bluuebunny/crossref_metadata_2025 huggingface dataset:
Treatment planning and verification of proton therapy using spot scanning: Initial experiences
Authors: Lomax Antony J. , Böhringer Terence , Bolsi Alessandra , Coray Doelf , Emert Frank , Goitein Gudrun , Jermann Martin , Lin Shixiong , Pedroni Eros , Rutz Hanspeter , Stadelmann Otto , Timmermann Beate , Verwey Jorn , Weber Damien C.
Published: November 2004

Since the end of 1996, we have treated more than 160 patients at PSI using spot‐scanned protons. The range of indications treated has been quite wide and includes, in the head region, base‐of‐skull sarcomas, low‐grade gliomas, meningiomas, and para‐nasal sinus tumors. In addition, we have treated bone sarcomas in the neck and trunk—mainly in the sacral area—as well as prostate cases and some soft tissue sarcomas. PTV volumes for our treated cases are in the range 20–4500 ml, indicating the flexibility of the spot scanning system for treating lesions of all types and sizes. The number of fields per applied plan ranges from between 1 and 4, with a mean of just under 3 beams per plan, and the number of fluence modulated Bragg peaks delivered per field has ranged from 200 to 45 000. With the current delivery rate of roughly 3000 Bragg peaks per minute, this translates into delivery times per field of between a few seconds to 20–25 min. Bragg peak weight analysis of these spots has shown that over all fields, only about 10% of delivered spots have a weight of more than 10% of the maximum in any given field, indicating that there is some scope for optimizing the number of spots delivered per field. Field specific dosimetry shows that these treatments can be delivered accurately and precisely to within (1 SD) orthogonal to the field direction and to within 1.5 mm in range. With our current delivery system the mean widths of delivered pencil beams at the Bragg peak is about 8 mm (σ) for all energies, indicating that this is an area where some improvements can be made. In addition, an analysis of the spot weights and energies of individual Bragg peaks shows a relatively broad spread of low and high weighted Bragg peaks over all energy steps, indicating that there is at best only a limited relationship between pencil beam weighting and depth of penetration. This latter observation may have some consequences when considering strategies for fast re‐scanning on second generation scanning gantries.
Performance of a commercial optical CT scanner and polymer gel dosimeters for 3‐D dose verification
Authors: Xu Y. , Wuu Cheng‐Shie , Maryanski Marek J.
Published: November 2004

Performance analysis of a commercial three‐dimensional (3‐D) dose mapping system based on optical CT scanning of polymer gels is presented. The system consists of polymer gels (MGS Research, Inc., Madison, CT), OCTOPUS™ laser CT scanner (MGS Research, Inc., Madison, CT), and an in‐house developed software for optical CT image reconstruction and 3‐D dose distribution comparison between the gel, film measurements and the radiation therapy treatment plans. Various sources of image noise (digitization, electronic, optical, and mechanical) generated by the scanner as well as optical uniformity of the polymer gel are analyzed. The performance of the scanner is further evaluated in terms of the reproducibility of the data acquisition process, the uncertainties at different levels of reconstructed optical density per unit length and the effects of scanning parameters. It is demonstrated that for gel phantoms held in cylindrical plastic containers, the relative dose distribution can be reproduced by the scanner with an overall uncertainty of about 3% within approximately 75% of the radius of the container. In regions located closer to the container wall, however, the scanner generates erroneous optical density values that arise from the reflection and refraction of the laser rays at the interface between the gel and the container. The analysis of the accuracy of the polymer gel dosimeter is exemplified by the comparison of the gel/OCT‐derived dose distributions with those from film measurements and a commercial treatment planning system (Cadplan, Varian Corporation, Palo Alto, CA) for a single field of x rays and a 3‐D conformal radiotherapy (3DCRT) plan. The gel measurements agree with the treatment plans and the film measurements within the “3%‐or‐” criterion throughout the usable, artifact‐free central region of the gel volume. Discrepancies among the three data sets are analyzed.
A method to test the reproducibility and to improve performance of computer‐aided detection schemes for digitized mammograms
Authors: Zheng Bin , Gur David , Good Walter F. , Hardesty Lara A.
Published: November 2004

The purpose of this study is to develop a new method for assessment of the reproducibility of computer‐aided detection (CAD) schemes for digitized mammograms and to evaluate the possibility of using the implemented approach for improving CAD performance. Two thousand digitized mammograms (representing 500 cases) with 300 depicted verified masses were selected in the study. Series of images were generated for each digitized image by resampling after a series of slight image rotations. A CAD scheme developed in our laboratory was applied to all images to detect suspicious mass regions. We evaluated the reproducibility of the scheme using the detection sensitivity and false‐positive rates for the original and resampled images. We also explored the possibility of improving CAD performance using three methods of combining results from the original and resampled images, including simple grouping, averaging output scores, and averaging output scores after grouping. The CAD scheme generated a detection score (from 0 to 1) for each identified suspicious region. A region with a detection score was considered as positive. The CAD scheme detected 238 masses (79.3% case‐based sensitivity) and identified 1093 false‐positive regions (average 0.55 per image) in the original image dataset. In eleven repeated tests using original and ten sets of rotated and resampled images, the scheme detected a maximum of 271 masses and identified as many as 2359 false‐positive regions. Two hundred and eighteen masses (80.4%) and 618 false‐positive regions (26.2%) were detected in all 11 sets of images. Combining detection results improved reproducibility and the overall CAD performance. In the range of an average false‐positive detection rate between 0.5 and 1 per image, the sensitivity of the scheme could be increased approximately 5% after averaging the scores of the regions detected in at least four images. At low false‐positive rate (e.g., per image), the grouping method alone could increase CAD sensitivity by 7%. The study demonstrated that reproducibility of a CAD scheme can be tested using a set of slightly rotated and resampled images. Because the reproducibility of true‐positive detections is generally higher than that of false‐positive detections, combining detection results generated from subsets of rotated and resampled images could improve both reproducibility and overall performance of CAD schemes.
A new radiation shielding block material for radiation therapy
Authors: Tajiri Minoru , Sunaoka Masayoshi , Fukumura Akifumi , Endo Masahiro
Published: November 2004

In recent years, lead has been recognized as a source of environmental pollution; this includes lead use for radiation shielding in radiotherapy. We looked for a new material that could be a lead substitute. We chose a material composed of tungsten and resin. We compared the attenuation coefficient of the material with those of lead and Lipowitz's metal, and found the material has a higher attenuation coefficient than the other two. The material may be used as a substitute for lead because it is easy to fabricate and friendly to the environment.
Dosimetric properties of magnetically collimated electron beams for radiation therapy
Authors: Ma Lijun
Published: November 2004

A method of generating magnetically collimated electron beams is developed and the dosimetric properties of magnetically collimated electrons are investigated. An in‐air magnetic collimator device was designed and constructed for the study. The magnetic collimator was placed above the exit port of a electron cone. Axial magnetic field of approximately 0.6 Tesla is generated inside the collimator via an array of permanent magnets. Fixed and rotational magnetically collimated electron beams were delivered and measured in phantoms. We found that magnetically collimated electron beams significantly lower the surface dose as compared with conventional electron beams. A magnetically collimated arc beam further reduces the surface dose to less than 20% of the maximum dose inside the target. The dose per monitor unit at for the magnetically collimated electron beams was significantly higher than that of the conventional electron beams. The use of magnetic collimation may lead to improved delivery techniques for breast and head and neck cancer treatments.
Limitations of a convolution method for modeling geometric uncertainties in radiation therapy: the radiobiological dose‐per‐fraction effect
Authors: Song William , Battista Jerry , Van Dyk Jake
Published: November 2004

The convolution method can be used to model the effect of random geometric uncertainties into planned dose distributions used in radiation treatment planning. This is effectively done by linearly adding infinitesimally small doses, each with a particular geometric offset, over an assumed infinite number of fractions. However, this process inherently ignores the radiobiological dose‐per‐fraction effect since only the summed physical dose distribution is generated. The resultant potential error on predicted radiobiological outcome [quantified in this work with tumor control probability (TCP), equivalent uniform dose (EUD), normal tissue complication probability (NTCP), and generalized equivalent uniform dose (gEUD)] has yet to be thoroughly quantified. In this work, the results of a Monte Carlo simulation of geometric displacements are compared to those of the convolution method for random geometric uncertainties of 0, 1, 2, 3, 4, and 5 mm (standard deviation). The ratios of 0.8, 1.5, 3, 5, and 10 Gy are used to represent the range of radiation responses for different tumors, whereas a single ratio of 3 Gy is used to represent all the organs at risk (OAR). The analysis is performed on a four‐field prostate treatment plan of 18 MV x rays. The fraction numbers are varied from 1–50, with isoeffective adjustments of the corresponding dose‐per‐fractions to maintain a constant tumor control, using the linear‐quadratic cell survival model. The average differences in TCP and EUD of the target, and in NTCP and gEUD of the OAR calculated from the convolution and Monte Carlo methods reduced asymptotically as the total fraction number increased, with the differences reaching negligible levels beyond the treatment fraction number of . The convolution method generally overestimates the radiobiological indices, as compared to the Monte Carlo method, for the target volume, and underestimates those for the OAR. These effects are interconnected and attributed to assuming an infinite number of fractions inherent in the implementation of the convolution technique, irrespective of the uniqueness of each treatment schedule. Based on the fraction numbers analyzed (1–50), and the range of fraction numbers normally used clinically , the convolution method can be used safely to estimate the effects of random geometric uncertainties on prostate treatment radiobiological outcomes, for both the target and the OAR. Although the results of this study is likely to apply to other clinical sites and treatment techniques other than the four‐field, further validation similar to those done in this study may be necessary prior to clinical implementation.
Energy Transfer Across a Metal Film Mediated by Surface Plasmon Polaritons
Authors: Andrew P. , Barnes W. L.
Published: November 2004

Coupled surface plasmon polaritons (SPPs) are shown to provide effective transfer of excitation energy from donor molecules to acceptor molecules on opposite sides of metal films up to 120 nanometers thick. This variant of radiative transfer should allow directional control over the flow of excitation energy with the use of suitably designed metallic nanostructures, with SPPs mediating transfer over length scales of 10
–7
to 10
–4
meters. In the emerging field of nanophotonics, such a prospect could allow subwavelength-scale manipulation of light and provide an interface to the outside world.
Reading Between the Lines
Authors: Sleigh Charlotte
Published: November 2004

An Elusive Victorian
The Evolution of Alfred Russel Wallace.
By Martin Fichman
. University of Chicago Press, Chicago, 2004. 392 pp. $40, £28. ISBN 0-226-24613-2.

Through an exploration of key themes, the author interprets Wallace's work as an attempt to integrate his scientific and humanistic interests in a unified vision of humanity's place in nature.
Serologic and Molecular Characterization of
Vibrio parahaemolyticus
Strains Isolated from Seawater and Fish Products of the Gulf of Mexico
Authors: Cabrera-García María Eugenia , Vázquez-Salinas Carlos , Quiñones-Ramírez Elsa Irma
Published: November 2004

The thermostable direct hemolysin (TDH) and TDH-related hemolysin (TRH) are the main virulence factors of
Vibrio parahaemolyticus
. We isolated
V. parahaemolyticus
from seawater, fish, and oysters obtained from the Pueblo Viejo Lagoon in Veracruz, determined the serogroups, phenotypically and genotypically characterized TDH and TRH, and investigated the presence of the
toxR
gene. A total of 46
V. parahaemolyticus
strains were isolated, and all of them amplified the 368-bp
toxR
gene fragment. The
trh
gene was not identified in any of the strains; 4 of the 46 strains were Kanagawa phenomenon (KP) positive and amplified the 251-bp
tdh
gene fragment. The most frequent serogroup was serogroup O3. This is the first report of the presence of KP-positive
tdh
-positive environmental
V. parahaemolyticus
strains in Mexico.
Diversity and Distribution of
Frankia
Strains Symbiotic with
Ceanothus
in California
Authors: Oakley Brian , North Malcolm , Franklin Jerry F. , Hedlund Brian P. , Staley James T.
Published: November 2004

Frankia
strains symbiotic with
Ceanothus
present an interesting opportunity to study the patterns and causes of
Frankia
diversity and distribution within a particular host infectivity group. We intensively sampled
Frankia
from nodules on
Ceanothus
plants along an elevational gradient in the southern Sierra Nevada of California, and we also collected nodules from a wider host taxonomic and geographic range throughout California. The two sampling scales comprised 36 samples from eight species of
Ceanothus
representing six of the seven major biogeographic regions in and around California. The primary objective of this study was to use a quantitative model to test the relative importance of geographic separation, host specificity, and environment in influencing the identity of
Ceanothus Frankia
symbionts as determined by ribosomal DNA sequence data. At both sampling scales,
Frankia
strains symbiotic with
Ceanothus
exhibited a high degree of genetic similarity.
Frankia
strains symbiotic with
Chamaebatia
(
Rosaceae
) were within the same clade as several
Ceanothus
symbionts. Results from a classification and regression tree model used to quantitatively explain
Frankia
phylogenetic groupings demonstrated that the only significant variable in distinguishing between phylogenetic groups at the more local sampling scale was host species. At the regional scale,
Frankia
phylogenetic groupings were explained by host species and the biogeographic province of sample collection. We did not find any significant correspondence between
Frankia
and
Ceanothus
phylogenies indicative of coevolution, but we concluded that the identity of
Frankia
strains inhabiting
Ceanothus
nodules may involve interactions between host species specificity and geographic isolation.
No Significant Contribution of Arbuscular Mycorrhizal Fungi to Transfer of Radiocesium from Soil to Plants
Authors: Joner E. J. , Roos P. , Jansa J. , Frossard E. , Leyval C. , Jakobsen I.
Published: November 2004

The diffuse pollution by fission and activation products following nuclear accidents and weapons testing is of major public concern. Among the nuclides that pose a serious risk if they enter the human food chain are the cesium isotopes
137
Cs and
134
Cs (with half-lives of 30 and 2 years, respectively). The biogeochemical cycling of these isotopes in forest ecosystems is strongly affected by their preferential absorption in a range of ectomycorrhiza-forming basidiomycetes. An even more widely distributed group of symbiotic fungi are the arbuscular mycorrhizal fungi, which colonize most herbaceous plants, including many agricultural crops. These fungi are known to be more efficient than ectomycorrhizas in transporting mineral elements from soil to plants. Their role in the biogeochemical cycling of Cs is poorly known, in spite of the consequences that fungal Cs transport may have for transfer of Cs into the human food chain. This report presents the first data on transport of Cs by these fungi by use of radiotracers and compartmented growth systems where uptake by roots and mycorrhizal hyphae is distinguished. Independent experiments in three laboratories that used different combinations of fungi and host plants all demonstrated that these fungi do not contribute significantly to plant uptake of Cs. The implications of these findings for the bioavailability of radiocesium in different terrestrial ecosystems are discussed.
Glutamine, Glutamate, and α-Glucosylglycerate Are the Major Osmotic Solutes Accumulated by
Erwinia chrysanthemi
Strain 3937
Authors: Goude Renan , Renaud Stéphanie , Bonnassie Sylvie , Bernard Théophile , Blanco Carlos
Published: November 2004

Erwinia chrysanthemi
is a phytopathogenic soil enterobacterium closely related to
Escherichia coli
. Both species respond to hyperosmotic pressure and to external added osmoprotectants in a similar way. Unexpectedly, the pools of endogenous osmolytes show different compositions. Instead of the commonly accumulated glutamate and trehalose,
E. chrysanthemi
strain 3937 promotes the accumulation of glutamine and α-glucosylglycerate, which is a new osmolyte for enterobacteria, together with glutamine. The amounts of the three osmolytes increased with medium osmolarity and were reduced when betaine was provided in the growth medium. Both glutamine and glutamate showed a high rate of turnover, whereas glucosylglycerate stayed stable. In addition, the balance between the osmolytes depended on the osmolality of the medium. Glucosylglycerate and glutamate were the major intracellular compounds in low salt concentrations, whereas glutamine predominated at higher concentrations. Interestingly, the ammonium content of the medium also influenced the pool of osmolytes. During bacterial growth with 1 mM ammonium in stressing conditions, more glucosylglycerate accumulated by far than the other organic solutes. Glucosylglycerate synthesis has been described in some halophilic archaea and bacteria but not as a dominant osmolyte, and its role as an osmolyte in
Erwinia chrysanthemi
3937 shows that nonhalophilic bacteria can also use ionic osmolytes.
Representative Freshwater Bacterioplankton Isolated from Crater Lake, Oregon
Authors: Page Kathleen A. , Connon Stephanie A. , Giovannoni Stephen J.
Published: November 2004

High-throughput culturing (HTC) methods that rely on dilution to extinction in very-low-nutrient media were used to obtain bacterial isolates from Crater Lake, Oregon. 16S rRNA sequence determination and phylogenetic reconstruction were used to determine the potential ecological significance of isolated bacteria, both in Crater Lake and globally. Fifty-five Crater Lake isolates yielded 16 different 16S rRNA gene sequences. Thirty of 55 (55%) Crater Lake isolates had 16S rRNA gene sequences with 97% or greater similarity to sequences recovered previously from Crater Lake 16S rRNA gene clone libraries. Furthermore, 36 of 55 (65%) Crater Lake isolates were found to be members of widely distributed freshwater groups. These results confirm that HTC is a significant improvement over traditional isolation techniques that tend to enrich for microorganisms that do not predominate in their environment and rarely correlate with 16S rRNA gene clone library sequences. Although all isolates were obtained under dark, heterotrophic growth conditions, 2 of the 16 different groups showed evidence of photosynthetic capability as assessed by the presence of
puf
operon sequences, suggesting that photoheterotrophy may be a significant process in this oligotrophic, freshwater habitat.
Differentiation of
Micromonospora
Isolates from a Coastal Sediment in Wales on the Basis of Fourier Transform Infrared Spectroscopy, 16S rRNA Sequence Analysis, and the Amplified Fragment Length Polymorphism Technique
Authors: Zhao Hongjuan , Kassama Yankuba , Young Michael , Kell Douglas B. , Goodacre Royston
Published: November 2004

A number of actinomycetes isolates were recovered from coastal sediments in Aberystwyth (Wales, United Kingdom) with standard isolation techniques. Most of them were putatively assigned to the genera
Streptomyces
and
Micromonospora
on the basis of their morphological characteristics, and there appeared to be no difference whether the isolation media contained distilled water or seawater. A group of 20
Micromonospora
isolates was selected to undergo further polyphasic taxonomic investigation. Three approaches were used to analyze the diversity of these isolates, 16S rDNA sequencing, fluorescent amplified fragment length polymorphism (AFLP), and Fourier transform infrared spectroscopy (FT-IR). The 16S rDNA sequence analysis confirmed that all of these isolates should be classified to the genus
Micromonospora
, and they were analyzed with a group of other
Micromonospora
16S rDNA sequences available from the Ribosomal Database Project. The relationships of the 20 isolates were observed after hierarchical clustering, and almost identical clusters were obtained with these three techniques. This has obvious implications for high-throughput screening for novel actinomycetes because FT-IR spectroscopy, which is a rapid and reliable whole-organism fingerprinting method, can be applied as a very useful dereplication tool to indicate which environmental isolates have been cultured previously.
Sequence and Expression Analysis of the
ompA
Gene of
Rickettsia peacockii
, an Endosymbiont of the Rocky Mountain Wood Tick,
Dermacentor andersoni
Authors: Baldridge Gerald D. , Burkhardt Nicole Y. , Simser Jason A. , Kurtti Timothy J. , Munderloh Ulrike G.
Published: November 2004

The transmission dynamics of Rocky Mountain spotted fever in Montana appears to be regulated by
Rickettsia peacockii
, a tick symbiotic rickettsia that interferes with transmission of virulent
Rickettsia rickettsii
. To elucidate the molecular relationships between the two rickettsiae and glean information on how to possibly exploit this interference phenomenon, we studied a major rickettsial outer membrane protein gene,
ompA
, presumed to be involved in infection and pathogenesis of spotted fever group rickettsiae (SFGR) but which is not expressed in the symbiont. Based on PCR amplification and DNA sequence analysis of the SFGR
ompA
gene, we demonstrate that
R. peacockii
is the most closely related of all known SFGR to
R. rickettsii
. We show that
R. peacockii
, originally described as East Side agent in
Dermacentor andersoni
ticks from the east side of the Bitterroot Valley in Montana, is still present in that tick population as well as in
D. andersoni
ticks collected at two widely separated locations in Colorado. The
ompA
genes of
R. peacockii
from these locations share three identical premature stop codons and a weakened ribosome binding site consensus sequence relative to
ompA
of
R. rickettsii
. The
R. peacockii ompA
promoter closely resembles that of
R. rickettsii
and is functional based on reverse transcription-PCR results. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis and Western blotting showed that OmpA translation products were not detected in cultured tick cells infected with
R. peacockii
. Double immunolabeling studies revealed actin tail structures in tick cells infected with
R. rickettsii
strain Hlp#2 but not in cells infected with
R. peacockii
.
Morphotypic Conversion inListeria monocytogenesBiofilm Formation: Biological Significance of Rough Colony Isolates
Authors: Monk Ian R. , Cook Gregory M. , Monk Brian C. , Bremer Philip J.
Published: November 2004

Adherence to a stainless steel surface selected isolates ofListeria monocytogeneswith enhanced surface colonization abilities and a change in phenotype from the common smooth colony morphology to a succession of rough colony morphotypes. Growth in broth culture of the best-adapted, surface-colonizing rough colony morphotype gave a smooth colony revertant. Comparative analysis revealed that the smooth and rough variants had similar phenotypic and biochemical characteristics (e.g., identical growth rates and tolerances to antibiotics and environmental stressors). Rough colony isolates, however, failed to coordinate motility or induce autolysis. The defect in autolysis of rough colony isolates, which involved impaired cellular localization of several peptidoglycan-degrading enzymes, including cell wall hydrolase A (CwhA), suggested a link to a secretory pathway defect. The genetic basis for the impairment was studied at the level of the accessory secretory pathway component SecA2. DNA sequencing of thesecA2gene in smooth and rough colony isolates found no mutations in the coding or promoter regions. Analysis of SecA2 expression with an integratedsecA2-FLAG tag construct found the protein to be upregulated in the rough and revertant backgrounds compared to the parental smooth colony isolate. A compensatory mechanism involving the SecA2 secretion pathway components is postulated to control smooth to rough interconversion ofL. monocytogenes. Such phenotypic variation may enhance the ability of this opportunistic pathogen to colonize environments as diverse as processing surfaces, food products, and animal hosts.
Ultrastructural Alterations of
Erwinia carotovora
subsp.
atroseptica
Caused by Treatment with Aluminum Chloride and Sodium Metabisulfite
Authors: Yaganza Elian-Simplice , Rioux Danny , Simard Marie , Arul Joseph , Tweddell Russell J.
Published: November 2004

Aluminum and bisulfite salts inhibit the growth of several fungi and bacteria, and their application effectively controls potato soft rot caused by
Erwinia carotovora
. In an effort to understand their inhibitory action, ultrastructural changes in
Erwinia carotovora
subsp.
atroseptica
after exposure (0 to 20 min) to different concentrations (0.05, 0.1, and 0.2 M) of these salts were examined by using transmission electron microscopy. Plasma membrane integrity was evaluated by using the SYTOX Green fluorochrome that penetrates only cells with altered membranes. Bacteria exposed to all aluminum chloride concentrations, especially 0.2 M, exhibited loosening of the cell walls, cell wall rupture, cytoplasmic aggregation, and an absence of extracellular vesicles. Sodium metabisulfite caused mainly a retraction of plasma membrane and cellular voids which were more pronounced with increasing concentration. Bacterial mortality was closely associated with SYTOX stain absorption when bacteria were exposed to either a high concentration (0.2 M) of aluminum chloride or prolonged exposure (20 min) to 0.05 M aluminum chloride or to a pH of 2.5. Bacteria exposed to lower concentrations of aluminum chloride (0.05 and 0.1 M) for 10 min or less, or to metabisulfite at all concentrations, did not exhibit significant stain absorption, suggesting that no membrane damage occurred or it was too weak to allow the penetration of the stain into the cell. While mortality caused by aluminum chloride involves membrane damage and subsequent cytoplasmic aggregation, sulfite exerts its effect intracellularly; it is transported across the membrane by free diffusion of molecular SO
2
with little damage to the cellular membrane.
New Vector for Efficient Allelic Replacement in Naturally Nontransformable, Low-GC-Content, Gram-Positive Bacteria
Authors: Arnaud Maryvonne , Chastanet Arnaud , Débarbouillé Michel
Published: November 2004

A shuttle vector designated pMAD was constructed for quickly generating gene inactivation mutants in naturally nontransformable gram-positive bacteria. This vector allows, on X-Gal (5-bromo-4-chloro-3-indolyl-β-
d-
galactopyranoside) plates, a quick colorimetric blue-white discrimination of bacteria which have lost the plasmid, greatly facilitating clone identification during mutagenesis. The plasmid was used in
Staphylococcus aureus
,
Listeria monocytogenes
, and
Bacillus cereus
to efficiently construct mutants with or without an associated antibiotic resistance gene.
Acetate Threshold Concentrations Suggest Varying Energy Requirements during Anaerobic Respiration byAnaeromyxobacter dehalogenans
Authors: He Qiang , Sanford Robert A.
Published: November 2004

Acetate threshold concentrations were determined under chlororespiring and Fe(III)-reducing conditions forAnaeromyxobacter dehalogenansstrain 2CP-C. The acetate threshold concentrations measured were 69 ± 4, 19 ± 8, and <1 nM for chlororespiration, amorphous Fe(III) reduction, and Fe(III) citrate reduction, respectively. Residual ΔGvalues of −75.4 kJ/mol of electrons for chlororespiration and −41.5 kJ/mol of electrons for amorphous Fe(III) reduction were calculated at the acetate threshold concentration. By comparing threshold concentrations for different metabolisms in a single organism, this study provides insight into the metabolic use of energy under different growth conditions.
CONTINUUM X-RAYS PRODUCED BY 60 keV- AND 80 keV- PROTON BOMBARDMENT
Authors: Chu T.C. , Ishii K. , Kikuchi M. , Murozono K. , Hsu C.C. , Morita S.
Published: November 2004

We measured continuum x-rays from an aluminium target bombarded with 60 keV- and 80 keV- proton beams. On the basis of the PWBA theory, we calculated the thick target yields of atomic bremsstrahlung and nuclear bremsstrahlung produced in very low energy ion-atom collisions and compared with the experiment. The present theory predicts that the main component of continuum x-rays produced in such low energy ion-atom collisions is the nuclear bremsstrahlung. The theory presents the yields of continuum x-rays about 5 times larger than the experimental ones, however, reproduces well the spectral shape.
FACILITY OF PIXE ANALYSIS AT TOHOKU UNIVERSITY
Authors: IWASAKI S. , ISHII K. , MATSUYAMA M. , MUROZONO K. , INOUE J. , TANAKA M. , YAMAZAKI H. , HONMA T. , FUJIOKA M. , ORIHARA H.
Published: November 2004

PIXE research at the 4.5-MV Dynamitron laboratory of the Faculty of Engineering, Tohoku University started as a joint project between Cyclotron and Radioisotope Center(CYRIC), Tohoku University, and the Dynamitron laboratory. The PIXE equipments including vertical beam in air PIXE system called ViaPIXE was installed at a vacant beam course of the Dynamitron laboratory. Some PIXE experiments conducted at this facility as well future PIXE research in this laboratory are briefly described.
QUANTITATIVE MEASUREMENT OF METAL ION CONCENTRATION OF PROTEINS SEPARATED BY ELECTROPHORESIS
Authors: WEBER G. , STRIVAY D. , MENENDEZ C. , SCHOEFS B. , BERTRAND M.
Published: November 2004

This communication is devoted to nature determination and quantification by PIXE of metals contained in proteins after their separation by PolyAcrylamide Gel Electrophoresis (PAGE). After the electrophoresis, the gel is dried and each track is scanned with a 2.5 MeV proton beam which triggers metal X-ray fluorescence and then, allows to determine the type of metals contained in an electrophoretic band. For quantitative determination of the amount of the metal contained inside the band, the characteristic X-ray peak area is compared with those obtained with polyacrylamide gels doped with the same metal. The normalization has been achieved by using RBS measurements on the gel itself.

The procedure presented seems to be a very useful multielementary method for the metal content analysis and for the determination of the metal amounts inside proteins after their separation by electrophoresis. Furthermore it allows to check if metals remain bound to proteins.
SIMULTANEOUS DETERMINA TION OF TRACE ELEMENTS IN SERA OF PATIENTS WITH ACUTE MYOCARDIAL INFARCTION BY PIXE -2-
Authors: MIURA Y. , ITOH C. , MIYAKAWA T. , NAKAI K. , HIRAMORI K. , SERA K. , FUTATSUGAWA S.
Published: November 2004

Vascular cell adhesion molecule-1 (VCAM-1) is transiently expressed on vascular endothelial cells in response to cytokines. It plays a major role in the adhesion of leucocytes to the endothelium by interaction with its ligand VLA-4, a member of the β1 integrin family.

We measured the serum concentration of the soluble VCAM-1 (sVCAM-1) in 114 patients with acute myocardial infarction (AMI) and 37 normal controls by enzyme-linked immunoassay in comparison with trace element concentration. sVCAM-1 levels were markedly higher ( mean ± SD =833.2 ± 328.9 ng/ml ) in the sera of patients with AMI than in normal controls ( mean ± SD = 549.5 ± 188.8 ng/ml , p<0.001). Using PIXE we also determined concentration of magnesium, manganese, iron, copper, zinc, selenium, and calcium in sera of 43 patients with AMI. There were no clear correlation between the sVCAM-1 concentration and the magnesium, manganese, copper, selenium, iron. But there were significant correlation between the sVCAM-1 concentration and the zinc, calcium (p<0.05).
PIXE IN THE EXPLORATION OF POLLUTION: SCOPE AND EXAMPLES
Authors: ROMO-KRÖGER CARLOS M.
Published: November 2004

The need to establish the elemental concentration profile for a clean environment and for a healthy organism is emphasized. Through several examples it is shown how PIXE has gained importance in elemental analysis in the fields of Medicine, Biology and Environment. Studies have been done on cancerous tumors and other diseased tissues. Elemental concentrations of blood, hair, teeth and nails have been correlated to specific diseases and to environmental pollution. Also plants, algae, lichens and tree rings have been analyzed as bio-sensors. The PIXE routines in four laboratories in Latinamerica are described. Their main environmental applications are in atmospheric aerosols, tree rings, waste water and others.
BIO-PIXE AND BIO-SXRF
Authors: YAO HUIYING , JIN CHENGZHI , ZHANG JINGXIA , WU BENJIE
Published: November 2004

Application of PiXE On biology, medicine and environment has been successful in the last twenty years. However, with the development of science and technique, lower detectable limit, sub-ppm sensitivity, more accurate quantitative analysis and the element chemical state information were presented which can not be achieved by PIXE. The synchrotron radiation as an excitation source to induce X-ray emission (SXRF) is a very powerful method with all the above requirements. In this paper the advantages of SXRF were discussed and compared with PIXE. The article shows our work on biological field by PIXE and SXRF also.
APPLICATIONS OF X-RAY EMISSION TO ELEMENTAL ANALYSIS OF FOODS
Authors: FLOCCHINI ROBERT G. , LAGUNAS-SOLAR MANUEL C. , PERLEY BRIAN P.
Published: November 2004

Trace element analysis via X-Ray Fluorescence (XRF) and Proton-Induced X-Ray Emission (PIXE) techniques were applied to several samples of fresh and processed foods. Thin samples of fresh fruits and vegetables, processed dry foods. and spices were included in these analyses. The results indicate that XRF and/or PIXE analysis is applicable to these types of samples but require special and simple modifications in sample preparation techniques, and the inclusion of new matrix type corrections for data analysis. However, the non-destructive nature, reproducibility, efficiency and high sensitivity that characterize these multi-element analytical procedures can provide new potential methods for detecting trace elements in foods and in many agricultural commodities. Toxic metals such as Hg, Pb. and As were detected in some foods. In addition, other essential or neutral trace elements such as Na, K, Mg, Ca, Cu, Cr, V, Zn, Mo, Fe, Mn, Ni, Se, Cl, S, and P were also detected. These and other elements can be analyzed rapidly and with high sensitivity for applications in process control and for certification of food quality. Developing these techniques and procedures specifically for food and for various agricultural products may provide new analytical options and help mitigate the expected impact of forthcoming regulations intended to establish limits and tolerance levels for micro toxicants and other essential nutrients in foods and agricultural products.
EFFECTS OF CISPLATIN ON ELEMENT DISTRIBUTION IN MOUSE KIDNEY TISSUE ASSAYED BY MULTIVARIATE STATISTICAL ANALYSIS
Authors: LIU NIANQING , DENG YUE , PAN JUXIANG , WU YINGRONG , ZHOU CHUANGNONG
Published: November 2004

The micro-SXRF scanning technique (size 150×150µ m 2) has been used to obtain the positional distributions of Zn, Cu, Fe, Mn, Br, Rb, K, Ca, Cl, S and Pt in cryo-section of the kidneys of normal mice treated with the anti-cancer drug cisplatin. The effect of cisplatin on element correlation was assayed by multivariate statistical analysis. The results of these examination imply that the elements affected by the cisplatin treatment are Zn and Fe.
SYNCHROTRON RADIATION X-RAY FLUORESCENCE ANALYSIS OF ELEMENTS IN HUMAN GASTRIC CANCER
Authors: SHAO HANRU , XU QING , HONG RONG , WU YINGRONG , CHAO ZHIYU , YE SIMAO , HAN YAJING
Published: November 2004

Synchrotron radiation microprobe XRF analysis has been used in the multielements analysis of human gastric cancer tissues. Elements of P, S, Cl, K, Ca, Ti, Mn, Fe, Cu, Zn, Se, Br and Rb were detected. The relative concentrations of P and K in cancer are higher than in normal tissue, but it is contrary for Cl, Ca, Se and Br.
CHEMICAL EFFECT ON X-RAY FLUORESCENCE YIELDS FOR CARBON
Authors: MUKOYAMA TAKESHI , NAKAMATSU HIROHIDE , ADACHI HIROHIKO
Published: November 2004

The chemical effect on K-shell fluorescence yields for carbon compounds has been estimated in a simple model based on the discrete-variational Xα molecular orbital calculations and the statistical scaling method. The calculated results show that there is a relation between the fluorescence yield and the effective number of 2p electrons in carbon, n2p. The behavior of the fluorescence yield as a function of n2p is in qualitatively agreement with the experimental data by proton impact. The present values for fluorescence yields of carbon oxides agree with other theoretical values.
TRACE ELEMENTAL ANALYSIS OF OTOLITHS OF ANADROMOUS FISH
Authors: Nagata Yoshihisa , Arai Nobuaki , Sakamoto Wataru , Tago Yasuhiko , Yoshida Koji
Published: November 2004

PIXE was adopted for analysis of trace elements in otoliths of anadromous fish, masu salmon Oncorhynchus masou masou and amago salmon O. masou ishikawae. Mn, Zn and Sr were detected in order of ppm. Two different types of spectra were obtained from masu salmon otoliths. The concentrations of Sr and Zn in the two types were quite different. The difference seems to be a result of the difference in periods when the individuals stayed in freshwater environment until they were caught. Amago salmon otoliths contain significantly less Sr than masu salmon otoliths. It is considered to be due to different migration pattern between the two subspecies. Anadromous fish generally experiences freshwater and sea water environment in its migration. Trace elemental concentrations in sea water is quite different from those in freshwater. The environment, which varies along with the migration, would affect the incorporation of trace elements into otoliths of anadromous fish.
A SIMPLE GEOMETRICAL STRUCTURE UNDERLYING SPEECH SIGNALS OF THE JAPANESE VOWEL /a/
Authors: TOKUDA ISAO , TOKUNAGA RYUJI , AIHARA KAZUYUKI
Published: November 2004

We provide several pieces of evidence for possible chaotic dynamics in the irregular behavior of normal speech signals of the Japanese vowel /a/. First, principal component analysis demonstrates that a simple geometric structure underlying the complex speech signal is well reconstructed in a three-dimensional delay-coordinate space. Observations of the reconstructed speech trajectory at multiple cross sections also display speech dynamics with stretching, folding and compressing. Second, Lyapunov spectrum analysis indicates sensitive dependence on initial conditions with a positive Lyapunov exponent for the speech signals of several different speakers. Third, nonlinear modeling analysis with an artificial neural network shows that the nonlinear dynamics of the vowel sound is well reproduced by a deterministic dynamical model.
ADAPTIVE SYNCHRONIZATION OF CHUA'S OSCILLATORS
Authors: CHUA LEON O. , YANG TAO , ZHONG GUO-QUN , WU CHAI WAH
Published: November 2004

In this letter, we study the use of adaptive controllers to maintain the synchronization of two Chua's oscillators when the channel and circuit parameters are time-varying. We present both computer simulation results and physical experimental results to verify the operation of the designs.
CLASSICAL SOLVABILITY AND UNIFORM ESTIMATES FOR THE STEADY STOKES SYSTEM IN DOMAINS WITH NONCOMPACT BOUNDARIES
Authors: PILECKAS K.
Published: November 2004

The stationary Stokes equations of a viscous incompressible fluid are considered in domains Ω with m > 1 outlets to infinity, which have in some coordinate system the following form [Formula: see text] where gi are functions satisfying the global Lipschitz condition and g'i (xn) → 0 as xn → ∞. In this paper we prove the solvability of the Stokes system with prescribed fluxes in weighted Hölder spaces and we show the pointwise decay of the solutions.
STUDY OF THE LIMIT BEHAVIOR OF A VISCOELASTIC MEDIUM WITH VERY SMALL OBSTACLES
Authors: CHALLAL S. , PAULIN J. SAINT JEAN
Published: November 2004

We study the asymptotic behavior of a viscous, barotropic and compressible fluid in a porous medium Ωε, (ε > 0) obtained by removing from an open set Ω some small obstacles [Formula: see text] with size aε ≪ ε. We establish that the fluid behaves differently depending on whether the size aε is greater than or smaller than a critical size cε. If it is greater than or equal to cε a convolution term appears in the limit problem. This corresponds to a long memory effect. On the contrary, if the size is smaller than cε, the fluid behaves as if there is no obstacle.
FINITE ELEMENT METHODS FOR THE PARABOLIC EQUATION WITH INTERFACES
Authors: DOUGALIS VASSILIOS A. , KAMPANIS NIKOLAOS A.
Published: November 2004

We consider the standard parabolic approximation of underwater acoustics in a medium consisting of fluid layers with depth- and range-dependent speed of sound and dissipation coefficients. In the case of horizontal layers we construct two types of finite element discretizations in the depth variable which treat the interfaces in different ways. We couple these methods with conservative Crank–Nicolson and implicit Runge–Kutta schemes in the range variable and analyze the stability and convergence of the resulting fully discrete methods. Using a change of variable technique, we show how these schemes may be extended to treat interfaces with range-dependent topography; we also couple them with a nonlocal ('impedance') bottom boundary condition. The methods are applied to several benchmark problems in the literature and their results are compared to those obtained from standard numerical codes.
Effects of the gap junction blocker glycyrrhetinic acid on gastrointestinal smooth muscle cells
Authors: Takeda Yukari , Ward Sean M. , Sanders Kenton M. , Koh Sang Don
Published: November 2004

In the tunica muscularis of the gastrointestinal (GI) tract, gap junctions form low-resistance pathways between pacemaker cells known as interstitial cells of Cajal (ICCs) and between ICC and smooth muscle cells. Coupling via these junctions facilitates electrical slow-wave propagation and responses of smooth muscle to enteric motor nerves. Glycyrrhetinic acid (GA) has been shown to uncouple gap junctions, but previous studies have shown apparent nonspecific effects of GA in a variety of tissues. We tested the effects of GA using isometric force measurements, intracellular microelectrode recordings, the patch-clamp technique, and the spread of Lucifer yellow within cultured ICC networks. In murine small intestinal muscles, β-GA (10 μM) decreased phasic contractions and depolarized resting membrane potential. Preincubation of GA inhibited the spread of Lucifer yellow, increased input resistance, and decreased cell capacitance in ICC networks, suggesting that GA uncoupled ICCs. In patch-clamp experiments of isolated jejunal myocytes, GA significantly decreased L-type Ca2+ current in a dose-dependent manner without affecting the voltage dependence of this current. The IC50 for Ca2+ currents was 1.9 μM, which is lower than the concentrations used to block gap junctions. GA also significantly increased large-conductance Ca2+-activated K+ currents but decreased net delayed rectifier K+ currents, including 4-aminopyridine and tetraethylammonium-resistant currents. In conclusion, the reduction of phasic contractile activity of GI muscles by GA is likely a consequence of its inhibitory effects on gap junctions and voltage-dependent Ca2+ currents. Membrane depolarization may be a consequence of uncoupling effects of GA on gap junctions between ICCs and smooth muscles and inhibition of K+ conductances in smooth muscle cells.
Metabolic and vascular support for the role of myoglobin in humans: a multiparametric NMR study
Authors: Duteil S. , Bourrilhon C. , Raynaud J. S. , Wary C. , Richardson R. S. , Leroy-Willig A. , Jouanin J. C. , Guezennec C. Y. , Carlier P. G.
Published: November 2004

In human muscle the role of myoglobin (Mb) and its relationship to factors such as muscle perfusion and metabolic capacity are not well understood. We utilized nuclear magnetic resonance (NMR) to simultaneously study the Mb concentration ([Mb]), perfusion, and metabolic characteristics in calf muscles of athletes trained long term for either sprint or endurance running after plantar flexion exercise and cuff ischemia. The acquisitions for 1H assessment of Mb desaturation and concentration, arterial spin labeling measurement of muscle perfusion, and 31P spectroscopy to monitor high-energy phosphate metabolites were interleaved in a 4-T magnet. The endurance-trained runners had a significantly elevated [Mb] (0.28 ± 0.06 vs. 0.20 ± 0.03 mmol/kg). The time constant of creatine rephosphorylation (τPCr), an indicator of oxidative capacity, was both shorter in the endurance-trained group (34 ± 6 vs. 64 ± 20 s) and negatively correlated with [Mb] across all subjects ( r = 0.58). The time to reach maximal perfusion after cuff release was also both shorter in the endurance-trained group (306 ± 74 vs. 560 ± 240 s) and negatively correlated with [Mb] ( r = 0.56). Finally, Mb reoxygenation rate tended to be higher in the endurance-trained group and was positively correlated with τPCr ( r = 0.75). In summary, these NMR data reveal that [Mb] is increased in human muscle with a high oxidative capacity and a highly responsive vasculature, and the rate at which Mb resaturates is well correlated with the rephosphorylation rate of Cr, each of which support a teleological role for Mb in O2 transport within highly oxidative human skeletal muscle.