FURTHER OBSERVATIONS OF TRIGEMINAL ANTIDROMIC POTENTIALS: POSSIBLE PHYSIOLOGICAL FUNCTION OF SENSORY ANTIDROMIC POTENTIALS.
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Cats↗
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Results for “Functional potential”
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Duration of the action potential as a function of the membrane potential in cardiac Purkinje fibres.
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Action Potentials↗
Structure-derived potentials and protein simulations.
There has recently been an explosion in the number of structure-derived potential functions that are based on the increasing number of high-resolution protein crystal structures. These functions differ principally in their reference states; the usual two classes correspond either to initial solvent exposure or to residue exposure of residues. Reference states are critically important for applications of these potentials functions. Inspection of the potential functions and their derivation can tell us not only about protein interaction strengths themselves, but can also provide suggestions for the design of better folding simulations. An appropriate goal in this field is achieving self-consistency between the details in the derivation of potentials and the applied simulations.
Amino Acids↗
Endogenously released L-dopa itself tonically functions to potentiate postsynaptic D2 receptor-mediated locomotor activities of conscious rats.
A non-effective dose of exogenously applied L-dopa itself stereoselectively potentiates postsynaptic D2 receptor-mediated locomotor activities of rats. We further attempted to clarify whether or not endogenously released L-dopa tonically functions to potentiate activities of these receptors, simultaneously monitoring locomotor activities and basal release of L-dopa and dopamine during striatal microdialysis in conscious rats. Quinpirole (1 mg/kg, s.c.) alone, a selective D2 agonist, increased locomotor activities and decreased basal L-dopa and dopamine release 20-140 min after injection. Pretreatment with alpha-methyl-p-tyrosine (3 mg/kg, i.p.), a tyrosine hydroxylase inhibitor, decreased locomotor activities and further decreased L-dopa release without modification of dopamine release, compared to quinpirole alone, whereas 3-hydroxybenzylhydrazine (100 mg/kg, i.p.), a central dopa decarboxylase inhibitor, further increased locomotor activities and markedly increased L-dopa release without modification of dopamine release. Endogenously released L-dopa itself functions tonically to potentiate activities of postsynaptic D2 receptors relevant to locomotor movement of rats.
Animals↗
Neural net representations of empirical protein potentials.
Recently, there has been considerable interest in deriving and applying knowledge-based, empirical potential functions for proteins. These empirical potentials have been derived from the statistics of interacting, spatially neighboring residues, as may be obtained from databases of known protein crystal structures. In this paper we employ neural networks to redefine empirical potential functions from the point of view of discrimination functions. This approach generalizes previous work, in which simple frequency counting statistics are used on a database of known protein structures. This generalization allows us to avoid restriction to strictly pairwise interactions. Instead of frequency counting to fix adjustable parameters, one now optimizes an objective function involving a neural network parameterized probability distribution. We show how our method reduces to previous work in special situations, but also allows extensions to include orders of interaction beyond pairwise interaction. Given the close packing of proteins, steric interactions etc., the inclusion of higher order interactions is critical for developing an accurate potential. A key feature in the approach we advocate is the development of a representation to describe the spatial location of interacting residues that exist in a sphere of small fixed radius around each residue. This is a "shape representation" problem that has a natural solution for the interaction neighborhoods of protein residues. We demonstrate in a series of numerical experiments that the neural network approach improves discrimination over that obtained by previous methodologies limited to pair-wise interactions.
Amino Acid Sequence↗
Assessment of left ventricular diastolic function and potential by quantitative analysis of left ventricular filling curves in patients with atrial fibrillation. A new algorithm for Doppler echocardiographic study.
To evaluate left ventricular (LV) diastolic function and potential, LV filling curves for 18 patients with atrial fibrillation (Af) were constructed and their positions and appearance were evaluated quantitatively by analysis of 95% maximal filling volume points and maximal curvature alteration points. The LV filling curves of group A (Af only) lay left superiorly, while those of group B (impaired LV diastolic function) were situated right inferiorly, all bending steeply. The LV filling curves of group C (mitral stenosis) bent slightly. The lowest normal filling volume points and compensation areas were calculated to evaluate LV diastolic function and were demonstrated to be very different in groups A and B. The lowest normal filling volume points of group C were similar to those of group A, but compensation areas were smaller, indicating a lower LV diastolic potential. It is concluded that the 95% maximal filling volume point, maximal curvature alteration point, lowest normal filling volume point and compensation area are effective indices for evaluating not only LV diastolic function but also the diastolic potential.
Algorithms↗
Potential energy functions: from consistent force fields to spectroscopically determined polarizable force fields.
We review our methodology for producing physically accurate potential energy functions, particularly relevant in the context of Lifson's goal of including frequency agreement as one of the criteria of a self-consistent force field. Our spectroscopically determined force field (SDFF) procedure guarantees such agreement by imposing it as an initial constraint on parameter optimization, and accomplishes this by an analytical transformation of ab initio "data" into the energy function format. After describing the elements of the SDFF protocol, we indicate its implementation to date and then discuss recent advances in our representation of the force field, in particular those required to produce an SDFF for the peptide group.
Acetamides↗
Recording of the event-related potentials during functional MRI at 3.0 Tesla field strength.
The feasibility of recording event-related potentials (ERP) during functional MRI (fMRI) scanning was studied. Using an alternating checkerboard stimulus in a blocked presentation, visually evoked potentials were obtained with their expected configuration and latencies. A clustered echoplanar imaging protocol was applied to observe the hemodynamic response due to the visual stimulus interleaved with measuring ERPs. Influences of the electrode/amplifier set up on MRI scanning and the scanning process on the recording of electrophysiological signals are reported and discussed. Artifacts overlaid on the electrophysiological recordings were corrected by post hoc filtering methods presented here. Implications and limitations of conducting combined ERP/fMRI experiments using higher-level cognitive stimuli are discussed. Magn Reson Med 44:277-282, 2000.
Adult↗
An all-atom, distance-dependent scoring function for the prediction of protein-DNA interactions from structure.
We have developed an all-atom statistical potential function for the prediction of protein-DNA interactions from their structures, and show that this method outperforms similar, lower-resolution statistical potentials in a series of decoy discrimination experiments. The all-atom formalism appears to capture details of atomic interactions that are missed by the lower-resolution methods, with the majority of the discriminatory power arising from its description of short-range atomic contacts. We show that, on average, the method is able to identify 90% of near-native docking decoys within the best-scoring 10% of structures in a given decoy set, and it compares favorably with an optimized physical potential function in a test of structure-based identification of DNA binding-sequences. These results demonstrate that all-atom statistical functions specific to protein-DNA interactions can achieve great discriminatory power despite the limited size of the structural database. They also suggest that the statistical scores may soon be able to achieve accuracy on par with more complex, physical potential functions.
Binding Sites↗
Somatic mutations within the untranslated regions of rearranged Ig genes in a case of classical Hodgkin's disease as a potential cause for the absence of Ig in the lymphoma cells.
Hodgkin-Reed-Sternberg (H-RS) cells are clonal B cells carrying Ig gene rearrangements. However, in situ hybridization methods failed to demonstrate Ig gene expression in H-RS cells of classical Hodgkin's disease (HD). Because somatic mutations rendering potentially functional Ig gene rearrangements nonfunctional were detected in some cases of the disease, it was speculated that H-RS cells in classical HD may have lost the ability to express antigen receptor as a rule. Recently, we established a novel cell line (L1236) from H-RS cells of a patient with mixed cellularity subtype of HD. L1236 cells harbor a potentially functional VH1 and a potentially functional Vkappa3 gene rearrangement. However, no antibody expression was detected. To show potential reasons for this lack of Ig expression, we analyzed the genomic organization of the Ig genes and their transcription in the primary and cultivated H-RS cells of this patient. The H-RS cells were found to have switched their isotype to IgG4, confirming their mature B-cell nature. By amplifying cDNA from L1236 cells as well as from frozen biopsy material transcripts of the Vkappa3 and the VH1 gene rearrangement were detected for both sources of cDNA. However, Northern blot hybridization of L1236 RNA failed to demonstrate VH1 and Vkappa3 transcripts, indicating only a low level of transcription. Sequence analysis of the promoter and leader regions of the VH1 gene rearrangement from L1236 cells as well as from lymphoma-affected tissue showed a somatic mutation in the conserved octamer motif of the promoter region. Somatic mutations were also detected within the 3' splice site of the leader intron and adjacent nucleotides in the rearranged Vkappa light chain gene, leading to aberrant splicing. These mutations might prevent the generation of adequate amounts of functional Ig gene transcripts as template for translation into protein. Thus, mutations in H-RS cells that prevent Ig gene expression might also be located outside the coding region of the Ig genes.
Base Sequence↗
[The potential energy function of the internal rotation for H2S2 molecule].
Using the perturbation theory without wave function, the analytical formula of the internal Rotation energies has been derived, and the potential energy function of internal rotation for H2S2 molecule has been determined using the published data for the torsional frequencies.
English Abstract↗
[Potential energy function of internal rotation for the molecules of (CX3)2Y type].
Studing on the molecules having M -tops of N -fold symmetries, decoupling the equation of motion for rotation and using the perturbation theory without wave function, the formula of the energies of internal rotation has been derived and the potential energy functions of internal rotation for (CH3)2O and (CF3)2CO have been determined.
English Abstract↗
Too many trees to see the forest: performance, event-related potential, and functional magnetic resonance imaging manifestations of integrative congenital prosopagnosia.
Neuropsychological, event-related potential (ERP), and functional magnetic resonance imaging (fMRI) methods were combined to provide a comprehensive description of performance and neurobiological profiles for K.W., a case of congenital prosopagnosia. We demonstrate that K.W.'s visual perception is characterized by almost unprecedented inability to identify faces, a large bias toward local features, and an extreme deficit in global/configural processing that is not confined to faces. This pattern could be appropriately labeled congenital integrative prosopagnosia, and accounts for some, albeit not all, cases of face recognition impairments without identifiable brain lesions. Absence of face selectivity is evident in both biological markers of face processing, fMRI (the fusiform face area [FFA]), and ERPs (N170). Nevertheless, these two neural signatures probably manifest different perceptual mechanisms. Whereas the N170 is triggered by the occurrence of physiognomic stimuli in the visual field, the deficient face-selective fMRI activation in the caudal brain correlates with the severity of global processing deficits. This correlation suggests that the FFA might be associated with global/configural computation, a crucial part of face identification.
Adult↗
The V kappa genes of the L regions and the repertoire of V kappa gene sequences in the human germ line.
Only 14 of the 25 V kappa genes and pseudogenes had been found before as parts of the L regions. The cloning and linking described in the accompanying report allowed us now to assign to Lp or Ld some V kappa genes which had been found before on scattered clones. In addition the sequences of several still unknown genes are reported here, thus completing the publication of the V kappa genes of the kappa locus as far as they are potentially functional or have only one or two 1-bp defects. Of the V kappa genes of the kappa locus, 32 are potentially functional, 16 have minor defects, 3 have both potentially functional and slightly defective alleles and 25 are pseudogenes which amounts to a repertoire of 76 V kappa-related gene sequences. The V kappa genes of the L regions are, within the subgroups, particularly similar to each other, which is in part due to common evolutionary origins and in part caused by gene conversion-like events. One donor-acceptor pair could be clearly identified, since converted and not-converted alleles of the acceptor gene were found. In other cases the duplicates of the converted genes served as non-converted controls.
Alleles↗
Optimal sequence selection in proteins of known structure by simulated evolution.
Rational design of protein structure requires the identification of optimal sequences to carry out a particular function within a given backbone structure. A general solution to this problem requires that a potential function describing the energy of the system as a function of its atomic coordinates be minimized simultaneously over all available sequences and their three-dimensional atomic configurations. Here we present a method that explicitly minimizes a semiempirical potential function simultaneously in these two spaces, using a simulated annealing approach. The method takes the fixed three-dimensional coordinates of a protein backbone and stochastically generates possible sequences through the introduction of random mutations. The corresponding three-dimensional coordinates are constructed for each sequence by "redecorating" the backbone coordinates of the original structure with the corresponding side chains. These are then allowed to vary in their structure by random rotations around free torsional angles to generate a stochastic walk in configurational space. We have named this method protein simulated evolution, because, in loose analogy with natural selection, it randomly selects for allowed solutions in the sequence of a protein subject to the "selective pressure" of a potential function. Energies predicted by this method for sequences of a small group of residues in the hydrophobic core of the phage lambda cI repressor correlate well with experimentally determined biological activities. This "genetic selection by computer" approach has potential applications in protein engineering, rational protein design, and structure-based drug discovery.
Algorithms↗
An ab initio study of the structure, torsional potential energy function, and electric properties of disilane, ethane, and their deuterated isotopomers.
Highly accurate ab initio computations of the molecular structure and properties, torsional potential energy function, and harmonic force field of disilane and ethane have been carried out. Equilibrium parameters as well as vibrational corrections have been evaluated. In addition, for these systems a vibrational averaging procedure has been employed for calculating the dipole moment of molecules which have no permanent dipole moment, i.e., SiH(3)SiD(3) and CH(3)CD(3). The molecular and spectroscopic properties calculated for ethane and its isotopomers provide a calibration against known experimental data, allowing us to estimate the reliability of our computed results for disilane for which there is much less experimental data. The goal of the present study is to predict the molecular parameters, with estimated uncertainties, that determine the microwave spectrum of SiH(3)SiD(3).
Journal Article↗
Potential energy functions for atomic-level simulations of water and organic and biomolecular systems.
An overview is provided on the development and status of potential energy functions that are used in atomic-level statistical mechanics and molecular dynamics simulations of water and of organic and biomolecular systems. Some topics that are considered are the form of force fields, their parameterization and performance, simulations of organic liquids, computation of free energies of hydration, universal extension for organic molecules, and choice of atomic charges. The discussion of water models covers some history, performance issues, and special topics such as nuclear quantum effects.
Biophysics↗
Assessment of potential macular function using a color saturation discrimination test in eyes with cataract.
PURPOSE: To study the efficacy of a color saturation discrimination test (CSDT) in assessing potential macular function in eyes with cataract. SETTING: Yamanashi Medical University and Nirasaki City Hospital, Yamanashi, Japan. METHODS: In this prospective study of 200 consecutive eyes with cataract, the thresholds of color saturation discrimination on 6 hues were measured with the CSDT. The CSDT program was run on a personal computer and cathode-ray tube color monitor. The preoperative CSDT scores and postoperative visual acuities were compared. In addition, preoperative laser interferometry (LI) and postoperative CSDT were performed on selected patients and the results compared with their preoperative CSDT results. RESULTS: Patients who had a CSDT score of 11 or more had a significantly lower postoperative visual acuity (P < .0001). The prevalence of neuroretinal abnormality postoperatively increased with the preoperative CSDT score. The CSDT score was not correlated with preoperative visual acuity (P = 1409). Cataract severity had little influence on the CSDT score. The preoperative results of the CSDT and Ll were correlated with the postoperative acuity, with the correlation coefficient being stronger with the CSDT (r = -0.338 and 0.276 for CSDT and Ll, respectively). CONCLUSION: The CSDT was effective in evaluating neuroretinal pathology and predicting postoperative acuity.
Cataract↗