell of Co(NH3)5OH23+, I, by dimethyl sulfoxide (DMSO) as DMSO gradually replaced water in the solvation shell of I were found to approach, and finally equal, the water‐exchange rate constant of I in aqueous media in accordance with expectation for a dissociative mechanism. Also the rate constants for the replacement of DMSO from the innercoordination shell of Co(NH3)5DMSO3+, II, by water as water replaced DMSO in the solvation shell of II were found to approach, and approximately equal, the DMSO‐exchange rate constant for II in liquid DMSO in accordance with expectation for a dissociative mechanism.The DMSO‐exchange rate constant for II in liquid DMSO was determined and found to be equal to (3.6 ± 0.8) × 10−4 sec−1 at 45°C.The dissociation quotient, [II] [NO3−]/[Co(NH3)5NO32+], was found to be equal to 0.28 ± 0.11 M at 45°C by NMR methods. The pseudo first‐order rate constants for anation of II by NO3− and the solvation of Co(NH3)5NO3 2+ by DMSO were determined at various temperatures.
A study of the collisional quenching of O(21D2) by the noble gases employing time‐resolved attenuation of atomic resonance radiation in the vacuum ultraviolet
Authors: Heidner R. F. , Husain D. 
Published: January 2005

AbstractElectronically excited oxygen atoms O(21D2) have been generated by the pulsed irradiation of ozone in the Hartley‐band continuum and monitored photoelectrically in absorption by time‐resolved attenuation of atomic resonance radiation at λ = 115.2 nm [O(31D2°) → O(21D2)]. Collisional quenching of the excited atom has been investigated for all the noble gases, and the first absolute values for the second‐order deactivation rate constants are reported. The resulting rate data are discussed in terms of a curve‐crossing mechanism based on existing spectroscopic data for the noble gas oxides. The absolute rate constants are compared with previous relative rate data for the deactivation of O(21D2) by the noble gases.