bluuebunny/crossref_metadata_2025_split huggingface dataset:
2D‐RNA‐coupling numbers: A new computational chemistry approach to link secondary structure topology with biological function
Authors: González‐díaz Humberto , Agüero‐chapin Guillermín , Varona Javier , Molina Reinaldo , Delogu Giovanna , Santana Lourdes , Uriarte Eugenio , Podda Gianni 
Published: February 2007

AbstractMethods for prediction of proteins, DNA, or RNA function and mapping it onto sequence often rely on bioinformatics alignment approach instead of chemical structure. Consequently, it is interesting to develop computational chemistry approaches based on molecular descriptors. In this sense, many researchers used sequence‐coupling numbers and our group extended them to 2D proteins representations. However, no coupling numbers have been reported for 2D‐RNA topology graphs, which are highly branched and contain useful information. Here, we use a computational chemistry scheme: (a) transforming sequences into RNA secondary structures, (b) defining and calculating new 2D‐RNA‐coupling numbers, (c) seek a structure‐function model, and (d) map biological function onto the folded RNA. We studied as example 1‐aminocyclopropane‐1‐carboxylic acid (ACC) oxidases known as ACO, which control fruit ripening having importance for biotechnology industry. First, we calculated τk(2D‐RNA) values to a set of 90‐folded RNAs, including 28 transcripts of ACO and control sequences. Afterwards, we compared the classification performance of 10 different classifiers implemented in the software WEKA. In particular, the logistic equation ACO = 23.8 · τ1(2D‐RNA) + 41.4 predicts ACOs with 98.9%, 98.0%, and 97.8% of accuracy in training, leave‐one‐out and 10‐fold cross‐validation, respectively. Afterwards, with this equation we predict ACO function to a sequence isolated in this work from Coffea arabica (GenBank accession DQ218452). The τ1(2D‐RNA) also favorably compare with other descriptors. This equation allows us to map the codification of ACO activity on different mRNA topology features. The present computational‐chemistry approach is general and could be extended to connect RNA secondary structure topology to other functions. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007
A comparative study of molecular dynamics in Cartesian and in internal coordinates: Dynamical instability in the latter caused by nonlinearity of the equations of motion
Authors: Lee Sang‐Ho , Palmo Kim , Krimm Samuel 
Published: February 2007

AbstractThe stability of a general molecular dynamics (MD) integration scheme is examined for simulations in generalized (internal plus external) coordinates (GCs). An analytic expression is derived for the local error in energy during each integration time step. This shows that the explicit dependence of the mass‐matrix on GCs, which makes the system's Lagrange equations of motion nonlinear, causes MD simulations in GCs to be less stable than those in Cartesian coordinates (CCs). In terms of CCs, the corresponding mass‐matrix depends only on atomic masses and thus atomistic motion is subject to the linear Newton equations, which makes the system more stable. Also investigated are two MD methods in GCs that utilize nonzero elements of the vibrational spectroscopic B‐matrices. One updates positions and velocities in GCs that are iteratively adjusted so as to conform to the velocity Verlet equivalent in GCs. The other updates positions in GCs and velocities in CCs that are adjusted to satisfy the internal constraints of the new constrained WIGGLE MD scheme. The proposed methods are applied to an isolated n‐octane molecule and their performances are compared with those of several CCMD schemes. The simulation results are found to be consistent with the analytic stability analysis. Finally, a method is presented for computing nonzero elements of B‐matrices for external rotations without imposing the Casimir–Eckart conditions. © 2007 Wiley Periodicals, Inc.J Comput Chem 2007
Influence of temperature, friction, and random forces on folding of the B‐domain of staphylococcal protein A: All‐atom molecular dynamics in implicit solvent
Authors: Jagielska Anna , Scheraga Harold A. 
Published: February 2007

AbstractThe influences of temperature, friction, and random forces on the folding of protein A have been analyzed. A series of all‐atom molecular dynamics folding simulations with the Amber ff99 potential and Generalized Born solvation, starting from the fully extended chain, were carried out for temperatures from 300 to 500 K, using (a) the Berendsen thermostat (with no explicit friction or random forces) and (b) Langevin dynamics (with friction and stochastic forces explicitly present in the system). The simulation temperature influences the relative time scale of the major events on the folding pathways of protein A. At lower temperatures, helix 2 folds significantly later than helices 1 and 3. However, with increasing temperature, the folding time of helix 2 approaches the folding times of helices 1 and 3. At lower temperatures, the complete formation of secondary and tertiary structure is significantly separated in time whereas, at higher temperatures, they occur simultaneously. These results suggest that some earlier experimental and theoretical observations of folding events, e.g., the order of helix formation, could depend on the temperature used in those studies. Therefore, the differences in temperature used could be one of the reasons for the discrepancies among published experimental and computational studies of the folding of protein A. Friction and random forces do not change the folding pathway that was observed in the simulations with the Berendsen thermostat, but their explicit presence in the system extends the folding time of protein A. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007
Accuracy of distributed multipoles and polarizabilities: Comparison between the LoProp and MpProp models
Authors: Söderhjelm P. , Krogh J. W. , Karlström G. , Ryde U. , Lindh R. 
Published: February 2007

AbstractLocalized multipole moments up to the fifth moment as well as localized dipole polarizabilities are calculated with the MpProp and the newly developed LoProp methods for a total of 20 molecules, predominantly derived from amino acids. A comparison of electrostatic potentials calculated from the multipole expansion obtained by the two methods withab initioresults shows that both methods reproduce the electrostatic interaction with an elementary charge with a mean absolute error of ∼1.5 kJ/mol at contact distance and less than 0.1 kJ/mol at distances 2 Å further out when terms up to the octupole moments are included. The polarizabilities are tested with homogenous electric fields and are found to have similar accuracy. The MpProp method gives better multipole moments unless diffuse basis sets are used, whereas LoProp gives better polarizabilities. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007
A 45‐ns molecular dynamics simulation of hemoglobin in water by vectorizing and parallelizing COSMOS90 on the earth simulator: Dynamics of tertiary and quaternary structures
Authors: Saito Minoru , Okazaki Isao 
Published: February 2007

AbstractMolecular dynamics (MD) simulations of human adult hemoglobin (HbA) were carried out for 45 ns in water with all degrees of freedom including bond stretching and without any artificial constraints. To perform such large‐scale simulations, one of the authors (M.S.) accelerated his own software COSMOS90 on the Earth Simulator by vectorization and parallelization. The dynamical features of HbA were investigated by evaluating root‐mean‐square deviations from the initial X‐ray structure (an oxy T‐state hemoglobin with PDB code: 1GZX) and root‐mean‐square fluctuations around the average structure from the simulation trajectories. The four subunits (α1, α2, β1, and β2) of HbA maintained structures close to their respective X‐ray structures during the simulations even though no constraints were applied to HbA in the simulations. Dimers α1β1 and α2β2 also maintained structures close to their respective X‐ray structures while they moved relative to each other like two stacks of dumbbells. The distance between the two dimers (α1β1 and α2β2) increased by 2 Å (7.4%) in the initial 15 ns and stably fluctuated at the distance with the standard deviation 0.2 Å. The relative orientation of the two dimers fluctuated between the initial X‐ray angle −100° and about −105° with intervals of a few tens of nanoseconds. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007
“Quasi flexible” automatic docking processing for studying stereoselective recognition mechanisms, part 2: Prediction of ΔΔG of complexation and 1H‐NMR NOE correlation
Authors: Alcaro S. , Gasparrini F. , Incani O. , Caglioti L. , Pierini M. , Villani C. 
Published: February 2007

AbstractThe purpose of this work is to apply the global molecular interaction evaluation (“Glob‐MolInE”) computational protocol to the study of two molecular complexes characterized by a chiral selector and a couple of enantiomeric selectands experimentally known to give large difference in the free energy of complexation much higher than the experimental error normally associated to the molecular mechanic calculations. We have considered the well known diastereomeric complexes between the selector (S)‐N‐(3,5‐dinitrobenzoyl)‐leucine‐n‐propylamide (S)‐1 and the selectands (R) or (S)‐N‐(2‐naphthyl)‐alanine methyl ester 2, widely studied by enantioselective HPLC, NMR and X‐ray. The experimental difference of free energy of complexation between [(S)‐1•(R)‐2] and [(S)‐1•(S)‐2] (−1.34 kcal/mol) was reproduced by the new computational protocol with an excellent confidence error. Detailed results about the conformational search, the “quasi‐flexible” docking and the thermodynamic estimation are presented in this work. A remarkable correlation between the theoretical results and experimental data (NOE measurements, X‐ray crystallographic structure of the [(S)‐1•(S)‐2] complex and the free energy of complexation) supports the validity of the computational approach and underline the importance of the conformational multiplicity in the definition of the macroscopic properties of the complex in solution. © 2007 Wiley Periodicals, Inc. J Comput Chem 2007
Commentaries on the placebo concept in psychotherapy
Authors: Thorn Beverly 
Published: February 2007

AbstractThis editorial note introduces the next five commentaries on the placebo effect in psychotherapy. These commentaries follow the July, 2005 publication of a special series of articles in the Journal of Clinical Psychology, entitled “The Placebo Concept in Psychotherapy.” © 2007 Wiley Periodicals, Inc. J Clin Psychol 63: 371–372, 2007.
Stability of negative self‐structures: A longitudinal comparison of depressed, remitted, and nonpsychiatric controls
Authors: Dozois David J. A. 
Published: February 2007

AbstractTo be considered a vulnerability marker for depression, a variable should, in addition to demonstrating sensitivity and specificity, also show evidence of temporal stability (i.e., remain present in the absence of depressive symptomatology). Although many cognitive factors are associated with depression, the majority of them appear to be episode rather than vulnerability markers. This study examined cognitive organization of positive and negative interpersonal and achievement content in clinically depressed, remitted, and nonpsychiatric controls. At initial assessment, a sample of 54 clinically depressed individuals and 37 never‐depressed controls completed self‐report measures of positive and negative automatic thoughts and two cognitive organizational tasks. They were retested 6 months later when half of the depressed group no longer met diagnostic criteria for major depression. Negative automatic thoughts decreased and positive automatic thoughts increased significantly in individuals who had improved clinically. The organization of negative interpersonal content remained stable despite symptom amelioration, but negative achievement content was less interconnected at follow‐up in those patients who had improved. The structure of relational schemas, in particular, appears to be stable and may be an important cognitive vulnerability factor for depression. © 2007 Wiley Periodicals, Inc. J Clin Psychol 63: 319–338, 2007.
The placebo effect: “Relatively large” and “robust” enough to survive another assault
Authors: Wampold Bruce E. , Imel Zac E. , Minami Takuya 
Published: February 2007

AbstractThe evidence related to the placebo effect is discussed, and it is emphasized that the descriptors “relatively large” and “robust” are appropriate in the context in which they were used. Basic science and clinical trials, when interpreted properly, have revealed that the placebo effect is indeed a real phenomenon. J. Hunsley and R. Westmacott (this issue) as well as A. Hróbjartsson and P. C. Gøtzsche (this issue) are concerned that B. E. Wampold, T. Minami, S. C. Tierney, T. W. Baskin, and K. S. Bhati (2005) overstated the clinical effects of placebo when it was never B. E. Wampold et al.'s (2005) intention to make inferences about clinical utility; however, it is shown that the placebo effect exceeds many accepted medical interventions. © 2007 Wiley Periodicals, Inc. J Clin Psychol 63: 401–403, 2007.
Interpreting the magnitude of the placebo effect: Mountain or molehill?
Authors: Hunsley John , Westmacott Robin 
Published: February 2007

AbstractThe ambiguity involved in interpreting numbers and words is central to Hróbjartsson and Gøtzsche's (this issue) claim of “powerful spin” in the Wampold, Minami, Tierney, Baskin, and Bhati (2005) re‐analysis of their meta‐analytic findings on the placebo effect in medicine. Meta‐analytic results reported by the two sets of authors are nearly identical, yet their conclusions differ dramatically. In our comment, we discuss the findings of the respective authors and consider options for representing and interpreting the magnitude of meta‐analytic effect size estimates. We conclude that although the meta‐analyses described indicate that placebo effects do exist and cannot be dismissed as unimportant, given contextual information, it is consistent with existing research to describe the obtained mean effect size for placebos in medicine as small in magnitude. © 2007 Wiley Periodicals, Inc. J Clin Psychol 63: 391–399, 2007.
Good grief and not‐so‐good grief: Countertransference in bereavement therapy
Authors: Hayes Jeffrey A. , Yeh Yun‐Jy , Eisenberg Alanna 
Published: February 2007

AbstractThis study examined the relationship between therapists' grief related to the death of a loved one and clients' perceptions of the process of bereavement therapy. Mail survey data were obtained from 69 client–therapist dyads. Results indicated that the extent to which therapists missed deceased loved ones was inversely related to client perceptions of therapist empathy, but not to client ratings of the alliance, session depth, or therapist credibility. Therapist acceptance of the death of a loved one was unrelated to any of the dependent measures. Results are discussed in terms of countertransference and its management. © 2007 Wiley Periodicals, Inc. J Clin Psychol 63: 345–355, 2007.
The story of placebo effects in medicine: Evidence in context
Authors: Wampold Bruce E. , Imel Zac E. , Minami Takuya 
Published: February 2007

AbstractIn 2005, in an article reviewing the evidence related to the placebo effect that was derived from clinical trials in medicine and psychotherapy, B. E. Wampold, T. Minami, S. C. Tierney, T. W. Baskin, and K. S. Bhati re‐analyzed studies contained in A. Hróbjartsson and P. C. Gøtzsche's (2001) meta‐analysis of trials that contained placebo and no‐treatment conditions. Whereas Hróbjartsson and Gøtzsche (2001) concluded that the placebo effect was weak at best, Wampold et al. (2005) concluded that it was “robust.” Hróbjartsson and Gøtzsche (this issue) challenged Wampold et al.'s (2005) conclusion, claiming essentially that the results of clinical trials containing placebo and no‐treatment conditions are not sufficient to claim that the placebo effect exists to any substantial degree. In this article, it is shown that when properly interpreted by considering theory, method, context, and related research, the results of clinical trials support the existence of a placebo effect. In short, the placebo effect appears in those instances where it is expected. © 2007 Wiley Periodicals, Inc. J Clin Psychol 63: 379–390, 2007.
Imaging and analysis of 3‐D structure using a dual beam FIB
Authors: McGrouther D. , Munroe P.R. 
Published: February 2007

AbstractThe application of focused ion beam instrumentation in the generation of three‐dimensional microstructural data is described. The methodologies used to acquire and manipulate this data are explained, and the technique is illustrated by a number of examples from the material sciences. The limitations of this method, and practical pointers to the generation of meaningful data, are also discussed. Microsc. Res. Tech., 2007. © 2007 Wiley‐Liss, Inc.
Subcellular imaging of isotopically labeled carbon compounds in a biological sample by ion microprobe (NanoSIMS)
Authors: Clode Peta L. , Stern Richard A. , Marshall Alan T. 
Published: February 2007

AbstractHere we demonstrate the technique of nanoscale secondary ion mass spectrometry, utilizing the Cameca NanoSIMS50® ion microprobe, to detect and image the metabolism of an isotopically labeled compound (NaH13CO3) in a biological sample. In particular, we have designed and verified protocols for imaging the subcellular distribution and determining the relative abundance of labeled 13C, within the coral Galaxea fascicularis. Analyses were conducted on 1‐μm thick sections of resin‐embedded material, using both scanned (mapping) and static (spot analysis) Cs+ primary ion beam of ∼100 nm diameter. Using these samples we establish that NanoSIMS has adequate mass resolution to reliably distinguish 13C from potential isobaric interference by 12C1H and that data extracted from ion maps are comparable to those acquired by spot analyses. Independent of the method of acquisition, ratioing of 13C to the naturally abundant 12C is essential if meaningful data, which can be statistically compared to standard and control samples, are to be obtained. These results highlight the potential of NanoSIMS for intracellular tracking of a variety of organic and inorganic compounds labeled with stable isotopes of C, N, O, S, P, and halogens. Microsc. Res. Tech., 2007. © 2007 Wiley‐Liss, Inc.
New bounds on the edge number of ak‐map graph
Authors: Chen Zhi‐Zhong 
Published: February 2007

AbstractIt is known that for every integerk ≥ 4, eachk‐map graph withnvertices has at mostkn− 2kedges. Previously, it was open whether this bound is tight or not. We show that this bound is tight fork = 4, 5. We also show that this bound is not tight for large enoughk(namely,k ≥ 374); more precisely, we show that for every$0 < \epsilon < {3 \over 328}$and for every integer$k \ge {140 \over {41\epsilon}}$, eachk‐map graph withnvertices has at most$({325 \over 328} + \epsilon){kn} - 2{k}$edges. This result implies the first polynomial (indeed linear) time algorithm for coloring a givenk‐map graph with less than 2kcolors for large enoughk. We further show that for every positive multiplekof 6, there are infinitely many integersnsuch that somek‐map graph withnvertices has at least$({11 \over 12}{k} + {1 \over 3}) {n}$edges. © 2007 Wiley Periodicals, Inc. J Graph Theory 55: 267–290, 2007
Anatomical and metabolic assessment of prostate using a 3‐Tesla MR scanner with a custom‐made external transceive coil: Healthy volunteer study
Authors: Kaji Yasushi , Kuroda Kagayaki , Maeda Takaki , Kitamura Yuri , Fujiwara Toshitaka , Matsuoka Yuichiro , Tamura Mitsuru , Takei Naoyuki , Matsuda Tsuyoshi , Sugimura Kazuro 
Published: February 2007

AbstractPurposeTo examine the possibility of using a 3 Tesla (T) magnetic resonance (MR) scanner with a custom‐made external coil to obtain ductal details of the prostate, high‐quality spectra, and metabolite mapping corresponding to prostate zonal anatomy in healthy volunteers.Materials and MethodsMRI and two‐dimensional (2D) chemical shift imaging (CSI) were performed in 16 healthy volunteers using a 3T scanner with a custom‐made external transmit‐receive (transceive) coil. Visualization of the prostatic duct‐like structure was analyzed on T2‐weighted (T2W) images. The resolution of the metabolite peaks and the distribution of metabolites in CSI were also assessed.ResultsIn the axial plane, 3‐mm‐thick images were better than 4‐mm‐thick images with the same voxel volume for assessing duct‐like structures and prostatic urethra. Differentiation between inner and outer citrate (Cit) peaks was frequently observed (29 out of 30). The mean peak area ratio of choline (Cho) plus creatine (Cr) over Cit in the peripheral zone (PZ) was significantly lower than in the transition zone (TZ) (P = 0.014).Conclusion3T MR examinations of the prostate using an external coil allow information to be collected about the details of duct‐like structures, the high‐quality spectra of Cit, and the zone‐specific distribution of metabolites. J. Magn. Reson. Imaging 2007. © 2007 Wiley‐Liss, Inc.
Effects of RF inhomogeneity at 3.0T on ramped RF excitation: Application to 3D time‐of‐flight MR angiography of the intracranial arteries
Authors: Eissa Amir M. , Wilman Alan H. 
Published: February 2007

AbstractPurposeTo demonstrate the effects of inherent RF inhomogeneity on ramped RF excitation at 3.0T, and to introduce a simple correction for improving visualization of distal intracranial arteries in three‐dimensional time‐of‐flight MR angiography (3D‐TOF‐MRA).Materials and MethodsAt 3.0T, the effects of RF inhomogeneity arising from RF interference were demonstrated for ramped RF excitation in intracranial 3D‐TOF‐MRA. Computer simulations and experiments on phantoms and eight normal volunteers were performed. Four different ramp shapes were tested as a possible means of countering the reduced RF field that affects the distal intracranial arteries.ResultsRF destructive interference alters the ramp pulse shape, which is problematic for vessels that proceed from the center to the edge of the brain. Increasing the ramp pulse slope was shown to be an effective yet simple correction to counter the falling‐off of the RF field toward the periphery of the head. With this approach, circle‐of‐Willis 3D‐TOF‐MRA studies had improved distal visibility.ConclusionRamped RF excitation is severely affected by RF interference at 3.0T, which makes the ramp profile suboptimal for distal intracranial blood vessels. A simple correction of the ramp slope can make a marked improvement. J. Magn. Reson. Imaging 2007. © 2007 Wiley‐Liss, Inc.