bluuebunny/crossref_metadata_2025_split huggingface dataset:
Operator recognition by the phage 434 cI repressor: MD simulations of free and bound 50‐bp DNA reveal important differences between the OR1 and OR2 sites
Authors: Hartmann Brigitte , Sullivan Michael R. , Harris Lester F. 
Published: January 2003

AbstractUsing molecular dynamics simulations in explicit solvent, we investigated the behavior of a 50‐bp DNA sequence containing the 434 bacteriophage operators OR1 and OR2 separated by an 8‐bp spacer. Two simulations of 1 ns each were carried out, with DNA alone and with DNA complexed to dimers of the R1–69 DNA binding domain of the phage 434 cI repressor protein at the OR1 and OR2 sites. Strong correlations among average structural parameters are observed between our simulations and available experimental data for the bound OR1/OR2 subsites. In the free state, some differences appear between the three relevant fragments (OR1, the spacer, and OR2). Unbound OR1 exhibits a large, shallow major groove into which the base atoms protrude and is also bent toward the major groove. This structure is maintained because structural fluctuations are weak. Unbound OR2 resembles canonical B‐DNA although the structural parameters show greater fluctuations, essentially due to a malleable step (the innermost CpA/TpG), absent in OR1. Complexation with the proteins slightly alters the base positions but strongly modifies the sugar and backbone motions. The most crucial repressor effects are changes in the flexibility of the OR1/OR2 sites. Structural fluctuations are enhanced for OR1, conferring a favorable energetic contribution to the OR1 binding, whereas they are reduced for OR2. Therefore, both structural and dynamic properties of DNA suggest OR1 is the most attractive site for the repressor, which may explain the different binding association constants observed for the OR1 and OR2 sites. Finally, we also investigated the impact of the protein on the DNA backbone dynamics and find that direct or indirect interactions facilitate the DNA structural variations required for achieving complementarity with the protein. © 2003 Wiley Periodicals, Inc. Biopolymers 68: 250–264, 2003
Surface electrostatic effects in oligonucleotide microarrays: Control and optimization of binding thermodynamics
Authors: Vainrub Arnold , Montgomery Pettitt B. 
Published: January 2003

AbstractWe present a theoretical thermodynamic framework for the design of more efficient oligonucleotide microarrays. A general thermodynamic relation is derived to describe the electrostatic surface effects on the binding of the assayed biomolecule to a surface‐tethered molecular probe. The relation is applied to analyze how the nucleic acid target, the oligonuleotide probe, and their DNA duplex electrostatic interactions with the surface affect the hybridization on DNA arrays. Taking advantage of a closed form exact solution of the linear Poisson–Boltzmann equation for a charged ion‐penetrable sphere in electrolyte solution interacting with a plane wall, we study the effects of the surface and solution conditions. Binding free energy is found as a function of the surface material, dielectric or metal, the surface charge density, linker molecule length, temperature, and added salt content. The charge or electric potential of the dielectric or metal surface, respectively, is shown to dominate the hybridization, especially at low added salt or short linker length. We predict that substantial enhancement of sensitivity, selectivity, and reliability of microarrays can be achieved by control of the surface conditions. As examples, we discuss how to overcome two limitations of current technologies: nonequal sensitivity of the probes with different GC and AT bases content, and poor match/mismatch discrimination. In addition, we suggest the design of microarray conditions where the tested nucleic acid is unfolded, thus making possible the screening of a larger sequence with single nucleotide resolution. These promising findings are discussed and further experimental tests suggested. © 2003 Wiley Periodicals, Inc. Biopolymers 68: 265–270, 2003
Molecular mass and chain conformation of carboxymethylated derivatives of β‐glucan from sclerotia of Pleurotus tuber‐regium
Authors: Zhang Mei , Zhang Lina , Chi Keung Cheung Peter 
Published: January 2003

AbstractSeven water‐insoluble (1 → 3)‐β ‐D‐glucan fractions TM8‐1 to TM8‐7 with weight‐average molecular mass Mw ranged from 2.22 to 77.4 × 104 obtained from the sclerotia of Pleurotus tuber‐regium were carboxymethylated to produce the water‐soluble fractions CTM8‐1 to CTM8‐7 with Mw ranged from 3.87 to 87.8 × 104. The degree of substitution (DS) of CTM8 fractions was analyzed by ir and elemental analysis (EA) to be 0.3–0.68. The Mw and the intrinsic viscosity [η] of the CTM8 fractions were measured by size‐exclusion chromatography combined with multiangle laser light scattering (SEC‐MALLS), MALLS, and viscometry in phosphate buffer solution (PBS) at 37°C. The dependencies of [η] and radius of gyration 〈s2〉z1/2 on Mw for the CTM8 samples were found to be [η] = (8.82 ± 0.03) × 10−3 Mw0.78 ± 0.04 (cm3 g−1) and 〈s2〉z1/2 = (3.09 ± 0.05) × 10−3 Mw0.75 ± 0.06 (nm) in the Mw range from 3.87 × 104 to 53.2 × 104. Based on current theories for wormlike chain model, the conformational parameters of the CTM8 were obtained to be 790 (nm−1) for ML, 9.6 (nm) for q, which were higher than those of the native TM8 fractions, suggesting a more extended flexible chain of CTM8 in PBS. On the whole, the CTM8 fractions showed higher antitumor activity than their corresponding TM8 fractions. In view of data from molecular parameters and bioactivity, the antitumor activity of the CTM8 fractions may be correlated to its water solubility and relatively extended chain. © 2002 Wiley Periodicals, Inc. Biopolymers 68: 150–159, 2003
Simulation of the bis‐(penicillamine) enkephalin in ammonium chloride solution: A comparison with sodium chloride
Authors: Marlow Gail E. , Pettitt B. Montgomery 
Published: January 2003

AbstractIn order to quantify specific ion effects, a simulation study of bis(penicllamine) enkephalin, also known as DPDPE, has been performed in aqueous ammonium chloride solution and has been compared to a previous simulation of DPDPE in aqueous sodium chloride solution. Global thermodynamics have been calculated for a model system and the solution environment around DPDPE has been characterized. Associations of ions with DPDPE have been investigated. The observed differences between sodium chloride solution and ammonium chloride solution suggest that individual cations affect the solvation and peptide binding properties of a given anion. © 2003 Wiley Periodicals, Inc. Biopolymers 68: 192–209, 2003
Folding of peptides characterized by c3Val, a highly constrained analogue of valine
Authors: Peggion Cristina , Formaggio Fernando , Crisma Marco , Toniolo Claudio , Jiménez Ana I. , Cativiela Carlos , Kaptein Bernard , Broxterman Quirinus B. , Saviano Michele , Benedetti Ettore 
Published: January 2003

AbstractUsing a combined chemical/chiral chromatographic approach we synthesized an N‐protected derivative of (R)–c3Val, a severely conformationally restricted Cα‐tetrasubstituted α‐amino acid characterized by a Cβ,β‐dimethylated cyclopropane system. A set of terminally protected derivatives and model peptides (to the heptamer level), containing one or two (R)–c3Val residues in combination with either Aib or Gly residues, was prepared by solution methods. A detailed solution and crystal‐state conformational investigation, based on Fourier transform infrared (FTIR) absorption, 1H‐NMR, and x‐ray diffraction techniques, performed in comparison with a similar study on related derivatives and peptides rich in (αMe)Val, the prototype of Cα‐tetrasubstituted α‐amino acids of this subfamily, allowed us to conclude the following: (a) c3Val is a good β‐bend and helix former, although less efficient than (αMe)Val. (b) The relationship between α‐carbon chirality and screw sense of the folded structure formed is the same as that of (αMe)Val, i.e., the (R)‐enantiomer has a strong left‐handed bias. (c) c3Val seems more prone than (αMe)Val to fold into a γ‐bend conformation. The conformational propensities of Cβ,β‐disubstituted Ac3c residues are also discussed in comparison with those of the parent cyclopropane residue. © 2002 Wiley Periodicals, Inc. Biopolymers 68: 178–191, 2003
The thermodynamic contribution of the 5‐methyl group of thymine in the two‐ and three‐stranded complexes formed by poly(dU) and poly(dT) with poly(dA)
Authors: Ross Philip D. , Howard Frank B. 
Published: January 2003

AbstractTo assess the thermodynamic contribution of the 5‐methyl group of thymine, we have studied the two‐stranded helical complexes poly(dA) · poly(dU) and poly(dA) · poly(dT) and the three‐stranded complexes—poly(dA) · 2poly(dU), poly(dA) · poly(dT) · poly(dU) and poly(dA) · 2poly(dT)—by differential scanning calorimetry, and uv optical melting experiments. The thermodynamic quantities associated with the 3 → 2, 2 → 1, and 3 → 1 melting transitions are found to vary with salt concentration and temperature in a more complex manner than commonly believed. The transition temperatures, Tm, are generally not linear in the logarithm of concentration or activity of NaCl. The change in enthalpy and in entropy upon melting varies with salt concentration and temperature, and a change in heat capacity accompanies each transition. The poly(dA) · 2poly(dU) triple helix is markedly different from poly(dA) · 2poly(dT) in both its CD spectrum and thermodynamic behavior, while the poly(dA) · poly(dT) · poly(dU) triple helix resembles poly(dA) · 2poly(dT) in these properties. In comparing poly(dA) · 2poly(dT) with either the poly(dA) · poly(dT) · poly(dU) or the poly(dA) · 2poly(dU) triplexes, the substitution of thymine for uracil in the third strand results in an enhancement of stability against the 3 → 2 dissociation of ΔΔG° = −135 ± 85 cal (mol A)−1 at 37°C. This represents a doubling of the absolute stability toward dissociation compared to the triplexes with poly(dU) as the third strand. The poly (dA) · poly (dT) duplex is more stable than poly(dA) · poly(dU) by ΔΔG° = −350 ± 60 cal (mol base pair)−1 at 37°C. Poly(dA) · poly(dT) has 50% greater stability than poly(dA) · poly(dU) as a result of the dT for dU substitution in the duplex. © 2003 Wiley Periodicals, Inc. Biopolymers 68: 210– 222, 2003
Initial multicenter experience with a novel distal protection filter during carotid artery stent implantation
Authors: Grube Eberhard , Colombo Antonio , Hauptmann Eugen , Londero Hugo , Reifart Nicolaus , Gerckens Ulrich , Stone Gregg W. 
Published: January 2003

AbstractAtheroembolization resulting in transient or permanent neurologic impairment is the most common complication of catheter‐based percutaneous carotid artery intervention. Protection of the distal cerebral vasculature during carotid stent implantation may enhance procedural safety. Carotid stent implantation with distal cerebral protection using the FilterWire EX was performed in 35 consecutive patients undergoing 36 procedures at six centers. The FilterWire was delivered and deployed successfully in all 36 cases, and embolic material was retrieved from 74% of procedures. The 30‐day rate of major adverse events (death, major or minor stroke) was 0%. Transient ipsilateral periprocedural neurologic ischemia developed in two patients (5.7%), both resolving within 30 min. Distal cerebral protection with the FilterWire during carotid stenting is feasible and safe, results in capture and extraction of atheroembolic debris in the majority of patients while affording uninterrupted cerebral perfusion, and in this initial multicenter experience was associated with a high rate of procedural success without major complications. Cathet Cardiovasc Intervent 2003;58:139–146. © 2003 Wiley‐Liss, Inc
The efficacy of using pulmonary vein wedge pressure for the estimation of pulmonary artery pressure in children with congenital heart disease
Authors: Toyono Manatomo , Harada Kenji , Tamura Masamichi , Yasuoka Kenji , Oyama Tomomi , Takada Goro 
Published: January 2003

AbstractThe objectives of this study were to assess the accuracy of pulmonary vein wedge pressure (PVWP) in estimating pulmonary artery pressure (PAP) in various types of congenital heart disease, including single‐ventricle physiology. The systolic, diastolic, and mean values of both PAPs and PVWPs were measured in 30 patients (a total of 46 points). Pulmonary artery pressure ranged from 13 to 74 (34 ± 15) mm Hg in systole, 5 to 25 (13 ± 6) mm Hg in diastole, and 6 to 48 (18 ± 10) mm Hg in mean. As a whole, good correlations between PAPs and PVWPs were observed (systole, r = 0.70; diastole, r = 0.85; mean, r = 0.82; P < 0.0001). However, with an increase in PAP, the discrepancy between PAPs and PVWPs increased. When the mean PVWP was more than 18 mm Hg, the mean PVWP in 14 of 24 (58%) underestimated the mean PAP by up to 22 mm Hg (mean difference, −1.7 ± 5.8 mm Hg). On the other hand, all of the patients with mean PVWPs less than 18 mm Hg (n = 22) had mean PAPs less than 18 mm Hg (r = 0.86; PAP = 1.11 × PVWP − 1.41; P < 0.0001), and the mean difference was −0.2 ± 1.8 mm Hg. The mean PVWP can accurately estimate the mean PAP in children with congenital heart disease who have a mean PVWP less than 18 mm Hg. Cathet Cardiovasc Intervent 2003;58:232–237. © 2003 Wiley‐Liss, Inc.
Directional coronary atherectomy vs. rotational atherectomy for the treatment of in‐stent restenosis of native coronary arteries
Authors: Sanchez Pedro L. , Rodriguez‐Alemparte Maximo , Colon‐Hernandez Pedro J. , Pomerantsev Eugene , Inglessis Ignacio , Mahdi Nasser A. , Leinbach Robert C. , Palacios Igor F. 
Published: January 2003

AbstractManagement of in‐stent restenosis has become a significant challenge in interventional cardiology. Since the mechanism of in‐stent restenosis is predominantly intimal hyperplasia, debulking techniques have been used to treat this condition. This study is a nonrandomized comparison of the immediate and long‐term results of directional coronary atherectomy (DCA; n = 58) vs. high‐speed rotational atherectomy (ROTA; n = 61) for the treatment of in‐stent restenosis of native coronary arteries. There were no in‐hospital deaths, Q‐wave myocardial infarctions, or emergency coronary artery bypass surgery in either group. DCA resulted in a larger postprocedural minimal luminal diameter of (2.57 ± 0.51 vs. 2.14 ± 0.37 mm; P < 0.0001) and a larger acute gain (1.83 ± 0.52 vs. 1.42 ± 0.48 mm; P < 0.0001). Furthermore, 12‐month clinically indicated target lesion revascularization (39% vs. 21%; P = 0.02) and long‐term follow‐up MACE (44% vs. 28%; P = 0.03) was greater in the ROTA group. The present study suggests that DCA appears to be superior to ROTA for the treatment of in‐stent restenosis of native coronary arteries. Compared to ROTA, the debulking effect of DCA leads to a larger postprocedure minimal luminal diameter, and a lower incidence of subsequent target lesion revascularization and MACE. Cathet Cardiovasc Intervent 2003;58:155–161. © 2003 Wiley‐Liss, Inc.
Balloon angioplasty and stenting of multiple intralobar pulmonary arterial stenoses in adult patients
Authors: Rothman Abraham , Levy Denis J. , Sklansky Mark S. , Grossfeld Paul D. , Auger William R. , Ajami Gholam H. , Behling Cynthia A. 
Published: January 2003

AbstractBalloon angioplasty and stent placement for pulmonary arterial stenoses in children are well‐established therapies. In contrast, management of isolated peripheral pulmonary arterial stenoses in adults remains relatively unexplored. Four women (ages 18–63 years) with multiple discrete intralobar pulmonary arterial stenoses were treated with balloon angioplasty. Initially, 4–5 stenoses were dilated in each patient. The mean minimum diameter of the stenoses increased from 1.3 to 3.1 mm (P < 0.001), and the mean ratio of right ventricular to aortic systolic pressure decreased from 0.92 to 0.62 (P < 0.05). Each patient had marked symptomatic improvement. However, three patients developed recurrence of symptoms 4–24 months after angioplasty, and two had angiographic evidence of restenosis at previously dilated sites. These restenoses were treated with repeat angioplasty or stent implantation (three stents in each patient). One of these two patients developed near‐occlusive restenosis of the stents and had successful bilateral lung transplantation. The other patient had a third catheterization with successful implantation of three additional stents. The third patient with recurrent symptoms died 2 years later, without further intervention. Transcutaneous catheter therapy for multiple intralobar pulmonary arterial stenoses in adults is highly successful acutely, but restenosis is common within several months. For some patients, balloon angioplasty and stent implantation may provide definitive management, while for others these procedures may serve as a bridge to lung transplantation. Cathet Cardiovasc Intervent 2003;58:252–260. © 2003 Wiley‐Liss, Inc.
Transcatheter occlusion of patent ductus arteriosus using a new angled Amplatzer duct occluder: Initial clinical experience
Authors: Masura Jozef , Gavora Pavol , Podnar Tomaž 
Published: January 2003

AbstractIn the present study, we report the initial clinical experience with the new angled Amplatzer duct occluder (ADO) for the percutaneous closure of patent ductus arteriosus (PDA). Percutaneous closure of PDA using standard ADO in infants and in patients with small PDA ampulla is difficult, or even impossible, due to protrusion of the aortic disk into the descending thoracic aorta. The aortic disk of an angled ADO is angled at 32° to the body of the device and concave toward the aorta to prevent protrusion of the disk into the aorta. Percutaneous closure of PDA was attempted in nine patients with a median age of 5.2 years (range, 0.5–12.7) and median weight of 20 kg (range, 4.9–55). Selection of the occluder and the implantation technique were similar to the standard ADO. The minimal PDA diameter ranged from 2.1 to 3.7 mm (median, 2.5 mm). Occluders were successfully implanted in all patients. Immediate complete PDA closure was achieved in all patients. There were no complications. The new angled ADO is a safe and effective device for PDA closure, particularly suitable for infants and patients with small PDA ampulla. Further studies and long‐term follow‐up are necessary to confirm our initial experience. Cathet Cardiovasc Intervent 2003;58:261–267. © 2003 Wiley‐Liss, Inc.
Restick following initial Angioseal use
Authors: Applegate Robert J. , Rankin Kevin M. , Little William C. , Kahl Frederic R. , Kutcher Michael A. 
Published: January 2003

AbstractThe Angioseal hemostatic device is currently in widespread use for arterial closure after both diagnostic and interventional procedures. Resticking of the artery in which an Angioseal device has been placed has been discouraged for up to 90 days after the initial device placement because of theoretical concerns of disruption or dislodgment of the hemostatic plug. However, no data are available to address this concern. We evaluated the incidence of vascular complications following restick of the artery in which an Angioseal device had been deployed ≤ 90 days previously in 181 patients. Restick occurred 1–7 days after device placement in 80 patients, 8–30 days in 34 patients, and 31–90 days in 66 patients. There were no major bleeding, vascular repair, vessel occlusion, or embolizations. Three large hematomas (1.7%) were noted. These data suggest that restick can be performed safely after initial Angioseal deployment. Cathet Cardiovasc Intervent 2003;58:181–184. © 2003 Wiley‐Liss, Inc.
Double scaling limit in the random matrix model: The Riemann‐Hilbert approach
Authors: Bleher Pavel M. , Its Alexander R. 
Published: January 2003

AbstractWe prove the existence of the double scaling limit in the unitary matrix model with quartic interaction, and we show that the correlation functions in the double scaling limit are expressed in terms of the integrable kernel determined by the ψ function for the Hastings‐McLeod solution to the Painlevé II equation. The proof is based on the Riemann‐Hilbert approach, and the central point of the proof is an analysis of analytic semiclassical asymptotics for the ψ function at the critical point in the presence of four coalescing turning points. © 2003 Wiley Periodicals, Inc.
Long‐time asymptotics of moving boundary problems using an Ehrenpreis‐type representation and its Riemann‐Hilbert nonlinearization
Authors: Fokas A. S. , Schultz P. F. 
Published: January 2003

AbstractA new method for solving boundary value problems for linear and integrable nonlinear PDEs has recently been introduced. For a linear evolution equation with dispersion relation ω(k), in a time‐dependent concave domain, 𝓁(t) < x < ∞, 𝓁″(t) < 0, this method yields the solution q(x, t) as a line integral in the complex k‐plane, whose integrand has explicit (x, t)‐dependence of the form exp[ikx − iω(k)t]. For a nonlinear integrable evolution equation the situation is similar, but the integrand also involves the solution M(x, t, k) to a Riemann‐Hilbert problem whose jump function also has explicit (x, t)‐dependence of exponential form. These representations for linear and for nonlinear evolution equations are convenient for the study of the long‐time asymptotics, using the stationary phase and the Deift‐Zhou methods, respectively. Here we study the long‐time asymptotics in a time‐dependent concave domain for a linear evolution equation with a spatial derivative of arbitrary order, and for the defocusing nonlinear Schrödinger equation. For completeness we also study the long‐time asymptotics for a linear evolution equation with a spatial derivative of arbitrary order in the fixed domain 0 < x < ∞. © 2003 Wiley Periodicals, Inc.
Quercetin, a bioflavonoid, reverses development of tolerance and dependence to morphine
Authors: Singh Amanpreet , Naidu Pattipati S. , Kulkarni Shrinivas K. 
Published: January 2003

AbstractQuercetin, a bioflavonoid (25 and 50 mg/kg), when chronically administered for 9 days, failed to produce any significant change in tail flick latency as compared to control mice. However, repeated administration of quercetin (25 and 50 mg/kg) for 9 days attenuated the development of tolerance to the analgesic effect of morphine (10 mg/kg). Quercetin (25 and 50 mg/kg) also suppressed naloxone (2 mg/kg)‐precipitated withdrawal jumps on day 10 in morphine‐tolerant mice. Pretreatment of mice with quercetin (10–50, ip) significantly reversed the morphine (5 mg/kg)‐induced delay in gastric transit, whereas a higher dose of quercetin (100 mg/kg) did not have any significant effect on morphine‐induced delay in gastric transit. Quercetin per se had no effect on gastric transit. In conclusion, the results of the present study suggest potential use of quercetin in alleviating the adverse effects of opioid treatment. Drug Dev. Res. 57:167–172, 2002. © 2003 Wiley‐Liss, Inc.