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A wavelet-based statistical analysis of FMRI data: I. motivation and data distribution modeling.

We propose a new method for statistical analysis of functional magnetic resonance imaging (fMRI) data. The discrete wavelet transformation is employed as a tool for efficient and robust signal representation. We use structural magnetic resonance imaging (MRI) and fMRI to empirically estimate the distribution of the wavelet coefficients of the data both across individuals and spatial locations. An anatomical subvolume probabilistic atlas is used to tessellate the structural and functional signals into smaller regions each of which is processed separately. A frequency-adaptive wavelet shrinkage scheme is employed to obtain essentially optimal estimations of the signals in the wavelet space. The empirical distributions of the signals on all the regions are computed in a compressed wavelet space. These are modeled by heavy-tail distributions because their histograms exhibit slower tail decay than the Gaussian. We discovered that the Cauchy, Bessel K Forms, and Pareto distributions provide the most accurate asymptotic models for the distribution of the wavelet coefficients of the data. Finally, we propose a new model for statistical analysis of functional MRI data using this atlas-based wavelet space representation. In the second part of our investigation, we will apply this technique to analyze a large fMRI dataset involving repeated presentation of sensory-motor response stimuli in young, elderly, and demented subjects.

Adult↗

[Experimental study of Raman spectra of magnesite at 297 K and at the pressure of 0.13-1 GPa].

The experimental study of Raman spectra of magnesite has been conducted at the pressure of 967 MPa and at the temperatureof 297 K using a cubic zirconia-anvil cell. The result shows that neither phase transition nor organic substances were observed during compression, and the Raman peak of magnesite shifted to higher frequency with increasing pressure. The relation between the pressure and the Raman peak position of magnesite (1094 cm(-1)) was obtained as follows: v (cm(-1)) = 0.007 44 x P(MPa) + 1 093.3. The value of dv/dP of magnesite is greater than the previous data obtained by Gillet, which was mostly taken under the mantle pressure. And at the ambient temperature, magnesite can be used as a pressure gauge, and the relation between the pressure and Raman shift of 1 094 cm(-1) peak position is given as following: P(MPa) = 125.8 x (deltavp) 1094 + 124.7 (1094 cm(-1) < vp < 1101 cm(-1)).

Algorithms↗

Influence of filler content on static properties of glass-reinforced bone cement.

A commercial acrylic bone cement was modified by the incorporation of different weight fractions of glass spheres. The influence of the filler proportion on the mechanical behavior was assessed. Composite cements were prepared by replacing part of the powder phase of the cement by an equivalent weight of glass particles, which resulted in an increase in the liquid-to-powder (L/P) ratio of the polymeric matrix. Dynamic mechanical analysis revealed an increase in residual monomer content with increasing filler proportion as a consequence of the increase in L/P. Flexural, compressive, and fracture properties of the cement with varying amounts of glass particles were measured. It was found that up to 50 wt% glass particles could be added with significant increases in flexural modulus and fracture toughness. The mechanical behavior was explained in terms of both the reinforcing effect of the filler and the plasticizing effect of the monomer. Glass-filled bone cements displayed superior workability compared with the standard cement, which was attributed to a decrease in the viscosity of the initial mix and the surface characteristics of the glass particles. The observed increase in fracture toughness could be rationalized through the application of proposed mechanisms for toughening of particle-reinforced polymers.

Acrylic Resins↗

DNA structure in human RNA polymerase II promoters.

The fact that DNA three-dimensional structure is important for transcriptional regulation begs the question of whether eukaryotic promoters contain general structural features independently of what genes they control. We present an analysis of a large set of human RNA polymerase II promoters with a very low level of sequence similarity. The sequences, which include both TATA-containing and TATA-less promoters, are aligned by hidden Markov models. Using three different models of sequence-derived DNA bendability, the aligned promoters display a common structural profile with bendability being low in a region upstream of the transcriptional start point and significantly higher downstream. Investigation of the sequence composition in the two regions shows that the bendability profile originates from the sequential structure of the DNA, rather than the general nucleotide composition. Several trinucleotides known to have high propensity for major groove compression are found much more frequently in the regions downstream of the transcriptional start point, while the upstream regions contain more low-bendability triplets. Within the region downstream of the start point, we observe a periodic pattern in sequence and bendability, which is in phase with the DNA helical pitch. The periodic bendability profile shows bending peaks roughly at every 10 bp with stronger bending at 20 bp intervals. These observations suggest that DNA in the region downstream of the transcriptional start point is able to wrap around protein in a manner reminiscent of DNA in a nucleosome. This notion is further supported by the finding that the periodic bendability is caused mainly by the complementary triplet pairs CAG/CTG and GGC/GCC, which previously have been found to correlate with nucleosome positioning. We present models where the high-bendability regions position nucleosomes at the downstream end of the transcriptional start point, and consider the possibility of interaction between histone-like TAFs and this area. We also propose the use of this structural signature in computational promoter-finding algorithms.

Algorithms↗

Active implementation of a consensus strategy improves diagnosis and management in suspected pulmonary embolism.

Our consensus-based strategy in the diagnostic management of patients with pulmonary embolism involves a perfusion lung scan, a ventilation lung scan, compression ultrasonography and pulmonary angiography, in sequence. We compared the diagnostic approach in patients with clinically suspected pulmonary embolism before the active implementation of this strategy (retrospective analysis of 618 patients, April 1992-March 1995) and after (prospective study of 250 patients, April 1995-March 1996), with another assessment 1 year later. The measured outcomes were: (i) final diagnosis of pulmonary embolism either directly by pulmonary angiography, indirectly by compression ultrasonography of the leg veins, or with a high probability from a ventilation/perfusion lung scan; (ii) prescription of anticoagulant therapy. Before strategy implementation, pulmonary embolism was adequately confirmed or excluded in 11% of patients with an abnormal perfusion lung scan; in 55% the diagnosis remained uncertain, but the patient received anticoagulants. After implementation, these figures were 58.5% and 13%, respectively. A modest further improvement was observed 1 year later. Active implementation of a consensus-based strategy in the diagnosis of pulmonary embolism increases definite diagnoses, and reduces the numbers treated with anticoagulants. It induces a rapid change in the diagnostic behaviour of physicians.

Algorithms↗

[Intraoperative monitoring of the function of the peroneal nerve in knee joint operations].

Operations on the knee are known to be associated with postoperative neurological complications. There is no consensus opinion on the causes of these complications. The aim of the present study was to develop a method for the intraoperative monitoring of the function of the common peroneal nerve. This was done as to identify intraoperative factors that might be responsible for reversible and irreversible neurological deficits. Computer-aided neuromonitoring is based on online digitizing of the surface EMG of the anterior tibial muscle. An algorithm continuously modifies the amplitude to determine the motor threshold. The method described has been used in 18 patients undergoing high tibial osteotomy. In 10 of the 18 patients, the nerve is rendered completely non-excitable after an average tourniquet application time of 59 min. This non-excitability was reversed on release of the tourniquet. In the remaining 8 patients, excitability was maintained throughout the ischaemic period, which did not exceed 60 minutes in any of the cases. Our method enables accurate quantification of the neural function throughout the entire operation, and convincingly documents the influence of ischaemia on peripheral nerve block.

Electromyography↗

From projection pursuit and CART to adaptive discriminant analysis?

While many efforts have been put into the development of nonlinear approximation theory and its applications to signal and image compression, encoding and denoising, there seems to be very few theoretical developments of adaptive discriminant representations in the area of feature extraction, selection and signal classification. In this paper, we try to advocate the idea that such developments and efforts are worthwhile, based on the theorerical study of a data-driven discriminant analysis method on a simple--yet instructive--example. We consider the problem of classifying a signal drawn from a mixture of two classes, using its projections onto low-dimensional subspaces. Unlike the linear discriminant analysis (LDA) strategy, which selects subspaces that do not depend on the observed signal, we consider an adaptive sequential selection of projections, in the spirit of nonlinear approximation and classification and regression trees (CART): at each step, the subspace is enlarged in a direction that maximizes the mutual information with the unknown class. We derive explicit characterizations of this adaptive discriminant analysis (ADA) strategy in two situations. When the two classes are Gaussian with the same covariance matrix but different means, the adaptive subspaces are actually nonadaptive and can be computed with an algorithm similar to orthonormal matching pursuit. When the classes are centered Gaussians with different covariances, the adaptive subspaces are spanned by eigen-vectors of an operator given by the covariance matrices (just as could be predicted by regular LDA), however we prove that the order of observation of the components along these eigen-vectors actually depends on the observed signal. Numerical experiments on synthetic data illustrate how data-dependent features can be used to outperform LDA on a classification task, and we discuss how our results could be applied in practice.

Algorithms↗

Conformity index: a review.

We present a critical analysis of the conformity indices described in the literature and an evaluation of their field of application. Three-dimensional conformal radiotherapy, with or without intensity modulation, is based on medical imaging techniques, three-dimensional dosimetry software, compression accessories, and verification procedures. It consists of delineating target volumes and critical healthy tissues to select the best combination of beams. This approach allows better adaptation of the isodose to the tumor volume, while limiting irradiation of healthy tissues. Tools must be developed to evaluate the quality of proposed treatment plans. Dosimetry software provides the dose distribution in each CT section and dose-volume histograms without really indicating the degree of conformity. The conformity index is a complementary tool that attributes a score to a treatment plan or that can compare several treatment plans for the same patient. The future of conformal index in everyday practice therefore remains unclear.

Algorithms↗

Scale-up feasibility in high-shear mixers: determination through statistical procedures.

The wet granulation scale-up of a formulation exhibiting plastic deformation behavior under compression was examined. Through experimental factorial design, the effect of solution level, mixing time, and mixer speed on granulation properties was investigated. Measurements of mean particle size, tapped density, bulk density, Carr's index, coarse-to-fine ratio, cumulative percentage, and flow rate were taken and compared among granulations. In addition, comparisons were done on the hardness of tablets made from the formulations. It was shown that the characteristics of the granulations made under different conditions were highly reproducible. The excipient system of microcrystalline cellulose and pregel starch was shown to be a very robust formulation that is resistant to changes in the scaling-up process in high-shear mixers.

Algorithms↗

Neuronal sensitivity to hyperoxia, hypercapnia, and inert gases at hyperbaric pressures.

As ambient pressure increases, hydrostatic compression of the central nervous system, combined with increasing levels of inspired Po2, Pco2, and N2 partial pressure, has deleterious effects on neuronal function, resulting in O2 toxicity, CO2 toxicity, N2 narcosis, and high-pressure nervous syndrome. The cellular mechanisms responsible for each disorder have been difficult to study by using classic in vitro electrophysiological methods, due to the physical barrier imposed by the sealed pressure chamber and mechanical disturbances during tissue compression. Improved chamber designs and methods have made such experiments feasible in mammalian neurons, especially at ambient pressures <5 atmospheres absolute (ATA). Here we summarize these methods, the physiologically relevant test pressures, potential research applications, and results of previous research, focusing on the significance of electrophysiological studies at <5 ATA. Intracellular recordings and tissue Po2 measurements in slices of rat brain demonstrate how to differentiate the neuronal effects of increased gas pressures from pressure per se. Examples also highlight the use of hyperoxia (<or=3 ATA O2) as a model for studying the cellular mechanisms of oxidative stress in the mammalian central nervous system.

Air Pressure↗

A three-dimensional mathematical model for predicting spinal joint force distribution during manual liftings.

OBJECTIVE: A three-dimensional dynamic mathematical model was developed to discover what loads are imposed on the lumbar structures by performance of asymmetric manual liftings. DESIGN: An external model was used to estimate the intersegmental resultant forces and moments at the L(5)/S(1) joint in this dynamic biomechanical model. Using an optimization algorithm, an internal model then distributed the intersegmental resultants to forces of muscle, disc, facet joints, and ligaments. BACKGROUND: To study the relation between large loads and low-back disorders, many biomechanical models have been developed. Most of the models were two-dimensional models discussed with symmetric activities. Some three-dimensional biomechanical models were static models or only included limited elements of the disc and muscles in the model. METHODS: A healthy young male subject was asked to perform asymmetric lift with bent knees. Dynamic data of body motion and ground reaction forces were monitored, and the EMG of six muscles were recorded simultaneously. A Newtonian equation was used to calculate the joint intersegmental resultant forces and moments. In the internal model, three components of the disc force, eight muscle forces, two ligament forces and two facet joint forces were computed. RESULTS: The correlation between the reaction moments from the upper and lower models of the external part were generally above 0.94, and the root mean square differences were below 19 Nm. In this internal model, the maximal disc compression was close to the data showed on the literature, and the estimation of muscle forces corresponded to the EMG activities. CONCLUSIONS: A three-dimensional biomechanical model has been developed and evaluated to estimate the spinal joint force distribution during asymmetric manual lifting activities.

Journal Article↗

Early experience with retrievable inferior vena cava filters in high-risk trauma patients.

BACKGROUND: This study describes the use of retrievable IVC filters in a select group of trauma patients at high risk for deep vein thrombosis (DVT) and pulmonary embolism (PE). STUDY DESIGN: Retrievable IVC filters were placed in selected trauma patients who met high-risk criteria for deep vein thrombosis and PE according to institutional clinical management guidelines. All filters were placed percutaneously in the interventional radiology suite. Indications for filter placement were based on injury complex, weight-bearing status, and contraindications to enoxaparin or pneumatic compression devices. IVC filters were either removed or maintained. RESULTS: Retrievable IVC filters were placed in 35 patients after blunt trauma. Twenty-six patients (74%) sustained at least one orthopaedic injury; 17 patients (49%) were diagnosed with a pelvis fracture. Activity was limited to bed rest or spinal precautions in 18 patients (51%). Enoxaparin was contraindicated in 32 patients (91%) and injuries precluded the use of pneumatic compression devices in 11 (31%). IVC filters were removed in 18 patients (51%), with no reported complications. Patients with orthopaedic injuries and pelvis fractures were less likely to have their filters maintained (p = 0.040). CONCLUSIONS: Retrievable IVC filters offer a versatile option for prophylaxis in trauma patients at high risk for PE. Filter retrieval potentially spares the longterm complications of permanent filters in younger trauma patients. Retrievable filters warrant consideration in patients who meet high-risk criteria for deep vein thrombosis or PE who cannot receive effective mechanical prophylaxis and in whom contraindications to anticoagulation are expected to be temporary.

Adult↗

Arbitrary-ratio image resizing using fast DCT of composite length for DCT-based transcoder.

We propose a fast arbitrary-ratio image resizing method for transcoding of the compressed images. The downsizing process in the discrete cosine transform (DCT) domain can be implemented by truncating high-frequency coefficients, whereas the upsizing process is implemented in the DCT domain by padding zero coefficients to the high-frequency part. The proposed method combines a fast inverse and forward DCT of composite length for arbitrary-ratio upsizing or downsizing. According to the resizing ratio, truncating the high-frequency coefficients and padding zeros are appropriately considered by combining the inverse DCT and forward DCT. The proposed method shows a good peak signal-to-noise ratio and less computational complexity compared with the spatial-domain and previous DCT-domain image resizing methods.

Algorithms↗

Estimating the entropy rate of spike trains via Lempel-Ziv complexity.

Normalized Lempel-Ziv complexity, which measures the generation rate of new patterns along a digital sequence, is closely related to such important source properties as entropy and compression ratio, but, in contrast to these, it is a property of individual sequences. In this article, we propose to exploit this concept to estimate (or, at least, to bound from below) the entropy of neural discharges (spike trains). The main advantages of this method include fast convergence of the estimator (as supported by numerical simulation) and the fact that there is no need to know the probability law of the process generating the signal. Furthermore, we present numerical and experimental comparisons of the new method against the standard method based on word frequencies, providing evidence that this new approach is an alternative entropy estimator for binned spike trains.

Action Potentials↗

Preliminary clinical application of contrast-enhanced MR portography.

The clinical application of contrast enhanced (CE) MR was evaluated. A total of 66 CE MR portograms were obtained by performing fast imaging with steady procession (FISP) technique on a 1.5-T Siemens magnetom vision. A maximum intensity projection algorithm was also employed to include all vessels in a single image. The patency of portal venous system, the presence and extent of varices were also evaluated. The results showed that all images had diagnostic quality. Main portal vein (MPV) and its 4th-6th level intrahepatic branches were visualized in 10 normal persons serving as control. The diameter of MPV, splenic vein and superior mesenteric vein was 1.02 +/- 0.21, 0.8 +/- 0.15, 0.8 +/- 0.26 cm respectively, which were significantly lower than that in portal hypertension patients (1.38 +/- 0.27, 1.26 +/- 0.18, 1.24 +/- 0.18 cm, respectively). In 23 preoperative cases of portal hypertension, dilated portal vein and tortuous enlarged splenic vein were found in 23 cases; esophageal and coronary varices in 12 and 19 cases, respectively. In 7 postoperative re-examined cases with portal hypertension, the flow velocity and flow of MPV were decreased in all cases and esophageal varices could still be observed in 3 cases. New vessels appeared in the great curvature of stomach in 2 cases. In 20 cases of liver carcinoma, occlusion of MPV or its intrahepatic branches were showed in 14, compression and dislocation of intrahepatic portal vein were found in 6. In other 6 cases, 2 were splenic venous thrombosis and 4 were tumors in the intestine or retro-peritoneum. It is concluded that three-dimensional CE MR portography is an accurate technique for evaluating the portal venous system. It is a reliable and noninvasive technique that can provide important information for the evaluation of patients' condition before TIPSS and liver transplantation.

Contrast Media↗

Binding of Mg2+ to single-stranded polynucleotides: hydration and optical studies.

The binding of Mg(2+) to single-stranded ribo- and deoxy-polynucleotides, poly(rA), poly(rU), poly(dA) and poly(dT), has been investigated in dilute aqueous solutions at pH 7.5 and 20 degrees C. A combination of ultrasound velocimetry, density, UV and CD spectroscopy have been employed to study hydration and spectral effects of Mg(2+) binding to the polynucleotides. Volume and compressibility effects of Mg(2+) binding to random-coiled poly(rU) and poly(dT) correspond to two coordination bonds probably between the adjacent phosphate groups. The same parameters for poly(rA)+Mg(2+) correspond to an inner-sphere complex with three-four direct contacts. However, almost no hydration effects are arising in binding to its deoxy analog, poly(dA), indicating mostly a delocalized binding mode. In agreement with hydration studies, optical investigations revealed almost no influence of Mg(2+) on poly(dA) properties, while it stabilizes and aggregates poly(rA) single-helix. The evidence presented here indicates that Mg(2+) are able to bind specifically to single-stranded polynucleotides, and recognize their composition and backbone conformation.

Algorithms↗

A tele-operated mobile ultrasound scanner using a light-weight robot.

This paper presents a new tele-operated robotic chain for real-time ultrasound image acquisition and medical diagnosis. This system has been developed in the frame of the Mobile Tele-Echography Using an Ultralight Robot European Project. A light-weight six degrees-of-freedom serial robot, with a remote center of motion, has been specially designed for this application. It holds and moves a real probe on a distant patient according to the expert gesture and permits an image acquisition using a standard ultrasound device. The combination of mechanical structure choice for the robot and dedicated control law, particularly nearby the singular configuration allows a good path following and a robotized gesture accuracy. The choice of compression techniques for image transmission enables a compromise between flow and quality. These combined approaches, for robotics and image processing, enable the medical specialist to better control the remote ultrasound probe holder system and to receive stable and good quality ultrasound images to make a diagnosis via any type of communication link from terrestrial to satellite. Clinical tests have been performed since April 2003. They used both satellite or Integrated Services Digital Network lines with a theoretical bandwidth of 384 Kb/s. They showed the tele-echography system helped to identify 66% of lesions and 83% of symptomatic pathologies.

Algorithms↗

RSHash: a fast and space-efficient hash table for k-mers.

SUMMARY: Large genomic data collections can be viewed as a continuous string of DNA characters. The essential operations for data structures indexing the k-mer content of such a string are lookup and locate. Lookup determines whether a query k-mer q exists in the string and locate returns all locations in the string where q is present. High-throughput DNA sequencing generates very many k-mer sets of size exceeding billions of characters. In such scenarios, memory consumption and query efficiency pose significant challenges to a data structure supporting the above mentioned queries. To address this problem, we describe a simple, compressed, static data structure for k-mers that answers lookup and can be extended for supporting locate. The general scheme follows the use of minimizers like the state-of-the art SSHash. However, instead of using minimum perfect hash functions our solution (RSHash for Rank-Select Hash) relies on bitvectors with rank and select support, a multiple layered minimizer scheme, and a clever buffering strategy. We can show that RSHash is on average 40% and in some cases up to two times faster than SSHash while having the same memory requirements. Indeed we can go as low as 8&#x2009;bits per canonical 31-mer on a human dataset. AVAILABILITY: https://github.com/jonsmcode/rshash.

Sequence Analysis, DNA↗