bluuebunny/crossref_metadata_2025 huggingface dataset:
Na+ Interaction with the Pore of Shaker B K+ Channels
Authors: Gómez-Lagunas Froylán
Published: July 2002

The Shaker B K+ conductance (GK) collapses (in a reversible manner) if the membrane is depolarized and then repolarized in, 0 K+, Na+-containing solutions (Gómez-Lagunas, F. 1997. J. Physiol. 499:3–15; Gómez-Lagunas, F. 1999. Biophys. J. 77:2988–2998). In this work, the role of Na+ ions in the collapse of GK in 0-K+ solutions, and in the behavior of the channels in low K+, was studied. The main findings are as follows. First, in 0-K+ solutions, the presence of Na+ ions is an important factor that speeds the collapse of GK. Second, external Na+ fosters the drop of GK by binding to a site with a Kd = 3.3 mM. External K+ competes, in a mutually exclusive manner, with Nao+ for binding to this site, with an estimated Kd = 80 μM. Third, NMG and choline are relatively inert regarding the stability of GK; fourth, with [Ko+] = 0, the energy required to relieve Nai+ block of Shaker (French, R.J., and J.B. Wells. 1977. J. Gen. Physiol. 70:707–724; Starkus, J.G., L. Kuschel, M. Rayner, and S. Heinemann. 2000. J. Gen. Physiol. 110:539–550) decreases with the molar fraction of Nai+ (XNa,i), in an extent not accounted for by the change in ΔμNa. Finally, when XNa,i = 1, GK collapses by the binding of Nai+ to two sites, with apparent Kds of 2 and 14.3 mM.
Some complements to the Jensen and Chebyshev inequalities and a problem of W. Walter
Authors: Malamud S.
Published: July 2002

Motivated by an integral inequality conjectured by W. Walter, we prove some general integral inequalities on finite intervals of the real line. In addition to supplying new proofs of Walter’s conjecture, the general inequalities furnish a reverse Jensen inequality under appropriate conditions and provide generalizations of Chebyshev’s integral inequality.
Periodic billiard orbits are dense in rational polygons
Authors: Boshernitzan M. , Galperin G. , Krüger T. , Troubetzkoy S.
Published: July 2002

We show that periodic orbits are dense in the phase space for billiards in polygons for which the angle between each pair of sides is a rational multiple of

π
.

\pi .
Empirical evidence for the Birch and Swinnerton-Dyer conjectures for modular Jacobians of genus 2 curves
Authors: Flynn E. , Leprévost Franck , Schaefer Edward , Stein William , Stoll Michael , Wetherell Joseph
Published: July 2002

This paper provides empirical evidence for the Birch and Swinnerton-Dyer conjectures for modular Jacobians of genus 2 curves. The second of these conjectures relates six quantities associated to a Jacobian over the rational numbers. One of these six quantities is the size of the Shafarevich-Tate group. Unable to compute that, we computed the five other quantities and solved for the last one. In all 32 cases, the result is very close to an integer that is a power of 2. In addition, this power of 2 agrees with the size of the 2-torsion of the Shafarevich-Tate group, which we could compute.
Some new error estimates for Ritz–Galerkin methods with minimal regularity assumptions
Authors: Schatz Alfred , Wang Junping
Published: July 2002

New uniform error estimates are established for finite element approximations

u
h

u_h

of solutions

u
u

of second-order elliptic equations

L

u
=
f

\mathcal {L} u = f

using only the regularity assumption

‖
u

‖
1

≤
c
‖
f

‖

−
1

\|u\|_1 \leq c\|f\|_{-1}

. Using an Aubin–Nitsche type duality argument we show for example that, for arbitrary (fixed)

ε
\varepsilon

sufficiently small, there exists an

h
0

h_0

such that for

0
>
h
>

h
0

0 > h > h_0

\[

‖
u
−

u
h

‖
0

≤
ε
‖
u
−

u
h

‖
1

.

\|u-u_h\|_0 \leq \varepsilon \|u-u_h\|_1.

\]
Here,

‖
⋅

‖
s

\|\cdot \|_s

denotes the norm on the Sobolev space

H
s

H^s

. Other related results are established.
A new parallel chasing algorithm for transforming arrowhead matrices to tridiagonal form
Authors: Oliveira Suely
Published: July 2002

Rutishauser, Gragg and Harrod and finally H.Y. Zha used the same class of chasing algorithms for transforming arrowhead matrices to tridiagonal form. Using a graphical theoretical approach, we propose a new chasing algorithm. Although this algorithm has the same sequential computational complexity and backward error properties as the old algorithms, it is better suited for a pipelined approach. The parallel algorithm for this new chasing method is described, with performance results on the Paragon and nCUBE. Comparison results between the old and the new algorithms are also presented.
Vector subdivision schemes and multiple wavelets
Authors: Jia Rong-Qing , Riemenschneider S. , Zhou Ding-Xuan
Published: July 2002

We consider solutions of a system of refinement equations written in the form

ϕ
=

∑

α
∈

Z

a
(
α
)
ϕ
(
2
⋅
−
α
)
,

\begin{equation*}\phi = \sum _{\alpha \in \mathbb {Z}} a(\alpha )\phi (2\cdot -\alpha ),\end{equation*}

where the vector of functions

ϕ
=
(

ϕ

1

,
…
,

ϕ

r

)

T

\phi =(\phi ^{1},\ldots ,\phi ^{r})^{T}

is in

(

L

p

(

R

)

)

r

(L_{p}(\mathbb {R}))^{r}

and

a
a

is a finitely supported sequence of

r
×
r

r\times r

matrices called the refinement mask. Associated with the mask

a
a

is a linear operator

Q

a

Q_{a}

defined on

(

L

p

(

R

)

)

r

(L_{p}(\mathbb {R}))^{r}

by

Q

a

f
:=

∑

α
∈

Z

a
(
α
)
f
(
2
⋅
−
α
)

Q_{a} f := \sum _{\alpha \in \mathbb {Z}} a(\alpha )f(2\cdot -\alpha )

. This paper is concerned with the convergence of the subdivision scheme associated with

a
a

, i.e., the convergence of the sequence

(

Q

a

n

f

)

n
=
1
,
2
,
…

(Q_{a}^{n}f)_{n=1,2,\ldots }

in the

L

p

L_{p}

-norm. Our main result characterizes the convergence of a subdivision scheme associated with the mask

a
a

in terms of the joint spectral radius of two finite matrices derived from the mask. Along the way, properties of the joint spectral radius and its relation to the subdivision scheme are discussed. In particular, the

L

2

L_{2}

-convergence of the subdivision scheme is characterized in terms of the spectral radius of the transition operator restricted to a certain invariant subspace. We analyze convergence of the subdivision scheme explicitly for several interesting classes of vector refinement equations. Finally, the theory of vector subdivision schemes is used to characterize orthonormality of multiple refinable functions. This leads us to construct a class of continuous orthogonal double wavelets with symmetry.
Generalized monotone schemes, discrete paths of extrema, and discrete entropy conditions
Authors: LeFloch Philippe , Liu Jian-Guo
Published: July 2002

Solutions of conservation laws satisfy the monotonicity property: the number of local extrema is a non-increasing function of time, and local maximum/minimum values decrease/increase monotonically in time. This paper investigates this property from a numerical standpoint. We introduce a class of fully discrete in space and time, high order accurate, difference schemes, called generalized monotone schemes. Convergence toward the entropy solution is proven via a new technique of proof, assuming that the initial data has a finite number of extremum values only, and the flux-function is strictly convex. We define discrete paths of extrema by tracking local extremum values in the approximate solution. In the course of the analysis we establish the pointwise convergence of the trace of the solution along a path of extremum. As a corollary, we obtain a proof of convergence for a MUSCL-type scheme that is second order accurate away from sonic points and extrema.
Strongly typical representations of the basic classical Lie superalgebras
Authors: Gorelik Maria
Published: July 2002

We describe the category of representations with a strongly typical central character of a basic classical Lie superalgebra in terms of representations of its even part.
Cell Cycle-dependent Assembly of a Gin4-Septin Complex
Authors: Mortensen Eric M. , McDonald Hayes , Yates John , Kellogg Douglas R.
Published: July 2002

Gin4, a Nim1-related kinase, is required in budding yeast for localization of the septins and for proper control of daughter cell growth during G2/M. Gin4 becomes hyperphosphorylated when cells enter mitosis, leading to activation of Gin4 kinase activity. In this study, we have used immunoaffinity chromatography to identify proteins that associate with Gin4 during mitosis, with the goal of finding targets of Gin4 kinase activity and proteins that play a role in Gin4 activation. We show that during mitosis Gin4 is assembled into a multiprotein complex that includes Nap1, Bni5, the septins, and at least two molecules of Gin4. The associated Gin4 molecules present in this complex phosphorylate each other, leading to Gin4 hyperphosphorylation. Furthermore, the Shs1 septin present in the complex undergoes Gin4-dependent phosphorylation during mitosis and appears to be a substrate of Gin4 in vitro, suggesting that it is a target of Gin4 kinase activity in vivo. Genetic data support the idea that Shs1 is an important target of Gin4 kinase activity. Association of Gin4 with the septins during mitosis requires Shs1, Nap1, Cla4, Elm1, and the kinase activities of Gin4 and Cdc28. Self-association of Gin4 molecules requires Shs1 but not Cla4 or Nap1. Previous work has suggested that the septins function together as a tight complex, and we found that the majority of the Shs1 in the cell is tightly bound to the other septins Cdc3, Cdc10, Cdc11, and Cdc12. Interestingly, however, Shs1 can bind to Gin4 and induce Gin4 oligomerization under conditions in which the Cdc11 septin does not bind to Gin4, suggesting that Shs1 can function independently of the other septins. Taken together, these findings suggest that highly regulated protein-binding events ensure that the Gin4 kinase is activated only during mitosis and only in association with Shs1, a likely in vivo substrate of Gin4. In addition, these results provide clues to how Gin4 may regulate the localization or function of the septins.
ProtEST: protein multiple sequence alignments from expressed
sequence tags
Authors: Cuff James A. , Birney Ewan , Clamp Michele E. , Barton Geoffrey J.
Published: July 2002

Motivation: An automatic sequence searching method (ProtEST) is described which constructs multiple protein sequence alignments from protein sequences and translated expressed sequence tags (ESTs). ProtEST is more effective than a simple TBLASTN search of the query against the EST database, as the sequences are automatically clustered, assembled, made non-redundant, checked for sequence errors, translated into protein and then aligned and displayed.

Results: A ProtEST search found a non-redundant, translated, error- and length-corrected EST sequence for &58% of sequences when single sequences from 1407 Pfam-A seed alignments were used as the probe. The average family size of the resulting alignments of translated EST sequences contained &10 sequences. In a cross-validated test of protein secondary structure prediction, alignments from the new procedure led to an improvement of 3.4% average Q3 prediction accuracy over single sequences.

Availability: The ProtEST method is available as an Internet World Wide Web service at http://barton.ebi.ac.uk/servers/protest.htmlThe Wise2 package for protein and genomic comparisons and the ProtESTWise script can be found at: http://www.sanger.ac.uk/Software/Wise2

Contact: geoff@ebi.ac.uk
Visualizing the spindle checkpoint in Drosophila spermatocytes
Authors: Rebollo Elena , González Cayetano
Published: July 2002

The spindle assembly checkpoint detects defects in spindle structure or in the alignment of the chromosomes on the metaphase plate and delays the onset of anaphase until defects are corrected. Thus far, the evidence regarding the presence of a spindle checkpoint during meiosis in male Drosophila has been indirect and contradictory. On the one hand, chromosomes without pairing partners do not prevent meiosis progression. On the other hand, some conserved components of the spindle checkpoint machinery are expressed in these cells and behave as their homologue proteins do in systems with an active spindle checkpoint. To establish whether the spindle checkpoint is active in Drosophila spermatocytes we have followed meiosis progression by time‐lapse microscopy under conditions where the checkpoint is likely to be activated. We have found that the presence of a relatively high number of misaligned chromosomes or a severe disruption of the meiotic spindle results in a significant delay in the time of entry into anaphase. These observations provide the first direct evidence substantiating the activity of a meiotic spindle checkpoint in male Drosophila.
Florid plaques in ovine PrP transgenic mice infected with an experimental ovine BSE
Authors: Crozet Carole , Bencsik Anna , Flamant Frédéric , Lezmi Stéphane , Samarut Jacques , Baron Thierry
Published: July 2002

The occurrence of the variant Creutzfeldt–Jakob disease (vCJD), related to bovine spongiform encephalopathy (BSE), raises the important question of the sources of human contamination. The possibility that sheep may have been fed with BSE‐contaminated foodstuff raises the serious concern that BSE may now be present in sheep without being distinguishable from scrapie. Sensitive models are urgently needed given the dramatic consequences of such a possible contamination on animal and human health. We inoculated transgenic mice expressing the ovine PrP gene with a brain homogenate from sheep experimentally infected with BSE. We found numerous typical florid plaques in their brains. Such florid plaques are a feature of vCJD in humans and experimental BSE infection in macaques. Our observation represents the first description, after a primary infection, of this hallmark in a transgenic mouse model. Moreover, these mice appear to be a promising tool in the search for BSE in sheep.
“At the Curve Exchange”: Postwar Beauty Culture and Working Women at Maidenform
Authors: Howard Vicki
Published: July 2002

Beauty culture shaped the work experiences of women factory operatives and office staff at the Maidenform company in complex ways during the 1940s and 1950s. Through advertising, the company newsletter, beauty contests, “Pin-Up of the Month” competitions, and the ultra-feminine form made possible by the company's brassieres and girdles, Maidenform helped define postwar commercial beauty culture. Maidenform employees also had a hand in defining beauty culture, making it an important part of workplace sociability. In the process of producing and consuming workplace beauty culture at Maidenform, women from a wide range of class and ethnic backgrounds participated in the dominant gender ideal fostered by their employer. At the same time, however, their work culture remained rooted in their own class and ethnic identities. This article will examine the ways in which working women at Maidenform used commercial beauty culture to negotiate these divergent identities.
Transgene overexpression of αB crystallin confers simultaneous protection against cardiomyocyte apoptosis and necrosis during myocardial ischemia and reperfusion
Authors: RAY PARTHA S. , MARTIN JODY L. , SWANSON ERIC A. , OTANI HAJIME , DILLMANN WOLFGANG H. , DAS DIPAK K
Published: July 2002

We investigated whether enhanced expression of αB crystallin, a stress‐inducible molecular chaperone of the small heat shock family, can protect myocardial contractile apparatus against ischemia reperfusion (I/R) injury. Transgenic mice overexpressing αB crystallin were generated using the 0.76 kb rat αB crystallin cDNA cloned into a pCAGGS plasmid driven by a human cytomegalovirus expression system. Southern analysis confirmed transgene integration and Northern and Western blotting characterized expression (3.1‐fold and 6.9‐fold elevations in myocardial mRNA and protein levels, respectively). Extent of functional recovery overa3hreperfusion period following a 20 min ischemic period in transgenic and wild‐type mouse hearts was assessed using an ex vivo work‐performing heart preparation. The transgenic group displayed significantly higher values of DP at R45 min (29.14±1.9mmHgvs. 17.6±0.7 mm Hg), R60 min (31.56±1.7mmHgvs. 17.8±0.8 mm Hg), and R75 min (32.5±2.2 mm Hg vs. 16.9±0.9 mm Hg), and of dLVP/dt at R45 min (1740.2±111.5 mm Hg.s−1 vs. 548.7±82.2 mm Hg.s−1) and R60 min (1199.8±104.6 mm Hg.s−1 vs. 466.9±61.1 mm Hg.s−1). The transgenic group also displayed development of less oxidative stress, decreased extent of infarction, and attenuated cardiomyocyte apoptotic cell death. Transgene overexpression of αB crystallin was therefore successful in diminishing the independent contributory effects of both necrosis and apoptosis on I/R‐induced cell death.—Ray, P. S., Martin, J. L., Swanson, E. A., Otani, H., Dillmann, W. H., Das, D. K. Transgene overexpression of aB crystallin confers simultaneous protection against cardiomyocyte apoptosis and necrosis during myocardial ischemia and reperfusion. FASEB J. 15, 393‐402 (2001)
Vegetation-climate feedbacks in a greenhouse world
Authors: Woodward F. I. , Lomas M. R. , Betts R. A.
Published: July 2002

The potential for feedbacks between terrestrial vegetation, climate, and the atmospheric CO
2
partial pressure have been addressed by modelling. Previous research has established that under global warming and CO
2
enrichment, the stomatal conductance of vegetation tends to decrease, causing a warming effect on top of the driving change in greenhouse warming. At the global scale, this positive feedback is ultimately changed to a negative feedback through changes in vegetation structure. In spatial terms this structural feedback has a variable geographical pattern in terms of magnitude and sign. At high latitudes, increases in vegetation leaf area index (LAI) and vegetation height cause a positive feedback, and warming through reductions in the winter snow–cover albedo. At lower latitudes when vegetation becomes more sparse with warming, the higher albedo of the underlying soil leads to cooling. However, the largest area effects are of negative feedbacks caused by increased evaporative cooling with increasing LAI. These effects do not include feedbacks on the atmospheric CO
2
concentration, through changes in the carbon cycle of the vegetation. Modelling experiments, with biogeochemical, physiological and structural feedbacks on atmospheric CO
2
, but with no changes in precipitation, ocean activity or sea ice formation, have shown that a consequence of the CO
2
fertilization effect on vegetation will be a reduction of atmospheric CO
2
concentration, in the order of 12% by the year 2100 and a reduced global warming by 0.7°C, in a total greenhouse warming of 3.9°C.
Aggregation and distribution of strains in microparasites
Authors: Lord C. C. , Barnard B. , Day K. , Hargrove J. W. , McNamara J. J. , Paul R. E. L. , Trenholme K. , Woolhouse M. E. J.
Published: July 2002

Recent research has shown that many parasite populations are made up of a number of epidemiologically distinct strains or genotypes. The implications of strain structure or genetic diversity for parasite population dynamics are still uncertain, partly because there is no coherent framework for the interpretation of field data. Here, we present an analysis of four published data sets for vector–borne microparasite infections where strains or genotypes have been distinguished: serotypes of African horse sickness (AHS) in zebra; types ofNannomonastrypanosomes in tsetse flies; parasite–induced erythrocyte surface antigen (PIESA) based isolates ofPlasmodium falciparummalaria in humans, and the merozoite surface protein 2 gene (MSP–2) alleles ofP. falciparumin humans and in anopheline mosquitoes. For each data set we consider the distribution of strains or types among hosts and any pairwise associations between strains or types. Where host age data are available we also compare age–prevalence relationships and estimates of the force–of–infection. Multiple infections of hosts are common and for most data sets infections have an aggregated distribution among hosts with a tendency towards positive associations between certain strains or types. These patterns could result from interactions (facilitation) between strains or types, or they could reflect patterns of contact between hosts and vectors. We use a mathematical model to illustrate the impact of host–vector contact patterns, finding that even if contact is random there may still be significant aggregation in parasite distributions. This effect is enhanced if there is non–random contact or other heterogeneities between hosts, vectors or parasites. In practice, different strains or types also have different forces of infection. We anticipate that aggregated distributions and positive associations between microparasite strains or types will be extremely common.
If neuroimaging is the answer, what is the question?
Authors: Kosslyn S. M.
Published: July 2002

It is unclear that we will come to a better understanding of mental processes simply by observing which neural loci are activated while subjects perform a task. Rather, I suggest here that it is better to come armed with a question that directs one to design tasks in ways that take advantage of the strengths of neuroimaging techniques (particularly positron emission tomography and functional magnetic resonance imaging). Here I develop a taxonomy of types of questions that can be easily addressed by such techniques. The first class of questions focuses on how information processing is implemented in the brain; these questions can be posed at a very coarse scale, focusing on the entire system that confers a particular ability, or at increasingly more specific scales, ultimately focusing on individual structures or processes. The second class of questions focuses on specifying when particular processes and structures are invoked; these questions focus on how one can use patterns of activation to infer that specific processes and structures were invoked, and on how processing changes in different circumstances. The use of neuroimaging to address these questions is illustrated with results from experiments on visual cognition, and caveats regarding the logic of inference in each case are noted. Finally, the necessary interplay between neuroimaging and behavioural studies is stressed.
Fibroblast growth factor receptor–dependent morphogenesis of theDrosophilamesoderm
Authors: Wilson Robert , Leptin Maria
Published: July 2002

TheDrosophilafibroblast growth factor (FGF) receptors Heartless and Breathless are required for the morphogenesis of the mesoderm and the tracheal system. In this article we discuss a number of questions relating to the morphogenesis of these tissues and speculate on poorly understood aspects of the underlying mechanisms. As yet a ligand has not been identified for Heartless, but in the case of Breathless the ligand may in some situations act as a chemotactic signal. We consider it unlikely that release of a distant chemotactic signal plays a role in the morphogenesis of the mesoderm. Instead we propose that the change in the mesoderm from an invaginated epithelium to a single layer of cells spread out on the ectoderm could be a result of the mesodermal cells trying to maximize their contact with the ectoderm. Exactly how the activation of the FGF receptors affects cell behaviour and leads to cell movement is not understood. The signal could simply be permissive, causing cells to become motile, or it could act as a directional signal for cells that are already motile, or perhaps provide both functions. Furthermore, it is unclear how signal transduction is coupled to morphological change. It seems unlikely that activation of transcription targets is essential for cell migration and it is possible that FGF signalling may have a direct effect on the cytoskeleton independent of the activation of the mitogen–activated protein kinase cascade. Analysis of the function ofdof, which encodes a cytoplasmic protein required for FGF signal transduction may provide an insight into these issues.
Protein synthesis in the dendrite
Authors: Tang Shao Jun , Schuman Erin M.
Published: July 2002

In neurons, many proteins that are involved in the transduction of synaptic activity and the expression of neural plasticity are specifically localized at synapses. How these proteins are targeted is not clearly understood. One mechanism is synaptic protein synthesis. According to this idea, messenger RNA (mRNA) translation from the polyribosomes that are observed at the synaptic regions provides a local source of synaptic proteins. Although an increasing number of mRNA species has been detected in the dendrite, information about the synaptic synthesis of specific proteins in a physiological context is still limited. The physiological function of synaptic synthesis of specific proteins in synaptogenesis and neural plasticity expression remains to be shown. Experiments aimed at understanding the mechanisms and functions f synaptic protein synthesis might provide important information about the molecular nature of neural plasticity.
Identification of Potential Interaction Networks Using Sequence-Based Searches for Conserved Protein-Protein Interactions or “Interologs”
Authors: Matthews Lisa R. , Vaglio Philippe , Reboul Jérôme , Ge Hui , Davis Brian P. , Garrels James , Vincent Sylvie , Vidal Marc
Published: July 2002

Protein interaction maps have provided insight into the relationships among the predicted proteins of model organisms for which a genome sequence is available. These maps have been useful in generating potential interaction networks, which have confirmed the existence of known complexes and pathways and have suggested the existence of new complexes and or crosstalk between previously unlinked pathways. However, the generation of such maps is costly and labor intensive. Here, we investigate the extent to which a protein interaction map generated in one species can be used to predict interactions in another species.
Arginine‐140 and isoleucine‐141 determine the 17β‐estradiol‐binding specificity of the sex‐steroid‐binding protein (SBP, or SHBG) of human plasma
Authors: Petra Philip H. , Adman Elinor T. , Orr William R. , Woodcock Katherine T. , Groff Christine , Sui Li‐Ming
Published: July 2002

Arginine‐140 and isoleucine‐141 were identified as key determinants of 17β‐estradiol (E2) binding affinity of the sex‐steroid‐binding protein (SBP, or SHBG) of human plasma. Amino acid residues that differ between human and rabbit SBP sequences were replaced in the human protein and the products tested for lowered E2binding activity as are seen in the rabbit protein. Only mutants containing either R140K or I141L replacements display an E2 equilibrium dissociation constant (Kd) higher than the wild type, reaching a value of 30 nM when both were present. The 5α‐dihydrotestosterone (DHT) equilibrium dissociation constant of these mutants was unaffected. The quadruple mutant M107I/I138V/R140K/I141L yielded an E2 Kd of 65 nM, significantly closer to the 80 nM rabbit SBP E2 Kd value. Although mutants containing the M107I and I138V replacements in the absence of R140K and I141L had normal E2 Kds, the presence of the M107I replacement in the quadruple mutant was necessary to obtain an accurate E2 Kd value by competitive Scatchard analysis. Molecular modeling using coordinates for the recently determined N‐terminal domain of human SBP revealed a significant shift of the F56 phenyl ring away from ring A of E2 in mutant models containing the R140K and I141L replacements. We conclude that R140 and I141 are required for sustaining the right proximity of the phenyl ring of F56 to ring A of 17β‐estradiol, thus optimizing the E2‐binding affinity of human SBP.
Substitution of conserved methionines by leucines in chloroplast small heat shock protein results in loss of redox‐response but retained chaperone‐like activity
Authors: Gustavsson Niklas , Kokke Bas P.A. , Anzelius Björn , Boelens Wilbert C. , Sundby Cecilia
Published: July 2002

During evolution of land plants, a specific motif occurred in the N‐terminal domain of the chloroplast‐localized small heat shock protein, Hsp21: a sequence with highly conserved methionines, which is predicted to form an amphipathic α‐helix with the methionines situated along one side. The functional role of these conserved methionines is not understood. We have found previously that treatment, which causes methionine sulfoxidation in Hsp21, also leads to structural changes and loss of chaperone‐like activity. Here, mutants of Arabidopsis thaliana Hsp21 protein were created by site‐directed mutagenesis, whereby conserved methionines were substituted by oxidation‐resistant leucines. Mutants lacking the only cysteine in Hsp21 were also created. Protein analyses by nondenaturing electrophoresis, size exclusion chromatography, and circular dichroism proved that sulfoxidation of the four highly conserved methionines (M49, M52, M55, and M59) is responsible for the oxidation‐induced conformational changes in the Hsp21 oligomer. In contrast, the chaperone‐like activity was not ultimately dependent on the methionines, because it was retained after methionine‐to‐leucine substitution. The functional role of the conserved methionines in Hsp21 may be to offer a possibility for redox control of chaperone‐like activity and oligomeric structure dynamics.
Site‐directed mutations of human hemoglobin at residue 35β: A residue at the intersection of the α1β1, α1β2, and α1α2 interfaces
Authors: Kavanaugh Jeffrey S. , Weydert Jamie A. , Rogers Paul H. , Arnone Arthur , Hui Hilda L. , Wierzba Anita M. , Kwiatkowski Laura D. , Paily Paul , Noble Robert W. , Bruno Stefano , Mozzarelli Andrea
Published: July 2002

Because Tyr35β is located at the convergence of the α1β1, α1β2, and α1α2 interfaces in deoxyhemoglobin, it can be argued that mutations at this position may result in large changes in the functional properties of hemoglobin. However, only small mutation‐induced changes in functional and structural properties are found for the recombinant hemoglobins βY35F and βY35A. Oxygen equilibrium‐binding studies in solution, which measure the overall oxygen affinity (the p50) and the overall cooperativity (the Hill coefficient) of a hemoglobin solution, show that removing the phenolic hydroxyl group of Tyr35β results in small decreases in oxygen affinity and cooperativity. In contrast, removing the entire phenolic ring results in a fourfold increase in oxygen affinity and no significant change in cooperativity. The kinetics of carbon monoxide (CO) combination in solution and the oxygen‐binding properties of these variants in deoxy crystals, which measure the oxygen affinity and cooperativity of just the T quaternary structure, show that the ligand affinity of the T quaternary structure decreases in βY35F and increases in βY35A. The kinetics of CO rebinding following flash photolysis, which provides a measure of the dissociation of the liganded hemoglobin tetramer, indicates that the stability of the liganded hemoglobin tetramer is not altered in βY35F or βY35A. X‐ray crystal structures of deoxy βY35F and βY35A are highly isomorphous with the structure of wild‐type deoxyhemoglobin. The βY35F mutation repositions the carboxyl group of Asp126α1 so that it may form a more favorable interaction with the guanidinium group of Arg141α2. The βY35A mutation results in increased mobility of the Arg141α side chain, implying that the interactions between Asp126α1 and Arg141α2 are weakened. Therefore, the changes in the functional properties of these 35β mutants appear to correlate with subtle structural differences at the C terminus of the α‐subunit.
High‐resolution regional hyperthermia treatment planning
Authors: Van de Kamer Jeroen B.
Published: July 2002

The major difficulties in electromagnetic regional hyperthermia are the occurrence of systematic stress and local high temperatures (hot spots). This thesis describes the development of a planning system to get more insight in hyperthermia treatments. The system is based on a finite‐difference time‐domain computer model to calculate the specific absorption rate (SAR) distribution within a patient. Segmenting a CT data set into fat, muscle, and bone and using literature‐based values of the dielectric properties results in the required dielectric patient model. Because the SAR computation on CT‐resolution (1×1×5 would require 310 days, this high‐resolution is down‐scaled to a lower resolution of 1 (computation time 2.8 hours). The use of the HTP system reveals the close relation between SAR distribution and patient anatomy, stressing the need for high‐resolution computations. For this purpose a method called quasistatic zooming has been developed: from the low‐resolution E‐field distribution the high‐resolution potential distribution at the surface of a small subvolume is calculated. With this potential distribution and the high‐resolution patient geometry, the high‐resolution SAR distribution is computed using a quasistatic SAR model. Repeating this procedure yields the high‐resolution SAR distribution for an arbitrary volume of interest. With this method it takes 4.3 days to compute CT‐resolution SAR distributions. SAR maxima that are predicted by both quasistatic zooming and high‐resolution SAR modeling are not predicted by low‐resolution computations and vice versa. Hence, zooming is required for reliable treatment planning. Whether SAR maxima lead to hot spots depends on local blood flow (discrete vasculature, local perfusion) and will be investigated in a succeeding project.
Treatment of macular degeneration with proton beams
Authors: Moyers M. F. , Galindo R. A. , Yonemoto L. T. , Loredo L. , Friedrichsen E. J. , Kirby M. A. , Slater J. D. , Slater J. M.
Published: July 2002

Subfoveal neovascular membranes (SNVMs) are a leading cause of severe visual loss in the elderly in the United States. Previously, the only treatment that could halt progression of this disease was laser photocoagulation, which was, however, accompanied by immediate reduction in visual acuity. A single narrow proton beam was used to irradiate 45 patients to either 8 or 14 Cobalt Gray Equivalent. The alignment technique and dosimetry of these treatments are described. The proton beam direction, range, and modulation were planned with the assistance of an eye‐specific planning program. A single anterior beam was used, with patients looking nasally toward a blinking fixation light at an angle of 30°. Patients were aligned using a light field projected through a slit collimator. Patients' positions were monitored during treatment with a short‐focal‐length camera. Depth dose in a flat phantom was measured with a small‐diameter parallel plate ionization chamber. Lateral profiles were measured at several depths with silver halide film. Each treatment session lasted 15 min, of which 1 min consisted of beam delivery. The proton beam stopped in the orbital cavity, delivering no primary proton dose to the brain. Dose to the center of the lens of the involved eye was less than 0.5% of the dose delivered to the macula. Treatments of SNVMs with proton beams require only a short visit to the hospital, little immobilization effort, and a minimal amount of treatment room and beam time. Compared to previous treatment trials using x‐ray beams, the dose to nonocular tissues is reduced significantly.
Evidence for an analytic perception of multiharmonic sounds in the bat, Megaderma lyra, and its possible role for echo spectral analysis
Authors: Krumbholz Katrin , Schmidt Sabine
Published: July 2002

For echolocation, the gleaning bat Megaderma lyra relies on short and broadband calls consisting of multiple harmonic components, each of which is downward frequency modulated. The harmonic components in M. lyra’s calls have a relatively small frequency excursion and do not overlap spectrally. Broadband calls of other bat species, on the other hand, often consist of only a few harmonics which are modulated over broad and sometimes overlapping frequency ranges. A call consisting of narrow and nonoverlapping harmonic components may provide a less complete representation of target structure than a call which consists of broadly modulated components. However, a multiharmonic call may help the bats to perceive local spectral changes in the echo from shifts in the peak frequencies of single harmonics, and thereby to extract additional information about the target. To assess this hypothesis, the accuracy with which M. lyra can analyze frequency shifts of single partials in multiharmonic complex tones was investigated. A two-alternative, forced-choice behavioral task was used to measure M. lyra’s frequency discrimination threshold for the third partial in complex tones whose spectral composition resembled that of the bat’s sonar calls. The discrimination threshold for the third partial in a 21.5-kHz harmonic tone amounted to about 2% and was similar to the bat’s pure-tone discrimination threshold at 64.5 kHz. Discrimination performance was essentially unaffected by random frequency changes of the other partials and by reducing stimulus duration from 50.5 to 1.5 ms. Both findings are in accordance with predictions made on the basis of the shape of M. lyra’s cochlear filters. The comparison between the observed frequency discrimination performance and a computational estimate of the expected frequency shift in the third harmonic of an echo reflected by a simple, two-front target showed that M. lyra’s frequency resolution is sufficient for analyzing the target-specific information conveyed by shifts in the peak frequency of single echo components.
Array element localization for towed marine seismic arrays
Authors: Dosso Stan E. , Riedel Michael
Published: July 2002

This paper presents an approach to array element localization (AEL) for towed marine seismic arrays based on regularized inversion of direct and bottom-reflected acoustic ray travel times picked from recorded seismic sections. Depth-sensor measurements at a number of points along the array are included as a priori estimates (with uncertainties) in the inversion. The smoothest array shape consistent with the acoustic data and prior estimates is determined by minimizing the array curvature or roughness. A smooth array shape is physically reasonable; in addition, minimizing curvature provides a priori information about the correlation between hydrophone positions that allows the estimation of both the offset and depth of hydrophones that record only one (or even no) acoustic arrival due to the shadowing effects of water-column refraction or reflection from arbitrary bathymetry. The AEL inversion is applied to a 102-sensor, 1.2-km towed array to correct receiver positions in the seismic velocity analysis of a seabed gas hydrate survey.
Auditory brainstem response recovery in the dolphin as revealed by double sound pulses of different frequencies
Authors: Popov Vladimir V. , Supin Alexander Ya. , Klishin Vladimir O.
Published: July 2002

Recovery of auditory brainstem responses (ABR) in a bottlenose dolphin was studied in conditions of double-pip stimulation when two stimuli in a pair differed in frequency and intensity. When the conditioning and test stimuli were of equal frequencies, the test response was markedly suppressed at short interstimulus intervals; complete recovery appeared at intervals from about 2 ms (when two stimuli were of equal intensity) to 10–20 ms (when the conditioning stimulus exceeded the test by up to 40 dB). When the two stimuli were of different frequencies, the suppression diminished and was almost absent at a half-octave difference even if the conditioning stimulus exceeded the test one by 40 dB. Frequency-dependence curves (ABR amplitude dependence on frequency difference between the two stimuli) had equivalent rectangular bandwidth from ±0.2 oct at test stimuli of 20 dB above threshold to ±0.5 oct at test stimuli of 50 dB above threshold.
Distortion product otoacoustic emission input/output functions in normal-hearing and hearing-impaired human ears
Authors: Dorn Patricia A. , Konrad-Martin Dawn , Neely Stephen T. , Keefe Douglas H. , Cyr Emily , Gorga Michael P.
Published: July 2002

DPOAE input/output (I/O) functions were measured at 7f2 frequencies (1 to 8 kHz; f2/f1=1.22) over a range of levels (−5 to 95 dB SPL) in normal-hearing and hearing-impaired human ears. L1-L2 was level dependent in order to produce the largest 2 f1-f2 responses in normal ears. System distortion was determined by collecting DP data in six different acoustic cavities. These data were used to derive a multiple linear regression model to predict system distortion levels. The model was tested on cochlear-implant users and used to estimate system distortion in all other ears. At most but not all f2’s, measurements in cochlear implant ears were consistent with model predictions. At all f2 frequencies, the ears with normal auditory thresholds produced I/O functions characterized by compressive nonlinear regions at moderate levels, with more rapid growth at low and high stimulus levels. As auditory threshold increased, DPOAE threshold increased, accompanied by DPOAE amplitude reductions, notably over the range of levels where normal ears showed compression. The slope of the I/O function was steeper in impaired ears. The data from normal-hearing ears resembled direct measurements of basilar membrane displacement in lower animals. Data from ears with hearing loss showed that the compressive region was affected by cochlear damage; however, responses at high levels of stimulation resembled those observed in normal ears.
Power flow in an aeroelastic plate backed by a reverberant cavity
Authors: Frampton Kenneth D. , Clark Robert L.
Published: July 2002

This paper investigates the modeling of an elastic plate coupled to a reverberant acoustic enclosure and subjected to convected fluid loading. The primary objective of this work is to quantify the effects of variations in external fluid convection velocity on power flow from the plate. The plate power flow constituents consist of injected power due to turbulent boundary layer (TBL) pressure disturbance, sound power radiated to the convected flow, sound power radiated to a reverberant cavity, and power dissipated through structural damping. Results indicate that variations in the convected fluid loading can significantly alter the balance in power flow. These results demonstrate the importance of including the effects of convected fluid loading in modeling the sound transmission through plates. Results also indicate that convected fluid loading serves to decrease the sound power radiated to the cavity as the external flow velocity increases. This effect, however, is overwhelmed by the increase in turbulent boundary layer pressures with the square of the flow speed. This work concludes with a discussion on the potential effectiveness of dissipative control strategies (be they active or passive) toward minimizing the sound transmitted to the cavity.
Modeling auditory processing of amplitude modulation. I. Detection and masking with narrow-band carriers
Authors: Dau Torsten , Kollmeier Birger , Kohlrausch Armin
Published: July 2002

This paper presents a quantitative model for describing data from modulation-detection and modulation-masking experiments, which extends the model of the “effective” signal processing of the auditory system described in Dau et al. [J. Acoust. Soc. Am. 99, 3615–3622 (1996)]. The new element in the present model is a modulation filterbank, which exhibits two domains with different scaling. In the range 0–10 Hz, the modulation filters have a constant bandwidth of 5 Hz. Between 10 Hz and 1000 Hz a logarithmic scaling with a constant Q value of 2 was assumed. To preclude spectral effects in temporal processing, measurements and corresponding simulations were performed with stochastic narrow-band noise carriers at a high center frequency (5 kHz). For conditions in which the modulation rate (fmod) was smaller than half the bandwidth of the carrier (Δf), the model accounts for the low-pass characteristic in the threshold functions [e.g., Viemeister, J. Acoust. Soc. Am. 66, 1364–1380 (1979)]. In conditions with fmod>Δf/2, the model can account for the high-pass characteristic in the threshold function. In a further experiment, a classical masking paradigm for investigating frequency selectivity was adopted and translated to the modulation-frequency domain. Masked thresholds for sinusoidal test modulation in the presence of a competing modulation masker were measured and simulated as a function of the test modulation rate. In all cases, the model describes the experimental data to within a few dB. It is proposed that the typical low-pass characteristic of the temporal modulation transfer function observed with wide-band noise carriers is not due to “sluggishness” in the auditory system, but can instead be understood in terms of the interaction between modulation filters and the inherent fluctuations in the carrier.
Observation and extraction of three-dimensional information on fish schools
Authors: Simmonds John , Gerlotto Francois , Fernandes Paul , MacLennan David
Published: July 2002

The paper describes the performance calibration and use of a 90-deg sector scanning sonar for the collection and extraction of information on the 3D structure of fish schools. The equipment, which consists of a 455-kHz 60-beam sector scanning sonar linked to a PC is described briefly. The specific calibration problems of a high-frequency instrument with multiple beams is discussed and calibration data from on-axis and beam shape measurements are presented. The deployment of the instrument for data collection at sea and the data collection methods are described. Examples of the data collected are given. A three-dimensional data processing algorithm is presented along with results of reconstruction from selected schools. The statistical properties of within school data are discussed along with indications of the precision of internal structures that can be evaluated using the sonar. The development of this system is supported by the European research program, AIR.
Physical modeling of individual head-related transfer functions (HRTFs)
Authors: Sottek Roland , Genuit Klaus
Published: July 2002

A model of HRTFs was developed based on the Ph.D. thesis of Genuit. The two basic ideas are (1) HRTFs can be described by the influence of a few acoustically relevant objects; first the head was modeled by a sphere and the pinna with cavum conchae by two elliptical disks with an eccentric cylindrical cave (ear canal). (2) Individual variations of HRTFs correspond to variations of geometrical parameters (diameter of sphere, dimensions of disks and cave,...); the position of the ear canal entrance point is the most important parameter. Simulation results were compared to HRTFs measured with an artificial head of well-known geometry. In general, a good correspondence between calculated and measured HRTFs was found. The correlation is significantly higher if the influence of shoulder/torso is considered, too, modeled by an additional rigid sphere. Second, the shape of head and shoulder/torso was approximated with oblate respective prolate spheroids in order to get even better results. Sound field calculation were performed using numerical methods (boundary element method, source simulation technique) and analytical methods (solution of the wave equation, use of Huygens’ integral formula). The interaction between the different reflecting and diffracting bodies was analyzed to validate a simplified model.
C-scan imaging in molten zinc by focused ultrasonic waves
Authors: Ihara Ikuo , Jen Cheng-Kuei , Ramos França Demartonne
Published: July 2002

Ultrasonic images of a small steel object immersed in molten zinc at 600 °C are obtained with high spatial resolution using a focused ultrasonic pulse-echo technique. The focused ultrasonic waves are generated by a spherical acoustic lens which has been machined at the probing end of a clad buffer rod. The backscattered echoes from the object surface have a signal-to-noise ratio of 35 dB at 10 MHz in molten zinc. The ability to provide high spatial resolution measurements in molten metal is demonstrated by comparing the results obtained in molten zinc with those obtained in water.