bluuebunny/crossref_metadata_2025 huggingface dataset:
Cooperative Mechanisms in the Activation Dependence of the Rate of Force Development in Rabbit Skinned Skeletal Muscle Fibers
Authors: Fitzsimons Daniel P. , Patel Jitandrakumar R. , Campbell Kenneth S. , Moss Richard L.
Published: July 2002

Regulation of contraction in skeletal muscle is a highly cooperative process involving Ca2+ binding to troponin C (TnC) and strong binding of myosin cross-bridges to actin. To further investigate the role(s) of cooperation in activating the kinetics of cross-bridge cycling, we measured the Ca2+ dependence of the rate constant of force redevelopment (ktr) in skinned single fibers in which cross-bridge and Ca2+ binding were also perturbed. Ca2+ sensitivity of tension, the steepness of the force-pCa relationship, and Ca2+ dependence of ktr were measured in skinned fibers that were (1) treated with NEM-S1, a strong-binding, non–force-generating derivative of myosin subfragment 1, to promote cooperative strong binding of endogenous cross-bridges to actin; (2) subjected to partial extraction of TnC to disrupt the spread of activation along the thin filament; or (3) both, partial extraction of TnC and treatment with NEM-S1. The steepness of the force-pCa relationship was consistently reduced by treatment with NEM-S1, by partial extraction of TnC, or by a combination of TnC extraction and NEM-S1, indicating a decrease in the apparent cooperativity of activation. Partial extraction of TnC or NEM-S1 treatment accelerated the rate of force redevelopment at each submaximal force, but had no effect on kinetics of force development in maximally activated preparations. At low levels of Ca2+, 3 μM NEM-S1 increased ktr to maximal values, and higher concentrations of NEM-S1 (6 or 10 μM) increased ktr to greater than maximal values. NEM-S1 also accelerated ktr at intermediate levels of activation, but to values that were submaximal. However, the combination of partial TnC extraction and 6 μM NEM-S1 increased ktr to virtually identical supramaximal values at all levels of activation, thus, completely eliminating the activation dependence of ktr. These results show that ktr is not maximal in control fibers, even at saturating [Ca2+], and suggest that activation dependence of ktr is due to the combined activating effects of Ca2+ binding to TnC and cross-bridge binding to actin.
The Persuasion Knowledge Model: How People Cope with Persuasion Attempts
Authors: Friestad Marian , Wright Peter
Published: July 2002

In theories and studies of persuasion, people's personal knowledge about persuasion agents' goals and tactics, and about how to skillfully cope with these, has been ignored. We present a model of how people develop and use persuasion knowledge to cope with persuasion attempts. We discuss what the model implies about how consumers use marketers' advertising and selling attempts to refine their product attitudes and attitudes toward the marketers themselves. We also explain how this model relates to prior research on consumer behavior and persuasion and what it suggests about the future conduct of consumer research.
A simple proof of the elliptical range theorem
Authors: Li Chi-Kwong
Published: July 2002

A short proof is given of the elliptical range theorem concerning the numerical range of a

2
×
2

2\times 2

complex matrix.
Isolated spectral points
Authors: Koliha J.
Published: July 2002

The paper studies isolated spectral points of elements of Banach algebras and of bounded linear operators in terms of the existence of idempotents, and gives an elementary characterization of spectral idempotents. It is shown that

0
0

is isolated in the spectrum of a bounded linear operator

T
T

if the (not necessarily closed) space

M
=
{
x
:

lim

n

‖

T
n

x

‖

1

/

n

=
0
}

M=\{x: \lim _{n}\|T^nx\|^{1/n}=0\}

is nonzero and complemented by a closed subspace

N
N

satisfying

T
N
⊂
N
⊂
T
X

TN\subset N\subset TX

.
Maximal Bennequin numbers and Kauffman polynomials of positive links
Authors: Tanaka Toshifumi
Published: July 2002

By using results of Yamada and of Yokota, concerning link diagrams and link polynomials, we give some relationships between maximal Bennequin numbers and Kauffman polynomials of positive links.
Turnpike property for extremals of variational problems with vector-valued functions
Authors: Zaslavski A.
Published: July 2002

In this paper we study the structure of extremals

ν
:
[
0
,
T
]
→

R
n

\nu \colon [0,T]\to R^n

of variational problems with large enough

T
T

, fixed end points and an integrand

f
f

from a complete metric space of functions. We will establish the turnpike property for a generic integrand

f
f

. Namely, we will show that for a generic integrand

f
f

, any small

ε
>
0

\varepsilon >0

and an extremal

ν
:
[
0
,
T
]
→

R
n

\nu \colon [0,T]\to R^n

of the variational problem with large enough

T
T

, fixed end points and the integrand

f
f

, for each

τ
∈
[

L
1

,
T
−

L
1

]

\tau \in [L_1, T-L_1]

the set

{
ν
(
t
)
:
t
∈
[
τ
,
τ
+

L
2

]
}

\{\nu (t)\colon t\in [\tau ,\tau +L_2]\}

is equal to a set

H
(
f
)

H(f)

up to

ε
\varepsilon

in the Hausdorff metric. Here

H
(
f
)
⊂

R
n

H(f)\subset R^n

is a compact set depending only on the integrand

f
f

and

L
1

>

L
2

>
0

L_1>L_2>0

are constants which depend only on

ε
\varepsilon

and

|

ν
(
0
)

|

|\nu (0)|

,

|

ν
(
T
)

|

|\nu (T)|

.
Computing 𝜋(𝑥): the Meissel, Lehmer, Lagarias, Miller, Odlyzko method
Authors: Deleglise M. , Rivat J.
Published: July 2002

Let

π
(
x
)

\pi (x)

denote the number of primes

≤
x

\le x

. Our aim in this paper is to present some refinements of a combinatorial method for computing single values of

π
(
x
)

\pi (x)

, initiated by the German astronomer Meissel in 1870, extended and simplified by Lehmer in 1959, and improved in 1985 by Lagarias, Miller and Odlyzko. We show that it is possible to compute

π
(
x
)

\pi (x)

in

O
(

x

2

/

3

log
2

⁡
x

)

O(\frac {x^{2/3}} {\log ^2x})

time and

O
(

x

1

/

3

log
3

⁡
x
log
⁡
log
⁡
x
)

O(x^{1/3}\log ^3x\log \log x)

space. The algorithm has been implemented and used to compute

π
(

10

18

)

\pi (10^{18})

.
Mutations inSaccharomyces cerevisiaeGeneSIR2Can Have Differential Effects on In Vivo Silencing Phenotypes and In Vitro Histone Deacetylation Activity
Authors: Armstrong Christopher M. , Kaeberlein Matt , Imai Shin Ichiro , Guarente Leonard
Published: July 2002

The yeast SIR2 gene and many of its homologs have been identified as NAD+-dependent histone deacetylases. To get a broader view of the relationship between the histone deacetylase activity of Sir2p and its in vivo functions we have mutated eight highly conserved residues in the core domain ofSIR2. These mutations have a range of effects on the ability of Sir2p to deacetylate histones in vitro and to silence genes at the telomeres and HM loci. Interestingly, there is not a direct correlation between the in vitro and in vivo effects in some of these mutations. We also show that the histone deacetylase activity of Sir2p is necessary for the proper localiztion of the SIR complex to the telomeres.
Stem Trace: an interactive visual tool for comparative RNA structure analysis.
Authors: Kasprzak W , Shapiro B
Published: July 2002

MOTIVATION: Stem Trace is one of the latest tools available in STRUCTURELAB, an RNA structure analysis computer workbench. The paradigm used in STRUCTURELAB views RNA structure determination as a problem of dealing with a database of a large number of computationally generated structures. Stem Trace provides the capability to analyze this data set in a novel, visually driven, interactive and exploratory way. In addition to providing graphs at a high level of ion, it is also connected with complementary visualization tools which provide orthogonal views of the same data, as well as drawing of structures represented by a stem trace. Thus, on top of being an analysis tool, Stem Trace is a graphical user interface to an RNA structural information database. RESULTS: We illustrate Stem Trace's capabilities with several examples of the analysis of RNA folding data performed on 24 strains of HIV-1, HIV-2 and SIV sequences around the HIV dimerization region. This dimer linkage site has been found to play a role in encapsidation, reverse transcription, recombination, and inhibition of translation. Our examples show how Stem Trace elucidates preservation of structures in this region across the various strains of HIV. AVAILABILITY: The program can be made available upon request. It runs on SUN, SGI and DEC (Compaq) Unix workstations.
E-CELL: software environment for whole-cell simulation.
Authors: Tomita M , Hashimoto K , Takahashi K , Shimizu T S , Matsuzaki Y , Miyoshi F , Saito K , Tanida S , Yugi K , Venter J C , Hutchison C A
Published: July 2002

MOTIVATION: Genome sequencing projects and further systematic functional analyses of complete gene sets are producing an unprecedented mass of molecular information for a wide range of model organisms. This provides us with a detailed account of the cell with which we may begin to build models for simulating intracellular molecular processes to predict the dynamic behavior of living cells. Previous work in biochemical and genetic simulation has isolated well-characterized pathways for detailed analysis, but methods for building integrative models of the cell that incorporate gene regulation, metabolism and signaling have not been established. We, therefore, were motivated to develop a software environment for building such integrative models based on gene sets, and running simulations to conduct experiments in silico. RESULTS: E-CELL, a modeling and simulation environment for biochemical and genetic processes, has been developed. The E-CELL system allows a user to define functions of proteins, protein-protein interactions, protein-DNA interactions, regulation of gene expression and other features of cellular metabolism, as a set of reaction rules. E-CELL simulates cell behavior by numerically integrating the differential equations described implicitly in these reaction rules. The user can observe, through a computer display, dynamic changes in concentrations of proteins, protein complexes and other chemical compounds in the cell. Using this software, we constructed a model of a hypothetical cell with only 127 genes sufficient for transcription, translation, energy production and phospholipid synthesis. Most of the genes are taken from Mycoplasma genitalium, the organism having the smallest known chromosome, whose complete 580 kb genome sequence was determined at TIGR in 1995. We discuss future applications of the E-CELL system with special respect to genome engineering. AVAILABILITY: The E-CELL software is available upon request. SUPPLEMENTARY INFORMATION: The complete list of rules of the developed cell model with kinetic parameters can be obtained via our web site at: http://e-cell.org/.
MaskerAid : a performance enhancement to RepeatMasker
Authors: Bedell Joseph A. , Korf Ian , Gish Warren
Published: July 2002

Summary: Identifying and masking repetitive elements is usually the first step when analyzing vertebrate genomic sequence. Current repeat identification software is sensitive but slow, creating a costly bottleneck in large-scale analyses. We have developed MaskerAid , a software enhancement to RepeatMasker that increased the speed of masking more than 30-fold at the most sensitive setting.

Availability: On request from the authors (see http://sapiens.wustl.edu/MaskerAid).

Contact: maskeraid@watson.wustl.edu

These authors contributed equally to this work.

* To whom correspondence should be addressed.

** Current address: Incyte Genomics, 4633 World Parkway Cir., St. Louis, MO 63134 USA, jbedell@incyte.com
RDP: detection of recombination amongst aligned sequences
Authors: Martin Darren , Rybicki Ed
Published: July 2002

Summary: Recombination Detection Program (RDP) is a program that applies a pairwise scanning approach to the detection of recombination amongst a group of aligned DNA sequences. The software runs under Windows95 and combines highly automated screening of large numbers of sequences with a highly interactive interface for examining the results of the analyses.

Availability: For academic purposes RDP is available free of charge from: http://www.uct.ac.za/depts/microbiology/microdescription.htm

Contact: darren@molbiol.uct.ac.za
The massively parallel genetic algorithm for RNA folding: MIMD

implementation and population variation
Authors: Shapiro Bruce A. , Wu Jin Chu , Bengali David , Potts Mark J.
Published: July 2002

A massively parallel Genetic Algorithm (GA) has been applied to RNA sequence folding on three different computer architectures. The GA, an evolution-like algorithm that is applied to a large population of RNA structures based on a pool of helical stems derived from an RNA sequence, evolves this population in parallel. The algorithm was originally designed and developed for a 16384 processor SIMD (Single Instruction Multiple Data) MasPar MP-2. More recently it has been adapted to a 64 processor MIMD (Multiple Instruction Multiple Data) SGI ORIGIN 2000, and a 512 processor MIMD CRAY T3E. The MIMD version of the algorithm raises issues concerning RNA structure data-layout and processor communication. In addition, the effects of population variation on the predicted results are discussed. Also presented are the scaling properties of the algorithm from the perspective of the number of physical processors utilized and the number of virtual processors (RNA structures) operated upon.

Contact: bshapiro@ncifcrf.gov; jcwu@ncifcrf.gov; bengalid@ncifcrf.gov; mark.potts@ieee.org

* To whom correspondence should be addressed.

4 Current address: HPC Applications Inc., 10080 Old Frederick Road, Ellicott City, MD 21042, USA.
The Rate of Return on Investment in Wine
Authors: Burton Benjamin J. , Jacobsen Joyce P.
Published: July 2002

Is wine an investment alternative to stocks and bonds? First, we review prior studies regarding the pecuniary rate of return to wine and other alternatives to financial assets. Next, we calculate the rate of return to holding red Bordeaux wine from 1986 to 1996 using a repeat‐sale regression. Finally, we contrast the financial performance of wine, both on an aggregate basis and for various portfolios, to that of other asset classes. We conclude that wine does not yield greater returns than financial assets, especially when the volatility of returns and transaction costs are taken into account.
Prothymosin α interacts with the CREB‐binding protein and potentiates transcription
Authors: Karetsou Zoe , Kretsovali Adroniki , Murphy Carol , Tsolas Orestes , Papamarcaki Thomais
Published: July 2002

Prothymosin α (ProTα) is a histone H1‐binding protein localized in sites of active transcription in the nucleus. We report here that ProTα physically interacts with the CREB‐binding protein (CBP), which is a versatile transcription co‐activator. Confocal laser scanning microscopy reveals that ProTα partially colocalizes with CBP in discrete subnuclear domains. Using transient transfections, we show that ProTα synergizes with CBP and stimulates AP1‐ and NF‐κB‐dependent transcription. Furthermore, overexpression of ProTα enhances the transactivation potential of CBP. These findings reveal a new function for ProTα in transcription activation, probably through CBP‐mediated recruitment to different promoters.
Cell cycle‐dependent expression of cyclooxygenase‐2 in human fibroblasts
Authors: Gilroy Derek W. , Saunders Michael A. , Sansores‐Garcia Leticia , Matijevic‐Aleksic Nena , Wu Kenneth K.
Published: July 2002

The purpose of this investigation is to determine whether the levels of cyclooxygenase‐2 (COX‐2) expression are cell cycle dependent. We used a serum‐starved human foreskin fibroblast model to determine changes in COX‐2 mRNA, protein, and promoter activity in response to stimulation with interleukin‐1β (IL‐1β) and phorbol 12‐myristate 13‐acetate (PMA) at G0, G1, S and G2/M phases of the cell cycle. IL‐1β (1 ng/ml) and PMA (100 nM) induced robust COX‐2 expression in the G0 cells, and the level of COX‐2 expression declined progressively after the cells had entered the cell cycle. The COX‐2 mRNA level at G1, S and G2/M phases of the cell cycle was 76%, 46%, and 30% of that at G0, respectively. A 5’‐flanking promoter fragment of COX‐2 constructed into a luciferase expression vector was transfected into cells. The promoter activity in response to PMA stimulation was significantly higher in G0 than in S phase cells. These results imply that G0 cells are the key players in inflammation and other COX‐2‐dependent pathophysiological processes. When the cells are in the proliferative phase, COX‐2 inducibility becomes restrained probably by an endogenous control mechanism to avoid COX‐2 mediated oxidative DNA damage.
The kinetics of nerve-evoked quantal secretion
Authors: Fesce Riccardo
Published: July 2002

Current views on quantal release of neurotransmitters hold that after the vesicle migrates towards release sites (active zones), multiple protein interactions mediate the docking of the vesicle to the presynaptic membrane and the formation of a multimolecular protein complex (the ‘fusion machine’) which ultimately makes the vesicle competent to release a quantum in response to the action potential. Classical biophysical studies of quantal release have modelled the process by a binomial system where n vesicles (sites) competent for exocytosis release a quantum, with probability
p
, in response to the action potential. This is likely to be an oversimplified model. Furthermore, statistical and kinetic studies have given results which are difficult to reconcile within this framework. Here, data are presented and discussed which suggest a revision of the biophysical model. Transient silencing of release is shown to occur following the pulse of synchronous transmitter release, which is evoked by the presynaptic action potential. This points to a schema where the vesicle fusion complex assembly is a reversible, stochastic process. Asynchronous exocytosis may occur at several intermediate stages in the process, along paths which may be differentially regulated by divalent cations or other factors. The fusion complex becomes competent for synchronous release (armed vesicles) only at appropriately organized sites. The action potential then triggers (deterministically rather than stochastically) the synchronous discharge of all armed vesicles. The existence of a specific conformation for the fusion complex to be competent for synchronous evoked fusion reconciles statistical and kinetic results during repetitive stimulation and helps explain the specific effects of toxins and genetic manipulation on the synchronization of release in response to an action potential.
Historical overview of research on the tobacco mosaic virus genome: genome organization, infectivity and gene manipulation
Authors: Okada Y.
Published: July 2002

Early in the development of molecular biology, TMV RNA was widely used as a mitochondrial RNA that could be purified easily, and it contributed much to research on protein synthesis. Also, in the early stages of elucidation of the genetic code, artificially produced TMV mutants were widely used and provided the first proof that the genetic code was non–overlapping. In 1982, Goeletet al.determined the complete TMV RNA base sequence of 6395 nucleotides. The four genes (130K, 180K, 30K and coat protein) could then be mapped at precise locations in the TMV genome. Furthermore it had become clear, a little earlier, that genes located internally in the genome were expressed via subgenomic mRNAs. The initiation site for assembly of TMV particles was also determined.

However, although TMV contributed so much at the beginning of the development of molecular biology, its influence was replaced by that ofEscherichia coliand its phages in the next phase. As recombinant DNA technology developed in the 1980s, RNA virus research became more detached from the frontier of molecular biology. To recover from this setback, a gene–manipulation system was needed for RNA viruses. In 1986, two such systems were developed for TMV, using full–length cDNA clones, by Dawson's group and by Okada's group. Thus, reverse genetics could be used to elucidate the basic functions of all proteins encoded by the TMV genome. Identification of the function of the 30K protein was especially important because it was the first evidence that a plant virus possesses a cell–to–cell movement function. Many other plant viruses have since been found to encode comparable ‘movement proteins’. TMV thus became the first plant virus for which structures and functions were known for all its genes. At the birth of molecular plant pathology, TMV became a leader again.

TMV has also played pioneering roles in many other fields. TMV was the first virus for which the amino acid sequence of the coat protein was determined and first virus for which cotranslational disassembly was demonstrated bothin vivoandin vitro. It was the first virus for which activation of a resistance gene in a host plant was related to the molecular specificity of a product of a viral gene. Also, in the field of plant biotechnology, TMV vectors are among the most promising. Thus, for the 100 years since Beijerinck's work, TMV research has consistently played a leading role in opening up new areas of study, not only in plant pathology, but also in virology, biochemistry, molecular biology, RNA genetics and biotechnology.
An evaluation of the potential triggers of photoinactivation of photosystem II in the context of a Stern–Volmer model for downregulation and the reversible radical pair equilibrium model
Authors: Oxborough Kevin , Baker Neil R.
Published: July 2002

Photoinactivation of photosystem II (PS II) is a light–dependent process that frequently leads to breakdown and replacement of the D1 polypeptide. Photoinhibition occurs when the rate of photoinactivation is greater than the rate at which D1 is replaced and results in a decrease in the maximum efficiency of PS II photochemistry. Down regulation, which increases non–radiative decay within PS II, also decreases the maximum efficiency of PS II photochemistry and plays an important role in protecting against photoinhibition by reducing the yield of photoinactivation. The yield of photoinactivation has been shown to be relatively insensitive to photosynthetically active photon flux density (PPFD). Formation of the P680 radical (P680
+
), through charge separation at PS II, generation of triplet–state P680 (
3
P680*), through intersystem crossing and charge recombination, and double reduction of the primary stable electron acceptor of PS II (the plastoquinone, Q
A
) are all potentially critical steps in the triggering of photoinactivation. In this paper, these processes are assessed using fluorescence data from attached leaves of higher plant species, in the context of a Stern–Volmer model for downregulation and the reversible radical pair equilibrium model. It is shown that the yield of P680
+
is very sensitive to PPFD and that downregulation has very little effect on its production. Consequently, it is unlikely to be the trigger for photoinactivation. The yields of
3
P680* generated through charge recombination or intersystem crossing are both less sensitive to PPFD than the yield of P680
+
and are both decreased by downregulation. The yield of doubly reduced Q
A
increases with incident photon flux density at low levels, but is relatively insensitive at moderate to high levels, and is greatly decreased by downregulation. Consequently,
3
P680* and doubly reduced Q
A
are both viable as triggers of photoinactivation.
Advanced database methodology for the Collation of Connectivity data on the Macaque brain (CoCoMac)
Authors: Stephan Klass E. , Kamper Lars , Bozkurt Ahmet , Burns Gully A. P. C. , Young Malcolm P. , Kötter Rolf
Published: July 2002

The need to integrate massively increasing amounts of data on the mammalian brain has driven several ambitious neuroscientific database projects that were started during the last decade. Databasing the brain's anatomical connectivity as delivered by tracing studies is of particular importance as these data characterize fundamental structural constraints of the complex and poorly understood functional interactions between the components of real neural systems. Previous connectivity databases have been crucial for analysing anatomical brain circuitry in various species and have opened exciting new ways to interpret functional data, both from electrophysiological and from functional imaging studies. The eventual impact and success of connectivity databases, however, will require the resolution of several methodological problems that currently limit their use. These problems comprise four main points: (i) objective representation of coordinate–free, parcellation–based data, (ii) assessment of the reliability and precision of individual data, especially in the presence of contradictory reports, (iii) data mining and integration of large sets of partially redundant and contradictory data, and (iv) automatic and reproducible transformation of data between incongruent brain maps.

Here, we present the specific implementation of the ‘collation of connectivity data on the macaque brain’ (CoCoMac) database (http://www.cocomac.org). The design of this database addresses the methodological challenges listed above, and focuses on experimental and computational neuroscientists' needs to flexibly analyse and process the large amount of published experimental data from tracing studies. In this article, we explain step–by–step the conceptual rationale and methodology of CoCoMac and demonstrate its practical use by an analysis of connectivity in the prefrontal cortex.
On the evolution of early development in the Nematoda
Authors: Goldstein Bob
Published: July 2002

The phylum Nematoda serves as an excellent model system for exploring how development evolves, using a comparative approach to developmental genetics. More than 100 laboratories are studying developmental mechanisms in the nematodeCaenorhabditis elegans, and many of the methods that have been developed forC. eleganscan be applied to other nematodes. This review summarizes what is known so far about steps in early development that have evolved in the nematodes, and proposes potential experiments that could make use of these data to further our understanding of how development evolves. The promise of such a comparative approach to developmental genetics is to fill a wide gap in our understanding of evolution—a gap spanning from mutations in developmental genes through to their phenotypic results, on which natural selection may act.
The silencing complex SAS-I links histone acetylation to the assembly of repressed chromatin by CAF-I and Asf1 in Saccharomyces cerevisiae
Authors: Meijsing Sebastiaan H. , Ehrenhofer-Murray Ann E.
Published: July 2002

The acetylation state of histones plays a central role in determining gene expression in chromatin. The reestablishment of the acetylation state of nucleosomes after DNA replication and chromatin assembly requires both deacetylation and acetylation of specific lysine residues on newly incorporated histones. In this study, the MYST family acetyltransferase Sas2 was found to interact with Cac1, the largest subunit of Saccharomyces cerevisiae chromatin assembly factor-I (CAF-I), and with the nucleosome assembly factor Asf1. The deletions ofCAC1 (cac1Δ), ASF1 (asf1Δ), andSAS2 (sas2Δ) had similar effects on gene silencing and were partially overlapping. Furthermore, Sas2 was found in a nuclear protein complex that included Sas4 and Sas5, a homolog of TAFII30. This complex, termed SAS-I, was also found to contribute to rDNA silencing. Furthermore, the observation that a mutation of H4 lysine 16 to arginine displayed the identical silencing phenotypes as sas2Δ suggested that it was the in vivo target of Sas2 acetylation. In summary, our data present a novel model for the reestablishment of acetylation patterns after DNA replication, by which SAS-I is recruited to freshly replicated DNA by its association with chromatin assembly complexes to acetylate lysine 16 of H4.
Structural investigations of the active‐site mutant Asn156Ala of outer membrane phospholipase A: Function of the Asn–His interaction in the catalytic triad
Authors: Snijder H.J. , Van Eerde J.H. , Kingma R.L. , Kalk K.H. , Dekker N. , Egmond M.R. , Dijkstra B.W.
Published: July 2002

Outer membrane phospholipase A (OMPLA) from Escherichia coli is an integral‐membrane enzyme with a unique His–Ser–Asn catalytic triad. In serine proteases and serine esterases usually an Asp occurs in the catalytic triad; its role has been the subject of much debate. Here the role of the uncharged asparagine in the active site of OMPLA is investigated by structural characterization of the Asn156Ala mutant. Asparagine 156 is not involved in maintaining the overall active‐site configuration and does not contribute significantly to the thermal stability of OMPLA. The active‐site histidine retains an active conformation in the mutant notwithstanding the loss of the hydrogen bond to the asparagine side chain. Instead, stabilization of the correct tautomeric form of the histidine can account for the observed decrease in activity of the Asn156Ala mutant.
Rapid measurement of Gd‐DTPA extraction fraction in a dialysis system using echo‐planar imaging
Authors: Niendorf Eric R. , Grist Thomas M. , Frayne Richard , Brazy Peter C. , Santyr Giles E.
Published: July 2002

Gd‐DTPA (Magnevist, Berlex, Wayne, NJ) extraction fractions (EF) have been measured for three dialysis filter types using an echo‐planar imaging (EPI) Look‐Locker measurement technique under conditions of fast and slow flow. The mean EF measured in Fresenius (Bad Homburg, Germany) F3, F6, and F8 dialysis filters were 0.015±0.005, 0.053±0.004, and 0.084±0.003, respectively, under conditions of fast flow which provided complete refreshment of spins in the intervals between read‐out pulse samples of the relaxation recovery. Data acquisition and post‐processing techniques were developed to extend the accuracy of the LL technique to systems with slow flow which did not provide complete refreshment of spins between samples of the recovery. A multi‐shot EPI LL interleaved acquisition of relaxation recovery space (IRRS) provided measurement accuracy comparable to the refreshed system, 10, but at the expense of increased scan times (factor of 2 or 3). Discarding the first few non‐equilibrium relaxation recovery samples from the fit allowed accurate estimation 10) with a single‐shot EPI LL method under conditions of slow flow. These EPI LL EF measurement methods may provide useful techniques for evaluating renal function in vivo.
Calibration and characterization of beta‐particle sources for intravascular brachytherapy
Authors: Soares C. G. , Halpern D. G. , Wang C.‐K.
Published: July 2002

The calibration of a catheter‐based system to be used for therapeutic radiation treatment to prevent restenosis following interventional coronary procedures is described. The primary dosimetry was performed ionometrically using an extrapolation chamber equipped with a 1‐mm diameter collecting electrode to measure absorbed dose in tissue equivalent plastic at a depth of 2 mm. These results are compared with measurements with radiochromic dye film, which is also used to characterize sources for axial and trans‐axial uniformity, and to determine dose distributions at various depths. A protocol for dose calculation based on that of AAPM TG43 is suggested for these sources, and examples of its use are given for the calculation of the enhancement effect on dose rate from a single seed source due to neighboring seeds. Monte Carlo calculations were also performed to validate the measured results.
Strategies to improve the signal and noise performance of active matrix, flat‐panel imagers for diagnostic x‐ray applications
Authors: Antonuk L. E. , Jee K.‐W. , El‐Mohri Y. , Maolinbay M. , Nassif S. , Rong X. , Zhao Q. , Siewerdsen J. H. , Street R. A. , Shah K. S.
Published: July 2002

A theoretical investigation of factors limiting the detective quantum efficiency (DQE) of active matrix flat‐panel imagers (AMFPIs), and of methods to overcome these limitations, is reported. At the higher exposure levels associated with radiography, the present generation of AMFPIs is capable of exhibiting DQE performance equivalent, or superior, to that of existing film‐screen and computed radiography systems. However, at exposure levels commonly encountered in fluoroscopy, AMFPIs exhibit significantly reduced DQE and this problem is accentuated at higher spatial frequencies. The problem applies both to AMFPIs that rely on indirect detection as well as direct detection of the incident radiation. This reduced performance derives from the relatively large magnitude of the square of the total additive noise compared to the system gain for existing AMFPIs. In order to circumvent these restrictions, a variety of strategies to decrease additive noise and enhance system gain are proposed. Additive noise could be reduced through improved preamplifier, pixel and array design, including the incorporation of compensation lines to sample external line noise. System gain could be enhanced through the use of continuous photodiodes, pixel amplifiers, or higher gain x‐ray converters such as lead iodide. The feasibility of these and other strategies is discussed and potential improvements to DQE performance are quantified through a theoretical investigation of a variety of hypothetical 200 μm pitch designs. At low exposures, such improvements could greatly increase the magnitude of the low spatial frequency component of the DQE, rendering it practically independent of exposure while simultaneously reducing the falloff in DQE at higher spatial frequencies. Furthermore, such noise reduction and gain enhancement could lead to the development of AMFPIs with high DQE performance which are capable of providing both high resolution radiographic images, at ∼100 μm pixel resolution, as well as variable resolution fluoroscopic images at 30 fps.
The impact of electron transport on the accuracy of computed dose
Authors: Arnfield Mark R. , Siantar Christine Hartmann , Siebers Jeffrey , Garmon Pamela , Cox Larry , Mohan Radhe
Published: July 2002

The aim of this work was to investigate the accuracy of dose predicted by a Batho power law correction, and two models which account for electron range: A superposition/convolution algorithm and a Monte Carlo algorithm. The results of these models were compared in phantoms with cavities and low‐density inhomogeneities. An idealized geometry was considered with inhomogeneities represented by regions of air and lung equivalent material. Measurements were performed with a parallel plate ionization chamber, thin TLDs (thermoluminescent dosimeters) and film. Dose calculations were done with a generalized Batho model, the Pinnacle collapsed cone convolution model (CCC), and the Peregrine Monte Carlo dose calculation algorithm. Absolute central axis and off axis dose data at various depths relative to interfaces of inhomogeneities were compared. Our results confirm that for a Batho correction, dose errors in the calculated depth dose arise from the neglect of electron transport. This effect increases as the field size decreases, as the density of the inhomogeneity decreases, and with the energy of incident photons. The CCC calculations were closer to measurements than the Batho model, but significant discrepancies remain. Monte Carlo results agree with measurements within the measurement and computational uncertainties.
Ferroelectricity: Measurement of the dielectric susceptibility of strontium titanate at low temperatures
Authors: Trainer Matthew
Published: July 2002

A cryogenic experiment determining the dielectric susceptibility of the ferroelectric substance, strontium titanate, in the 90- to 300-K temperature range is described. Evidence is presented for a structural phase transition in strontium titanate at 110 K. The experiment is suitable for advanced students.
An introduction to electrical resistivity in geophysics
Authors: Herman Rhett
Published: July 2002

Physicists are finding that the skills they have learned in their training may be applied to areas beyond traditional physics topics. One such field is that of geophysics. This paper presents the electrical resistivity component of an undergraduate geophysics course at Radford University. It is taught from a physics perspective, yet the application of the theory to the real world is the overriding goal. The concepts involved in electrical resistivity studies are first discussed in a general sense, and then they are studied through the application of the relevant electromagnetic theory. Since geology majors comprise the bulk of the students in this class, the math used is only that which is typically required of geology majors. The final results are given in a form that practicing geophysicists may use in the field. A method is presented for constructing an inexpensive apparatus for measuring electrical resistivity in both a tabletop laboratory setting and in the field. This apparatus is truly “plug and play” since its assembly and use requires only the most basic knowledge of electronics. This apparatus is tested in a tabletop laboratory setting as well as in two field surveys.
Completeness of the energy eigenfunctions for the one-dimensional δ-function potential
Authors: Patil S. H.
Published: July 2002

We develop energy eigenfunctions for the one-dimensional δ-function potential, with well-defined parity and appropriate orthogonalization. We use these elementary functions to present an explicit demonstration of the completeness of the energy eigenfunctions. It provides a simple illustration of an essential quantum mechanical property, which is pedagogically important.
Dynamic photoelastic study of the transient stress field in solids during shock wave lithotripsy
Authors: Xi Xufeng , Zhong Pei
Published: July 2002

Photoelastic and shadowgraph imaging techniques were used to visualize the propagation and evolution of stress waves, and the resultant transient stress fields in solids during shock wave lithotripsy. In parallel, theoretical analysis of the wavefront evolution inside the solids was performed using a ray-tracing method. Excellent agreement between the theoretical prediction and experimental results was observed. Both the sample size and geometry were found to have a significant influence on the wave evolution and associated stress field produced inside the solid. In particular, characteristic patterns of spalling damage (i.e., transverse and longitudinal crack formation) were observed using plaster-of-Paris cylindrical phantoms of rectangular and circular cross sections. It was found that the leading tensile pulse of the reflected longitudinal wave is responsible for the initiation of microcracks in regions inside the phantom where high tensile stresses are produced. In addition, the transmitted shear wave was found to play a critical role in facilitating the extension and propagation of the microcrack.
On reducing vibration transmission in a two-dimensional cantilever truss structure using geometric optimization and active vibration control techniques
Authors: Anthony D. K. , Elliott S. J.
Published: July 2002

Four optimization strategies were used to improve the average vibration isolation between the base and the end of a 10-m long two-dimensional (2D) cantilever truss structure. These were combinations of optimizing the structure geometry and the application of active vibration control (AVC) with optimal actuator positions. A power distribution analysis to investigate the mechanisms by which each strategy achieves reductions in the vibration transmission is reported. The trade-off is also explored between the freedom allowed in the size of the geometric changes and the number of actuators used in an AVC system to achieve a given level of vibration attenuation.
Regularization methods for near-field acoustical holography
Authors: Williams Earl G.
Published: July 2002

The reconstruction of the pressure and normal surface velocity provided by near-field acoustical holography (NAH) from pressure measurements made near a vibrating structure is a linear, ill-posed inverse problem due to the existence of strongly decaying, evanescentlike waves. Regularization provides a technique of overcoming the ill-posedness and generates a solution to the linear problem in an automated way. We present four robust methods for regularization; the standard Tikhonov procedure along with a novel improved version, Landweber iteration, and the conjugate gradient approach. Each of these approaches can be applied to all forms of interior or exterior NAH problems; planar, cylindrical, spherical, and conformal. We also study two parameter selection procedures, the Morozov discrepancy principle and the generalized cross validation, which are crucial to any regularization theory. In particular, we concentrate here on planar and cylindrical holography. These forms of NAH which rely on the discrete Fourier transform are important due to their popularity and to their tremendous computational speed. In order to use regularization theory for the separable geometry problems we reformulate the equations of planar, cylindrical, and spherical NAH into an eigenvalue problem. The resulting eigenvalues and eigenvectors couple easily to regularization theory, which can be incorporated into the NAH software with little sacrifice in computational speed. The resulting complete automation of the NAH algorithm for both separable and nonseparable geometries overcomes the last significant hurdle for NAH.
An energy-conserving one-way coupled mode propagation model
Authors: Abawi Ahmad T.
Published: July 2002

The equations of motion for pressure and displacement fields in a waveguide have been used to derive an energy-conserving, one-way coupled mode propagation model. This model has three important properties: First, since it is based on the equations of motion, rather than the wave equation, instead of two coupling matrices, it only contains one coupling matrix. Second, the resulting coupling matrix is anti-symmetric, which implies that the energy among modes is conserved. Third, the coupling matrix can be computed using the local modes and their depth derivatives. The model has been applied to two range-dependent cases: Propagation in a wedge, where range dependence is due to variations in water depth and propagation through internal waves, where range dependence is due to variations in water sound speed. In both cases the solutions are compared with those obtained from the parabolic equation (PE) method.
Effective medium approach to linear acoustics in bubbly liquids
Authors: Kargl Steven G.
Published: July 2002

Linear wave propagation through a bubbly liquid has seen a resurgence of interest because of proposed “corrections” to the lowest-order approximation of an effective wave number obtained from Foldy’s exact multiple scattering theory [Foldy, Phys. Rev. 67, 107 (1945)]. An alternative approach to wave propagation through a bubbly liquid reduces the governing equations for a two-phase medium to an effective medium. Based on this approach, Commander and Prosperetti [J. Acoust. Soc. Am. 85, 732 (1989)] derive an expression for the lowest-order approximation to an effective wave number. At this level of approximation the bubbles interact with only the mean acoustic field without higher-order rescattering. That is, the field scattered from a bubble may interact with one or more new bubbles in the distribution, but a portion of that scattered field may not be scattered back to any previous bubble. The current article shows that modifications to the results of Commander and Prosperetti lead to a new expression for the effective wave number, which properly accounts for all higher orders of multiple scattering.
Factors contributing to bone conduction: The middle ear
Authors: Stenfelt Stefan , Hato Naohito , Goode Richard L.
Published: July 2002

Measurement of the motion of the malleus umbo and stapes footplate during bone conduction (BC) stimulation was conducted in vitro in 26 temporal bones using a laser Doppler vibrometer over the frequency range 0.1 to 10 kHz. For lower frequencies, both ossicular sites followed the motion of the temporal bone. The differential motion between the malleus and the surrounding bone was greater than the differential motion of the stapes footplate; both resonated near 1.5 kHz. Different lesions were shown to affect the response: (1) a mass attached to the umbo lowered the resonance frequency of the ossicular vibration; (2) fixation of either the malleus or stapes increased the stiffness and shifted the resonance frequency upward; and (3) dislocation of the incudo-stapedial joint did not significantly affect the ossicular vibration. The sound radiated from the tympanic membrane was approximately 85 dB SPL at an umbo differential velocity of 1 mm/s for low frequencies in an open ear canal and about 10 dB higher for an occluded one; at higher frequencies (above 2 kHz) resonances of the canal determine the response. It was also found that the motion between the footplate and promontory was within 5 dB when the specimen was stimulated orthogonal to the vibration direction of the ossicles than in line with the same. Measurement of the differential motion of the umbo in one live human skull gave similar response as the average result from the temporal bone specimens.
The connection between sound production and jet structure of the supersonic impinging jet
Authors: Henderson Brenda
Published: July 2002

An experimental investigation into the sound-producing characteristics of moderately and highly underexpanded supersonic impinging jets exhausting from a round convergent nozzle is presented. The production of large plate tones by impingement on a square plate with a side dimension equal to 12 nozzle exit diameters is studied using random and phase-locked shadowgraph photography. Discrete frequency sound is produced in the near-wall region of the jet when a Mach disk occurs upstream of the standoff shock wave. Tones cease when the plate distance is approximately 2.2 free-jet cell lengths and the first and second shock waves are located in the free-jet positions. The production of impulsive sound appears to be associated with the collapse of the standoff shock wave during a portion of the oscillation cycle. Results from unsteady plate-pressure measurements indicate that plane-wave motion occurs in the impingement region and a secondary pressure maximum is observed on the plate adjacent to the flow region where sound appears to originate.
YIN, a fundamental frequency estimator for speech and music
Authors: de Cheveigné Alain , Kawahara Hideki
Published: July 2002

An algorithm is presented for the estimation of the fundamental frequency (F0) of speech or musical sounds. It is based on the well-known autocorrelation method with a number of modifications that combine to prevent errors. The algorithm has several desirable features. Error rates are about three times lower than the best competing methods, as evaluated over a database of speech recorded together with a laryngograph signal. There is no upper limit on the frequency search range, so the algorithm is suited for high-pitched voices and music. The algorithm is relatively simple and may be implemented efficiently and with low latency, and it involves few parameters that must be tuned. It is based on a signal model (periodic signal) that may be extended in several ways to handle various forms of aperiodicity that occur in particular applications. Finally, interesting parallels may be drawn with models of auditory processing.