Dilation of subglacial sediment governs incipient surge motion in glaciers with deformable beds

Glacier surges are quasi-periodic episodes of rapid ice flow that arise from increases in slip rate at the ice–bed interface. The mechanisms that trigger and sustain surges are not well understood. Here, we develop a new model of incipient surge motion for glaciers underlain by sediments to explore how surges may arise from slip instabilities within a thin layer of saturated, deforming subglacial till. Our model represents the evolution of internal friction, porosity and pore water pressure within the till as functions of the rate and history of shear deformation, and couples the till mechanics to a simple ice-flow model. Changes in pore water pressure govern incipient surge motion, with less permeable till facilitating surging because dilation-driven reductions in pore water pressure slow the rate at which till tends towards a new steady state, thereby allowing time for the glacier to thin dynamically. The reduction of overburden (and thus effective) pressure at the bed caused by dynamic thinning of the glacier sustains surge acceleration in our model. The need for changes in both the hydromechanical properties of the till and the thickness of the glacier creates restrictive conditions for surge motion that are consistent with the rarity of surge-type glaciers and their geographical clustering.

The Reference Image Database to Evaluate Response to therapy in lung cancer (RIDER) project: a resource for the development of change-analysis software

Critical to the clinical evaluation of effective novel therapies for lung cancer is the early and accurate determination of tumor response, which requires an understanding of the sources of uncertainty in tumor measurement and subsequent attempts to minimize their effects on the assessment of the therapeutic agent. The Reference Image Database to Evaluate Response (RIDER) project seeks to develop a consensus approach to the optimization and benchmarking of software tools for the assessment of tumor response to therapy and to provide a publicly available database of serial images acquired during lung cancer drug and radiation therapy trials. Images of phantoms and patient images acquired under situations in which tumor size or biology is known to be unchanged also will be provided. The RIDER project will create standardized methods for benchmarking software tools to reduce sources of uncertainty in vital clinical assessments such as whether a specific tumor is responding to therapy.

Comparing pairwise and simultaneous joint registrations of decorrelating interval exams using entropic graphs

The interest in registering a set of images has quickly risen in the field of medical image analysis. Mutual information (MI) based methods are well-established for pairwise registration but their extension to higher dimensions (multiple images) has encountered practical implementation difficulties. We extend the use of alpha mutual information (alphaMI) as the similarity measure to simultaneously register multiple images. alphaMI of a set of images can be directly estimated using entropic graphs spanning feature vectors extracted from the images, which is demonstrated to be practically feasible for joint registration. In this paper we are specifically interested in monitoring malignant tumor changes using simultaneous registration of multiple interval MR or CT scans. Tumor scans are typically a decorrelating sequence due to the cycles of heterogeneous cell death and growth. The accuracy of joint and pairwise registration using entropic graph methods is evaluated by registering several sets of interval exams. We show that for the parameters we investigated simultaneous joint registration method yields lower average registration errors compared to pairwise. Different degrees of decorrelation in the serial scans are studied and registration performance suggests that an appropriate scanning interval can be determined for efficiently monitoring lesion changes. Different levels of observation noise are added to the image sequences and the experimental results show that entropic graph based methods are robust and can be used reliably for multiple image registration.

Assessment of the functional diffusion map (fDM) as an imaging biomarker for early stratification of glioma clinical response

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Background: Current assessment of glioma treatment response relies on changes in the product of the maximal perpendicular tumor diameters at 2 months following treatment. Due to the fact that patients with malignant glioma have high mortality rates and a short median survival (about 41 weeks), the ability to stratify these tumors into responsive and non-responsive categories prior to treatment completion would allow for individualization of treatment. Changes in glioma water diffusion values were quantified using diffusion MRI as a biomarker for therapeutic-induced changes in tumor cellularity. Methods: A total of 37 patients with Grade III/IV supratentorial malignant gliomas (restricted to anaplastic astrocytomas (Grade III) and glioblastomas/sarcomas (Grade IV)) into a clinical imaging study. Standard and diffusion MRI scans pre-treatment and at 3 weeks post-initiation of chemo- and/or radio-therapy were acquired. Images were co-registered to pretreatment scans, and changes in tumor water diffusion values were calculated and displayed as a functional diffusion map (fDM) for correlation with clinical response. Results: Analysis of the patient data revealed that the fDM volumes of total detected diffusion change (VT) was able to statistically discriminate (P<0.001) between the stable disease (SD) and progressive disease (PD) patient populations 3 weeks into therapy. Patients classified as PD by fDM analysis at 3 weeks were found to have a shorter OS in the PD group compared with SD patients (median survival, 8.0 versus 18.2 months; p<0.01). The fDM measurements provided an early biomarker for response, TTP and OS in malignant glioma patients. Conclusions: This novel imaging biomarker (fDM) was found to be a viable and early predictor of WHO clinical outcome. This clinical study strongly supports the hypothesis that fDM analysis provides a sensitive measure of therapeutic-induced changes in tumor cellularity, which can thereby serve as a predictive clinical surrogate marker for treatment response. Further evaluation of this imaging biomarker is ongoing.

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Automated generation of a four-dimensional model of the liver using warping and mutual information

The use of mutual information (MI) based alignment to map changes in liver shape and position from exhale to inhale was investigated. Inhale and exhale CT scans were obtained with intravenous contrast for six patients. MI based alignment using thin-plate spine (TPS) warping was performed between each inhale and exhale image set. An expert radiation oncologist identified corresponding vessel bifurcations on the exhale and inhale CT image and the transformation for identified points was determined. This transformation was then used to determine the accuracy of the MI based alignment. The reproducibility of the vessel bifurcation identification was measured through repeat blinded vessel bifurcation identification. Reproducibility [standard deviation (SD)] in the L/R, A/P, and I/S directions was 0.11, 0.09, and 0.14 cm, respectively. The average absolute difference between the transformation obtained using MI based alignment and the vessel bifurcation in the L/R, A/P, and I/S directions was 0.13 cm (SD=0.10 cm), 0.15 cm (SD=0.12 cm), and 0.15 cm (SD-0.14 cm), respectively. These values are comparable to the reproducibility of bifurcation identification, indicating that MI based alignment using TPS warping is accurate to within measurement error and is a reliable tool to aid in describing deformation that the liver undergoes from the exhale to inhale state.

Effects of locally-delivered human macrophage products and estrogen on murine inflammatory bone resorption

The objective of this study was to use an in vivo model of periodontitis (mouse calvaria) to quantify the effects of local release of secreted human macrophage products, 17beta-estradiol (E2), and proinflammatory lipopolysaccharide (LPS) on histologic bone resorption. Human THP-1 monocytes (106) were converted to macrophage phenotype by 500 ng/ml phorbol 12-myristate- 13-acetate (PMA) and treated as follows: no stimulation or Escherichia coli LPS (10 microg/ml) alone or in combination with a physiologic dose of E2 (100 pg/ml) for 24 h in RPMI/10% FBS, washed extensively, then incubated for 24 h in serum-free media. Supernatant products were concentrated and incorporated into a 4% (w/v) methylcellulose gel. Separate gels were incorporated with the following: LPS (500 microg/animal) alone, high dose of E2 (10 ng/animal) alone, a combination of LPS + E2, or gel only (controls). Loaded or control gels were placed into a polylactic acid occlusive dome, inserted subcutaneously over the calvaria of mature ovariectomized ICR Swiss mice (8 mice x 7 groups x 2 times [5/14 days] = 112 animals), then calvaria were evaluated histologically. Macrophage stimulation with LPS alone, but not LPS in combination with E2, produced supernatants which upregulated osteoclast numbers in the suture area compared to gel controls at 5 days (p = 0.009). The addition of LPS directly to the local delivery gels significantly upregulated osteoclasts in endosteal surfaces compared to gel controls at 5 days (p = 0.024) and at 14 days (p = 0.025). The addition of E2 to LPS down-regulated resorption to a level not different from gel controls at 14 days. This in vivo model appears effective in studying inflammatory bone resorption, which may be inhibited by E2 directly or through its influence on secreted macrophage products.

Identification of functionally important amino-terminal arginines of Agrobacterium tumefaciens ADP-glucose pyrophosphorylase by alanine scanning mutagenesis

Treatment of the Agrobacterium tumefaciens ADP-glucose pyrophosphorylase with the arginyl reagent phenylglyoxal resulted in complete desensitization to fructose 6-phosphate (F6P) activation, and partial desensitization to pyruvate activation. The enzyme was protected from desensitization by ATP, F6P, pyruvate, and phosphate. Alignment studies revealed that this enzyme contains arginine residues in the amino-terminal region that are relatively conserved in similarly regulated ADP-glucose pyrophosphorylases. To functionally evaluate the role(s) of these arginines, alanine scanning mutagenesis was performed to generate the following enzymes: R5A, R11A, R22A, R25A, R32A, R33A, R45A, and R60A. All of the enzymes, except R60A, were successfully expressed and purified to near homogeneity. Both the R5A and R11A enzymes displayed desensitization to pyruvate, partial activation by F6P, and increased sensitivity to phosphate inhibition. Both the R22A and R25A enzymes exhibited reduced V(max) values in the absence of activators, lower apparent affinities for ATP and F6P, and reduced sensitivities to phosphate. The presence of F6P restored R22A enzyme activity, while the R25A enzyme exhibited only approximately 1.5% of the wild-type activity. The R32A enzyme displayed an approximately 11.5-fold reduced affinity for F6P while exhibiting behavior identical to that of the wild type with respect to pyruvate activation. Both the R33A and R45A enzymes demonstrated a higher activity than the wild-type enzyme in the absence of activators, no response to F6P, partial activation by pyruvate, and desensitization to phosphate inhibition. These altered enzymes were also insensitive to phenylglyoxal. The data demonstrate unique functional roles for these arginines and the presence of separate subsites for the activators.

Regional mu opioid receptor regulation of sensory and affective dimensions of pain

The endogenous opioid system is involved in stress responses, in the regulation of the experience of pain, and in the action of analgesic opiate drugs. We examined the function of the opioid system and mu-opioid receptors in the brains of healthy human subjects undergoing sustained pain. Sustained pain induced the regional release of endogenous opioids interacting with mu-opioid receptors in a number of cortical and subcortical brain regions. The activation of the mu-opioid receptor system was associated with reductions in the sensory and affective ratings of the pain experience, with distinct neuroanatomical involvements. These data demonstrate the central role of the mu-opioid receptors and their endogenous ligands in the regulation of sensory and affective components of the pain experience.

3D spatial compounding of ultrasound images using image-based nonrigid registration

Medical ultrasound images are often distorted enough to significantly limit resolution during compounding (i.e., summation of images from multiple views). A new, volumetric image registration technique has been used successfully to enable high spatial resolution in three-dimensional (3D) spatial compounding of ultrasound images. Volumetric ultrasound data were acquired by scanning a linear matrix array probe in the elevational direction in a focal lesion phantom and in a breast in vivo. To obtain partly uncorrelated views, the volume of interest was scanned at five different transducer tilt angles separated by 4 degrees to 6 degrees. Pairs of separate views were registered by an automatic procedure based on a mutual information metric, using global full affine and thin-plate spline warping transformations. Registration accuracy was analyzed automatically in the phantom data, and manually in vivo, yielding average registration errors of 0.31 mm and 0.65 mm, respectively. In the vicinity of the warping control points, registrations obtained with warping transformations were significantly more accurate than full affine registrations. Compounded images displayed the expected reduction in speckle noise and increase in contrast-to-noise ratio (CNR), as well as better delineation of connective tissues and reduced shadowing. Compounding also revealed some apparent low contrast lobulations that were not visible in the single-sweep images. Given expected algorithmic and hardware enhancements, nonrigid, image-based registration shows great promise for reducing tissue motion and refraction artifacts in 3D spatial compounding.

Cloning and sequencing of glycogen metabolism genes from Rhodobacter sphaeroides 2.4.1. Expression and characterization of recombinant ADP-glucose pyrophosphorylase

A 6-kb DNA fragment of the Rhodobacter sphaeroides 2.4.1 glg operon was cloned from a genomic library using a polymerase chain reaction probe coding for part of the ADP-glucose pyrophosphorylase (glgC) gene. The DNA fragment was sequenced and found to harbor complete open reading frames for the glgC and glgA (glycogen synthase) genes and partial sequences corresponding to glgP (glycogen phosphorylase) and glgX (glucan hydrolase/transferase) genes. The genomic fragment also contained an apparent truncated sequence corresponding to the C-terminus of the glgB gene (branching enzyme). The presence of active branching enzyme activity in crude sonicates of Rb. sphaeroides cells indicates that the genome contains a full-length glgB at another location. The structure of this operon in relation to other glg operons is further discussed. The deduced sequence of the ADP-glucose pyrophosphorylase enzyme is compared to other known ADP-glucose pyrophosphorylase sequences and discussed in relation to the allosteric regulation of this enzyme family. The glgC gene was subcloned in the vector pSE420 (Invitrogen) for high-level expression in E. coli. The successful overexpression of the recombinant enzyme allowed for the purification of over 35 mg of protein from 10 g of cells, representing a dramatic improvement over enzyme isolation from the native strain. The recombinant enzyme was purified to near homogeneity and found to be physically, immunologically, and kinetically identical to the native enzyme, verifying the fidelity of the cloning step.

Characterization of ADP-glucose pyrophosphorylase from Rhodobacter sphaeroides 2.4.1: evidence for the involvement of arginine in allosteric regulation

ADP-glucose pyrophosphorylase (ADPGlc PPase, EC 2.7.7.27) from Rhodobacter sphaeroides 2.4.1 has been purified to near homogeneity. The enzyme reacted in Western blots to polyclonal antibodies raised against other bacterial ADPGlc PPases. The purified enzyme was found to be activated by fructose 6-phosphate, fructose 1,6-bisphosphate, and pyruvate and inhibited by phosphate, phosphoenolpyruvate, ADP, and pyridoxal phosphate. Kinetic studies indicate that AMP, while having little effect on kinetic parameters at pH 8 in the absence of effectors, is a specific ligand for an allosteric site(s). Treatment of the purified enzyme with the arginyl reagents 2,3-butanedione and phenylglyoxal resulted in desensitization of the enzyme to both activation and inhibition by metabolites. Phosphate, fructose 6-phosphate, and AMP were found to protect the enzyme against allosteric desensitization supportive of these metabolites interacting at common site(s) or with a common enzyme form. As a first step in cloning the gene coding for this enzyme, a polymerase chain reaction fragment was generated from genomic DNA using primers based on amino terminal sequencing data and a highly conserved region in known ADPGlc PPases. The sequence of this fragment and position of amino terminal arginines in comparison to other known ADPGlc PPases is discussed in relation to the kinetic and chemical modification data.

Motion correction in fMRI via registration of individual slices into an anatomical volume

An automated retrospective image registration based on mutual information is adapted to a multislice functional magnetic resonance imaging (fMRI) acquisition protocol to provide accurate motion correction. Motion correction is performed by mapping each slice to an anatomic volume data set acquired in the same fMRI session to accommodate inter-slice head motion. Accuracy of the registration parameters was assessed by registration of simulated MR data of the known truth. The widely used rigid body volume registration approach based on stacked slices from the time series data may hinder statistical accuracy by introducing inaccurate assumptions of no motion between slices for multislice fMRI data. Improved sensitivity and specificity of the fMRI signal from mapping-each-slice-to-volume method is demonstrated in comparison with a stacked-slice correction method by examining functional data from two normal volunteers. The data presented in a standard anatomical coordinate system suggest the reliability of the mapping-each-slice-to-volume method to detect the activation signals consistent between the two subjects.

Semiautomatic registration of volumetric ultrasound scans

We demonstrate the ability to register easily and accurately volumetric ultrasound scans without significant data preprocessing or user intervention. Two volumetric ultrasound breast scan data sets were acquired from two different patients with breast cancer. Volumetric scan data were acquired by manually sweeping a linear array transducer mounted on a linear slider with a position encoder. The volumetric data set pairs consisted of color flow and/or power mode Doppler data sets acquired serially on the same patients. A previously described semiautomatic registration method based on maximizing mutual information was used to determine the transform between data sets. The results suggest that, even for the deformable breast, three-dimensional full affine transforms can be sufficient to obtain clinically useful registrations; warping may be necessary for increased registration accuracy. In conclusion, mutual information-based automatic registration as implemented on modern workstations is capable of yielding clinically useful registrations in times <35 min.

Site-directed mutagenesis of a regulatory site of Escherichia coli ADP-glucose pyrophosphorylase: the role of residue 336 in allosteric behavior

Site-directed mutagenesis was used to probe the role of glycine residue 336 in the regulatory properties of Escherichia coli ADP-glucose pyrophosphorylase. This residue was previously found to be changed from glycine to aspartate in the gene of an Escherichia coli mutant strain. The mutant enzyme had altered kinetic properties, including higher activity in the absence of the activator fructose 1,6-bisphosphate (FBP), higher apparent affinity for FBP and substrates, and lower apparent affinity for the inhibitor AMP. The observed changes in activity were caused by this single mutation, because the aspartate mutant was prepared from the wild-type gene. The kinetic properties of the site-directed mutant are identical to those of the enzyme from the mutant strain. A series of mutants was prepared to explore the effects of charge, size, shape, and hydrophobicity of the amino acid at residue 336 on the enzyme regulatory properties. All of the mutants, except for the lysine and arginine enzymes, were expressed and purified for kinetic analysis. The glycine-336 residue is able to tolerate diverse substitutions without compromise of catalytic activity. A range of allosteric changes was observed, with the most dramatic effects seen with the highly active aspartate enzyme and the low-activity G336Q mutant, which exhibited lower apparent affinities for activator and substrates and higher apparent affinity for inhibitor. The altered allosteric properties of the G336D mutant enzyme were almost completely abolished by substitution of asparagine. Thus, the aspartate negative charge is essential for the altered binding of effectors.

A kinetic study of site-directed mutants of Escherichia coli ADP-glucose pyrophosphorylase: the role of residue 295 in allosteric regulation

The effects of amino acid substitutions at residue 295 on the regulatory properties of Escherichia coli ADP-glucose pyrophosphorylase were studied. In previous studies, this residue, altered from proline to serine (P295S) in the gene of a mutant strain of E. coli, resulted in a high-activity form of enzyme [higher activity in absence of activator fructose 1,6-bisphosphate (FBP), higher apparent affinity for FBP and substrates, and lower apparent affinity for the inhibitor, AMP]. The effects of size and charge on this site were explored by replacing Pro with Gly, Asp, Asn, Gln, or Glu. All mutant enzymes were expressed and purified for kinetic analysis. All mutant enzymes, to varying extents, were in more active form than the wild-type enzyme. Enzymes with a substituted negative charge (P295D, P295E) had the highest activity in the absence of FBP, while the P295G enzyme was most similar to the wild type. The P295D and P295E enzymes had the lowest apparent affinities for AMP; this effect was partially abolished by the neutral substitutions P295N and P295Q. Another mutation, G336D, had previously been found to produce an even higher activity enzyme form. In order to examine interactions between substitutions at the 295 and 336 positions, the double mutant P295D-G336D was constructed and characterized. The double mutant enzyme was more active in the absence of FBP, with a higher affinity for FBP and a lower apparent affinity for AMP than either single mutated enzyme. The significance of residue 295 in regulation is discussed.

Retrospective correction of surface coil MR images using an automatic segmentation and modeling approach

The use of surface coils in magnetic resonance imaging offers significant improvements in the signal-to-noise ratio over volume coils for many applications. However, the inhomogeneous reception profile of surface coils hampers their usefulness by introducing significant nonuniformities or intensity variations which can vary by greater than six-fold across the sample. In this study, we evaluated an automatic technique for retrospective correction of intensity variations observed in a high-resolution surface coil MR image of the rat brain obtained using an adiabatic magnetic resonance imaging sequence. The images are shown to have a coefficient of variation less than 12% following application of this correction algorithm. This image intensity correction technique can be applied retrospectively to all data sets and corrects both sample/patient dependent effects (e.g. attenuation of overlying tissue) or sample independent effects (e.g. coil geometry or position). This approach should also prove valuable in improving regions of interest analysis, volume histograms and thresholding techniques.

Demonstration of accuracy and clinical versatility of mutual information for automatic multimodality image fusion using affine and thin-plate spline warped geometric deformations

This paper applies and evaluates an automatic mutual information-based registration algorithm across a broad spectrum of multimodal volume data sets. The algorithm requires little or no pre-processing, minimal user input and easily implements either affine, i.e. linear or thin-plate spline (TPS) warped registrations. We have evaluated the algorithm in phantom studies as well as in selected cases where few other algorithms could perform as well, if at all, to demonstrate the value of this new method. Pairs of multimodal gray-scale volume data sets were registered by iteratively changing registration parameters to maximize mutual information. Quantitative registration errors were assessed in registrations of a thorax phantom using PET/CT and in the National Library of Medicine's Visible Male using MRI T2-/T1-weighted acquisitions. Registrations of diverse clinical data sets were demonstrated including rotate-translate mapping of PET/MRI brain scans with significant missing data, full affine mapping of thoracic PET/CT and rotate-translate mapping of abdominal SPECT/CT. A five-point thin-plate spline (TPS) warped registration of thoracic PET/CT is also demonstrated. The registration algorithm converged in times ranging between 3.5 and 31 min for affine clinical registrations and 57 min for TPS warping. Mean error vector lengths for rotate-translate registrations were measured to be subvoxel in phantoms. More importantly the rotate-translate algorithm performs well even with missing data. The demonstrated clinical fusions are qualitatively excellent at all levels. We conclude that such automatic, rapid, robust algorithms significantly increase the likelihood that multimodality registrations will be routinely used to aid clinical diagnoses and post-therapeutic assessment in the near future.

Ultrasonic characterization of in vitro osteoarthritic articular cartilage with validation by confocal microscopy

The majority of adults over the age of 65 y develop osteoarthritis (OA), a joint disease characterized by degeneration of articular cartilage and subchondral sclerosis. Early in the disease, the articular cartilage surface begins to change histologically from a smooth to a rough or fibrillated appearance. A prerequisite for any chondroprotective pharmacological intervention is detection of OA in its preclinical phase. Current diagnostic imaging modalities, such as radiographs or (nuclear) magnetic resonance imaging, either cannot directly image the cartilage surface or lack sufficient resolution to detect surface fibrillations. We have developed an ultrasonic technique that can be used to characterize these surface fibrillations directly. We present our in vitro results with validation by laser-based confocal microscopic imaging.

Mutual information for automated unwarping of rat brain autoradiographs

An automated multimodal warping based on mutual information metric (MI) as a mapping cost function is demonstrated. Mutual information (I) is calculated from a two-dimensional (2D) gray scale histogram of an image pair, and MI (= -I) provides a matching cost function which can be effective in registration of two- or three-dimensional data sets independent of modality. Most histological image data, though information rich and high resolution, present nonlinear deformations due to the specimen sectioning and need reconstitution into deformation-corrected volumes prior to geometric mapping to an anatomical volume for spatial analyses. Section alignment via automatic 2D registrations employing MI as a global cost function and thin-plate-spline (TPS) warping is applied to deoxy-D-[14C]glucose autoradiographic image slices of a rat brain with video reference images of the uncut block face to reconstitute a cerebral glucose metabolic volume data. Unlike the traditional feature-based TPS warping algorithms, initial control points are defined independently from feature landmarks. Registration quality using automated multimodal image warping is validated by comparing MIs of the image pair registered by automated affine registration and manual warping method. The MI proves to be a robust objective matching cost function effective for automatic multimodality warping for 2D data sets and can be readily applied to volume registrations.