Ground- and excited-state properties of DNA base molecules from plane-wave calculations using ultrasoft pseudopotentials

We present equilibrium geometries, vibrational modes, dipole moments, ionization energies, electron affinities, and optical absorption spectra of the DNA base molecules adenine, thymine, guanine, and cytosine calculated from first principles. The comparison of our results with experimental data and results obtained by using quantum chemistry methods show that in specific cases gradient-corrected density-functional theory (DFT-GGA) calculations using ultrasoft pseudopotentials and a plane-wave basis may be a numerically efficient and accurate alternative to methods employing localized orbitals for the expansion of the electron wave functions.

Relaxation channels of two-vibron bound states in alpha-helix proteins

Relaxation channels for two-vibron bound states in an anharmonic alpha-helix protein are studied. According to a recently established small polaron model [V. Pouthier, Phys. Rev. E 68, 021909 (2003)], it is shown that the relaxation originates in the interaction between the dressed anharmonic vibrons and the remaining phonons. This interaction is responsible for the occurrence of transitions between two-vibron eigenstates mediated by both phonon absorption and phonon emission. At biological temperature, the relaxation rate does not significantly depend on the nature of the two-vibron states involved in the process. The lifetime for both bound and free states is of the same order of magnitude and ranges between 0.1 and 1.0 ps for realistic parameter values. By contrast, the relaxation channels strongly depend on the nature of the two-vibron states which is a consequence of the breatherlike behavior of the two-vibron bound states.

Effect of different vibration frequencies on heart rate variability and driving fatigue in healthy drivers

OBJECTIVE

This investigation was to assess the effect of different vibration frequencies on heart rate variability (HRV) and driving fatigue in healthy subjects during simulated driving, by the use of power spectrum analysis and subjective evaluation.

MATERIALS AND METHODS

Sixty healthy subjects (29.6+/-3.3 years) were randomly divided into three groups, A, B and C, and the subjects of each group participated in the simulated driving for 90 min with vertical sinusoidal vibration (acceleration 0.05 g) of 1.8 Hz (group A), 6 Hz (group B) and no vibration (group C), respectively. Low-frequency (LF) and high-frequency (HF) components of HRV, reflecting sympathetic and parasympathetic activities, and the LF:HF ratio, indicating sympathovagal balance, were measured throughout all periods. All indices of HRV were calculated in the pre-experiment period, mid-experiment period and end-experiment period, and were analyzed by repeated measures analysis of variance. Subjective responses to a questionnaire were obtained after the simulated task for the three groups.

RESULTS

Significant differences in all indices of HRV were observed between different experiment periods and between any two groups. The ratings of subjective fatigue exhibited significant differences between any two groups.

CONCLUSION

The drivers' fatigue ratings were associated with vibration frequencies in simulated driving. The study quantitatively demonstrated that different effects on autonomic nerve activities were induced by different vibration frequencies.

Resonant ultrasound spectroscopy measurements of the elastic constants of human dentin

The technique of resonant ultrasound spectroscopy (RUS) was used to measure the second-order elastic constants of hydrated human dentin. Specimens were placed between two transducers, and the resonant frequencies of vibration were measured between 0.5 and 1.4 MHz. The elastic constants determined from the measured resonant frequencies in hydrated dentin exhibited slight hexagonal anisotropy, with the stiffest direction being perpendicular to the axis of the tubules (E11 = 25.1GPA) This hexagonal anisotropy was small (E33/E11 = 0.92), and almost disappeared when the specimens were dried. In addition, there was a pronounced anisotropy in the Poisson's ratio of wet dentin: v21 = 0.45; v31 = 0.29. With drying in air, this anisotropy vanished: v21 = v31 = 0.29. The isotropic Young's modulus of dried dentin was 28.1 GPa. RUS shows promise for determining the elastic constants in mineralized tissues.

A Comparison of Two Methods of Enhancing Implant Primary Stability

BACKGROUND

Surgical technique and implant design have an effect on the primary stability of oral implants, which in turn increases resistance to implant micromotion during healing.

PURPOSE

This study was designed to compare the parameters associated with implant insertion using two different methods of enhancing implant primary stability and to identify any relationship between these parameters and changes in the stability of implants during the initial 6-month healing period following implant insertion. A comparison was made between two methods of enhancing primary implant stability: method 1, standard Brånemark System implants (Nobel Biocare AB, Gothenburg, Sweden) inserted with a technique designed to enhance primary stability, and method 2: Brånemark Mk IV implants (Nobel Biocare AB) inserted according to the manufacturer's instructions.

MATERIALS AND METHODS

Thirteen patients were selected for inclusion in the study. A total of 42 implants were placed. Insertion torque data were recorded, and bone quality at the implant site was assessed at implant insertion. Resonance frequency analysis measurements were taken at implant insertion as well as at second-stage surgery 6 months later.

RESULTS

A statistically significant difference was recorded between the mean maximum insertion torque for type 4 bone and bone types 2 and 3. No significant difference was recorded between bone types 2 and 3. A significantly lower resonance frequency value was seen for standard implants placed into type 4 bone (p < .05). Across all implant types a significant difference in the energy required when inserting implants into type 4 bone and bone types 2 and 3 was seen. A significantly lower mean energy requirement was seen between the Mk IV implants placed into type 4 bone and the other combinations of implant types and bone.

CONCLUSIONS

Within the limitations of this study, the results agree with the manufacturer's claim that when compared with standard implants, the design of the Mk IV implant increases implant primary stability with a reduction in the energy imparted into the bone at the implant site.

Supersonic shear imaging: a new technique for soft tissue elasticity mapping

Supersonic shear imaging (SSI) is a new ultrasound-based technique for real-time visualization of soft tissue viscoelastic properties. Using ultrasonic focused beams, it is possible to remotely generate mechanical vibration sources radiating low-frequency, shear waves inside tissues. Relying on this concept, SSI proposes to create such a source and make it move at a supersonic speed. In analogy with the "sonic boom" created by a supersonic aircraft, the resulting shear waves will interfere constructively along a Mach cone, creating two intense plane shear waves. These waves propagate through the medium and are progressively distorted by tissue heterogeneities. An ultrafast scanner prototype is able to both generate this supersonic source and image (5000 frames/s) the propagation of the resulting shear waves. Using inversion algorithms, the shear elasticity of medium can be mapped quantitatively from this propagation movie. The SSI enables tissue elasticity mapping in less than 20 ms, even in strongly viscous medium like breast. Modalities such as shear compounding are implementable by tilting shear waves in different directions and improving the elasticity estimation. Results validating SSI in heterogeneous phantoms are presented. The first in vivo investigations made on healthy volunteers emphasize the potential clinical applicability of SSI for breast cancer detection.

Non-Gaussian statistics of the vibrational fluctuations of myoglobin

Experiments on the dynamics of vibrational fluctuations in myoglobin revealed an interesting behavioral cross-over occurring in the range 180-200 K. In this temperature range the mean square displacement of atomic positions versus temperature sharply increases its slope, indicating the dissociation of CO from the heme group. In this paper we develop a theoretical model that provides a framework for the quantitative description of this phenomenon. The basis of our calculations is an assumption of an effective potential with multiple local minima. In particular, we consider a quartic potential in place of the simple quadratic. We then use non-Gaussian statistics to obtain a relationship between the mean square displacement and model parameters. We compare our model to published experimental data and show that it can describe the data set using physically meaningful parameters which are fitted to the experimental data. In the process we verify the Gaussian approximation's applicability only to the low-temperature régime. In the high-temperature limit, however, deviations from the Gaussian approximation are due to the double-well nature of our effective potential. We find that the published datasets showing the thermal transition display the qualitative trends predicted by appropriate algebraic approximations to our predicted myoglobin behavior.

Vibration characteristics and function of atelectatic segments in the tympanic membrane in fresh human cadaveric temporal bones

Dimeric segments are commonly encountered in otological practice. They may be associated with a mild conductive hearing loss and often coexist with other tympanic membrane and middle ear abnormalities. Some otologists have advocated surgical management but the consequences of dimeric segment stiffening, shielding or excision and grafting on acoustic transfer to the stapes footplate has been poorly explored. In this study, laser Doppler vibrometry was used to measure vibrations at the tympanic membrane and the stapes footplate in the fresh cadaveric human temporal bone. The dimeric segment vibrates more than the adjacent, thicker normal tympanic membrane. Shielding or excision and grafting of the dimeric segment with thicker and stiffer materials has little effect on displacement at the stapes footplate.

Assignment validation software suite for the evaluation and presentation of protein resonance assignment data

We present a set of utilities and graphical user interface (GUI) tools for evaluating the quality of protein resonance assignments. The Assignment Validation Software (AVS) suite, together with new GUI features in the AutoAssign software package, provides a set of reports and graphs for validating protein resonance assignment data before its use in structure analysis and/or submission to the BioMagResBank (BMRB). Input includes a listing of resonance assignments and a summary of sequential connectivity data (i.e. triple resonance, NOE, or other data) used in deriving the assignments. These tools are useful for evaluating the accuracy of protein resonance assignments determined by either automated or manual methods.

Implant Stability, Tissue Conditions, and Patient Self-Evaluation after Treatment with Osseointegrated Implants in the Posterior Mandible

BACKGROUND

Implant treatment in the posterior mandible is considered challenging because of bone resorption and the presence of the inferior alveolar nerve, which may result in the use of short implants.

PURPOSE

To evaluate implant stability, tissue conditions, and patient opinion after treatment with implant-supported bridges in the posterior mandible.

MATERIALS AND METHODS

Thirty-four patients treated with implant-supported bridges in the posterior mandible according to a two-stage protocol were clinically and radiographically examined and interviewed after a mean functional time of 3.9 years. One hundred five Brånemark implants (Nobel Biocare AB, Gothenburg, Sweden) were placed in premolar and molar regions to support 40 bridges. Twenty-eight implants were placed anterior to the mental foramen, and 77 implants were placed posterior to the mental foramen. Bridges were supported either by two or by three implants. After 2 to 6 years, the bridges were removed to analyze the resonance frequency of the implants with the use of a special instrument (Osstell instrument, Integration Diagnostics AB, Gothenburg, Sweden), and an implant stability quotient (ISQ) was recorded for each implant.

RESULTS

One implant was lost. An ISQ range of 59 to 90 (mean, 70.05) expressed stability of fully integrated implants in the posterior mandible. Significantly higher (p < .024) ISQ values were found in implants in three-implant bridges when compared with implants in two-implant bridges. There were no differences in ISQ values between molars/premolars, implant types, implant widths, implant lengths, anchoring depth, or uni- or bilateral mandibular bridges. Good mucosal health in the periimplant soft tissue and minor bone resorption around the implants were observed. Patients were generally very satisfied with the treatment outcome.

CONCLUSIONS

High implant stability can be reached in the posterior mandible. The implants were more stable in three-implant bridges than in two-implant bridges. The patients were highly satisfied with the treatment, and few complications were seen.

A vibrator prevents streaming during close-arterial infusion into the kidney

Close-arterial infusion of test substances allows one to study the responses of a selected vascular bed without inducing confounding systemic effects. Unfortunately, laminar flow patterns within the artery cause streaming of the injected factor, so that distribution within the target organ is not homogeneous. We describe a reliable method of overcoming these problems. Specifically, we attach a vibrator (i-Vibe egg) to the syringe containing the test substance. We showed that, without vibration, infusion of a solution of Evans blue (0.5% wt/vol) results in uneven distribution of the dye in the kidney. Vibration of the syringe during infusion allows for uniform coloration of the kidney surface. There is also functional improvement of drug distribution during vibration. Renal blood flow was measured during intrarenal infusion of phenylephrine (150 μl, 0.05–0.5 μg). Vibration caused a significant leftward shift in the dose-response curve, i.e., the phenylephrine-induced reduction in renal blood flow was enhanced by vibration. This cheap, simple method for ensuring adequate mixing of intra-arterially infused substances will facilitate not only the study of renal function in the rat but also infusion of test and therapeutic substances into other organs.

Penile vibratory stimulation in the marmoset monkey: a practical alternative to electro-ejaculation, yielding ejaculates of enhanced quality

The availability of sufficient amounts of spermatozoa of high quality is one of the main limiting factors in reproductive research and development of reproductive technologies in marmoset monkeys (Callithrix jacchus). Penile vibrostimulation (PVS) has been successfully used in semen collection in the squirrel monkey but with poor success rate in the marmoset. We report here on an improved protocol for PVS with a success rate of almost 90%. Ejaculates obtained by PVS were of enhanced quality compared with those obtained by rectal probe electro-ejaculation (RPE). PVS ejaculates contained on average three to fourfold higher numbers of total and motile spermatozoa. Assessment of sperm kinematics using computer-assisted sperm analysis indicated that there are also functional differences between spermatozoa collected by PVS and RPE. Marmoset spermatozoa in samples obtained by RPE swim in a more convoluted manner compared with those obtained by PVS.

Measuring the nonlinear elastic properties of tissue-like phantoms

A direct mechanical system simultaneously measuring external force and deformation of samples over a wide dynamic range is used to obtain force-displacement curves of tissue-like phantoms under plain strain deformation. These measurements, covering a wide deformation range, then are used to characterize the nonlinear elastic properties of the phantom materials. The model assumes incompressible media, in which several strain energy potentials are considered. Finite-element analysis is used to evaluate the performance of this material characterization procedure. The procedures developed allow calibration of nonlinear elastic phantoms for elasticity imaging experiments and finite-element simulations.

Effects of whole-body vibration exercise on the endocrine system of healthy men

Whole-body vibration is reported to increase muscle performance, bone mineral density and stimulate the secretion of lipolytic and protein anabolic hormones, such as GH and testosterone, that might be used for the treatment of obesity. To date, as no controlled trial has examined the effects of vibration exercise on the human endocrine system, we performed a randomized controlled study, to establish whether the circulating concentrations of glucose and hormones (insulin, glucagon, cortisol, epinephrine, norepinephrine, GH, IGF-1, free and total testosterone) are affected by vibration in 10 healthy men [age 39 +/- 3, body mass index (BMI) of 23.5 +/- 0.5 kg/m2, mean +/- SEM]. Volunteers were studied on two occasions before and after standing for 25 min on a ground plate in the absence (control) or in the presence (vibration) of 30 Hz whole body vibration. Vibration slightly reduced plasma glucose (30 min: vibration 4.59 +/- 0.21, control 4.74 +/- 0.22 mM, p=0.049) and increased plasma norepinephrine concentrations (60 min: vibration 1.29 +/- 0.18, control 1.01 +/- 0.07 nM, p=0.038), but did not change the circulating concentrations of other hormones. These results demonstrate that vibration exercise transiently reduces plasma glucose, possibly by increasing glucose utilization by contracting muscles. Since hormonal responses, with the exception of norepinephrine, are not affected by acute vibration exposure, this type of exercise is not expected to reduce fat mass in obese subjects.

A pilot study of reference vibrotactile perception thresholds on the fingertip obtained with Malaysian healthy people using ISO 13091-1 equipment

The purpose of this paper is to clarify the reference vibrotactile perception thresholds (VPT) for healthy people in Malaysia. The measurement equipment standard, ISO 13091-1, of the vibrotactile perception thresholds for the assessment of nerve dysfunction and the analysis and interpretation of measurements at the fingertips standard, ISO 13091-2, were published in ISO/TC108/SC4/WG8 on 2001 and 2003 individually. In the ISO 13091-2 standard, the reference VPT data were obtained from few research papers. Malaysian people's VPT data don't include to this standard. In Malaysia, when the VPT is using to diagnose of the hand-arm vibration syndrome, the reference VPT data need to compare with the worker's ones. But, Malaysia does not have the reference VPT data yet. So, in this paper, the VPT was measured by using ISO 13091-1 standard equipment to obtain the reference data for Malaysian people. And these data were compared with the ISO reference data on the ISO 13091-2 standard. From the comparison of these data, it was clear that the Malaysian healthy people's VPT data were consistent with the reference data of the ISO 13091-2 standard.

Isomers of HSCO: IR absorption spectra of t-HSCO in solid Ar

Irradiation of an Ar matrix sample containing H2S and CO (or OCS) with an ArF excimer laser at 193 nm yields trans-HSCO (denoted t-HSCO). New lines at 1823.3, 931.6, and 553.3 cm(-1) appear after photolysis and their intensity enhances after annealing; secondary photolysis at 248 nm diminishes these lines and produces OCS and CO. These lines are assigned to C-O stretching, HSC-bending, and C-S stretching modes of t-HSCO, respectively, based on results of 13C-isotopic experiments and theoretical calculations. Theoretical calculations using density-functional theories (B3LYP and PW91PW91) predict four stable isomers of HSCO: t-HSCO, c-HSCO, HC(O)S, and c-HOCS, listed in increasing order of energy. According to calculations with B3LYP/aug-cc-pVTZ, t-HSCO is planar, with bond lengths of 1.34 A (H-S), 1.81 A (S-C), and 1.17 A (C-O), and angles angle HSC congruent with 93.4 degrees and angle SCO congruent with 128.3 degrees; it is more stable than c-HSCO and HC(O)S by approximately 9 kJ mol(-1) and more stable than c-HOCS by approximately 65 kJ mol(-1). Calculated vibrational wave numbers, IR intensities, and 13C-isotopic shifts for t-HSCO fit satisfactorily with experimental results. This new spectral identification of t-HSCO provides information for future investigations of its roles in atmospheric chemistry.

A psychophysical test of the vibration theory of olfaction

At present, no satisfactory theory exists to explain how a given molecule results in the perception of a particular smell. One theory is that olfactory sensory neurons detect intramolecular vibrations of the odorous molecule. We used psychophysical methods in humans to test this vibration theory of olfaction and found no evidence to support it.

Reverse propagation of sound in the gerbil cochlea

It is commonly believed that the cochlea emits sounds through backward-traveling waves. In the present experiment using a scanning-laser interferometer, I detected forward-traveling but not backward-traveling waves and found that the stapes vibrates earlier than the basilar membrane. These results contradict the current theory and show that the ear emits sounds through the cochlear fluids as compression waves rather than along the basilar membrane as backward-traveling waves.

Multiple-bandwidth photoacoustic tomography

Photoacoustic tomography, also referred to as optoacoustic tomography, employs short laser pulses to generate ultrasonic waves in biological tissues. The reconstructed images can be characterized by the convolution of the structure of samples, the laser pulse and the impulse response of the ultrasonic transducer used for detection. Although the laser-induced ultrasonic waves cover a wide spectral range, a single transducer can receive only part of the spectrum because of its limited bandwidth. To systematically analyse this problem, we constructed a photoacoustic tomographic system that uses multiple ultrasonic transducers simultaneously, each at a different central frequency. The photoacoustic images associated with the different transducers were compared and analysed. The system was tested by imaging both mouse brains and phantom samples. The vascular vessels in the brain were revealed by all of the transducers, but the image resolutions differed. The higher frequency detectors provided better image resolution while the lower frequency detectors delineated the major structural traits with a higher signal-noise ratio.

Modal Damping for Monitoring Bone Integrity and Osteoporosis

We applied a noninvasive method to assess bone structural integrity. The method is based on the measurement of the dynamic characteristics of the bone (quality factor and modal damping factor) by applying vibration excitation in the range of acoustic frequencies, in the form of an acoustic sweep signal. Excised sheep femora were tested to detect changes in modal damping, density (kg/m3), bone mineral density (kg/m2) and bone mineral (hydroxyapatite) percentage. The changes were recorded after each time of chemical treatment of the bones performed to gradually cause mineral removal, thus simulating osteoporosis. It was shown that the change in quality factor and damping was in all cases on average equal or greater to the change in all other measured characteristics, thus strengthening the potential of the proposed method to become a valuable assessment tool for monitoring bone integrity and osteoporosis.

Modes and Balance of Energy in the Piezoelectric Cochlear Outer Hair Cell Wall

Here, we analyze energy transformations in the outer hair cell and its effectiveness as a piezoelectric-type actuator in the cochlea. The major modes of energy are introduced, and a method to estimate the coefficients of their tension-dependence is proposed. Next, we derive balance of the mechanical and electrical parts of energy, and show two forms of the active energy associated with the motors driving electromotility. The two forms of the active energy, stored mechanical energy, and external electrical work are then introduced as functions of voltage and applied force. We use the energy balance to introduce and estimate the effectiveness of the cell’s electromotile response.

Adhesion and rupture of liposomes mediated by electrostatic interaction monitored by thickness shear mode resonators

Adhesion and spreading of negatively charged unilamellar vesicles composed of POPG/POPC and DPPG/DPPC on positively charged self-assembly monolayers of 11-amino-1-undecanethiol were monitored by means of thickness shear mode (TSM) resonators with a fundamental frequency of 5 MHz. Changes of frequency and motional resistance upon vesicle adsorption were recorded as a function of surface charge density and lyotropic phase state of the lipids. From the readout of the TSM resonator, changes of the shape of the vesicles as well as the formation of supported lipid bilayers can be inferred in a quantitative manner. Increasing surface charge densities on the vesicles, which are tunable by the POPG content, led to decreasing frequency and resistance changes. At very high PG content, a lower limit of 3-12 Hz was found, indicative of the formation of planar bilayers due to vesicle rupture induced by the strong electrostatic interaction forces. Vesicles composed of DPPG/DPPC were less susceptible to deformation and rupture, a fact that can be attributed to the higher bending rigidity of DPPG/DPPC liposomes. More than 70 mol% of DPPG were needed to induce adhesion-controlled rupture of surface-attached vesicles, while only 30-50% of POPG were sufficient to form planar lipid bilayers on the quartz.

Accurate and efficient description of protein vibrational dynamics: Comparing molecular dynamics and Gaussian models

Current all-atom potential based molecular dynamics (MD) allows the identification of a protein's functional motions on a wide-range of timescales, up to few tens of nanoseconds. However, functional, large-scale motions of proteins may occur on a timescale currently not accessible by all-atom potential based MD. To avoid the massive computational effort required by this approach, several simplified schemes have been introduced. One of the most satisfactory is the Gaussian network approach based on the energy expansion in terms of the deviation of the protein backbone from its native configuration. Here, we consider an extension of this model that captures in a more realistic way the distribution of native interactions due to the introduction of effective side-chain centroids. Since their location is entirely determined by the protein backbone, the model is amenable to the same exact and computationally efficient treatment as previous simpler models. The ability of the model to describe the correlated motion of protein residues in thermodynamic equilibrium is established through a series of successful comparisons with an extensive (14 ns) MD simulation based on the AMBER potential of HIV-1 protease in complex with a peptide substrate. Thus, the model presented here emerges as a powerful tool to provide preliminary, fast yet accurate characterizations of protein near-native motion.