bluuebunny/crossref_metadata_2025 huggingface dataset:
A longevity assurance gene homolog of tomato mediates resistance to
Alternaria alternata
f. sp.
lycopersici
toxins and fumonisin B
1
Authors: Brandwagt Bas F. , Mesbah Laurent A. , Takken Frank L. W. , Laurent Pascal L. , Kneppers Tarcies J. A. , Hille Jacques , Nijkamp H. John J.
Published: July 2002

The phytopathogenic fungus
Alternaria alternata
f. sp. lycopersici (AAL) produces toxins that are essential for pathogenicity of the fungus on tomato (
Lycopersicon
esculentum
). AAL toxins and fumonisins of the unrelated fungus
Fusarium moniliforme
are sphinganine-analog mycotoxins (SAMs), which cause inhibition of sphingolipid biosynthesis
in vitro
and are toxic for some plant species and mammalian cell lines. Sphingolipids can be determinants in the proliferation or death of cells. We investigated the tomato
A
lternaria
s
tem
c
anker (
Asc
) locus, which mediates resistance to SAM-induced apoptosis. Until now, mycotoxin resistance of plants has been associated with detoxification and altered affinity or absence of the toxin targets. Here we show that SAM resistance of tomato is determined by
Asc-1
, a gene homologous to the yeast longevity assurance gene
LAG1
and that susceptibility is associated with a mutant
Asc-1
. Because both sphingolipid synthesis and
LAG1
facilitate endocytosis of glycosylphosphatidylinositol-anchored proteins in yeast, we propose a role for
Asc-1
in a salvage mechanism of sphingolipid-depleted plant cells.
Nucleocytoplasmic Recycling of the Nuclear Localization Signal Receptor α Subunit In Vivo Is Dependent on a Nuclear Export Signal, Energy, and RCC1
Authors: Boche Irene , Fanning Ellen
Published: July 2002

Nuclear protein import requires a nuclear localization signal (NLS) receptor and at least three other cytoplasmic factors. The α subunit of the NLS receptor, Rag cohort 1 (Rch1), enters the nucleus, probably in a complex with the β subunit of the receptor, as well as other import factors and the import substrate. To learn more about which factors and/or events end the import reaction and how the import factors return to the cytoplasm, we have studied nucleocytoplasmic shuttling of Rch1 in vivo. Recombinant Rch1 microinjected into Vero or tsBN2 cells was found primarily in the cytoplasm. Rch1 injected into the nucleus was rapidly exported in a temperature-dependent manner. In contrast, a mutant of Rch1 lacking the first 243 residues accumulated in the nuclei of Vero cells after cytoplasmic injection. After nuclear injection, the truncated Rch1 was retained in the nucleus, but either Rch1 residues 207–217 or a heterologous nuclear export signal, but not a mutant form of residues 207–217, restored nuclear export. Loss of the nuclear transport factor RCC1 (regulator of chromosome condensation) at the nonpermissive temperature in the thermosensitive mutant cell line tsBN2 caused nuclear accumulation of wild-type Rch1 injected into the cytoplasm. However, free Rch1 injected into nuclei of tsBN2 cells at the nonpermissive temperature was exported. These results suggested that RCC1 acts at an earlier step in Rch1 recycling, possibly the disassembly of an import complex that contains Rch1 and the import substrate. Consistent with this possibility, incubation of purified RanGTP and RCC1 with NLS receptor and import substrate prevented assembly of receptor/substrate complexes or stimulated their disassembly.
An Oligodendrocyte Cell Adhesion Molecule at the Site of Assembly of the Paranodal Axo-Glial Junction
Authors: Tait Steven , Gunn-Moore Frank , Collinson J. Martin , Huang Jeffery , Lubetzki Catherine , Pedraza Liliana , Sherman Diane L. , Colman David R. , Brophy Peter J.
Published: July 2002

Two major isoforms of the cell adhesion molecule neurofascin NF186 and NF155 are expressed in the central nervous system (CNS). We have investigated their roles in the assembly of the node of Ranvier and show that they are targeted to distinct domains at the node. At the onset of myelination, NF186 is restricted to neurons, whereas NF155 localizes to oligodendrocytes, the myelin-forming glia of the CNS. Coincident with axon ensheathment, NF155 clusters at the paranodal regions of the myelin sheath where it localizes in apposition to the axonal adhesion molecule paranodin/contactin-associated protein (Caspr1), which is a constituent of the septate junction-like axo-glial adhesion zone. Immunoelectron microscopy confirmed that neurofascin is a glial component of the paranodal axo-glial junction. Concentration of NF155 with Caspr1 at the paranodal junctions of peripheral nerves is also a feature of Schwann cells. In Shiverer mutant mice, which assemble neither compact CNS myelin nor normal paranodes, NF155 (though largely retained at the cell body) is also distributed at ectopic sites along axons, where it colocalizes with Caspr1. Hence, NF155 is the first glial cell adhesion molecule to be identified in the paranodal axo-glial junction, where it likely interacts with axonal proteins in close association with Caspr1.
Biogenesis of the Protein Storage Vacuole Crystalloid
Authors: Jiang Liwen , Phillips Thomas E. , Rogers Sally W. , Rogers John C.
Published: July 2002

We identify new organelles associated with the vacuolar system in plant cells. These organelles are defined biochemically by their internal content of three integral membrane proteins: a chimeric reporter protein that moves there directly from the ER; a specific tonoplast intrinsic protein; and a novel receptor-like RING-H2 protein that traffics through the Golgi apparatus. Highly conserved homologues of the latter are expressed in animal cells. In a developmentally regulated manner, the organelles are taken up into vacuoles where, in seed protein storage vacuoles, they form a membrane-containing crystalloid. The uptake and preservation of the contents of these organelles in vacuoles represents a unique mechanism for compartmentalization of protein and lipid for storage.
Diacylglycerol Kinase ζ Regulates Ras Activation by a Novel Mechanism
Authors: Topham Matthew K. , Prescott Stephen M.
Published: July 2002

Guanine nucleotide exchange factors (GEFs) activate Ras by facilitating its GTP binding. Ras guanyl nucleotide-releasing protein (GRP) was recently identified as a Ras GEF that has a diacylglycerol (DAG)-binding C1 domain. Its exchange factor activity is regulated by local availability of signaling DAG. DAG kinases (DGKs) metabolize DAG by converting it to phosphatidic acid. Because they can attenuate local accumulation of signaling DAG, DGKs may regulate RasGRP activity and, consequently, activation of Ras. DGKζ, but not other DGKs, completely eliminated Ras activation induced by RasGRP, and DGK activity was required for this mechanism. DGKζ also coimmunoprecipitated and colocalized with RasGRP, indicating that these proteins associate in a signaling complex. Coimmunoprecipitation of DGKζ and RasGRP was enhanced in the presence of phorbol esters, which are DAG analogues that cannot be metabolized by DGKs, suggesting that DAG signaling can induce their interaction. Finally, overexpression of kinase-dead DGKζ in Jurkat cells prolonged Ras activation after ligation of the T cell receptor. Thus, we have identified a novel way to regulate Ras activation: through DGKζ, which controls local accumulation of DAG that would otherwise activate RasGRP.
A subset of dynamic actin rearrangements in Drosophila requires the Arp2/3 complex
Authors: Hudson Andrew M. , Cooley Lynn
Published: July 2002

The Arp2/3 complex has been shown to dramatically increase the slow spontaneous rate of actin filament nucleation in vitro, and it is known to be important for remodeling the actin cytoskeleton in vivo. We isolated and characterized loss of function mutations in genes encoding two subunits of the Drosophila Arp2/3 complex: Arpc1, which encodes the homologue of the p40 subunit, and Arp3, encoding one of the two actin-related proteins. We used these mutations to study how the Arp2/3 complex contributes to well-characterized actin structures in the ovary and the pupal epithelium. We found that the Arp2/3 complex is required for ring canal expansion during oogenesis but not for the formation of parallel actin bundles in nurse cell cytoplasm and bristle shaft cells. The requirement for Arp2/3 in ring canals indicates that the polymerization of actin filaments at the ring canal plasma membrane is important for driving ring canal growth.
Integrin αMβ2-Mediated Cell Migration to Fibrinogen and Its Recognition Peptides
Authors: Forsyth Christopher B. , Solovjov Dmitry A. , Ugarova Tatiana P. , Plow Edward F.
Published: July 2002

Leukocyte migration is the hallmark of inflammation, and integrin αMβ2 and its ligand fibrinogen (Fg) are key participants in this cellular response. Cells expressing wild-type or mutant αMβ2 and Fg or its derivatives have been used to dissect the molecular requirements for this receptor–ligand pair to mediate cell migration. The major conclusions are that (a) Fg, its D fragment, and its P1 and P2 αMβ2 recognition peptides support a chemotactic response; (b) when the I domain of αL was replaced with the I domain of αM, the chimeric receptor supported cell migration to Fg; however, the αM subunit, containing the I domain but lacking the β2 subunit, supported migration poorly, thus, the αMI domain is necessary but not sufficient to support chemotaxis, and efficient migration requires the β2 subunit and αMI domain; and (c) in addition to supporting cell migration, P2 enhanced αMβ2-mediated chemotaxis to Fg and the P1 peptide. This activation was associated with exposure of the activation-dependent epitope recognized by monoclonal antibody 7E3 and was observed also with human neutrophils. Taken together, these data define specific molecular requirements for αMβ2 to mediate cell migration to Fg derivatives and assign a novel proinflammatory activity to the P2 peptide.
Construction of local 𝐶¹ quartic spline elements for optimal-order approximation
Authors: Chui Charles , Hong Dong
Published: July 2002

This paper is concerned with a study of approximation order and construction of locally supported elements for the space

S
4
1

(
Δ
)

S_4^1(\Delta )

of

C
1

C^1

p
p

pp

(piecewise polynomial) functions on an arbitrary triangulation

Δ
\Delta

of a connected polygonal domain

Ω
\Omega

in

R

2

\Bbb R^2

. It is well known that even when

Δ
\Delta

is a three-directional mesh

Δ

(
1
)

\Delta ^{(1)}

, the order of approximation of

S
4
1

(

Δ

(
1
)

)

S_4^1(\Delta ^{(1)})

is only 4, not 5. The objective of this paper is two-fold: (i) A local Clough-Tocher refinement procedure of an arbitrary triangulation

Δ
\Delta

is introduced so as to yield the optimal (fifth) order of approximation, where locality means that only a few isolated triangles need refinement, and (ii) locally supported Hermite elements are constructed to achieve the optimal order of approximation.
Computing all power integral bases in orders of totally real cyclic sextic number fields
Authors: Gaál István
Published: July 2002

An algorithm is given for determining all power integral bases in orders of totally real cyclic sextic number fields. The orders considered are in most cases the maximal orders of the fields. The corresponding index form equation is reduced to a relative Thue equation of degree 3 over the quadratic subfield and to some inhomogeneous Thue equations of degree 3 over the rationals. At the end of the paper, numerical examples are given.
TheDrosophilaNuclear Lamina Protein YA Binds to DNA and Histone H2B with Four Domains
Authors: Yu Jing , Wolfner Mariana F.
Published: July 2002

Dramatic changes occur in nuclear organization and function during the critical developmental transition from meiosis to mitosis. TheDrosophila nuclear lamina protein YA binds to chromatin and is uniquely required for this transition. In this study, we dissected YA's binding to chromatin. We found that YA can bind to chromatin directly and specifically. It binds to DNA but not RNA, with a preference for double-stranded DNA (linear or supercoiled) over single-stranded DNA. It also binds to histone H2B. YA's binding to DNA and histone H2B is mediated by four domains distributed along the length of the YA molecule. A model for YA function at the end ofDrosophila female meiosis is proposed.
Spindle Checkpoint Requires Mad1-bound and Mad1-free Mad2
Authors: Chung Eunah , Chen Rey-Huei
Published: July 2002

The spindle checkpoint prevents anaphase from occurring until all chromosomes have attached properly to the mitotic spindle. The checkpoint components Mad1 and Mad2 associate with unattached kinetochores and are probably involved in triggering the checkpoint. We now demonstrate that in Xenopus egg extracts Mad1 and Mad2 form a stable complex, whereas a fraction of Mad2 molecules is not bound to Mad1. The checkpoint establishment and maintenance are lost upon titrating out free Mad2 with an excess of Mad1 or a truncated Mad1 (amino acids 326–718, Mad1C) that contains the Mad2-binding region. Mad1N (amino acids 1–445) that binds kinetochores, but not Mad2, reduces Mad1 and Mad2 at kinetochores and abolishes checkpoint maintenance. Furthermore, the association between Mad2 and Cdc20, the activator for the anaphase-promoting complex, is enhanced under checkpoint-active condition compared with that at metaphase. Immunodepletion analysis shows that the Mad1-free Mad2 protein is unable to bind Cdc20, consistent with the model that kinetochore localization of Mad2 facilitates the formation of Mad2–Cdc20 complex. This study demonstrates that the ratio between Mad1 and Mad2 is critical for maintaining a pool of Mad1-free Mad2 that is necessary for the spindle checkpoint. We propose that Mad2 may become activated and dissociated from Mad1 at kinetochores and is replenished by the pool of Mad1-free Mad2.
A systematic approach to dynamic programming in bioinformatics
Authors: Giegerich Robert
Published: July 2002

Motivation: Dynamic programming is probably the most popular programming method in bioinformatics. Sequence comparison, gene recognition, RNA structure prediction and hundreds of other problems are solved by ever new variants of dynamic programming. Currently, the development of a successful dynamic programming algorithm is a matter of experience, talent and luck. The typical matrix recurrence relations that make up a dynamic programming algorithm are intricate to construct, and difficult to implement reliably. No general problem independent guidance is available.

Results: This article introduces a systematic method for constructing dynamic programming solutions to problems in biosequence analysis. By a conceptual splitting of the algorithm into a recognition and an evaluation phase, algorithm development is simplified considerably, and correct recurrences can be derived systematically. Without additional effort, the method produces an early, executable prototype expressed in a functional programming language. The method is quite generally applicable, and, while programming effort decreases, no overhead in terms of ultimate program efficiency is incurred.

Contact: robert@techfak.uni-bielefeld.de

Work partially supported by a grant from the Australian National University.
Characterization of the folding degree of proteins
Authors: Estrada Ernesto
Published: July 2002

Motivation: The characterization of the folding degree of chains is central to the elucidation of structure--function relationships in proteins. Here we present a new index for characterizing the folding degree of a (protein) chain. This index shows a range of features that are desirable for the study of the relation between structure and function in proteins.

Results: A novel index characterizing the folding degree of (protein) chains is developed based on the spectral moments of a matrix representing the dihedral angles (φ, ω and ε) of the protein main chain. The proposed index is normalized to the chain size, is not correlated to the gyration radius of the backbone chain and is able to distinguish between structures for which the sum of the main-chain dihedral angles is identical. The index is well correlated to the percentages of helix and strand in proteins, shows a linear dependence with temperature changes, and is able to differentiate among protein families.

Availability: On request from the author.

Contact: estrada66@yahoo.com
Presynaptic mitochondria and the temporal pattern of neurotransmitter release
Authors: Brodin Lennart , Bakeeva Lora , Shupliakov Oleg
Published: July 2002

Mitochondria are critical for the function of nerve terminals as the cycling of synaptic vesicle membrane requires an efficient supply of ATP. In addition, the presynaptic mitochondria take part in functions such as Ca
2+
buffering and neurotransmitter synthesis. To learn more about presynaptic mitochondria, we have examined their organization in two types of synapse in the lamprey, both of which are glutamatergic but are adapted to different temporal patterns of activity. The first is the giant lamprey reticulospinal synapse, which is specialized to transmit phasic signals (i.e. bursts of impulses). The second is the synapse established by sensory dorsal column axons, which is adapted to tonic activity. In both cases, the presynaptic axons were found to contain two distinct types of mitochondria; small ‘synaptic’ mitochondria, located near release sites, and larger mitochondria located in more central parts of the axon. The size of the synapse–associated mitochondria was similar in both types of synapse. However, their number differed considerably. Whereas the reticulospinal synapses contained only single mitochondria within 1 micrometre distance from the edge of the active zone (on average 1.2 per active zone, range of 1–3), the tonic dorsal column synapses were surrounded by clusters of mitochondria (4.5 per active zone, range of 3–6), with individual mitochondria sometimes apparently connected by intermitochondrial contacts. In conjunction with studies of crustacean neuromuscular junctions, these observations indicate that the temporal pattern of transmitter release is an important determinant of the organization of presynaptic mitochondria.
An ancestral nuclear protein assembly: Crystal structure of the Methanopyrus kandleri histone
Authors: Fahrner Richard L. , Cascio Duilio , Lake James A. , Slesarev Alexei
Published: July 2002

Eukaryotic histone proteins condense DNA into compact structures called nucleosomes. Nucleosomes were viewed as a distinguishing feature of eukaryotes prior to ideication of histone orthologs in methanogens. Although evolutionarily distinct from methanogens, the methane‐producing hyperthermophile Methanopyrus kandleri produces a novel, 154‐residue histone (HMk). Amino acid sequence comparisons show that HMk differs from both methanogenic and eukaryotic histones, in that it contains two histone‐fold ms within a single chain. The two HMk histone‐fold ms, N and C terminal, are 28% identical in amino acid sequence to each other and ∼21% identical in amino acid sequence to other histone proteins. Here we present the 1.37‐Å‐resolution crystal structure of HMk and report that the HMk monomer structure is homologous to the eukaryotic histone heterodimers. In the crystal, HMk forms a dimer homologous to [H3–H4]2 in the eukaryotic nucleosome. Based on the spatial similarities to structural ms found in the eukaryotic nucleosome that are important for DNA‐binding, we infer that the Methanopyrus histone binds DNA in a manner similar to the eukaryotic histone tetramer [H3–H4]2.
Development of a computer‐aided diagnosis system for chest x‐ray helical CT images (in Japanese)
Authors: Lee Yongbum
Published: July 2002

A computerized detection scheme of lung nodules in helical x‐ray CT images was developed for computer‐aided diagnosis (CAD) systems. We propose a novel template‐matching technique based on a genetic algorithm (GA template matching) for detecting nodules existing within the lung area; the GA was used to determine the target position in the observed image efficiently and to select an adequate template image from several reference patterns for quick template matching. In addition, a conventional template matching was employed to detect nodules existing on the lung wall area (lung wall template matching), where semicircular models were used as reference patterns; the semicircular models were rotated according to the angle of the target point on the contour of the lung wall. After initial detection of candidates using the two template‐matching methods, we extracted a total of 13 feature values and used them to eliminate false–positive findings. Twenty clinical cases involving a total of 557 sectional images were used in this study. Seventy‐one nodules out of 98 were correctly detected by our scheme (i.e., a detection rate of about 72%), with the number of false positives at approximately 1.1 per sectional image. An application of the CAD system for helical CT images with graphic user interface was developed.
Self‐absorption correction for and stents: Dose point kernel calculations versus Monte Carlo
Authors: Reynaert N. , Häfeli U. O.
Published: July 2002

Monte Carlo simulations of dose distributions around radioactive stents are very time intensive. Thus, in order to calculate the dose distribution around a stent, we chose to test a point kernel method, a method which is known to be faster but the accuracy of which has not been established for this application. The dose point kernel method, which takes into account absorption in the strut material was based on different beta‐emitting point source distributions in water by itself and surrounded by steel spheres of different thicknesses. This information was input into an integration routine that modeled either a Palmaz–Schatz or Multilink stent. The dose distributions around and stents calculated with the dose point kernel method were compared to those calculated using EGS4 and MCNP 4B Monte Carlo methods. The resulting correction for self‐absorption in steel was distance dependent and averaged 1.12 for and 1.25 for stents. The dose point kernel method gave nearly identical results to these full Monte Carlo simulations and was thus used to calculate the dose distributions around a stent. Although has a half‐life of only 17 hours, it is posited to be useful for radioactive restenosis prevention, given that a recently developed rapid electrodeposition procedure allows stents to be made radioactive, at predetermined activities, within 15 minutes. The dose point kernel calculations of a ‐coated Multilink stent were compared to its radiochromic film measurements. The dose fall‐off agreed with the calculations within 5% over 0.4 to 3.5 mm from the stent surface. The dose point kernel method is a valuable tool to determine depth dose distributions around activated stents taking into account the detailed geometry and the self‐absorption in the struts. It not only requires much less processing time than Monte Carlo methods, but also allows the use of higher resolutions in modeling the geometry, which leads to more accurate self‐absorption correction factors.
A method for measuring the ionization fraction due to the chamber wall (α) and assessing its characteristics
Authors: Kappas C. , Rosenwald J. C. , Panitsa E.
Published: July 2002

To calibrate a megavoltage therapy beam using an ionization chamber, it is necessary to know the fraction of the ionization arising in the chamber wall when this is made of a material different than the medium. A method for measuring the ionization fraction produced by electrons arising in the chamber wall (α) is presented here. The method uses three measurements at the same point in a medium in order to calculate α. These measurements are made using the examined chamber with and without a buildup cap and one reference chamber of wall material equivalent to the medium (i.e., in our case, Al and A‐150 were used as wall materials for the examined and the reference chamber, respectively). Using this method, it is possible to calculate α in the medium for a series of irradiation conditions and assess its characteristics. Two main conclusions came out of this assessment. The first one is the independence of α from the wall material, even if this is aluminum (α is only dependent on wall thickness expressed in ). The second one is that α depends on the irradiation conditions; it increases with field size and depth.
Evaluation of three contrast correction methods for digital subtraction in dental radiography: An in vitro study
Authors: Likar Boštjan , Pernuš Franjo
Published: July 2002

In the present in vitro study we test the efficacy of three most often used contrast correction methods to reduce contrast mismatches that can adversely affect digital subtraction in dental radiography. Five radiographs of the lower molars of a beagle dog with an included reference aluminium wedge were radiographed with different exposure times, captured by a monochrome CCD video camera and digitized. To study only the contrast correction effects, the influences of projective geometry and physical noise from the camera and the analog‐to‐digital conversion were eliminated by simulating bone loss in digital copies of the five reference radiographic images. Each copy in which loss was simulated was contrast corrected by all methods and subtracted from its original image. Four parameters were defined to test the potential of a method to correct grey level values between two images without corrupting real changes. The ODTF (optical density thickness function) method, which is based on a function relating grey level values of the aluminium wedge image and the corresponding thicknesses of the wedge, induced less contrast correction error than the CDF (cumulative density function) and the LSQA (least square quadratic approximation) methods. Therefore, the ODTF method may detect more subtle changes than the other two methods. The experiments indicate that less error is induced by a contrast correction method which uses a grey level mapping function based on the density distribution in a region representing a reference structure. Moreover, CDF, ODTF, and LSQA functions obtained from the reference structure density distribution may be applied for objective contrast enhancements and for standardization of image quality, while the ODTF function also allows bone change volume estimations.
Application of the scaling factor method to estimation of beta dose distributions for dissimilar media separated by a planar interface
Authors: Marcu Silviu M. , Prestwich William V.
Published: July 2002

The most accurate method of calculating beta dose distribution currently relies on the Monte Carlo technique. The major drawback of the method is the long computing time required to follow a large number of “electron histories” in order to achieve good statistics, which makes the method unattractive for practical radiation therapy. A way to avoid the Monte Carlo calculations for homogeneous media was suggested by Cross and co‐workers (AECL Report Nos. 7617, 1982; 10521, 1992), and is known as the “scaling factor” method. It consists of the determination of the depth dose distribution in a medium based on known data about the dose distribution in an arbitrary reference medium (e.g., air, water) by the use of a scaling factor on distance and a closely related renormalization factor imposed by energy conservation. This work is an attempt to extend the applicability of the scaling factor method to dissimilar media to a planar interface. The investigation was done for an isotropic source of the radioisotope and an interface between water and medium “i,” where medium “i” could be any medium with atomic number in the range The method was checked using three randomly chosen elements and each forming planar interfaces with water at either 100 or Discrepancies of less than 5% were detected (acceptable for practical radiotherapy) for the depth within which at least 95% of the initial energy is deposited.
Improvement of the fluorine‐18 fluorodeoxyglucose images in simultaneous F‐18 FDG/Tc‐99m collimated spect imaging
Authors: Knešaurek Karin , Machac Josef
Published: July 2002

Collimated F‐18 FDG SPECT imaging has been shown to be an acceptable alternative to F‐18 FDG PET imaging for evaluating injured but viable myocardium. Ultra‐high‐energy (UHE) imaging is usually performed in simultaneous F‐18 FDG/Tc‐99m MIBI studies. The main limitations of this technique are degradation of the Tc‐99m MIBI images due to F‐18 downscatter to the Tc‐99m window, and loss of resolution in Tc‐99m images caused by using a UHE rather than a low‐energy collimator. The quality of F‐18 images has not been addressed. In our clinical and phantom studies we have found that F‐18 images are inferior to simultaneously acquired Tc‐99m MIBI images. This paper compares two correction methods for F‐18 FDG images in a realistic cardiac phantom study. One approach is subtractive scatter correction, which employs a third 410 keV energy window image to estimate scatter. The other approach is based on restoration. The phantom acquisition was performed with 7.2 MBq of F‐18 and 22.2 MBq of Tc‐99m injected into the left ventricular (LV) wall. Three inserts, 3 cm, 2 cm, and 1 cm in diameter, were placed in the LV wall to simulate infarcts. Circumferential profiles were drawn from three successive short‐axis slices and compared with true phantom data. The differences were calculated as root‐mean‐square error (rmse). Scatter correction improved rmse only while restoration improved rmse when compared with raw data. The same differences, measured as rmse, were and for raw, scatter corrected, and restored F‐18 data, respectively, when compared with Tc‐99m window 140 keV data. The amount of noise, measured as root‐mean‐square % (rms%) was for the Tc‐99m image, for the F‐18 restored image, for the raw F‐18 image, and for the scatter corrected F‐18 image. The contrast measured for 2 cm and 3 cm inserts was and for F‐18 raw data, and for the scatter corrected F‐18 image, and and for the restored F‐18 image. The contrast was and for the Tc‐99m 140 keV window image. The restoration approach provided F‐18 images of better contrast and detectibility than uncorrected or scatter corrected F‐18 images. Restored F‐18 images match better with the simultaneously acquired Tc‐99m images.
Optimization of inverse treatment planning using a fuzzy weight function
Authors: Li Rui‐Ping , Yin Fang‐Fang
Published: July 2002

A fuzzy approach has been applied to inverse treatment planning optimization in radiation therapy. The proposed inverse‐planning algorithm optimizes both the intensity‐modulated beam (IMB) and the normal tissue prescription. In the IMB optimization, we developed a fast‐monotonic‐descent (FMD) method that has the property of fast and monotonic convergence to the minimum for a constrained quadratic objective function. In addition, a fuzzy weight function is employed to express the vague knowledge about the importance of matching the calculated dose to the prescribed dose in the normal tissue. Then, a validity function is established to optimize the normal tissue prescription. The performance of this new fuzzy prescription algorithm has been compared to that based on hard prescription methods for two treatment geometries. The FMD method presented here both provides a full‐analytical solution to the optimization of intensity‐modulated beams, and guarantees fast and monotonic convergence to the minimum. It has been shown that the fuzzy inverse planning technique is capable of achieving an optimal balance between the objective of matching the calculated dose to the prescribed dose for the target volume and the objective of minimizing the normal tissue dose.
A gain nonuniformity correction for multislice volumetric CT scanners
Authors: Besson Guy , Hu Hui , Xie Min , He David , Seidenschnur George , Bromberg Neil
Published: July 2002

This paper presents a calibration and correction method for detector cell gain variations. A key functionality of current CT scanners is to offer variable slice thickness to the user. To provide this capability in multislice volumetric scanners, while minimizing costs, it is necessary to combine the signals of several detector cells in when the desired slice thickness is larger than the minimum provided by a single cell. These combined signals are then pre‐amplified, digitized, and transmitted to the system for further processing. The process of combining the output of several detector cells with nonuniform gains can introduce numerical errors when the impinging x‐ray signal presents a variation along over the range of combined cells. These numerical errors, which by nature are scan dependent, can lead to artifacts in the reconstructed images, particularly when the numerical errors vary from channel‐to‐channel (as the filtered‐backprojection filter includes a high‐pass filtering along the channel direction, within a given slice). A projection data correction algorithm has been developed to subtract the associated numerical errors. It relies on the ability of calibrating the individual cell gains. For effectiveness and data flow reasons, the algorithm works on a single slice basis, without slice‐to‐slice exchange of information. An initial error vector is calculated by applying a high‐pass filter to the projection data. The essence of the algorithm is to correlate that initial error vector, with a calibration vector obtained by applying the same high‐pass filter to various combinations of the cell gains (each combination representing a basis function for a expansion). The solution of the least‐square problem, obtained via singular value decomposition, gives the coefficients of a polynomial expansion of the signal slope and curvature. From this information, and given the cell gains, the final error vector is calculated and subtracted from the projection data.
Truncation of blood curves to enhance imaging and therapy with monoclonal antibodies
Authors: Williams Lawrence E. , Liu An , Wu Anna M. , Yazaki Paul J. , Yamauchi Dave M. , Lopatin George , Raubitschek Andrew A. , Wong Jeffrey Y. C.
Published: July 2002

Targeting of monoclonal antibody (Mab) to solid tumor sites is a function of the blood curve of activity versus time. It has been suggested that the blood curve be artificially reduced to approach zero so that the contrast between tumor and blood uptake is maximized. We analyzed tumor uptake as a function of the time of blood curve truncation. By using a convolution approach, we were able to find the optimal times for setting the blood curve to zero in either diagnostic or therapeutic animal examples. Two iodinated anti‐CEA engineered fragments, diabody and minibody, were considered using previous data from nude mouse studies involving the LS174T colorectal tumor model. Figures of merit (FOMs) were used to compare ordinary and truncated blood curves and their associated tumor accumulations. Using a label, it was seen that the appropriate time for diagnostic truncation occurred when tumor uptake, as measured, was a maximum. The corresponding point for therapy (with as a label) was at infinite time. We also demonstrated that the use of traditional indices led to ambiguities in the choice of truncation times. The traditional therapy index, the ratio of the integral of the tumor uptake to the integral of the blood uptake, was found to be a numerical constant independent of This ratio was proved to be the integral of the tumor impulse response function. Use of such convolution techniques to assess truncation of the perfused material is probably also applicable to multistep processes as well as to lesion targeting with other tumor‐specific pharmaceuticals.
Enhancing electromagnetism experiments with clamp-on ammeters
Authors: Henry Dennis C.
Published: July 2002

Experiments designed to illustrate the principles embodied in Ampere’s Law and Faraday’s Law often depend on the knowledge of the number of turns of wire on various types of laboratory coils. The lack of direct measurement of this parameter can be overcome with the use of inexpensive (<$85) digital clamp-on ammeters. The meters themselves illustrate the connection between the current enclosed by a closed path and the line integral of the magnetic intensity H around that contour. In this paper we present laboratory exercises that make essential use of clamp-on ammeters.
Generating a fractal using a capacitor
Authors: Tufillaro Nicholas B.
Published: July 2002

Digital communications systems often drive electronic circuits with signals that generate fractals. This paper describes a simple example, a triangular wave form executing a random walk applied to a circuit consisting of a capacitor and a resistor is used to generate a Cantor “middle third” set. This example can be used as part of a physics demonstration or an introductory lab.
Causality, the Coulomb field, and Newton’s law of gravitation
Authors: Rohrlich F.
Published: July 2002

Causality in classical field theories must be inserted by hand by choosing the retarded solution. It is shown how apparent contradictions in the Coulomb gauge can be resolved and that a causal Coulomb field exists despite the appearance to the contrary. Similarly, it is shown how Newtonian gravitation leads from action-at-a-distance to a causal field when a first-order correction for space–time curvature is applied.
Sound speed without entropy
Authors: Morris S. J. S.
Published: July 2002

The propagation speed c of an infinitesimal pressure step is obtained as a compatibility condition on the system of equations derived from the thermal equation of state and balances of mass, momentum, and total energy. Because the entropy is not introduced during the derivation, c is given initially in terms of the pressure, volume υ per unit mass, and derivatives of the internal energy. An identity using only the first law of thermodynamics is then used to show that c=γυKT , where γ is the specific heat ratio, and KT is the isothermal bulk modulus. This derivation differs from existing ones as the entropy is not used to obtain the result for c, but only to interpret it.
Superposition solutions to the Schrödinger equation
Authors: Williams H. Thomas
Published: July 2002

I present a method in the spirit of Green’s functions for generating bound state solutions to the Schrödinger equation. The method is demonstrated by generating ground state and excited state solutions to the one-dimensional, time-independent Schrödinger equation. Its applicability to the radial equation for two and three dimensions is also discussed.
Neutrino oscillations: A relativistic example of a two-level system
Authors: Sassaroli Elisabetta
Published: July 2002

Neutrino flavor oscillations are discussed in terms of an explicit model. This model consists of two coupled Dirac equations with three parameters: the electron neutrino mass, the muon neutrino mass, and a coefficient which describes the possibility that the neutrino can flip flavor. The system is diagonalized to obtain the exact eigenvalues and eigenfunctions. The system is then quantized and the neutrino flavor wave functions are derived directly from the quantized fields. It is shown that neutrino flavor oscillation probabilities are recovered in a quantum field theory treatment only in the ultrarelativistic limit.
A laboratory demonstration of the three-dimensional nature of in-line holography
Authors: Baez Albert V. , Castro George
Published: July 2002

An experiment is described in which two semi-transparent reticles and a photographic plate separated by several centimeters are illuminated by a monochromatic point source in a typical in-line configuration. The resulting shadowgram is a hologram that contains information from both reticles. Illuminating this complex hologram with a similar point source with the reticles removed produces reconstructed real images at two separate locations whose coordinates are predicted from simple theory, and also produces virtual images of the reticles at their original coordinates. This experimentally confirms the three-dimensional capability of an in-line hologram. As imaging devices such as charge-coupled device sensors become cheaper and of higher resolution, a simple demonstration of this aspect of holograms, which can be projected to an audience, can be observed by sliding the image sensor along the axis.
Measuring the interaction force between a high temperature superconductor and a permanent magnet
Authors: Valenzuela S. O. , Jorge G. A. , Rodrı́guez E.
Published: July 2002

Repulsive and attractive forces are both possible between a superconducting sample and a permanent magnet, and they can give rise to magnetic levitation or free-suspension phenomena, respectively. We show experiments to quantify this magnetic interaction, which represents a promising field with regard to short-term technological applications of high temperature superconductors. The measuring technique employs an electronic balance and a rare-earth magnet that induces a magnetic moment in a melt-textured YBa2Cu3O7 superconductor immersed in liquid nitrogen. The simple design of the experiments allows a fast and easy implementation in the advanced physics laboratory with a minimum cost. Actual levitation and suspension demonstrations can be done simultaneously as a help to interpret magnetic force measurements.
Electromagnetic radiation from sinusoidal currents
Authors: Thévenet C.
Published: July 2002

We study the electromagnetic field radiated by high-frequency electric currents in infinite conducting cylinders, with longitudinal or solenoidal flows. We show that the behavior of the radiated fields is very different for radiofrequencies and for higher frequencies. When ωa/c is large (where a is the cylinder radius), the radiated power varies very rapidly as a function of the frequency and is almost zero for certain values.
Mode frequency pulling in He–Ne lasers
Authors: Lindberg Åsa M.
Published: July 2002

In this experiment, the frequency separation between two longitudinal He–Ne laser modes is studied. A description is given of the physics that causes a change in the frequency separation when the modes are observed at various positions in the gain profile. The frequency separation is measured with a fast photodetector in combination with a counter as a function of the mode intensity ratio. The intensity ratio is monitored with a scanning Fabry–Perot interferometer. For a scan of the two modes through the gain profile, a frequency separation change of ∼30 kHz was observed.
Creating a virtual physics department
Authors: Suson Daniel J. , Hewett Lionel D. , McCoy Jim , Nelson Vaughn
Published: July 2002

The number of students graduating from the majority of physics programs throughout the nation is on the order of three students per year per department. This low number represents a problem for those programs that are located at schools which measure success by how many graduates a program creates. This was the problem faced by the physics departments located in three schools in the Texas A&M University System. A solution which alleviated our immediate concerns, and how it is evolving into a “virtual” department, is described.
Measuring the electrical conductivity of the earth
Authors: Avants Brian , Soodak Dustin , Ruppeiner George
Published: July 2002

We describe an undergraduate experiment for measuring the electrical conductivity of the earth with a four-electrode Wenner array, at scales approaching tens of meters. When analyzed in the context of a simple two-layer model of the earth, such measurements yield information about what is underground. In our case, this is the depth of the water table and the electrical conductivity of both the upper dry layer and the lower water-saturated layer. We also performed conductivity measurements in a water tank, to test the theory in a known situation. The experiments are discussed in the context of several boundary value problems in electricity and magnetism.
The form of magnetic work in a fundamental thermodynamic equation for a paramagnet
Authors: Barrett Martin , Macdonald Alan
Published: July 2002

Magnetic work takes two forms in the thermodynamics of a paramagnet as developed in many textbooks. We observe that in the case when the lattice energy is excluded, the form δW=BdM cannot be used in a fundamental thermodynamic equation. This shows that there are thermodynamic systems with no fundamental thermodynamic equation.
Napier’s logarithms
Authors: Bruce Ian
Published: July 2002

The development of Napier’s logarithms is traced from their beginnings in the construction of tables of numbers in geometric progression. These numbers are found using a kinematic model. The equivalent of a first-order differential equation arises. This is integrated numerically to give another set of corresponding numbers (logarithms) in arithmetic progression. The two sets of numbers are presented as a calculating device in the form of tables.
Optical Bloch equations: Informal motivation without the Schrödinger equation
Authors: Supplee James M.
Published: July 2002

We briefly review the classical model of a Lorentz atom interacting with an optical field. We then ask how the equations describing the atom’s behavior should be modified to include atomic energy level quantization. Simply discussing what modifications make sense provides a strong plausibility argument for the optical Bloch equations. Contrasted with the standard derivation, this argument is less rigorous but has a certain pedagogical appeal: It simply assumes two atomic states with energy difference ℏω, rather than invoking the Schrödinger equation. Also, because our goal is more-or-less to guess the correct equations with minimal formalism, this discussion focuses on the physical meaning of the Bloch equations.
Resource Letter IMCF-1: Inertially and magnetically confined fusion
Authors: Post Richard F.
Published: July 2002

This Resource Letter is intended to introduce the reader to the history of fusion research, and to provide references covering the research since its first beginnings and up to the present for those who wish to dig deeper.
Interference fringes from stabilized diode lasers
Authors: Basano Lorenzo , Ottonello Pasquale
Published: July 2002

Interference fringes produced by a pair of intracavity stabilized diode laser beams, each impinging separately on one aperture of a double slit, are recorded on a linear charge-coupled device array. The peculiar result of the experiment is that the fringe system is found to persist for a time of the order of 1 ms and loses contrast for longer integration times. This implies that the individual linewidths of the two beams from the stabilized lasers are narrower than 1 kHz and that the average drift rates of the central peaks are far less than 0.1 MHz/s. The device was built within the advanced undergraduate electronics laboratory of the department of physics and represents a considerable improvement over previous demonstration apparatuses used to detect interference fringes from independent lasers.
A unified model for reverberation and submerged object scattering in a stratified ocean waveguide
Authors: Makris Nicholas C. , Ratilal Purnima
Published: July 2002

A unified model for reverberation and submerged target scattering in a stratified medium is developed from wave theory. The advantage of the unified approach is that it enables quantitative predictions to be made of the target-echo-to-reverberation ratio in an ocean waveguide. Analytic expressions are derived for both deterministic and stochastic scattering from the seafloor and subseafloor. Asymptotic techniques are used to derive expressions for the scattering of broadband waveforms from distant objects or surfaces. Expressions are then obtained for the scattered field after beamforming with a horizontal line array. The model is applied to problems of active detection in shallow water. Sample calculations for narrow-band signals indicate that the detection of submerged target echoes above diffuse seafloor reverberation is highly dependent upon water column and sediment stratification as well as array aperture, source, receiver, and target locations, in addition to the scattering properties of the target and seafloor. The model is also applied to determine the conditions necessary for echo returns from discrete geomorphologic features of the seafloor and subseafloor to stand prominently above diffuse seafloor reverberation. This has great relevance to the geologic clutter problem encountered by active sonar systems operating in shallow water, as well as to the remote sensing of underwater geomorphology.