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PubMed1998

Reconstructing hominid Y evolution: X-homologous block, created by X-Y transposition, was disrupted by Yp inversion through LINE-LINE recombination.

The human X and Y chromosomes share many blocks of similar DNA sequence. We conducted mapping and nucleotide sequencing studies of extensive, multi-megabase homologies between Yp and Xq21, which do not recombine during male meiosis. We confirmed and built upon previous evidence that a Yp inversion had occurred during evolution: a single contiguous segment of Xq21 is homologous to two non-contiguous segments of Yp. We precisely defined and sequenced the inversion breakpoints, obtaining evidence that the inversion was mediated by recombination between LINE-1 elements in otherwise non-homologous regions. This inversion appears to have followed a single transposition of an approximately 4 Mb segment from the X to the Y chromosome. These events jointly account for the present arrangement of Yp-Xq21 homologous sequences. Based on Southern blotting studies of primates and of humans drawn from diverse populations, we conclude that both the X-Y transposition and the subsequent, LINE-mediated Yp inversion occurred after the divergence of hominid and chimp lineages but before the radiation of extant human populations. This evolutionary scenario is consistent with our finding of 99.3 +/- 0.2% nucleotide identity between the X and Y chromosomes within the transposed region, which suggests that the transposition occurred approximately 3-4 million years ago, near the time of emergence of Homo . Comparative sequencing of the entire human X and Y chromosomes may reveal a succession of transpositions, inversions and other rearrangements underlying the complex pattern of sequence similarities between the present-day sex chromosomes. With the possible exception of cubitus valgus, phenotypic features of Turner syndrome are absent in individuals monosomic for Yp-Xq21 homologous sequences, suggesting that most of the critical 'Turner genes' are found elsewhere on the X and Y chromosomes.

Base Sequence↗
PubMed1982

Long terminal repeat (LTR)-derived recombination of retroviral DNA: sequence analyses of an aberrant clone of baboon endogenous virus DNA which carries an inversion from the LTR to the gag region.

Nucleotide sequences of a cloned proviral DNA of baboon endogenous virus M7 were analyzed, which carried an internal inversion. The inversion of 2.2 kilobase pairs was occurred between the junction of two tandem LTRs and a site locating in the p30 region of the gag gene. The ATAA sequence was a target for recombination generating the inversion, which was duplicated at both ends of the inverted segment. AAA and CA were lost at the 5'- and 3'-ends of the LTRs by the inversion, respectively. On both sides of the target sequence, long AG-rich stretches were detected, which may specify the site of recombination together with the target sequence. The characteristic base changes in the inversion are concluded to result from an illegitimate recombination associated with LTRs, as well as in case of provirus integration into the host cell DNA. We propose and discuss models to explain the processes of recombination to generate both inversion and integration.

Amino Acid Sequence↗
PubMed2006

Visualizing bacterial tRNA identity determinants and antideterminants using function logos and inverse function logos.

Sequence logos are stacked bar graphs that generalize the notion of consensus sequence. They employ entropy statistics very effectively to display variation in a structural alignment of sequences of a common function, while emphasizing its over-represented features. Yet sequence logos cannot display features that distinguish functional subclasses within a structurally related superfamily nor do they display under-represented features. We introduce two extensions to address these needs: function logos and inverse logos. Function logos display subfunctions that are over-represented among sequences carrying a specific feature. Inverse logos generalize both sequence logos and function logos by displaying under-represented, rather than over-represented, features or functions in structural alignments. To make inverse logos, a compositional inverse is applied to the feature or function frequency distributions before logo construction, where a compositional inverse is a mathematical transform that makes common features or functions rare and vice versa. We applied these methods to a database of structurally aligned bacterial tDNAs to create highly condensed, birds-eye views of potentially all so-called identity determinants and antideterminants that confer specific amino acid charging or initiator function on tRNAs in bacteria. We recovered both known and a few potentially novel identity elements. Function logos and inverse logos are useful tools for exploratory bioinformatic analysis of structure-function relationships in sequence families and superfamilies.

Base Sequence↗
PubMed2002

Generalized emissivity inverse problem.

Inverse problems have recently drawn considerable attention from the physics community due to of potential widespread applications [K. Chadan and P. C. Sabatier, Inverse Problems in Quantum Scattering Theory, 2nd ed. (Springer Verlag, Berlin, 1989)]. An inverse emissivity problem that determines the emissivity g(nu) from measurements of only the total radiated power J(T) has recently been studied [Tao Wen, DengMing Ming, Xianxi Dai, Jixin Dai, and William E. Evenson, Phys. Rev. E 63, 045601(R) (2001)]. In this paper, a new type of generalized emissivity and transmissivity inverse (GETI) problem is proposed. The present problem differs from our previous work on inverse problems by allowing the unknown (emissivity) function g(nu) to be temperature dependent as well as frequency dependent. Based on published experimental information, we have developed an exact solution formula for this GETI problem. A universal function set suggested for numerical calculation is shown to be robust, making this inversion method practical and convenient for realistic calculations.

Journal Article↗
PubMed2006

Inversion formula of multifractal energy dissipation in three-dimensional fully developed turbulence.

The concept of inverse statistics in turbulence has attracted much attention in recent years. It is argued that the scaling exponents of the direct structure functions and the inverse structure functions satisfy an inversion formula. This proposition has already been verified by numerical data using the shell model. However, no direct evidence was reported for experimental three-dimensional turbulence. We propose to test the inversion formula using experimental data of three-dimensional fully developed turbulence by considering the energy dissipation rates instead of the usual efforts on the structure functions. The moments of the exit distances are shown to exhibit nice multifractality. The inversion formula between the direct and inverse exponents is then verified.

Journal Article↗
PubMed2003

Broadband ultrasonic transducers using a LiNbO3 plate with a ferroelectric inversion layer.

Some heat treatment of a lithium niobate (LiNbO3) plate induces domain inversion, thereby yielding a ferroelectric inversion layer. In such a piezoelectric plate with an inversion layer, even-order thickness-extensional modes, as well as odd-order modes, can be excited piezoelectrically. Therefore, the ultrasonic transducer using such a piezoelectric plate is expected to operate over a wide frequency range. In this paper, it is shown that broadband ultrasonic transducers can be obtained at a certain thickness ratio of inversion layer to plate, and that the transducer characteristics differ depending on whether the inversion layer is on the front side or on the backside. The broadband characteristics are experimentally demonstrated by fabricating transducers with 9 MHz or 75 MHz center frequency using 36 degrees rotated Y-cut LiNbO3 plates with a ferroelectric inversion layer.

Journal Article↗
PubMed2005

An analytical model of multilayer ultrasonic transducers with an inversion layer.

Inversion layer ultrasonic transducers have been investigated recently as an interesting approach in wideband transducer design. In this paper we present an analytical model of multilayer ultrasonic transducers with an inversion layer. Our analysis of the wave propagation problem of an inversion layer transducer includes a functional decomposition of the electrical input impedance. It becomes clear from this decomposition that an inversion layer transducer can be modeled as three elements in series connection, i.e., a clamped capacitance, a classical motional impedance, and a coupled motional impedance. The first two elements make up the classical model of a single element transducer. The coupled motional impedance describes the coupled interaction between the regular and the inverted piezoelectric sublayers, and thus reflects the effect of an inversion layer. We present examples which show that inversion layer transducers are advantageous in achieving such useful features as dual-frequency operation mode as used in harmonic imaging or broadband performance desired in most ultrasonic applications.

Journal Article↗
PubMedDate not supplied

Effect of alpha-adrenoceptor subtype-selective inverse agonists on non-pregnant and late-pregnant cervical resistance in vitro in the rat.

1. The aim of the present study was to compare and elucidate the effects of alpha(1)-adrenoceptor (alpha(1)-AR) subtype-selective inverse agonists on non-pregnant and late-pregnant rat cervical tone. 2. Cervical resistance was investigated in in vitro stretching tests in the absence or presence of alpha(1)-AR subtype-selective inverse agonists (WB 4101, AH 11110A and BMY 7378; all at 10(-6) mol/L), whereas the mRNA levels and density of the alpha(1)-AR subtypes and the G-protein-activating effects of the inverse agonists were determined by reverse transcription-polymerase chain reaction, western blot and [(35)S]-GTPgammaS binding techniques, respectively. 3. The inverse agonists did not cause any change in resistance in non-pregnant and 18-day-pregnant samples. WB 4101 increased cervical resistance from Day 20, whereas AH 11110A had no effect and BMY 7378 exhibited such an action only on Day 21. Phenylephrine (10(-4) mol/L) had no effect on cervical resistance on Day 22. The mRNA levels and density of all alpha(1)-AR subtypes were increased on Day 18, but no further changes were observed after that. The [(35)S]-GTPgammaS binding studies revealed increased G-protein activation of alpha(1A)-AR and a moderate G-protein activation of alpha(1B)- and alpha(1D)-AR. The effect of WB 4101 to increase [(35)S]-GTPgammaS binding was blocked by pertussis toxin (50 ng/mL). Phenylephrine caused a slight and significant decrease in the amount of activated G-protein on Day 22. 4. The effects of inverse agonists on the alpha(1A)-AR can enhance cervical resistance in the late-pregnant rat in vitro. This action is mediated, at least in part, by a pertussis toxin-sensitive G(i)-protein. This effect of the alpha(1A)-AR inverse agonist WB 4101 may offer a new therapeutic target in the prevention of premature labour.

Adrenergic alpha-Agonists↗
PubMed2004

Free-breathing renal MR angiography with steady-state free-precession (SSFP) and slab-selective spin inversion: initial results.

BACKGROUND: The aim of our study was the investigation of a novel navigator-gated three-dimensional (3D) steady-state free-precession (SSFP) sequence for free-breathing renal magnetic resonance angiography (MRA) without contrast medium, and to examine the advantage of an additional inversion prepulse for improved contrast. METHODS: Eight healthy volunteers (mean age 29 years) and eight patients (mean age 53 years) were investigated on a 1.5 Tesla MR system (ACS-NT, Philips, Best, The Netherlands). Renal MRA was performed using three navigator-gated free-breathing cardiac-triggered 3D SSFP sequences [repetition time (TR) = 4.4 ms, echo time (TE) = 2.2 ms, flip angle 85 degrees, spatial resolution 1.25 x 1.25 x 4.0 mm(3), scanning time approximately 1 minute 30 seconds]. The same sequence was performed without magnetization preparation, with a non-slab selective and a slab-selective inversion prepulse. Signal-to-noise ratio (SNR), contrast-to-noise (CNR) vessel length, and subjective image quality were compared. RESULTS: Three-dimensional SSFP imaging combined with a slab-selective inversion prepulse enabled selective and high contrast visualization of the renal arteries, including the more distal branches. Standard SSFP imaging without magnetization preparation demonstrated overlay by veins and renal parenchyma. A non-slab-selective prepulse abolished vessel visualization. CNR in SSFP with slab-selective inversion was 43.6 versus 10.6 (SSFP without magnetization preparation) and 0.4 (SSFP with non-slab-selective inversion), P < 0.008. CONCLUSION: Navigator-gated free-breathing cardiac-triggered 3D SSFP imaging combined with a slab-selective inversion prepulse is a novel, fast renal MRA technique without the need for contrast media.

Adult↗
PubMed1995

Continuous heart rate variability monitoring through complex demodulation implemented with the fast Fourier transform and its inverse.

UNLABELLED: A new method for the analysis of 24-hour heart rate variability (HRV) using complex demodulation (CDM) implemented with the fast Fourier transform (FFT) and its inverse is described. In a control group with palpitations and dizzy spells (n = 30, 47.2 +/- 16.7 years) the relationship between HRV parameters and subject age was investigated. CDM was used to obtain the amplitude and frequency of the low frequency (LF) and high frequency (HF) oscillations for 8 diurnal hours and 4 nocturnal hours. Differences between the two periods were seen in the LF/HF ratio (2.2 +/- 0.6 vs 1.5 +/- 0.6; P < 0.0001), HF amplitudes (12 +/- 6 vs 17 +/- 7 normalized units, P < 0.05), and in the mean frequency of the LF oscillations (0.078 +/- 0.008 vs 0.073 +/- 0.007 Hz, P < 0.01). During the daytime, age was inversely correlated to HF amplitude (r = -0.60), directly correlated to HF mean central frequency (r = 0.40), inversely correlated to LF amplitude (r = -0.55), and likewise inversely correlated to LF mean central frequency (r = -0.74, P < 0.001). At night, age was only inversely correlated to HF amplitude and to LF mean central frequency. CONCLUSIONS: Continuous HRV monitoring through CDM implemented with the FFT and its inverse differentiates the periods of diurnal activity and nocturnal rest as an expression of two different activity states of the autonomic nervous system. It allows nonstationary analysis, and separately provides mean and instantaneous oscillation amplitude and frequency. Subject age is not equally related to mean amplitude and frequency of a given oscillation.

Adolescent↗
PubMed2005

Intrinsic risk factors for inversion ankle sprains in females--a prospective study.

Ankle sprains are extremely common. However, very little is known about the variables that predispose individuals to these injuries. The purpose of this study was to examine prospectively intrinsic risk factors for inversion sprains in a young physically active female population. One hundred and fifty-nine female physical education students were evaluated for several possible intrinsic risk factors for inversion sprains at the beginning of their academic study. The evaluated intrinsic risk factors included anthropometrical and physical characteristics, ankle joint position sense, isokinetic ankle muscle strength, lower leg alignment characteristics, postural control and muscle reaction time during a sudden inversion perturbation. All sports injuries were registered during 1-3 years and exposure to sport was recorded (mean: 15.33+/-4.33 h a week). Thirty-two (20%) of the 159 females sprained their ankle. The number of ankle sprains per 1000 h of sports exposure was 0.75. The Cox regression analysis revealed that females with less accurate passive joint inversion position sense [hazard ratio (HR): 1.08, 95% confidence interval (CI): 1.02-1.14 for absolute error at 15 degrees inversion], a higher extension range of motion at the first metatarsophalangeal joint (HR: 1.03, 95% CI: 1.00-1.06) and less coordination of postural control (HR: 0.96, 95% CI: 0.93-1.00 for endpoint excursion; HR: 0.94, 95% CI: 0.89-0.99 for maximal endpoint excursion) are at greater risk of an ankle sprain. The findings of this study suggest that effective prevention and conservative rehabilitation of ankle inversion sprains should include attention to these variables.

Adolescent↗
PubMed2007

Effect of inversion and ankle bracing on peroneus longus Hoffmann reflex.

This study examined peroneus longus (PL) Hoffmann reflex (H-reflex) during sudden inversion perturbation of the ankle/foot complex under an ankle brace and non-brace condition. Ten healthy subjects volunteered. H-reflexes were tested on the up-sloping portion of the recruitment curve, utilizing a control trial M-wave above motor threshold to maintain consistency between subjects and conditions. The PL H/maximum M-wave (M(max)) ratio was established using the PL H-reflex and PL M(max) peak-to-peak measures. The mean ratio across five trials for each subject under each ankle brace (brace, no brace) and surface (flat, inversion) conditions was utilized for analysis. The 1 x 4 repeated measures ANOVA revealed a significant main effect for treatment condition (P<0.0001). The PL H/M(max) ratio significantly increased during sudden inversion-no ankle brace condition compared with the flat surface no-ankle brace condition (P=0.04). Application of an ankle brace had no effect on PL H/M(max) ratio during inversion (P=0.78). During this study PL H/M(max) ratios increased during an inversion perturbation in healthy ankles. This is believed to occur due to heightened sensorimotor demand placed on the nervous system during this motion. Moreover, application of an ankle brace during inversion does not appear to affect PL H/M(max) ratio.

Adult↗
PubMed2003

Inversion polymorphisms and natural selection in Trimerotropis pallidipennis (Orthoptera).

Grasshoppers have been much less studied than Drosophila when it comes to inversion polymorphisms, despite the occurrence of this rearrangement in several species of grasshoppers. In the present study, 354 males from a natural population of the New World species Trimerotropis pallidipennis, polymorphic for 6 pericentric inversions in 4 chromosome pairs, were sampled at the beginning and at the end of the adult life span. This sampling, along with the fact that generations in this grasshopper are annual and discrete, was done to detect differential adult male longevity among karyotypes and departures from formal null models, such as gametic phase equilibrium. These methods allow the detection of natural selection taking place in the wild. The comparison between age classes showed that some inversions were significantly more frequent in one sample, thus revealing the operation of natural selection. Gametic phase disequilibrium was detected in the sample of aged males but not in the sample of young ones. Furthermore, here we aim to detect the phenotypic targets of longevity selection by examining morphometric characters, in order to have a clearer idea of the relation between inversions and natural selection in this species. These results corroborate previous studies that suggested that the inversions are involved in natural selection, and an adaptive model has been proposed for the pattern of inversion frequencies throughout several populations at different altitudes and latitudes.

Animals↗
PubMed2003

Real-time inverse planning for Gamma Knife radiosurgery.

The challenges of real-time Gamma Knife inverse planning are the large number of variables involved and the unknown search space a priori. With limited collimator sizes, shots have to be heavily overlapped to form a smooth prescription isodose line that conforms to the irregular target shape. Such overlaps greatly influence the total number of shots per plan, making pre-determination of the total number of shots impractical. However, this total number of shots usually defines the search space, a pre-requisite for most of the optimization methods. Since each shot only covers part of the target, a collection of shots in different locations and various collimator sizes selected makes up the global dose distribution that conforms to the target. Hence, planning or placing these shots is a combinatorial optimization process that is computationally expensive by nature. We have previously developed a theory of shot placement and optimization based on skeletonization. The real-time inverse planning process, reported in this paper, is an expansion and the clinical implementation of this theory. The complete planning process consists of two steps. The first step is to determine an optimal number of shots including locations and sizes and to assign initial collimator size to each of the shots. The second step is to fine-tune the weights using a linear-programming technique. The objective function is to minimize the total dose to the target boundary (i.e., maximize the dose conformity). Results of an ellipsoid test target and ten clinical cases are presented. The clinical cases are also compared with physician's manual plans. The target coverage is more than 99% for manual plans and 97% for all the inverse plans. The RTOG PITV conformity indices for the manual plans are between 1.16 and 3.46, compared to 1.36 to 2.4 for the inverse plans. All the inverse plans are generated in less than 2 min, making real-time inverse planning a reality.

Algorithms↗
PubMed2006

Inverse plan optimization accounting for random geometric uncertainties with a multiple instance geometry approximation (MIGA).

Radiotherapy treatment plans that are optimized to be highly conformal based on a static patient geometry can be degraded by setup errors and/or intratreatment motion, particularly for IMRT plans. To achieve improved plans in the face of geometrical uncertainties, direct simulation of multiple instances of the patient anatomy (to account for setup and/or motion uncertainties) is used within the inverse planning process. This multiple instance geometry approximation (MIGA) method uses two or more instances of the patient anatomy and optimizes a single beam arrangement for all instances concurrently. Each anatomical instance can represent expected extremes or a weighted distribution of geometries. The current implementation supports mapping between instances that include distortions, but this report is limited to the use of rigid body translations/ rotations. For inverse planning, the method uses beamlet dose calculations for each instance, with the resulting doses combined using a weighted sum of the results for the multiple instances. Beamlet intensities are then optimized using the inverse planning system based on the cost for the composite dose distribution. MIGA can simulate various types of geometrical uncertainties, including random setup error and intratreatment motion. A limited number of instances are necessary to simulate Gaussian-distributed errors. IMRT plans optimized using MIGA show significantly less degradation in the face of geometrical errors, and are robust to the expected (simulated) motions. Results for a complex head/neck plan involving multiple target volumes and numerous normal structures are significantly improved when the MIGA method of inverse planning is used. Inverse planning using MIGA can lead to significant improvements over the use of simple PTV volume expansions for inclusion of geometrical uncertainties into inverse planning, since it can account for the correlated motions of the entire anatomical representation. The optimized plan results reflect the differing patient geometry situations which can be important near the surface or heterogeneities. For certain clinical situations, the MIGA optimization approach can correct for a significant part of the degradation of the plan caused by the setup uncertainties.

Artifacts↗
PubMed2001

Tomographic inversion of geoacoustic properties in a range-dependent shallow-water environment.

This paper presents a matched-field tomographic method to estimate the geoacoustic properties of the ocean bottom for a range-dependent medium in shallow water. The inversion method has been developed in order to interpret experimental data from the Haro Strait PRIMER sea trial. This experiment was carried out in June '96 and used low-frequency broadband signals that were received on three vertical line arrays. Inversion of the data is particularly difficult because of the complex bathymetry of the Haro Strait experimental site. For this inversion, a range-dependent ray code was developed to solve the forward problem, allowing an arbitrarily layered bottom environment. The inversion scheme is based on modeling the propagation time and the amplitude of the recorded data, and a simple new cost function is proposed. The signal ray paths are identified automatically using a simple process that compares calculated and measured travel times. Data from multiple source positions are used to invert the range dependence of the geoacoustic model. The environment is separated into segments, and within each segment the inversion is carried out layer by layer for a multilayer geoacoustic model. Starting with the topmost layer, the range-dependent thickness and sound speed are estimated via a Monte Carlo method. Inversion results are presented for synthetic and experimental data from the Haro Strait sea trial.

Journal Article↗
PubMed2005

Geoacoustic inversion with ships as sources.

Estimation of geoacoustic parameters using acoustic data from a surface ship was performed for a shallow water region in the Gulf of Mexico. The data were recorded from hydrophones in a bottom mounted, horizontal line array (HLA). The techniques developed to produce the geoacoustic inversion are described, and an efficient method for geoacoustic inversion with broadband beam cross-spectral data is demonstrated. The performance of cost functions that involve coherent or incoherent sums over frequency and one or multiple time segments is discussed. Successful inversions for the first sediment layer sound speed and thickness and some of the parameters for the deeper layers were obtained with the surface ship at nominal ranges of 20, 30, or 50 water depths. The data for these inversions were beam cross-spectra from four subapertures of the HLA spanning a little more than two water depths. The subaperture beams included ten frequencies equally spaced in the 120-200 Hz band. The values of the geoacoustic parameters from the inversions are validated by comparisons with geophysical observations and with the parameter values from previous inversions by other invesigators, and by comparing transmission loss (TL) measured in the experiment with modeled TL based on the inverted geoacoustic parameters.

Journal Article↗
PubMed2005

The effects of ignored seabed variability in geoacoustic inversion.

Geoacoustic inversion using a matched-field inversion algorithm is a well-established technique for estimating the geoacoustic parameters of the seabed. This paper demonstrates how parameter estimation can be affected by unknown or wishfully ignored random range dependence of the true environment when the inversion model is--for practicality--assumed to be range independent. Simulations with controlled statistics were carried out using a simple shallow water model: an isospeed water column over a homogeneous elastic halfspace. The inversion parameters included water depth, compressional speed in the seabed, seabed density, and compressional wave attenuation. On average the environment is range independent: some parameters are constant while other parameters are random with range-independent means and variances. A Parabolic Equation underwater acoustic propagation model is used to calculate the simulated data fields for the range-dependent environment as well as to calculate the model fields for the range-independent inversion model. The Adaptive Simplex Simulated Annealing inversion algorithm is used to estimate the best-fit solution. It is found that ignoring the variability of even a single geoacoustic parameter leads to significant and correlated uncertainty (bias and variance) in the estimation of all inverted parameters. Results are presented for range variation of compressional sound speed and water depth.

Journal Article↗