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E L Madsen

Publications and source records attributed to E L Madsen.

At least 19 recordsLinked to original sources
PubMed2007

Normal and shear strain estimation using beam steering on linear-array transducers.

In current ultrasound elastography, only the axial component of the displacement vector is estimated and used to produce strain images. A method was recently proposed by our group to estimate both the axial and lateral components of a displacement vector following a uniaxial compression. Previous work evaluated the technique using both simulations and a mechanically translated phased array transducer. In this paper, we present initial results using beam steering on a linear array transducer attached to a commercial scanner to acquire echo signals for estimating 2-D displacement vectors. Single-inclusion and anthropomorphic breast phantoms with different boundary properties between the inclusion and background material are imaged by acquiring echo data along beam lines ranging from -15 degrees to 15 degrees relative to the compression direction. 1-D cross-correlation is used to calculate "angular displacements" in each acquisition direction, yielding axial and lateral components of the displacement vector. Strain tensor components are estimated from these displacements. Features on shear strain images generated for the inclusion phantom agree with those predicted using FEA analysis. Experimental results demonstrate the utility of this technique on clinical scanners. Shear strain tensors obtained using this method may provide useful information for the differentiation of benign from malignant tumors. For the linear array transducer used in this study, the optimum angular increment is around 3 degrees. However, more work is required for the selection of an appropriate value for the maximum beam angle for optimal performance of this technique.

Humans↗
PubMed2004

Characterization in Pseudomonas putida Cg1 of nahR and its role in bacterial survival in soil.

Sequencing, RFLP analyses and experiments utilizing a lacZ transcriptional reporter fused to the promoter regions of nahR and nahG in Pseudomonas putida Cg1 confirmed that regulation of naphthalene degradation in both P. putida Cg1 and the type strain, P. putida NCIB 9816-4, is consistent with that of NAH7 from P. putida G7. Two nahR knockout strains (RK1 and Cg1-NAHR from P. putida NCIB 9816-4 and Cg1, respectively) showed a growth defect in the presence of naphthalene as sole carbon and energy source. We hypothesized that nahR influences ecological fitness of bacteria in naphthalene-contaminated soil and tested this hypothesis using both parent and nahR-knockout strains introduced to soil microcosms with and without added naphthalene. After 21 days, loss of cell viability was pronounced in the presence of added naphthalene crystals for nahR mutants of both test bacteria, relative to the wild types. Diminished viable counts were attributed to toxicity. Thus, our data indicated that NahR in P. putida Cg1 is virtually identical to its homologues in other pseudomonads and that nahR is required for resistance to naphthalene toxicity, hence the persistence of bacterial cells in soil with high concentrations of naphthalene.

Bacterial Proteins↗
PubMed2003

Discovery of a bacterium, with distinctive dioxygenase, that is responsible for in situ biodegradation in contaminated sediment.

Microorganisms maintain the biosphere by catalyzing biogeochemical processes, including biodegradation of organic chemical pollutants. Yet seldom have the responsible agents and their respective genes been identified. Here we used field-based stable isotopic probing (SIP) to discover a group of bacteria responsible for in situ metabolism of an environmental pollutant, naphthalene. We released 13C-labeled naphthalene in a contaminated study site to trace the flow of pollutant carbon into the naturally occurring microbial community. Using GC/MS, molecular biology, and classical microbiological techniques we documented 13CO2 evolution (2.3% of the dose in 8 h), created a library of 16S rRNA gene clones from 13C labeled sediment DNA, identified a taxonomic cluster (92 of 95 clones) from the microbial community involved in metabolism of the added naphthalene, and isolated a previously undescribed bacterium (strain CJ2) from site sediment whose 16S rRNA gene matched that of the dominant member (48%) of the clone library. Strain CJ2 is a beta proteobacterium closely related to Polaromonas vacuolata. Moreover, strain CJ2 hosts the sequence of a naphthalene dioxygenase gene, prevalent in site sediment, detected before only in environmental DNA. This investigative strategy may have general application for elucidating the bases of many biogeochemical processes, hence for advancing knowledge and management of ecological and industrial systems that rely on microorganisms.

Bacteria↗
PubMed2003

Survival of naphthalene-degrading Pseudomonas putida NCIB 9816-4 in naphthalene-amended soils: toxicity of naphthalene and its metabolites.

Survival of naphthalene-degrading Pseudomonas putida NCIB 9816-4 was measured in nonsterile soil samples (coal tar-contaminated and pristine) with and without added crystalline naphthalene over a period of 21 days. A 2-3 log decrease in cfu occurred in the presence, but not absence, of added naphthalene. We used aqueous suspensions of crystalline naphthalene to explore potential mechanisms of its toxicity on the test bacterium under aerobic conditions. Measurements of dissolved naphthalene in medium indicated that uptake by P. putida NCIB 9816-4 maintained naphthalene at concentrations well below saturation. Accumulation of catechol was documented by high-performance liquid chromatography and gas chromatography/mass spectrometry in the presence of 0.5% (w/v) naphthalene crystals. Transient catechol accumulation was highest when cells entered stationary phase. A decrease in catechol concentration correlated with the development of brown color in the medium. Brown pigment accumulation correlated with a decrease in viable cell counts. These results suggested that catechol, related compounds, and their condensation products can accumulate to toxic levels in stationary phase P. putida NCIB 9816-4 cells. We hypothesize that the same mechanism of toxicity may occur under the nutrient-limited conditions expected in soil.

Biodegradation, Environmental↗
PubMed2003

Respiration of 13C-labeled substrates added to soil in the field and subsequent 16S rRNA gene analysis of 13C-labeled soil DNA.

Our goal was to develop a field soil biodegradation assay using (13)C-labeled compounds and identify the active microorganisms by analyzing 16S rRNA genes in soil-derived (13)C-labeled DNA. Our biodegradation approach sought to minimize microbiological artifacts caused by physical and/or nutritional disturbance of soil associated with sampling and laboratory incubation. The new field-based assay involved the release of (13)C-labeled compounds (glucose, phenol, caffeine, and naphthalene) to soil plots, installation of open-bottom glass chambers that covered the soil, and analysis of samples of headspace gases for (13)CO(2) respiration by gas chromatography/mass spectrometry (GC/MS). We verified that the GC/MS procedure was capable of assessing respiration of the four substrates added (50 ppm) to 5 g of soil in sealed laboratory incubations. Next, we determined background levels of (13)CO(2) emitted from naturally occurring soil organic matter to chambers inserted into our field soil test plots. We found that the conservative tracer, SF(6), that was injected into the headspace rapidly diffused out of the soil chamber and thus would be of little value for computing the efficiency of retaining respired (13)CO(2). Field respiration assays using all four compounds were completed. Background respiration from soil organic matter interfered with the documentation of in situ respiration of the slowly metabolized (caffeine) and sparingly soluble (naphthalene) compounds. Nonetheless, transient peaks of (13)CO(2) released in excess of background were found in glucose- and phenol-treated soil within 8 h. Cesium-chloride separation of (13)C-labeled soil DNA was followed by PCR amplification and sequencing of 16S rRNA genes from microbial populations involved with (13)C-substrate metabolism. A total of 29 full sequences revealed that active populations included relatives of Arthrobacter, Pseudomonas, Acinetobacter, Massilia, Flavobacterium, and Pedobacter spp. for glucose; Pseudomonas, Pantoea, Acinetobacter, Enterobacter, Stenotrophomonas, and Alcaligenes spp. for phenol; Pseudomonas, Acinetobacter, and Variovorax spp. for naphthalene; and Acinetobacter, Enterobacter, Stenotrophomonas, and Pantoea spp. for caffeine.

Bacteria↗
PubMed2003

Tissue-mimicking oil-in-gelatin dispersions for use in heterogeneous elastography phantoms.

A ten-month study is presented of materials for use in heterogeneous elastography phantoms. The materials consist of gelatin with or without a suspension of microscopic safflower oil droplets. The highest volume percent of oil in the materials is 50%. Thimerosal acts as a preservative. The greater the safflower oil concentration, the lower the Young's modulus. Elastographic data for heterogeneous phantoms, in which the only variable is safflower oil concentration, demonstrate stability of inclusion geometry and elastic strain contrast. Young's modulus ratios (elastic contrasts) producible in a heterogeneous phantom are as high as 2.7. The phantoms are particularly useful for ultrasound elastography. They can also be employed in MR elastography, although the highest achievable ratio of longitudinal to transverse relaxation times is considerably less than is the case for soft tissues.

Elasticity↗
PubMed2002

Diversity of 16S rDNA and naphthalene dioxygenase genes from coal-tar-waste-contaminated aquifer waters.

Microbial diversity in four wells along a groundwater flowpath in a coal-tar-waste-contaminated aquifer was examined using RFLP analysis of both 16S rDNA and naphthalene dioxygenase (NDO) genes. Amplified ribosomal DNA restriction analysis (ARDRA) relied upon eubacteria-specific primers to generate four clone libraries. From each library, 100 clones were randomly picked for analysis. Sixty percent of 400 clones contained unique ARDRA patterns. Diversity indices calculated for each community were high (Shannon-Weaver, H = 3.53 to 3.69). Clones representing ARDRA patterns found in the highest abundance were sequenced (31 total). Sequences related to aerobic bacteria (e.g., Nitrospira, Methylomonas, and Gallionella) predominated among those retrieved from the uncontaminated area of the site, whereas sequences related to facultatively aerobic and anaerobic bacteria (e.g. Azoarcus, Syntrophus, and Desulfotomaculum) predominated among those retrieved from contaminated areas of the site. Using NDO-specific primers and low-stringency PCR conditions, variability in RFLP patterns was only detected in community-derived DNA (3 of 4 wells) and not in 5 newly isolated naphthalene-degrading pure cultures. The ARDRA patterns of the pure culture isolates were not found in the clone libraries. Polymorphisms in community 16S rDNA and NDO genes found in well-water microorganisms reflected distinctive geochemical conditions across the site. Sequences related to sulfate-reducing bacteria were found in groundwater that contained sulfide, while sequences related to Gallionella, Syntrophus, and nitrate-reducing aromatic hydrocarbon-degrading bacteria were found in groundwater that contained ferrous iron, methane, and naphthalene, respectively.

Bacteria, Aerobic↗
PubMed2002

Geochemical and physiological evidence for mixed aerobic and anaerobic field biodegradation of coal tar waste by subsurface microbial communities.

We used geochemical analyses of groundwater and laboratory-incubated microcosms to investigate the physiological responses of naturally occurring microorganisms to coal-tar-waste constituents in a contaminated aquifer. Waters were sampled from wells along a natural hydrologic gradient extending from uncontaminated (1 well) into contaminated (3 wells) zones. Groundwater analyses determined the concentrations of carbon and energy sources (pollutants or total organic carbon), final electron acceptors (oxygen, nitrate, sulfate), and metabolic byproducts (dissolved inorganic carbon [DIC], alkalinity, methane, ferrous iron, sulfide, Mn2+). In the contaminated zone of the study site, concentrations of methane, hydrogen, alkalinity, and DIC were enhanced, while dissolved oxygen and nitrate were depleted. Field-initiated biodegradation assays using headspace-free serum bottle microcosms filled with groundwater examined metabolism of the ambient organic contaminants (naphthalene, 2-methylnaphthalene, benzothiophene, and indene) by the native microbial communities. Unamended microcosms from the contaminated zone demonstrated the simultaneous degradation of several coal-tar-waste constituents at the in situ temperature (10 degrees C). Lag phases prior to the onset of biodegradation indicated the prevalence of both aerobic and anaerobic conditions in situ. Electron acceptor-amended microcosms from the most contaminated well waters demonstrated only aerobic naphthalene degradation. Collectively, the geochemical and microbial evidence show that biodegradation of coal-tar-waste constituents occurs via both aerobic and anaerobic terminal electron accepting processes at this site.

Bacteria, Aerobic↗
PubMed2002

Elastographic imaging using a handheld compressor.

Elastography is an emerging imaging modality that allows noninvasive imaging of tissue stiffness changes and stiffness values associated with pathology or as a result of therapy. However, many currently-used systems for elastography rely on a fixed geometry transducer and compressor system for imaging. This configuration is disadvantageous for imaging difficult-to-reach regions that are currently accessible with conventional ultrasound. In this paper, we describe a handheld, portable stepper motor controlled system for elastography. This system may reduce motion and jitter errors that are prevalent in completely 'freehand elastography' that employs hand-induced compressions using the transducer. The latter also requires collection of large amounts of data and use of strain estimation algorithms that may not be sensitive to phase changes or use additional preprocessing to minimize decorrelation effects. The stepper motor controlled handheld system provides controlled compressions and synchronized data acquisition. Our technique yields elastograms of a low-contrast phantom that have contrast levels and contrast-to-noise ratios that are comparable to those obtained with a fixed geometry system.

Animals↗
PubMed2001

Further biogeochemical characterization of a trichloroethene-contaminated fractured dolomite aquifer: electron source and microbial communities involved in reductive dechlorination.

A recent article presented geochemical and microbial evidence establishing metabolic adaptation to and in-situ reductive dechlorination of trichloroethene (TCE) in a fractured dolomite aquifer. This study was designed to further explore site conditions and microbial populations and to explain previously reported enhancement of reductive dechlorination by the addition of pulverized dolomite to laboratory microcosms. A survey of groundwater geochemical parameters (chlorinated ethenes, ethene, H2, CH4, DIC, DOC, and delta13C values for CH4, DIC, and DOC) indicated that in situ reductive dechlorination was ongoing and that an unidentified pool of organic carbon was contributing, likely via microbial respiration, to the large and relatively light on-site DIC pool. Petroleum hydrocarbons associated with the dolomite rock were analyzed by GC/MS and featured a characteristically low delta13C value. Straight chain hydrocarbons were extracted from the dolomite previously found to stimulate reductive dechlorination; these were particularly depleted in hexadecane (HD). Thus, we hypothesized that HD and related hydrocarbons might be anaerobically respired and serve both as the source of on-site DIC and support reductive dechlorination of TCE. Microcosms amended with pulverized dolomite demonstrated reductive dechlorination, whereas a combusted dolomite amendment did not. HD-amended microcosms were also inactive. Therefore, the stimulatory factor in the pulverized dolomite was heat labile, but that component was not HD. Amplified Ribosomal DNA Restriction Analysis (ARDRA) of the microbial populations in well waters indicated that a relatively low diversity, sulfur-transforming community outside the plume was shifted toward a high diversity community including Dehalococcoides ethenogenes-type microorganisms inside the zone of contamination. These observations illustrate biogeochemical intricacies of in situ reductive dechlorination reactions.

Bacteria, Anaerobic↗
PubMed2001

Low-reflection-coefficient liquid interfaces for system characterization.

The use of liquid brominated hydrocarbons to form a planar reflecting interface with water is described. Gravity-based planar reflecting surfaces with known reflection coefficients can be used in system characterization for quantitative ultrasonics, and a set of surfaces with a range of reflection coefficients allows calibration of the output power and receiver gain of ultrasonic imaging systems. The substances reported here are immiscible in water and form interfaces with water, resulting in a broad range of acoustic reflection coefficients. Reflection coefficients were measured at temperatures from 18-24 degrees C for "pure" substances and for mixtures of two brominated hydrocarbons. Results show that reflection coefficients are weakly dependent on temperature and that, at a specific temperature, a significant range of arbitrarily small reflection coefficients is available, in the case of the mixtures, by the appropriate choice of weight-percents of the two brominated hydrocarbons.

Hydrocarbons, Brominated↗
PubMed2001

Improved method for determining resolution zones in ultrasound phantoms with spherical simulated lesions.

Quantification of ultrasound (US) imager performance simulating human observers is addressed using size-dependent lesion signal-to-noise ratio (LSNR) analysis of images of spherical simulated lesions in phantoms. LSNR values obtained over a broad range of image depths can be used with a single detectability threshold to determine the depth range over which lesions of a given size and contrast are deemed to be detectable, yielding a performance metric. Optimal LSNR analysis requires a priori knowledge of lesion locations in the image so that LSNR values relate to the center of each lesion. Phantoms having a regular array of accurately positioned spherical simulated lesions are described, along with easily employed and robust software that accurately determines lesion locations in images, even when only a few are detectable by visual inspection. The software accounts for image spatial calibration inaccuracies and accommodates sector, curvilinear, etc., formats. The minimum number of equivalent lesions to yield an acceptable mean (counteracting speckle variations) also is addressed.

Image Processing, Computer-Assisted↗
PubMed2001

Serum lactate dehydrogenase isoenzyme 1 and relapse in patients with nonseminomatous testicular germ cell tumors clinical stage I.

Serum lactate dehydrogenase isoenzyme 1 catalytic concentration (S-LD-1) was measured at the time of orchiectomy in 104 patients with nonseminomatous testicular germ cell tumors (NSTGCT) clinical stage I who participated in a randomized study comparing surveillance after orchiectomy (group I) and radiotherapy (group II). For 68 patients, S-LD-1 was measured in a serum sample before or on the day of the orchiectomy. Twenty-seven patients (40%) had elevated S-LD-1; median 102 U/L (range 41-335). For the remaining 36 patients. S-LD-1 was measured in a serum sample after orchiectomy: 8 of these patients (22%) had elevated S-LD-1. S-LD-1 was normalized shortly after surgery in most patients with a preorchiectomy elevated S-LD-1. Fifteen of the 68 patients relapsed: 9 out of 27 with an elevated S-LD-1 and 6 out of 41 patients with normal S-LD-1 (p = 0.13, Fisher's exact test). In group 1, those with a preoperatively elevated S-LD-1 had a lower 8-years' relapse-free survival than those with a normal S-LD-1 (40% vs. 80%, p = 0.003, log-rank test). The role of S-LD-1 in the staging, prognostication and monitoring of patients with NSGCT clinical stage I should be further explored in a large, prospective study.

Adolescent↗
PubMed2001

Tissue mimicking materials for a multi-imaging modality prostate phantom.

Materials that simultaneously mimic soft tissue in vivo for magnetic resonance imaging (MRI), ultrasound (US), and computed tomography (CT) for use in a prostate phantom have been developed. Prostate and muscle mimicking materials contain water, agarose, lipid particles, protein, Cu++, EDTA, glass beads, and thimerosal (preservative). Fat was mimicked with safflower oil suffusing a random mesh (network) of polyurethane. Phantom material properties were measured at 22 degrees C. (22 degrees C is a typical room temperature at which phantoms are used.) The values of material properties should match, as well as possible, the values for tissues at body temperature, 37 degrees C. For MRI, the primary properties of interest are T1 and T2 relaxations times, for US they are the attenuation coefficient, propagation speed, and backscatter, and for CT, the x-ray attenuation. Considering the large number of parameters to be mimicked, rather good agreement was found with actual tissue values obtained from the literature. Using published values for prostate parenchyma, T1 and T2 at 37 degrees C and 40 MHz are estimated to be about 1,100 and 98 ms, respectively. The CT number for in vivo prostate is estimated to be 45 HU (Hounsfield units). The prostate mimicking material has a T1 of 937 ms and a T2 of 88 ms at 22 degrees C and 40 MHz; the propagation speed and attenuation coefficient slope are 1,540 m/s and 0.36 dB/cm/MHz, respectively, and the CT number of tissue mimicking prostate is 43 HU. Tissue mimicking (TM) muscle differs from TM prostate in the amount of dry weight agarose, Cu++, EDTA, and the quality and quantity of glass beads. The 18 microm glass beads used in TM muscle increase US backscatter and US attenuation; the presence of the beads also has some effect on T1 but no effect on T2. The composition of tissue-mimicking materials developed is such that different versions can be placed in direct contact with one another in a phantom with no long term change in US, MRI, or CT properties. Thus, anthropomorphic phantoms can be constructed.

Adipose Tissue↗
PubMed2001

Serum lactate dehydrogenase isoenzyme 1 and prediction of death in patients with metastatic testicular germ cell tumors.

The International Germ Cell Cancer Collaborative Group study of patients with metastatic testicular germ cell tumors showed that catalytic concentration of serum lactate dehydrogenase (S-LD), serum alpha-fetoprotein concentration (S-AFP), and serum human chorionic gonadotropin concentration (S-hCG) predicted death from tumor. The recent international TNM classification (T primary tumor, N lymph node metastasis, M distant metastasis) is based on these results. The aim of our study was to evaluate whether catalytic concentration of S-LD isoenzyme 1 (S-LD-1) was a better predictor than the criteria used for the international classification. In an evaluation series of 44 patients from Odense University Hospital, Denmark, a raised S-LD-1 (>1.0 x upper limit of reference values) had a predictive value for death from tumor in 5-years observation of 46%. The predictive value was 46% for S-LD, 25% for S-AFP, and 40% for S-hCG. A normal SLD-1 had a predictive value for survival over 5-years observation of 100%. It was 81% for S-LD, 75% for SAFP, and 77% for S-hCG. The fraction of the patients who died of tumor and had a raised tumor marker value was 100% for S-LD-1, 46% for S-LD, 9% for S-AFP, and 18% for S-hCG. The fraction of patients with a normal serum tumor marker value among those who survived was 61% for S-LD-1, 81% for S-LD, 94% for SAFP, and 94% for S-hCG. A validation series of 37 patients treated at the University of Texas MD Anderson Cancer Center showed similar findings. Combining the patients in the two series, a raised value of SLD-1 classified more patients into a subgroup with an impaired survival (53%) than S-LD (35%), S-AFP (6%), or S-hCG (11%), and the high risk subgroups based on the international classification (40%). The findings have implications for the staging and treatment of patients with metastatic testicular germ cell tumors.

Biomarkers, Tumor↗
PubMed2000

Use of substrate responsive-direct viable counts to visualize naphthalene degrading bacteria in a coal tar-contaminated groundwater microbial community.

A microscopy-based method was developed to distinguish naphthalene-degrading bacteria within the microbial community of a coal tar-contaminated groundwater system. Pure cultures of Pseudomonas putida NCIB 9816-4 were used to develop the substrate responsive-direct viable count (SR-DVC) method. Cells were concentrated on membrane filters, placed on agar plates of Stanier's minimal basal salts media containing antibiotics (nalidixic acid, piromidic acid, pipemidic acid, and cephalexin), and exposed to vapors of naphthalene. Following brief incubation, samples were fixed in 2% formaldehyde and examined by epifluorescent microscopy. Pure cultures displayed the expected cell elongation response to the SR-DVC assay and required a minimum incubation time of 9 h for differentiation of elongated cells. When applied to groundwater samples from the study site, naphthalene responsive cells in the groundwater community were easily distinguished from unresponsive cells and debris (350+/-180 substrate responsive cells/ml, relative to negative controls with no added growth substrate). In an attempt to reduce background counts of elongated bacteria and fungi, the SR-DVC procedure was modified by adding a wash step prior to incubation and a fungal inhibitor, cyclohexamide, to the plates. When groundwater samples were subjected to the modified procedure, only cells in washed samples showed a significant response to naphthalene (150+/-25 cells/ml), indicating the presence of inhibitory substances in the groundwater. Variations in response of the groundwater microbial community to the two SR-DVC procedures suggest that subsurface conditions (microbial and chemical composition) vary temporally. SR-DVC allows the phenotypes of individual naturally occurring cells to be assessed.

Bacteria↗