bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comparative study of the COX‐1 and COX‐2 isozymes bound to lipid membranes
Authors: Wan Shunzhou , Coveney Peter V. 
Published: October 2008

AbstractThe monotopic proteins COX‐1 and ‐2 in dimeric form bound to lipid bilayer membranes are studied using molecular dynamics simulations within an aqueous environment. The 25‐ns simulations are performed for both isozymes with arachidonic acid bound in the cyclooxygenase sites. The interactions between the enzymes and the lipids are analyzed, providing insight into the attachment mechanism of monotopic proteins to membranes. Our study reveals some key differences between the two isozymes that include the orientations at which they sit on the surface of the membranes and the depths to which they embed within the membranes. The differences in membrane association of the isozymes indicate that they may integrate distinctively with the same membrane, and/or with different membranes or their lipid components. Our results indicate that arachidonic acid can be bound in the cyclooxygenase active site in distinct catalytically competent conformations that lead to certain hydroperoxy acids; and the arachidonic acid and/or cyclooxygenase sites undergo a conformational change which makes only one subunit of each homodimer catalytically active. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009
Interaction of two functional groups through the benzene ring: Theory and experiment
Authors: Böhm Stanislav , Exner Otto 
Published: October 2008

AbstractEnergies of 132 benzene para bis‐derivatives calculated within the framework of the density functional theory at the level B3LYP/6‐311+G(d,p)//B3LYP/6‐311+G(d,p) were used for correlations of two types. Correlation with the experimental enthalpies of formation clearly revealed that the published experimental data are generally not dependable and may be loaded with errors of more than 10 kJ mol−1. On the other hand, the calculated relative energies are biased so that the interaction of the two substituents is systematically overestimated. This shortcoming was insignificant for our correlations of the second type, in which the interaction of substituents expressed in terms of isodesmic reactions was analyzed depending on the effects of inductive and resonance. The results depended strongly on the character of substituents. When one substituent is an electron donor and the other is an acceptor, the inductive‐resonance model works and the classical resonance picture is adequate. With two acceptor substituents, this model is still acceptable with lower precision (as crossed conjugation), but with two donors it fails completely and may be acceptable only for a much restricted subclass of strong donors. Many correlations described in the literature must be viewed with great caution when they are based only on a relatively small number of data, in which substituents of different types are not represented in a comparable number. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
CASSCF and multireference CI with singles and doubles study of low‐lying valence and Rydberg states of 2H‐tetrazole
Authors: de Souza Miguel A. F. , Ventura Elizete , Araújo Regiane C. M. U , Ramos Mozart N. , do Monte Silmar A. 
Published: October 2008

AbstractComplete active space self‐consistent field (CASSCF) and multireference CI with singles and doubles (MR‐CISD) calculations [including extensivity corrections, at MR‐CISD+Q and multireference averaged quadratic coupled cluster (MR‐AQCC) levels] have been performed to characterize the low‐lying valence and the Rydberg states of 2H‐tetrazole. The highest level results (MR‐AQCC/d′‐aug′‐cc‐pVDZ) indicate the following ordering of the valence singlet excited states: S1 (n–π*), 6.06 eV; S2 (n–π*), 6.55 eV; S3 (π–π*), 6.55 eV. The MR‐CISD+Q/d′‐aug′‐cc‐pVDZ results indicate the same ordering, but at slight higher energies: 6.16, 6.68, and 6.69 eV, respectively. According to our MR‐CISD+Q/d′‐aug′‐cc‐pVDZ results, the next two states are Rydberg states, at 7.69 eV (π–3s) and 7.89 eV (n–3s). The calculated energies of these two states, as well as their proximity, are consistent with the conclusion reached by Palmer and Beveridge (Chem Phys 1987, 111, 249) that the first band of the photoelectron spectrum of 2H‐tetrazole is likely to be associated to the first two ionizations processes (of π and N lone pair electrons), at energies close to 11.3 eV. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009
An efficient grid‐based scheme to compute QTAIM atomic properties without explicit calculation of zero‐flux surfaces
Authors: Rodríguez Juan I. , Köster Andreas M. , Ayers Paul W. , Santos‐Valle Ana , Vela Alberto , Merino Gabriel 
Published: October 2008

AbstractWe introduce a method to compute atomic properties according to the “quantum theory of atoms in molecules.” An integration grid in real space is partitioned into subsets, ωi. The subset, ωi, is composed of all grid points contained in the atomic basin, Ωi, so that integration over Ωiis reduced to simple quadrature over the points in ωi. The partition is constructed from deMon2k's atomic center grids by following the steepest ascent path of the density starting from each point in the grid. We also introduce a technique that exploits the cellular nature of the grid to make the algorithm faster. The performance of the method is tested by computing properties of atoms and nonnuclear attractors (energies, charges, dipole, and quadrupole moments) for a set of representative molecules. © 2008 Wiley Periodicals, Inc. J Comput Chem 2009
The nitrogen edge‐doped effect on the static first hyperpolarizability of the supershort single‐walled carbon nanotube
Authors: Xu Hong‐Liang , Wang Fang‐Fang , Li Zhi‐Ru , Wang Bing‐Qiang , Wu Di , Chen Wei , Yu Guang‐Tao , Gu Feng Long , Aoki Yuriko 
Published: October 2008

AbstractThe nitrogen edge‐doped effect on the structure, dipole moment, and first hyperpolarizability of the supershort single‐walled carbon nanotube (5, 0) has been studied systematically. For the nitrogen edge‐doped effect on the structure, the mean diameter on the nitrogen‐doped side (Du) decreases as the number of doped‐nitrogen (n) increases (4.044 (1) > 3.991 (2) > 3.941 (3) > 3.891 (4) > 3.844 Å (5)). Significantly, the nitrogen edge‐doped effects on the dipole moment and first hyperpolarizability are revealed for the first time and these new effects are dramatic for the supershort single‐walled carbon nanotube (5, 0). Among the β0 values of these seven nitrogen‐doped structures, the largest β0 (3155 au) is larger by almost 450 times than the very small β0 (7 au) of undoped structure (D5h). For nitrogen‐doped structures, the order of the β0 values is 3155 (1) > 2677 (2A) ≈ 2817 (2B) > 1465 (3A) ≈ 1458 (3B) > 670 (4) > 254 au (5), which shows two interesting relationships between the β0 value and nitrogen‐doped number: (1) the smaller the nitrogen‐doped number, the larger the β0 value. (2) The structures with the same number of doped‐nitrogen have almost the same β0 values (1465 for 3A and 1458 au for 3B). As for the frequency‐dependent β (−ω; ω, 0) and β (−2ω; ω, ω), the dependence on the nitrogen‐doped number (n) is similar to the case of static β0. For β (−2ω; ω, ω) values at ω = 0.005 au are 3220 (1) > 2720 (2A) ≈ 2862 (2B) > 1480 (3A) ≈ 1477 (3B) > 676 (4) > 256 au (5). In addition, the important monotonic dependences of the β value on the Du and electronic spatial extent 〈R2〉 are also observed. The new knowledge of influence the β value will be beneficial to design high‐performance nonlinear optical (NLO) materials. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Conformational transition pathway in the allosteric process of calcium‐induced recoverin: Molecular dynamics simulations
Authors: Li Ji‐Lai , Geng Cai‐Yun , Bu Yuxiang , Huang Xu‐Ri , Sun Chia‐Chung 
Published: October 2008

AbstractRecoverin is an important neuronal calcium sensor (NCS) protein, which have been implicated in a wide range of Ca2+ signaling events in neurons and photoreceptors. To characterize the conformational transition of recoverin from the myristoyl sequestered state to the extrusion state, a series of conventional molecular dynamics (CMD) and targeted molecular dynamics (TMD) simulations were performed. The 36.8 ns long CMD and TMD simulations on recoverin revealed a reliably conformational transition pathway, which can be viewed as a sequential two‐stage process. A very important mechanistic conclusion from the present TMD simulations is that the hydrophobic and hydrophilic interactions modulate the allostery cooperatively in the conformational transition pathway. In the first stage, three salt‐bridges broken between Lys‐84 and Gly‐124, between Lys‐5 and Glu‐103 and between Gly‐16 and Lys‐97 are major components to destabilize the structure of state T and trigger the swivel of the N‐ and C‐terminal domains. In the second stage, the rupture of H‐bond Phe‐56‐O…H(O)‐Thr‐21 leads to the two helices of EF‐1 apart from each other, destabilizing the hydrophobic interactions of the myristoyl group with its environment, whereas the making of H‐bond Leu‐108‐O…H(O)‐Ser‐72 helps the interfacial domain maintain its structural integrity during the course of the myristoyl extrusion. The molecular dynamics simulations results are beneficial to understanding the mechanism of how and why NCS proteins make progress in the photo‐signal transduction processes. Further experimental and theoretical studies are still very desirable. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Notes on quantitative structure‐properties relationships (QSPR) (1): A discussion on a QSPR dimensionality paradox (QSPR DP) and its quantum resolution
Authors: Carbó‐Dorca Ramon , Gallegos Ana , Sánchez Ángel J. 
Published: October 2008

AbstractClassical quantitative structure‐properties relationship (QSPR) statistical techniques unavoidably present an inherent paradoxical computational context. They rely on the definition of a Gram matrix in descriptor spaces, which is used afterwards to reduce the original dimension via several possible kinds of algebraic manipulations. From there, effective models for the computation of unknown properties of known molecular structures are obtained. However, the reduced descriptor dimension causes linear dependence within the set of discrete vector molecular representations, leading to positive semi‐definite Gram matrices in molecular spaces. To resolve this QSPR dimensionality paradox (QSPR DP) here is proposed to adopt as starting point the quantum QSPR (QQSPR) computational framework perspective, where density functions act as infinite dimensional descriptors. The fundamental QQSPR equation, deduced from employing quantum expectation value numerical evaluation, can be approximately solved in order to obtain models exempt of the QSPR DP. The substitution of the quantum similarity matrix by an empirical Gram matrix in molecular spaces, build up with the original non manipulated discrete molecular descriptor vectors, permits to obtain classical QSPR models with the same characteristics as in QQSPR, that is: possessing a certain degree of causality and explicitly independent of the descriptor dimension. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2009
Examination of selected atmospheric and orographic effects on monthly precipitation of Taiwan using the ASOADeK model
Authors: Guan Huade , Hsu Huang‐Hsiung , Makhnin Oleg , Xie Hongjie , Wilson John L. 
Published: October 2008

AbstractCharacterization and quantification of precipitation spatial variability are required for many studies, such as those in hydrology, ecology, forestry and agriculture. In mountainous terrains (e.g. Taiwan), interactions of moist air mass with underlying complex topography result in increased but often predictable precipitation spatial variability. When these interactions are quantitatively captured, they can contribute to precipitation mapping. In this paper, we applied a recently developed multivariate regression model [auto‐searched orographic and atmospheric effects de‐trended kriging (ASOADeK) regression] to examine selected atmospheric and orographic effects: atmospheric moisture gradient (MG), terrain elevation (Z), terrain aspect and related moisture flux direction (MFD), on Taiwan mean monthly precipitation climatology, primarily based on a dense gauge network (about 110 gauges per 10 000 km2). The results indicate that (1) the regression captures over 50% of spatial variability in mean monthly precipitation over the whole Taiwan island, with improved performance when the regression is applied to sectional regions; (2) the atmospheric MG and MFD are significant factors explaining mean monthly precipitation spatial variability in Taiwan, whereas the elevation effect is not as significant; (3) when the data of sectional regions are applied in the regression, the inferred MFDs vary in a certain range, indicating slightly different climate setting between northern and southern parts of Taiwan; (4) the degree of agreement between the ASOADeK regression‐inferred MFDs and local observed prevailing winds is systemic, and can be used to explain the contrast of rainfall seasonality patterns between the northern part and the rest of Taiwan; and (5) a gauge network of 50 gauges per 10 000 km2 is sufficient to capture the orographic effect on mean monthly precipitation distribution. Copyright © 2008 Royal Meteorological Society
Preliminary 10Be chronology for the last deglaciation of the western margin of the Greenland Ice Sheet
Authors: Rinterknecht Vincent , Gorokhovich Yuri , Schaefer Joerg , Caffee Marc 
Published: October 2008

AbstractThe now acknowledged thinning of the Greenland Ice Sheet raises concerns about its potential contribution to future sea level rise. In order to appreciate the full extent of its contribution to sea level rise, reconstruction of the ice sheet's most recent last deglaciation could provide key information on the timing and the height of the ice sheet at a time of rapid climate readjustment. We measured 10Be concentrations in 12 samples collected along longitudinal and altitudinal transects from Sisimiut to within 10 km of the Isunguata Sermia Glacier ice margin on the western coast of Greenland. Along the longitudinal transect, we collected three perched boulders and two bedrocks. In addition, we sampled seven perched boulders along a vertical transect in a valley within 10 km of the Isunguata Sermia Glacier ice margin. Our pilot dataset constrains the height of the ice sheet during the Last Glacial Maximum (LGM) between 500 m and 840 m (including the 120 m relative sea level depression at the time of the LGM, 21 ka BP). From the transect we estimate the thinning of the ice sheet at the end of the deglaciation between 12.3 ± 1.5 10Be ka (n = 2) and 8.3 ± 1.2 10Be ka (n = 3) to be ∼6 cm a−1 over this time period. Direct dating of the retreat of the western margin of the Greenland Ice Sheet has the potential to better constrain the retreat rate of the ice margin, the thickness of the former ice sheet as well as its response to climate change. Copyright © 2008 John Wiley & Sons, Ltd.
Kinetics and products of chlorine atom initiated oxidation of HCF2OCF2OCF2CF2OCF2H and HCF2O(CF2O)n‐(CF2CF2O)mCF2H
Authors: Wallington T. J. , Hurley M. D. , Javadi M. S. , Nielsen O. J. 
Published: October 2008

AbstractSmog chamber/FTIR techniques were used to measure k(Cl + HCF2OCF2OCF2‐CF2OCF2H) = k(Cl + HCF2O(CF2O)n(CF2CF2O)mCF2H) = (5.0 ± 1.4) × 10−17 cm3 molecule−1 s−1 in 700 Torr of N2/O2 diluent at 296 ± 1 K. The Cl‐initiated atmospheric oxidation of HCF2OCF2OCF2CF2OCF2H and the sample of HCF2O(CF2O)n(CF2CF2O)mCF2H used in this work gave COF2 in molar yields of (476 ± 36)% and (859 ± 63)%, respectively, with no other observable carbon containing products (i.e., essentially complete conversion of both hydrofluoropolyethers into COF2). The results are discussed with respect to the atmospheric chemistry and environmental impact of hydrofluoropolyethers of the general formula HCF2O(CF2O)n(CF2CF2O)mCF2H. © 2008 Wiley Periodicals, Inc. Int J Chem Kinet 40: 819–825, 2008
Physical therapy in Parkinson's disease: Evolution and future challenges
Authors: Keus Samyra H.J. , Munneke Marten , Nijkrake Maarten J. , Kwakkel Gert , Bloem Bastiaan R. 
Published: October 2008

AbstractEven with optimal medical management using drugs or neurosurgery, patients with Parkinson's disease (PD) are faced with progressively increasing mobility problems. For this reason, many patients require additional physical therapy. Here, we review the professional evolution and scientific validation of physical therapy in PD, and highlight several future challenges. To gain insight in ongoing, recently completed or published trials and systematic reviews, we performed a structured literature review and contacted experts in the field of physical therapy in PD. Following publication of the first controlled clinical trial in 1981, the quantity and quality of clinical trials evaluating the efficacy of physical therapy in PD has evolved rapidly. In 2004 the first guideline on physical therapy in PD was published, providing recommendations for evidence‐based interventions. Current research is aiming to gather additional evidence to support specific intervention strategies such as the prevention of falls, and to evaluate the implementation of evidence into clinical practice. Although research focused on physical therapy for PD is a relatively young field, high‐quality supportive evidence is emerging for specific therapeutic strategies. We provide some recommendations for future research, and discuss innovative strategies to improve the organization of allied health care in PD, making evidence‐based care available to all PD patients. © 2008 Movement Disorder Society
Functional effects of local thyroid hormone administration after sciatic nerve injury in rats
Authors: Papakostas Ioannis , Mourouzis Iordanis , Mourouzis Kostas , Macheras Georgios , Boviatsis Efstathios , Pantos Constantinos 
Published: October 2008

AbstractThis study investigates potential functional effects of thyroid hormone (T3) on peripheral nerve regeneration in rats. Forty adult male Lewis rats were included in this study. After complete transection of the right sciatic nerve, the gap between the stumps was bridged with a silicone tube. In the first experimental group (group A, n = 12), T3 solution was used to fill the tube, whereas a sterile buffer solution was used in nontreated rats, (group B, n = 12). Additionally, sham operation with surgical incision and mobilization of the sciatic nerve without any other intervention was performed (group C, n = 10). In a few animals, α‐segment of the nerve was excised and the stumps were reversed to exclude the possibility of regeneration (group D, n = 6). The process of peripheral nerve regeneration was assessed by functional indices at 3, 6, 9, 13, and 17 weeks postoperatively. Mid‐stance angle, at the ankle, measured in degrees, was used as a kinematic index and the withdrawal reflex (measured in grams of applied force) was used to evaluate the return of sensory function. Kinematic indexes were not different between the groups A and B at all time points of the evaluation. Sensory function was significantly different in T3‐treated animals compared with buffer‐treated control group (x vs. y, P = 0.031) at 9 weeks. Thereafter, sensory function was comparable between groups. In conclusion, T3 seems to accelerate the return of sensory function after complete transection of the sciatic nerves in Lewis rats without a significant effect on motor nerve recovery. © 2008 Wiley‐Liss, Inc. Microsurgery, 2009.
Fibrin glue application in microvascular anastomosis: Comparative study of two free flaps series
Authors: Cho Alvaro B. , Wei Teng Hsiang , Torres Luciano Ruiz , Júnior Rames Mattar , Rugiero Gustavo Mantovani , Aita Márcio Aurélio 
Published: October 2008

AbstractBackground: Since the first experiments with fibrin glue application in microvascular anastomoses in 1977, several studies have reported its benefits on suture reduction and anastomosis decreased time. In spite of that, clinical experience has been limited to two neurosurgical and two replantation case series, all of them with good results. This study was conducted to evaluate the feasibility and the potential benefits of fibrin glue application in free flaps. Methods: We performed 24 free flaps in 24 patients, from March 2005 to June 2006. Twenty were included in this study. They were divided into two groups according to the anastomosis technique: conventional group (n = 7 patients) and fibrin glue group (n = 13 patients). In the conventional group, the anastomosis was performed with interrupted sutures, whereas in the fibrin glue group, they were performed using less sutures and fibrin glue application. Results: The application of fibrin glue cut by half the number of sutures required to complete the anastomoses. The mean arterial and venous anastomotic times in the conventional group were 27.2 and 24.0 minutes, respectively. In the fibrin glue group, they were 13.6 and 12.6 minutes, respectively. All these differences were statistically significant. There was no significant difference of ischemic time between two groups (P = 0.26). The survival rate of the flaps was similar in both groups: 84.6% (11 of 13) in the fibrin glue group and 85.7% (6 of 7) in the conventional group (P = 1.0). Conclusions: Fibrin glue application in free flaps was feasible and allowed us to complete the anastomoses with fewer sutures and less time. The survival rate of the flaps was not adversely affected by the fibrin glue. © 2008 Wiley‐Liss, Inc. Microsurgery, 2009.
Neovascularization and free microsurgical transfer of in vitro cartilage‐engineered constructs
Authors: Hoang Nguyen The , Hoehnke Christoph , Hien Pham Thu , Mandlik Veronika , Feucht Achim , Staudenmaier Rainer 
Published: October 2008

AbstractCartilage tissue engineering shows to have tremendous potential for the reconstruction of three‐dimensional cartilage defects. To ensure survival, shape, and function, in vitro cartilage‐engineered constructs must be revascularized. This article presents an effective method for neovascularization and free microsurgical transfer of these in vitro constructs. Twelve female Chinchilla Bastard rabbits were used. Cartilage‐engineered constructs were created by isolating chondrocytes from auricular biopsies, amplifying in monolayer culture, and then seeding them onto polycaprolactone scaffolds. In each prefabricated skin flap, three in vitro cartilage‐engineered constructs (2 × 2 × 0.5 cm) and one construct without cells (served as the control) were implanted beneath an 8 × 15 cm random‐pattern skin flap, neovascularized by implantation of an arteriovenous vascular pedicle with maximal blood flow. Six weeks later, the neovascularized flaps with embedded cartilage‐engineered constructs were completely removed based on the newly implanted vascular pedicle, and then freely retransferred into position using microsurgery. Macroscopic observation, selective microangiography, histology, and immunohistochemistry were performed to determine the construct vitality, neovascularization, and new cartilage formation. The results showed that all neovascularized skin flaps with embedded constructs were successfully free‐transferred as free flaps. The implanted constructs were well integrated and protected within the flap. All constructs were well neovascularized and showed histologically stability in both size and form. Immunohistology showed the existence of cartilage‐like tissue with extracellular matrix neosynthesis. © 2008 Wiley‐Liss, Inc. Microsurgery, 2009.