bluuebunny/crossref_metadata_2025_split huggingface dataset:
RECOORD: A recalculated coordinate database of 500+ proteins from the PDB using restraints from the BioMagResBank
Authors: Nederveen Aart J. , Doreleijers Jurgen F. , Vranken Wim , Miller Zachary , Spronk Chris A.E.M. , Nabuurs Sander B. , Güntert Peter , Livny Miron , Markley John L. , Nilges Michael , Ulrich Eldon L. , Kaptein Robert , Bonvin Alexandre M.J.J. 
Published: April 2005

AbstractState‐of‐the‐art methods based on CNS and CYANA were used to recalculate the nuclear magnetic resonance (NMR) solution structures of 500+ proteins for which coordinates and NMR restraints are available from the Protein Data Bank. Curated restraints were obtained from the BioMagResBank FRED database. Although the original NMR structures were determined by various methods, they all were recalculated by CNS and CYANA and refined subsequently by restrained molecular dynamics (CNS) in a hydrated environment. We present an extensive analysis of the results, in terms of various quality indicators generated by PROCHECK and WHAT_CHECK. On average, the quality indicators for packing and Ramachandran appearance moved one standard deviation closer to the mean of the reference database. The structural quality of the recalculated structures is discussed in relation to various parameters, including number of restraints per residue, NOE completeness and positional root mean square deviation (RMSD). Correlations between pairs of these quality indicators were generally low; for example, there is a weak correlation between the number of restraints per residue and the Ramachandran appearance according to WHAT_CHECK (r = 0.31). The set of recalculated coordinates constitutes a unified database of protein structures in which potential user‐ and software‐dependent biases have been kept as small as possible. The database can be used by the structural biology community for further development of calculation protocols, validation tools, structure‐based statistical approaches and modeling. The RECOORD database of recalculated structures is publicly available from http://www.ebi.ac.uk/msd/recoord. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Does structural and chemical divergence play a role in precluding undesirable protein interactions?
Authors: Jiménez José L. 
Published: April 2005

AbstractTo understand the evolutionary forces establishing, maintaining, breaking, or precluding protein–protein interactions, a comprehensive data set of protein complexes has been analyzed to examine the overlap between protein interfaces and the most conserved or divergent protein surface areas. The most divergent areas tend to be found predominantly away from protein interfaces, although when found at interfaces, they are associated with specific lack of cross‐reactivity between close homologues, like in antibody–antigen complexes. Moreover, the amino acid composition of highly variable regions is significantly different from any other protein surfaces. The variable regions present higher structural plasticity as a result of insertions and deletions, and favor charged over hydrophobic residues, a known strategy to minimize aggregation. This suggests that (1) a rapid rate of mutations at these regions might be continuously altering their properties, making difficult the coadaptation, in shape and chemical complementarity, to potential interacting partners; and (2) the existence of some form of selective pressure for variable areas away from interfaces to accumulate charged residues, perhaps as an evolutionary mechanism to increase solubility and minimize undesirable interactions within the crowded cellular environment. Finally, these results are placed into the context of the aberrant oligomerization of sickle‐cell anemia hemoglobin and prion proteins. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Electron ionization fragmentation mechanisms of different substituted 2,3‐dihydro‐ and 2,3,4,5‐tetrahydro‐1,5‐benzothiazepines
Authors: Ansari Farzana Latif , Hussain Latif , Nasir Saima , Sultana Sajida 
Published: April 2005

AbstractThe electron ionization induced fragmentations of ten biologically significant 2,3‐dihydro‐1,5‐benzothiazepines and the corresponding 2,3,4,5‐tetrahydro‐1,5‐benzothiazepines have been studied by low‐ and high‐resolution mass spectrometry. The fragmentations follow a general pattern, the details of which are discussed with respect to the nature and position of the substituent in the aromatic ring. The dihydro‐ and tetrahydro‐1,5‐benzothiazepines both undergo fragmentation through four routes (A–D). However, the most significant fragmentation takes place through route A, leading to the elimination of ring A or ring B of the molecule. The difference between the fragmentation patterns of dihydro‐ and tetrahydro‐1,5‐benzothiazepines appears mainly in route E where a phenylallylhydroxybenzene cation appears in all tetrahydro‐1,5‐benzothiazepines but is not observed in the corresponding dihydro derivatives. Copyright © 2005 John Wiley & Sons, Ltd.
Mappings of finite distortion: discreteness and openness for quasi-light mappings
Authors: Koskela Pekka , Hencl Stanislav 
Published: April 2005

Let

f \in W^{1,n}(\Omega ,\mathbb{R}^{n})

be a continuous mapping so that the components of the preimage of each

y \in \mathbb{R}^{n}

are compact. We show that

f

is open and discrete if

|Df(x)|^{n}⩽K(x)J_{f}(x)

a.e. where

K(x)⩾1

and

K^{n−1}/ \Phi (\mathrm{\log }(e + K)) \in L^{1}(\Omega )

for a function

Φ

that satisfies

\int _{1}^{\infty }1/ \Phi (t)\:\mathrm{d}t = \infty

and some technical conditions. This divergence condition on

Φ

is shown to be sharp.

Résumé

Soit

f \in W^{1,n}(\Omega ,\mathbb{R}^{n})

une application continue telle que les composantes connexes de la préimage de tat point

y \in \mathbb{R}^{n}

est compacte. On démontre que

f

est ouverte et discrète si

|Df(x)|^{n}⩽K(x)J_{f}(x)

p.p. oi

K(x)⩾1

et

K^{n−1}/ \Phi (\mathrm{\log }(e + K)) \in L^{1}(\Omega )

pour une fonction

Φ

telle que

\int _{1}^{\infty }1/ \Phi (t)\:\mathrm{d}t = \infty

et vérifiant des conditions techniques. La condition de divergence de l'intégrale est optimale.
On backward-time behavior of the solutions to the 2-D space periodic Navier–Stokes equations
Authors: Dascaliuc Radu 
Published: April 2005

In 1995, Constantin, Foias, Kukavica, and Majda had shown that the 2-D space periodic Navier–Stokes equations have a rich set of the solutions that exist for all times

t \in \mathbb{R}

and grow exponentially in Sobolev

H^{1}

norm when

t\rightarrow −\infty

. In the present note we show that these solutions grow exponentially (when

t\rightarrow −\infty

) in any Sobolev

H^{m}

norm (

m⩾2

) provided the driving force is bounded in

H^{m−1}

norm.

Résumé

En 1995 Constantin, Foias, Kukavica et Majda ont demontré que les équations de Navier–Stokes périodiques dans

\mathbb{R}^{2}

possèdent un ensemble ample des solutions qui existent pour tout temps

t \in \mathbb{R}

et qui ont une croissance exponentielle (pour

t\rightarrow −\infty

) dans l'espace de Sobolev

H^{1}

. Dans cet article nous montrons que ces solutions ont aussi une croissance exponentielle (pour

t\rightarrow −\infty

) dans tout espace de Sobolev

H^{m}

(

m⩾2

) à condition que la force soit dans l'espace de Sobolev

H^{m−1}

.
Multi-bump type nodal solutions having a prescribed number of nodal domains: I
Authors: Wang Zhi-Qiang , Liu Zhaoli 
Published: April 2005

This paper is concerned with analyzing their nodal property of multi-bump type sign-changing solutions constructed by Coti Zelati and Rabinowitz [Comm. Pure Appl. Math. 45 (1992) 1217]. In some cases we provide both upper and lower bounds on the number of nodal domains for these solutions.

Résumé
Cet article concerne l'analyse de la propriété nodale des solutions de multi-bosse changeant de signe, construites par Coti Zelati et Rabinowitz [Comm. Pure Appl. Math. 45 (1992) 1217]. Dans certain cas, nous obtenons la borne supérieure et inférieure de nombre des domaines nodales de ces solutions.
Pointwise curvature estimates for F-stable hypersurfaces
Authors: Winklmann Sven 
Published: April 2005

We consider immersed hypersurfaces in euclidean

\mathbb{R}^{n + 1}

which are stable with respect to an elliptic parametric functional of the form

\mathcal{F}(X) = \int _{M}F(N)\:\mathrm{d}\mu

. We prove a pointwise curvature estimate provided that

n⩽5

and

F

is sufficiently close to the area integrand. This extends the pointwise curvature estimates of Schoen, Simon and Yau [Acta Math. 134 (1975) 275] for stable minimal hypersurfaces in

\mathbb{R}^{n + 1}

and of Simon [Math. Z. 154 (1977) 265] for minimizers of

\mathcal{F}

. Our result follows from an integral curvature estimate and a generalized Simons inequality that were established recently [Calc. Var. Partial Differential Equations (2004), DOI: 10.1007/S00526-004-0306-5], together with a Moser type iteration argument.

Résumé

Nous considérons des hypersurfaces dans l'espace euclidien

\mathbb{R}^{n + 1}

qui sont stables par rapport à une fonctionnelle paramétrique elliptique de la forme

\mathcal{F}(X) = \int _{M}F(N)\:\mathrm{d}\mu

. Nous démontrons une estimation ponctuelle de la courbure sous l'hypothèse

n⩽5

et

F

est suffisamment proche de l'intégrande aire. Ce résultat étend l'estimation ponctuelle de la courbure obtenue par Schoen, Simon et Yau [Acta Math. 134 (1975) 275] pour les hypersurfaces minimales stables de

\mathbb{R}^{n + 1}

et par Simon [Math. Z. 154 (1977) 265] pour les minimiseurs de

F

. Une estimation intégrale de la courbure, une inégalité de Simons généralisée, établie récemment dans [Calc. Var. Partial Differential Equations (2004), DOI : 10.1007/S00526-004-0306-5], ainsi qu'un argument itératif de type Moser nous permet d'obtenir cette estimation ponctuelle.
Pharmacological left ventricular reverse remodeling in elderly patients receiving optimal therapy for chronic heart failure
Authors: Cioffi Giovanni , Tarantini Luigi , De Feo Stefania , Pulignano Giovanni , Del Sindaco Donatella , Stefenelli Carlo , Opasich Cristina 
Published: April 2005

AbstractBackground and aims:In recent years, reversal of established left ventricular (LV) dilatation has been increasingly recognized in middle‐aged patients with dilated cardiomyopathy receiving angiotensin‐converting enzyme (ACE) inhibitors and/or beta‐blockers. We performed this prospective study to evaluate whether optimized therapy for heart failure also induces LV reverse remodeling in older patients.Methods:One hundred and twenty‐four patients aged >70 years with LV ejection fraction <40% underwent clinical and echocardiographic evaluation at baseline and after 1 year. During the early stage of follow‐up, pharmacological therapy was optimized. LV reverse remodeling was defined as a reduction in LV end‐diastolic volume >25% from baseline to final evaluation.Results:LV reverse remodeling was recognized in 32 patients (26%). Compared to the subjects who did not improve LV geometry, those with reverse remodeling had, at baseline, higher arterial blood pressure, lower serum creatinine levels, shorter duration of symptoms of heart failure, more frequently received beta‐blocker therapy and had predominantly nonischemic aetiology. The variables associated with the development of reverse remodeling in the multivariate analysis were shorter duration of symptoms of heart failure (Odds ratio: 7.7; CI: 2.5–23.3, p=0.0001) and beta‐blocker therapy (Odds ratio: 6.0; CI: 1.6–23.3, p=0.01).Conclusions:LV reverse remodeling takes place in elderly as well as in younger heart failure patients. A significant proportion of elderly patients undergoes this favourable process which occurs prevalently in patients receiving beta‐blocker therapy with a short history of cardiac disease.
Beneficial effects of add‐on hydrochlorothiazide in rats with myocardial infarction optimally treated with quinapril
Authors: Westendorp Bart , Schoemaker Regien G. , Buikema Hendrik , de Zeeuw Dick , Boomsma Frans , van Gilst Wiek H. , van Veldhuisen Dirk J. 
Published: April 2005

AbstractBackground:The antihypertensive and renoprotective effects of ACE inhibitor (ACEi) therapy are enhanced by inducing a negative sodium balance. Whether this strategy also improves outcome of chronic ACEi treatment after myocardial infarction (MI) is unknown. Therefore, we investigated whether hydrochlorothiazide (HCTZ) or dietary sodium restriction further improves survival in ACEi‐treated rats with MI.Methods:MI was induced by coronary ligation. After 2 weeks rats were randomised to quinapril (QUI), HCTZ added to quinapril (QUI+HCTZ), or low sodium diet added to quinapril (QUI+LS). Survival was monitored for 62 weeks, after which left ventricular (LV) pressures were measured and blood for neurohumoral characterisation was collected. A separate group of rats, subjected to the same procedure, was evaluated after 35 weeks.Results:After 62 weeks, mortality was comparable in all groups. However, survival was improved by HCTZ until 35 weeks. This effect on survival was paralleled by decreased proteinuria and LV end‐diastolic pressures in QUI+HCTZ rats at 35, but not 62 weeks. Plasma renin activity was significantly decreased in QUI+HCTZ rats at 35 weeks. Contrary to HCTZ, LS added to QUI caused no benefit.ConclusionsAdding HCTZ, but not LS, to quinapril improved survival, neurohumoral status, and proteinuria during the early chronic phase of experimental post‐MI LV dysfunction. Since no adverse effects were observed, HCTZ may safely be used to improve ACEi therapy.
Incident atrial fibrillation and mortality in older adults with heart failure
Authors: Ahmed Ali , Perry Gilbert J. 
Published: April 2005

AbstractWe studied 944 hospitalized heart failure patients 65 years and older to examine the impact of incident atrial fibrillation on mortality. Patients were categorized into four groups based on past medical history and admission electrocardiogram: (1) no (neither past nor current), (2) incident (newly diagnosed), (3) past and (4) chronic (past and current) atrial fibrillation. The primary outcome was 4‐year all‐cause mortality. Bivariate and multivariable Cox proportion hazards analyses were used to determine risk of all‐cause mortality. In the multivariable model, we adjusted for various demographic and clinical covariates. Compared with patients who never had atrial fibrillation, those with incident atrial fibrillation had a 57% higher risk of death (unadjusted hazard ratio, 1.57; 95% confidence interval, 1.22–2.03). After adjustment for other covariates the association remained unchanged (adjusted hazard ratio, 1.41; 95% confidence interval, 1.08–1.83). Past or chronic atrial fibrillation was not associated with increased risk of death.
Pulsed radiofrequency applied to dorsal root ganglia causes a selective increase in ATF3 in small neurons
Authors: Hamann Wolfgang , Abou‐Sherif Sherif , Thompson Stephen , Hall Susan 
Published: April 2005

AbstractBackground This is a “proof of concept study” to test the hypothesis that pulsed radiofrequency, PRF, produces cell stress at the primary afferent level without signs of overt thermal damage. We assumed that cell stress would result in impairment of normal function, and used the expression of activating transcription factor 3, ATF3, as an indicator of cellular “stress”.Methods PRF (20 ms of 500‐kHz RF pulses, delivered at a rate of 2 Hz; maximum temperature 42 °C) was delivered either to the sciatic nerve of adult rats in mid thigh, or to the L4 anterior primary ramus just distal to the intervertebral foramen. Controls were sham‐operated or L4 axotomised. All tissues were examined 14 days after surgery. The percentage of CGRP‐ or ATF3‐positive DRG neuronal somata was calculated using image analysis software (SigmaScan Pro 4).Results ATF3 expression was upregulated in L4 DRG neuronal cell bodies, irrespective of their size, after axotomy. It was also upregulated significantly (p < 0.002) and selectively, in small and medium calibre L4 DRG neurons, when PRF was applied close to the DRG just distal to the intervertebral foramen. PRF did not produce any obvious cellular changes in the nerve or L4 DRG neurons when applied to the sciatic nerve in mid‐thigh.Conclusion PRF has a biological effect, unlikely to be related to overt thermal damage. It appears to be selective in that it targets the group of neurons whose axons are the small diameter C and Aδ nociceptive fibres.
Polyamines preferentially interact with bent adenine tracts in double-stranded DNA
Authors: Lindemose Søren , Nielsen Peter E. , Møllegaard Niels Erik 
Published: April 2005

Abstract
Polyamines, such as putrescine, spermidine and spermine, have indirectly been linked with the regulation of gene expression, and their concentrations are typically increased in cancer cells. Although effects on transcription factor binding to cognate DNA targets have been demonstrated, the mechanisms of the biological action of polyamines is poorly understood. Employing uranyl photo-probing we now demonstrate that polyamines at submillimolar concentrations bind preferentially to bent adenine tracts in double-stranded DNA. These results provide the first clear evidence for the sequence-specific binding of polyamines to DNA, and thereby suggest a mechanism by which the cellular effects of polyamines in terms of differential gene transcriptional activity could, at least partly, be a direct consequence of sequence-specific interactions of polyamines with promoters at the DNA sequence level.
Differential Effects of MK801 and Lorazepam on Heart Rate Variability in Adolescent Rhesus Monkeys (Macaca Mulatta)
Authors: Bennett Allyson J , DePetrillo Paolo B 
Published: April 2005

Abstract:

Previous research shows that ketamine significantly alters cardiac signal regulation in rhesus monkeys, however relatively little is known about the mechanism for this effect. In the study reported here the relative contributions of NMDA receptor activation on cardiac signal dynamics were determined by administering a specific NMDA antagonist, MK801, to rhesus monkeys. The general effects of sedation were assessed by measuring cardiac response to lorazepam, a sedative drug without direct NMDA receptor activity. Electrocardiographic signal dynamics were examined before and after I.V. administration of either MK801 (0.16 mg/kg) or lorazepam (0.48 mg/kg). Inter-beat interval time series data were analyzed in the frequency domain after Fourier transform, and a nonlinear measure of autocorrelation, the Hurst exponent (H), was derived. After MK801 administration, log [HF /Total power] increased post-infusion (M = 1.11, SD = 0.45) compared with pre-infusion values [M = −0.19, SD = 0.32, F(1,4) = 19.49, P = 0.01] while H decreased, mean pre versus post 0.52+/−S.D. 0.10 versus 0.01+/− 0.05, P = 0.0002. Lorazepam administration did not significantly alter heart rate variability measures obtained in the frequency or nonlinear domains. To our knowledge, this is the first study that has defined the effects of peripherally administered MK801 on cardiovascular dynamics in primates and establishes that peripheral administration of NMDA antagonists result in large increases the high-frequency components of cardiac rhythm and increased heart rate variability compatible with MK801-associated increases in parasympathetic outflow.
Endogenous Estrogens Increase Postischemic Hyperemia in the Skin Microcirculation
Authors: Stojanovic Vesna , Küng Fides , Spieker Lukas E , Binggeli Christian , Sudano Isabella , Hayoz Daniel , Lüscher Thomas F , Noll Georg 
Published: April 2005

Abstract:

Estrogens have been recognized as a major regulator of vascular tone and structure, particularly in the skin. The objective of this study was to investigate the effects of endogenous estrogens on the skin microcirculation. Skin blood flow was measured at the forearm at rest and during postischemic hyperemia using laser Doppler flowmetry in 32 healthy women (mean age 34.5 ± 3.9 years) involved in an in-vitro fertilization program. Women were treated for 10 to 12 days with gonadotropin-releasing hormone agonist (total dose 40.3 ± 3.3 mg) and human menopausal gonadotropin (1942 ± 801 IE) or follicle-stimulating hormone (2544 ± 1071 IE) according to individual estrogen levels. Plasma estrogen levels increased from 132 ± 90 pmol/L (36 ± 25 pg/mL) to 8471 ± 4386 pmol/L (2308 ± 1195 pg/mL) during treatment (P < 0.0001). Maximal hyperemic blood flow increased from 353 ± 81% before treatment to 516 ± 144% after hormonal stimulation (P < 0.0001), whereas basal skin flow was not altered. This study shows that endogenous estrogens enhance the postischemic hyperemic response of the skin microcirculation.
Mediation of the Effect of Nicotine on Kir6.1 Channels by Superoxide Anion Production
Authors: Hanna Salma Toma , Cao Kun , Sun Xianfeng , Wang Rui 
Published: April 2005

Abstract:

KATP channels are a complex of regulatory sulfonylurea receptor subunits and the pore-forming inward rectifiers such as Kir6.1. Using the whole-cell patch-clamp technique, we investigated the interaction of nicotine with the Kir6.1 subunit as well as the underlying mechanism. Stable expression of Kir6.1 in HEK-293 cells yielded a detectable inward rectifier KATP current. This inward current was significantly inhibited by PNU-37883A and by a specific anti-Kir6.1 antibody. Nicotine at 30 and 100 μM increased Kir6.1 currents by 42 ± 11.8% and 26.2 ± 14.6%, respectively (n = 4-6, P < 0.05). In contrast, nicotine at 1-3 mM inhibited Kir6.1 currents (P < 0.05). Nicotine at 100 μM increased the production of superoxide anion (O2
.-) by 20.3 ± 5.7%, whereas at 1 mM it significantly decreased the production of O2
.- by 37.7 ± 4.3%. Coapplication of hypoxanthine (HX) and xanthine oxidase (XO) to the transfected HEK-293 cells resulted in a significant and reproducible increase in Kir6.1 currents (P < 0.05). The stimulatory effect of HX/XO on Kir6.1 current was abolished by tempol, a scavenger of O2
.-. Tempol also abolished the stimulatory effect of 30 μM nicotine on Kir6.1 currents. In conclusion, nicotine stimulates Kir6.1 channel at least in part through the production of O2
.-.
Triptans Induce Vasoconstriction of Human Arteries and Veins from the Thoracic Wall
Authors: Wackenfors Angelica , Jarvius Malin , Ingemansson Richard , Edvinsson Lars , Malmsjö Malin 
Published: April 2005

Abstract:

A common side effect of migraine treatment with triptans is chest symptoms. The origin of these symptoms is not known. The aim of the present study was to examine the vasocontractile effect of triptans in human arteries and veins from the thoracic wall and in coronary artery bypass grafts. In vitro pharmacology experiments showed that the 5-hydroxytryptamine (5-HT) type 1B and 1D receptor agonists, eletriptan, naratriptan, rizatriptan, sumatriptan, and zolmitriptan, induced vasoconstriction in the thoracic blood vessels from 38% to 57% of the patients. 5-carboxamidotryptamine (5-CT) and sumatriptan elicited a vasoconstriction that was antagonized by the 5-HT1B receptor antagonist SB224289, whereas the 5-HT1D receptor antagonist BRL115572 had no effect. 5-HT induced a contraction that was inhibited by the 5-HT2A receptor antagonist ketanserin. 5-HT2A, 5-HT1B, and 5-HT1D receptor mRNA levels were detected by real-time PCR in all blood vessels studied. In conclusion, triptans induce vasoconstriction in arteries and veins from the thoracic wall, most likely by activation of 5-HT1B receptors. This response could be observed in only 38% to 57% of the patients, which may provide an explanation for why a similar number of patients experience chest symptoms as a side effect of migraine treatment with triptans.