bluuebunny/crossref_metadata_2025 huggingface dataset:
Periodic solutions in periodic state-dependent delay equations and population models
Authors: Li Yongkun , Kuang Yang
Published: July 2002

Sufficient and realistic conditions are obtained for the existence of positive periodic solutions in periodic equations with state-dependent delay. The method involves the application of the coincidence degree theorem and estimations of uniform upper bounds on solutions. Applications of these results to some population models are presented. These application results indicate that seasonal effects on population models often lead to synchronous solutions. In addition, we may conclude that when both seasonality and time delay are present and deserve consideration, the seasonality is often the generating force for the often observed oscillatory behavior in population densities.
Characterizations of contraction 𝐶-semigroups
Authors: Li Miao , Huang Falun
Published: July 2002

A

C
C

-semigroup

{
T
(
t
)

}

t
≥
0

\{T(t)\}_{t\ge 0}

is of contractions if

‖
T
(
t
)
x
‖
≤
‖
C
x
‖

\|T(t)x\|\le \|Cx\|

for

t
≥
0

t\ge 0

,

x
∈
X

x\in X

. Using the Hille-Yosida space, we completely characterize the generators of contraction

C
C

-semigroups. We also give the Lumer-Phillips theorem for

C
C

-semigroups in several special cases.
Timelike periodic trajectories in spatially compact Lorentz manifolds
Authors: Sánchez Miguel
Published: July 2002

A result on the existence of timelike periodic trajectories in a general class of Lorentzian manifolds

R

×
M

\mathbb R{}\times M

, with compact

M
M

, is obtained. The proof is based on arguments concerning closed geodesics and causality theory.
Robin boundary value problems on arbitrary domains
Authors: Daners Daniel
Published: July 2002

We develop a theory of generalised solutions for elliptic boundary value problems subject to Robin boundary conditions on arbitrary domains, which resembles in many ways that of the Dirichlet problem. In particular, we establishLpL_p-LqL_q-estimates which turn out to be the best possible in that framework. We also discuss consequences to the spectrum of Robin boundary value problems. Finally, we apply the theory to parabolic equations.
Multi-bump orbits homoclinic to resonance bands
Authors: Kaper Tasso , Kovacic Gregor
Published: July 2002

We establish the existence of several classes of multi-bump orbits homoclinic to resonance bands for completely-integrable Hamiltonian systems subject to small-amplitude Hamiltonian or dissipative perturbations. Each bump is a fast excursion away from the resonance band, and the bumps are interspersed with slow segments near the resonance band. The homoclinic orbits, which include multi-bump Šilnikov orbits, connect equilibria and periodic orbits in the resonance band. The main tools we use in the existence proofs are the exchange lemma with exponentially small error and the existence theory of orbits homoclinic to resonance bands which make only one fast excursion away from the resonance bands.
A Construction of the Level 3 Modules for the Affine Lie Algebra 𝐴₂⁽²⁾ and a New Combinatorial Identity of the Rogers-Ramanujan Type
Authors: Capparelli Stefano
Published: July 2002

We obtain a vertex operator construction of level 3 standard representations for the affine Lie algebra

A
2

(
2
)

A_2^{(2)}

. As a corollary, we also get new conbinatorial identities.
Error estimates for the finite element approximation of linear elastic equations in an unbounded domain
Authors: Han Houde , Bao Weizhu
Published: July 2002

In this paper we present error estimates for the finite element approximation of linear elastic equations in an unbounded domain. The finite element approximation is formulated on a bounded computational domain using a nonlocal approximate artificial boundary condition or a local one. In fact there are a family of nonlocal approximate boundary conditions with increasing accuracy (and computational cost) and a family of local ones for a given artificial boundary. Our error estimates show how the errors of the finite element approximations depend on the mesh size, the terms used in the approximate artificial boundary condition, and the location of the artificial boundary. A numerical example for Navier equations outside a circle in the plane is presented. Numerical results demonstrate the performance of our error estimates.
Changes in the performances of filter media during clogging and cleaning cycles
Authors: Callé S. , Bémer D. , Thomas D. , Contal P. , Leclerc D.
Published: July 2002

The performance of two filter media used in industrial air cleaning were studied both in the initial state (new filter) and after a number of collection and pulse pressure cleaning cycles. The main difference between them is that one has anti-clogging properties and the other does not. The test aerosol is composed of alumina particles with a median volumetric diameter of 2.6 μm (MMAD=4.8 μm) generated at a concentration of 700 mg m−3. Filtration took place at a velocity of 2 cm s−1. Two parameters, namely pressure drop and efficiency, were monitored according to the collection and cleaning cycles. The comparison of the filtration efficiency of the two media and that of the corresponding industrial dust separator at the end of the cycles showed a close agreement. The separation efficiency calculated with a new medium (corresponding to initial switch-on of the installation) was low and increased very quickly during the cycles. Finally, a phenomenological model was developed to represent the increase in pressure drop of a filter medium after cleaning and was found to be in close agreement with the experimental values.
Rose: generating sequence families.
Authors: Stoye J , Evers D , Meyer F
Published: July 2002

MOTIVATION: We present a new probabilistic model of the evolution of RNA-, DNA-, or protein-like sequences and a software tool, Rose, that implements this model. Guided by an evolutionary tree, a family of related sequences is created from a common ancestor sequence by insertion, deletion and substitution of characters. During this artificial evolutionary process, the 'true' history is logged and the 'correct' multiple sequence alignment is created simultaneously. The model also allows for varying rates of mutation within the sequences, making it possible to establish so-called sequence motifs. RESULTS: The data created by Rose are suitable for the evaluation of methods in multiple sequence alignment computation and the prediction of phylogenetic relationships. It can also be useful when teaching courses in or developing models of sequence evolution and in the study of evolutionary processes. AVAILABILITY: Rose is available on the Bielefeld Bioinformatics WebServer under the following URL: http://bibiserv.TechFak.Uni-Bielefeld.DE/rose/ The source code is available upon request. Contact: folker@TechFak.Uni-Bielefeld.DE
JOY: protein sequence-structure representation and analysis.
Authors: Mizuguchi K , Deane C M , Blundell T L , Johnson M S , Overington J P
Published: July 2002

MOTIVATION: JOY is a program to annotate protein sequence alignments with three-dimensional (3D) structural features. It was developed to display 3D structural information in a sequence alignment and to help understand the conservation of amino acids in their specific local environments. RESULTS:: The JOY representation now constitutes an essential part of the two databases of protein structure alignments: HOMSTRAD (http://www-cryst.bioc.cam.ac.uk/homstrad ) and CAMPASS (http://www-cryst.bioc.cam.ac. uk/campass). It has also been successfully used for identifying distant evolutionary relationships. AVAILABILITY: The program can be obtained via anonymous ftp from torsa.bioc.cam.ac.uk from the directory /pub/joy/. The address for the JOY server is http://www-cryst.bioc.cam.ac.uk/cgi-bin/joy.cgi. CONTACT: kenji@cryst.bioc.cam.ac.uk
Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations.
Authors: Henikoff S , Henikoff J G , Pietrokovski S
Published: July 2002

MOTIVATION: As databanks grow, sequence classification and prediction of function by searching protein family databases becomes increasingly valuable. The original Blocks Database, which contains ungapped multiple alignments for families documented in Prosite, can be searched to classify new sequences. However, Prosite is incomplete, and families from other databases are now available to expand coverage of the Blocks Database. RESULTS: To take advantage of protein family information present in several existing compilations, we have used five databases to construct Blocks+, a unified database that is built on the PROTOMAT/BLOSUM scoring model and that can be searched using a single algorithm for consistent sequence classification. The LAMA blocks-versus-blocks searching program identifies overlapping protein families, making possible a non-redundant hierarchical compilation. Blocks+ consists of all blocks derived from PROSITE, blocks from Prints not present in PROSITE, blocks from Pfam-A not present in PROSITE or Prints, and so on for ProDom and Domo, for a total of 1995 protein families represented by 8909 blocks, doubling the coverage of the original Blocks Database. A challenge for any procedure aimed at non-redundancy is to retain related but distinct families while discarding those that are duplicates. We illustrate how using multiple compilations can minimize this potential problem by examining the SNF2 family of ATPases, which is detectably similar to distinct families of helicases and ATPases. AVAILABILITY: http://blocks.fhcrc.org/
Progenetix.net: an online repository for molecular cytogenetic
aberration data
Authors: Baudis Michael , Cleary Michael L.
Published: July 2002

Summary: Through sequencing projects and, more recently, array-based expression analysis experiments, a wealth of genetic data has become accessible via online resources. In contrast, few of the (molecular-) cytogenetic aberration data collected in the last decades are available in a format suitable for data mining procedures. www.progenetix.net is a new online repository for previously published chromosomal aberration data, allowing the addition of band-specific information about chromosomal imbalances to oncologic data analysis efforts.

Availability: http://www.progenetix.net

Contact: mbaudis@stanford.edu

* To whom correspondence should be addressed.
TMCompare: transmembrane region sequence and structure
Authors: Togawa R. C. , Antoniw J. F. , Mullins J. G. L.
Published: July 2002

Summary: TMCompare is an alignment and visualization tool for comparison of sequence information for membrane proteins contained in SWISS-PROT entries, with structural information contained in PDB files. The program can be used for:

 detection of breaks in α helical structure of transmembrane regions;  examination of differences in coverage between PDB and SWISS-PROT files;  examination of annotation differences between PDB files and associated SWISS-PROT files;  examination and comparison of assigned PDB α helix regions and assigned SWISS-PROT transmembrane regions in linear sequence (one letter code) format;  examination of these differences in 3D using the CHIME plugin, allowing;  analysis of the α and non-α content of transmembrane regions.
Long-range control of expression in yeast
Authors: Mannila Heikki , Patrikainen Anne , Seppänen Jouni
   K. , Kere Juha
Published: July 2002

Contact: juha.kere@biosci.ki.se

* To whom correspondence should be addressed.
Modulation of ISWI function by site‐specific histone acetylation
Authors: Corona Davide F V , Clapier Cedric R , Becker Peter B , Tamkun John W
Published: July 2002

Mutations in Drosophila ISWI, a member of the SWI2/SNF2 family of chromatin remodeling ATPases, alter the global architecture of the male X chromosome. The transcription of genes on this chromosome is increased 2‐fold relative to females due to dosage compensation, a process involving the acetylation of histone H4 at lysine 16 (H4K16). Here we show that blocking H4K16 acetylation suppresses the X chromosome defects resulting from loss of ISWI function in males. In contrast, the forced acetylation of H4K16 in ISWI mutant females causes X chromosome defects indistinguishable from those seen in ISWI mutant males. Increased expression of MOF, the histone acetyltransferase that acetylates H4K16, strongly enhances phenotypes resulting from the partial loss of ISWI function. Peptide competition assays revealed that H4K16 acetylation reduces the ability of ISWI to interact productively with its substrate. These findings suggest that H4K16 acetylation directly counteracts chromatin compaction mediated by the ISWI ATPase.
Short-course therapy of acute cystitis: a brief review of therapeutic strategies
Authors: Tice Alan D.
Published: July 2002

Acute cystitis is one of the commonest medical problems encountered by primary care physicians. It affects more women than men (8:1), but the incidence among men is increasing. Uncomplicated cystitis by definition occurs in healthy patients with a normal urinary tract, whereas complicated cystitis implies a predisposing or underlying condition. A narrow range of aetiological agents is responsible for most uncomplicated cystitis in women (Escherichia coli in 80% of cases). Recently, however, pathogens usually associated with sexually transmitted disease have been implicated. In women with typical symptoms of acute uncomplicated cystitis, an abbreviated laboratory work-up followed by empirical therapy is recommended. Single-dose and 3 day regimens of co-trimoxazole and the quinolones are as effective as longer regimens and have a higher eradication rate than other commonly used antimicrobials. Relapse rates are slightly higher with single-dose therapy. With this success rate plus the reduced cost and improved patient compliance, these regimens have replaced traditional 5 to 14 day courses of treatment. With increasing resistance of the common urinary pathogens to amoxycillin and, now, co-trimoxazole, the quinolones are a logical choice for empirical therapy of uncomplicated urinary tract infections.
The importance of diagnosing genital herpes
Authors: Cusini Marco , Ghislanzoni Massimo
Published: July 2002

Genital herpes is the result of infection by herpes simplex virus type 2 (HSV-2) and, to a lesser extent, HSV-1. Recent years have seen a rise in the prevalence of genital HSV infection in both industrialized and developing countries. The main factors attributed to the spread of HSV infection include asymptomatic virus shedding, and under-recognition and under-diagnosis of the disease. At the level of the individual patient, genital herpes is associated with significant psychosocial morbidity and complications such as neonatal herpes, the result of transmission of HSV from mother to baby. HSV-2 infection is also implicated in the transmission and acquisition of human immunodeficiency virus (HIV). As genital HSV infection has substantial public health implications, increased awareness of the disease and its prevalence, together with better use of diagnostic tests, may be one step towards more effective management and infection control.
Molecular instability in theCOII–tRNALysintergenic region of the human mitochondrial genome: multiple origins of the 9–bp deletion and heteroplasmy for expanded repeats
Authors: Thomas Mark G. , Cook Charles E. , Miller Kevin W. P. , Warin Michael J. , Hagelberg Erika
Published: July 2002

We have identified two individuals from Glasgow in Scotland who have a deletion of one of two copies of the cytochrome oxidise II (COII) intergenic 9–bp sequence motif CCCCCTCTA, located between theCOIIandtRNALysgenes of the human mitochondrial genome. Although this polymorphism is common in Africa and Asia, it has not been reported in Northern Europe. Analysis of the mitochondrial DNA control region sequences of these two individuals suggests that they belong to a lineage that originated independently of the previously characterized African and Asian 9–bp deleted lineages. Among the Scottish population we have also identified a maternal lineage of three generations exhibiting heteroplasmy for two, three and four copies of the CCCCCTCTA motif. Polymerase chain reaction amplification across theCOII–tRNALysintergenic region of these individuals gives different ratios of the three product lengths that are dependent on the concentration of the DNA–binding dye crystal violet. To investigate whether changes in repeat number were generatedde novo, we constructed clones containing known numbers of the CCCCCTCTA motif. In the presence of high concentrations of crystal violet we obtained two, three and four copies of this motif when the amplification template contained only four copies. Various DNA–binding drugs are known to stabilize bulged structures in DNA and contribute to the process of slipped–strand–mispairing during DNA replication. These results suggest that theCOII–tRNALysintergenic region is unstable owing to slipped–strand mispairing. Although sequences containing four copies of the CCCCCTCTA motif are less stablein vitro, we observed an increase in the proportion of mitochondrial genomes with four repeats between a mother and a daughter in the heteroplasmic lineage. From this we conclude that drift in the germ–line lineage is a main factor in the maintenance or loss of heteroplasmy.
Converging levels of analysis in the cognitive neuroscience of visual attention
Authors: Duncan John
Published: July 2002

Experiments using behavioural, lesion, functional imaging and single neuron methods are considered in the context of a neuropsychological model of visual attention. According to this model, inputs compete for representation in multiple visually responsive brain systems, sensory and motor, cortical and subcortical. Competition is biased by advance priming of neurons responsive to current behavioural targets. Across systems competition is integrated such that the same, selected object tends to become dominant throughout. The behavioural studies reviewed concern divided attention within and between modalities. They implicate within–modality competition as one main restriction on concurrent stimulus identification. In contrast to the conventional association of lateral attentional focus with parietal lobe function, the lesion studies show attentional bias to be a widespread consequence of unilateral cortical damage. Although the clinical syndrome of unilateral neglect may indeed be associated with parietal lesions, this probably reflects an assortment of further deficits accompanying a simple attentional imbalance. The functional imaging studies show joint involvement of lateral prefrontal and occipital cortex in lateral attentional focus and competition. The single unit studies suggest how competition in several regions of extrastriate cortex is biased by advance priming of neurons responsive to current behavioural targets. Together, the concepts of competition, priming and integration allow a unified theoretical approach to findings from behavioural to single neuron levels.
Molecular mechanisms involved in bacterial speck disease resistance of tomato
Authors: Gu Yong–Qiang , Martin Gregory B.
Published: July 2002

An important recent advance in the field of plant–microbe interactions has been the cloning of genes that confer resistance to specific viruses, bacteria, fungi or nematodes. Disease resistance (R) genes encode proteins with predicted structural motifs consistent with them having roles in signal recognition and transduction. The future challenge is to understand howRgene products specifically perceive defence–eliciting signals from the pathogen and transduce those signals to pathways that lead to the activation of plant defence responses. In tomatoes, the Pto kinase (product of thePto Rgene) confers resistance to strains of the bacterial speck pathogen,Pseudomonas syringaepv.tomato, that carry the corresponding avirulence geneavrPto. Resistance to bacterial speck disease is initiated by a mechanism involving the physical interaction of the Pto kinase and the AvrPto protein. This recognition event initiates signalling events that lead to defence responses including an oxidative burst, the hypersensitive response and expression of pathogenesis–related genes. Pto–interacting (Pti) proteins have been identified that appear to act downstream of the Pto kinase and our current studies are directed at elucidating the roles of these components.
The organization of mature T–cell pools
Authors: Tanchot Corinne , Fernandes Henrique Veiga , Rocha Benedita
Published: July 2002

To deal with exogenous pathogens the peripheral T–cell compartment requires diverse repertoires (as those of naive cells) and efficient responses, the latter dependent on the persistence of memory cells. In the present work we show that (i) naive and memory cells differ in the type of interactions required for survival and division; (ii) they are segregated into independent ecological niches; (iii) that the size of each niche is controlled by independent homeostatic mechanisms; and (iv) that naive T cells do not have intrinsic life spans, surviving in the absence of thymus output but being continuously substituted by thymus export. The independent homeostatic regulation of the naive and memory T–cell pools guarantees the maintenance of versatile and efficient repertoires throughout life as well as the persistence of the naive T–cell pool after the thymus atrophies at puberty.
Were vertebrates octoploid?
Authors: Furlong Rebecca F. , Holland Peter W. H.
Published: July 2002

It has long been suggested that gene and genome duplication play important roles in the evolution of organismal complexity. For example, work by Ohno proposed that two rounds of whole genome doubling (tetraploidy) occurred during the evolution of vertebrates: the extra genes permitting an increase in physiological and anatomical complexity. Several modifications of this ‘two tetraploidies’ hypothesis have been proposed, taking into account accumulating data, and there is wide acceptance of the basic scheme. In the past few years, however, several authors have raised doubts, citing lack of direct support or even evidence to the contrary. Here, we review the evidence for and against the occurrence of tetraploidies in early vertebrate evolution, and present a new compilation of molecular phylogenetic data for amphioxus. We argue that evidence in favour of tetraploidy, based primarily on genome and gene family analyses, is strong. Furthermore, we show that two observations used as evidence against genome duplication are in fact compatible with the hypothesis: but only if the genome doubling occurred by two closely spaced sequential rounds of autotetraploidy. We propose that early vertebrates passed through an autoautooctoploid phase in the evolution of their genomes.
A crucial component of the endoderm formation pathway, CASANOVA, is encoded by a novel sox-related gene
Authors: Dickmeis Thomas , Mourrain Philippe , Saint-Etienne Laure , Fischer Nadine , Aanstad Pia , Clark Matthew , Strähle Uwe , Rosa Frédéric
Published: July 2002

casanova (cas) mutant zebrafish embryos lack endoderm and develop cardia bifida. In a substractive screen for Nodal-responsive genes, we isolated an HMG box-containing gene,10J3, which is expressed in the endoderm. Thecas phenotype is rescued by overexpression of 10J3and can be mimicked by 10J3-directed morpholinos. Furthermore, we identified a mutation within 10J3 coding sequence that cosegregates with the cas phenotype, clearly demonstrating that cas is encoded by 10J3. Epistasis experiments are consistent with an instructive role forcas in endoderm formation downstream of Nodal signals and upstream of sox17. In the absence of casactivity, endoderm progenitors differentiate into mesodermal derivatives. Thus, cas is an HMG box-containing gene involved in the fate decision between endoderm and mesoderm that acts downstream of Nodal signals.
Ablation of NF1 function in neurons induces abnormal development of cerebral cortex and reactive gliosis in the brain
Authors: Zhu Yuan , Romero Mario I. , Ghosh Pritam , Ye Zhengyi , Charnay Patrick , Rushing Elizabeth J. , Marth Jamey D. , Parada Luis F.
Published: July 2002

Neurofibromatosis type 1 (NF1) is a prevalent genetic disorder that affects growth properties of neural-crest-derived cell populations. In addition, approximately one-half of NF1 patients exhibit learning disabilities. To characterize NF1 function both in vitro and in vivo, we circumvent the embryonic lethality of NF1 null mouse embryos by generating a conditional mutation in the NF1 gene usingCre/loxP technology. Introduction of a Synapsin I promoter driven Cre transgenic mouse strain into the conditional NF1 background has ablated NF1 function in most differentiated neuronal populations. These mice have abnormal development of the cerebral cortex, which suggests that NF1 has an indispensable role in this aspect of CNS development. Furthermore, although they are tumor free, these mice display extensive astrogliosis in the absence of conspicuous neurodegeneration or microgliosis. These results indicate that NF1-deficient neurons are capable of inducing reactive astrogliosis via a non-cell autonomous mechanism.
Epigenetic variation in Arabidopsis disease resistance
Authors: Stokes Trevor L. , Kunkel Barbara N. , Richards Eric J.
Published: July 2002

Plant pathogen resistance is mediated by a large repertoire of resistance (R) genes, which are often clustered in the genome and show a high degree of genetic variation. Here, we show that anArabidopsis thaliana R-gene cluster is also subject to epigenetic variation. We describe a heritable but metastable epigenetic variant bal that overexpresses the R-like geneAt4g16890 from a gene cluster on Chromosome 4. The balvariant and Arabidopsis transgenics overexpressing theAt4g16890 gene are dwarfed and constitutively activate the salicylic acid (SA)-dependent defense response pathway. Overexpression of a related R-like gene also occurs in the ssi1(suppressor of SA insensitivity1) background, suggesting that ssi1 is mechanistically related to bal.
High probability of disrupting a disulphide bridge mediated by an endogenous excited tryptophan residue
Authors: Neves‐Petersen Maria Teresa , Gryczynski Zygmunt , Lakowicz Joseph , Fojan Peter , Pedersen Shona , Petersen Evamaria , Bjørn Petersen Steffen
Published: July 2002

It is well known that ultraviolet (UV) radiation may reduce or even abolish the biological activity of proteins and enzymes. UV light, as a component of sunlight, is illuminating all light‐exposed parts of living organisms, partly composed of proteins and enzymes. Although a considerable amount of empirical evidence for UV damage has been compiled, no deeper understanding of this important phenomenon has yet emerged. The present paper presents a detailed analysis of a classical example of UV‐induced changes in three‐dimensional structure and activity of a model enzyme, cutinase from Fusarium solani pisi. The effect of illumination duration and power has been investigated. A photon‐induced mechanism responsible for structural and functional changes is proposed. Tryptophan excitation energy disrupts a neighboring disulphide bridge, which in turn leads to altered biological activity and stability. The loss of the disulphide bridge has a pronounced effect on the fluorescence quantum yield, which has been monitored as a function of illumination power. A general theoretical model for slow two‐state chemical exchange is formulated, which allows for calculation of both the mean number of photons involved in the process and the ratio between the quantum yields of the two states. It is clear from the present data that the likelihood for UV damage of proteins is directly proportional to the intensity of the UV radiation. Consistent with the loss of the disulphide bridge, a complex pH‐dependent change in the fluorescence lifetimes is observed. Earlier studies in this laboratory indicate that proteins are prone to such UV‐induced radiation damage because tryptophan residues typically are located as next spatial neighbors to disulphide bridges. We believe that these observations may have far‐reaching implications for protein stability and for assessing the true risks involved in increasing UV radiation loads on living organisms.
Rapid screening for improved solubility of small human proteins produced as fusion proteins in Escherichia coli
Authors: Hammarström Martin , Hellgren Niklas , van den Berg Susanne , Berglund Helena , Härd Torleif
Published: July 2002

A prerequisite for structural genomics and related projects is to standardize the process of gene overexpression and protein solubility screening to enable automation for higher throughput. We have tested a methodology to rapidly subclone a large number of human genes and screen these for expression and protein solubility in Escherichia coli. The methodology, which can be partly automated, was used to compare the effect of six different N‐terminal fusion proteins and an N‐terminal 6*His tag. As a realistic test set we selected 32 potentially interesting human proteins with unknown structures and sizes suitable for NMR studies. The genes were transferred from cDNA to expression vectors using subcloning by recombination. The subcloning yield was 100% for 27 (of 32) genes for which a PCR fragment of correct size could be obtained. Of these, 26 genes (96%) could be overexpressed at detectable levels and 23 (85%) are detected in the soluble fraction with at least one fusion tag. We find large differences in the effects of fusion protein or tag on expression and solubility. In short, four of seven fusions perform very well, and much better than the 6*His tag, but individual differences motivate the inclusion of several fusions in expression and solubility screening. We also conclude that our methodology and expression vectors can be used for screening of genes for structural studies, and that it should be possible to obtain a large fraction of all NMR‐sized and nonmembrane human proteins as soluble fusion proteins in E. coli.
Microdosimetry spectra of the Loma Linda proton beam and relative biological effectiveness comparisons
Authors: Coutrakon G. , Cortese J. , Ghebremedhin A. , Hubbard J. , Johanning J. , Koss P. , Maudsley G. , Slater C. R. , Zuccarelli C. , Robertson J.
Published: July 2002

Protons have long been recognized as low LET radiation in radiotherapy. However, a detailed account of LET (linear energy transfer) and RBE (relative biological effectiveness) changes with incident beam energy and depth in tissue is still unresolved. This issue is particularly important for treatment planning, where the physical dose prescription is calculated from a RBE using cobalt as the reference radiation. Any significant RBE changes with energy or depth will be important to incorporate in treatment planning. In this paper we present microdosimetry spectra for the proton beam at various energies and depths and compare the results to cell survival studies performed at Loma Linda. An empirically determined biological weighting function that depends on lineal energy is used to correlate the microdosimetry spectra with cell survival data. We conclude that the variations in measured RBE with beam energy and depth are small until the distal edge of the beam is reached. On the distal edge, protons achieve stopping powers as high as 100 keV/μm, which is reflected in the lineal energy spectra taken there. Lineal energy spectra 5 cm beyond the distal edge of the Bragg peak also show a high LET component but at a dose rate 600 times smaller than observed inside the proton field.
An analysis of the relationship between radiosensitivity and volume effects in tumor control probability modeling
Authors: Buffa Francesca M. , Fenwick John D. , Nahum Alan E.
Published: July 2002

The dependence of local tumor control probability (tcp) on tumor volume is analyzed and discussed with the help of radiobiological modeling; in particular the impact of possible correlations between mean tumor radiosensitivity and tumor dimensions on the tcp volume dependence is explored. The linear‐quadratic Poissonian tumor control probability (tcp) model was modified to account for the possible dependence of clonogenic cell density and radiosensitivity parameters on tumor volume; then the original and modified versions of the model were fitted to published clinical and laboratory tumor control data. These different versions of the tcp model often fitted tumor control data equally well, because of the high degree of correlation between the parameters. Nevertheless the results were very different from a physical point of view and we suggest that sometimes it is possible to choose between equally good fits on the basis of physical considerations. Possible links between the volume dependence of the mean radiosensitivity and the degree of tumor hypoxia were also analyzed through a comparison of the results of the tcp fit to published measurements of oxygen tension in tumors.
Quality assurance for a treatment planning system in scanned ion beam therapy
Authors: Jäkel O. , Hartmann G. H. , Karger C. P. , Heeg P. , Rassow J.
Published: July 2002

Conformal radiation therapy using dynamic beam delivery systems like scanned ion beams requires concise quality assurance procedures for the complete treatment planning process. For the heavy ion therapy facility at GSI, Darmstadt, a quality assurance program for the treatment planning system (TPS) has been developed. It covers the development and updating of software, data protection and safety, and the application of soft‐ and hardware. The tests also apply to the geometrical precision of imaging devices and the geometrical and dosimetrical verification of dose distributions in different phantoms. The quality assurance program addresses acceptance and constancy tests of the treatment planning program. Results of the acceptance tests served as a basis for its governmental approval. Two main results of the acceptance tests are representative for the overall performance of the system. (1) The geometrical uncertainty that could be achieved for the target point definition, setup accuracy, field contouring, and field alignment is typically 1.5 mm. The uncertainty for the setup verification using digitally reconstructed radiographs (DRR's) is limited to 2 mm. (2) The mean deviations between measured and planned dose values is 3% for standardized cases in a water phantom and up to 6% for more complicated treatment configurations.
An economic analogy to thermodynamics
Authors: Saslow Wayne M.
Published: July 2002

We develop analogies between economic systems and thermodynamics, and show how economic quantities can characterize the state of an economic system in equilibrium. We argue that just as a physical system in thermodynamic equilibrium requires a nonmechanical variable (the temperature T) to specify its state, so does an economic system. In addition, both systems must have a corresponding conjugate quantity, the entropy S. We also develop economic analogies to the free energy, Maxwell relations, and the Gibbs–Duhem relationship. Assuming that economic utility can be measured, we develop an operational definition of an economic temperature scale. We also develop an analogy to statistical mechanics, which leads to Gaussian fluctuations.
Resonant response of complex shell structures
Authors: Photiadis Douglas M. , Houston Brian H. , Williams E. G. , Bucaro J. A.
Published: July 2002

Resonances of shell structures play a prominent role in determining their acoustic characteristics. Among the most important of such characteristics are radiated noise, scattering, and self-noise levels. The nature of the structural resonances, for example the number of modes within a particular frequency band or the overall spatial dependence of the response, determines the importance of these phenomena in various contexts and what steps may be taken to modify their acoustic impact. In the past, knowledge of the resonant response of highly idealized systems has been used to guide the development of quiet platforms. The results of a scale model investigation of the effects of increased complexity on the nature of the resonances of submerged shell structures are reported. Effects presented here are flexural Bloch mode resonances, localized resonances resulting from structural irregularity, and the effects of non-axisymmetry on these phenomena. The implications of these results on acoustic design and the development of systems is discussed.
Simultaneous effects on vowel duration in American English: A covariance structure modeling approach
Authors: Erickson Molly L.
Published: July 2002

The powerful techniques of covariance structure modeling (CSM) long have been used to study complex behavioral phenomenon in the social and behavioral sciences. This study employed these same techniques to examine simultaneous effects on vowel duration in American English. Additionally, this study investigated whether a single population model of vowel duration fits observed data better than a dual population model where separate parameters are generated for syllables that carry large information loads and for syllables that specify linguistic relationships. For the single population model, intrinsic duration, phrase final position, lexical stress, post-vocalic consonant voicing, and position in word all were significant predictors of vowel duration. However, the dual population model, in which separate model parameters were generated for (1) monosyllabic content words and lexically stressed syllables and (2) monosyllabic function words and lexically unstressed syllables, fit the data better than the single population model. Intrinsic duration and phrase final position affected duration similarly for both the populations. On the other hand, the effects of post-vocalic consonant voicing and position in word, while significant predictors of vowel duration in content words and stressed syllables, were not significant predictors of vowel duration in function words or unstressed syllables. These results are not unexpected, based on previous research, and suggest that covariance structure analysis can be used as a complementary technique in linguistic and phonetic research.
Coding of the fundamental frequency in continuous interleaved sampling processors for cochlear implants
Authors: Geurts Luc , Wouters Jan
Published: July 2002

In this study the perception of the fundamental frequency (F0) of periodic stimuli by cochlear implant users is investigated. A widely used speech processor is the Continuous Interleaved Sampling (CIS) processor, for which the fundamental frequency appears as temporal fluctuations in the envelopes at the output. Three experiments with four users of the LAURA (Registered trade mark of Philips Hearing Implants, now Cochlear Technology Centre Europe) cochlear implant were carried out to examine the influence of the modulation depth of these envelope fluctuations on pitch discrimination. In the first experiment, the subjects were asked to discriminate between two SAM (sinusoidally amplitude modulated) pulse trains on a single electrode channel differing in modulation frequency (δf=20%). As expected, the results showed a decrease in the performance for smaller modulation depths. Optimal performance was reached for modulation depths between 20% and 99%, depending on subject, electrode channel, and modulation frequency. In the second experiment, the smallest noticeable difference in F0 of synthetic vowels was measured for three algorithms that differed in the obtained modulation depth at the output: the default CIS strategy, the CIS strategy in which the F0 fluctuations in the envelope were removed (FLAT CIS), and a third CIS strategy, which was especially designed to control and increase the depth of these fluctuations (F0 CIS). In general, performance was poorest for the FLAT CIS strategy, where changes in F0 are only apparent as changes of the average amplitude in the channel outputs. This emphasizes the importance of temporal coding of F0 in the speech envelope for pitch perception. No significantly better results were obtained for the F0 CIS strategy compared to the default CIS strategy, although the latter results in envelope modulation depths at which sub-optimal scores were obtained in some cases of the first experiment. This indicates that less modulation is needed if all channels are stimulated with synchronous F0 fluctuations. This hypothesis is confirmed in a third experiment where subjects performed significantly better in a pitch discrimination task with SAM pulse trains, if three channels were stimulated concurrently, as opposed to only one.
Ants are deaf
Authors: Roces Flavio , Tautz Jürgen
Published: July 2002

Workers of a number of ant species produce vibrational signals, a phenomenon called “stridulation,” with a specialized organ located on their gasters. Even though stridulation can be heard by humans as faint air-borne sound, it has repeatedly been shown that ants are insensitive to the air-borne components of such signals. Instead, they are highly responsive to their substrate-borne components. Contrary to this view, it has recently been claimed that fire ants can hear stridulatory signals produced by nest mates as near-field sound, and that there is no evidence of signal transmission through the substrate in ants. In the present letter, this view is challenged by calculating the amplitude of the near-field particle oscillation around a stridulating ant, and by comparing it with the sensitivity threshold of the ant sensory receptors. The amplitude is shown to be at least 50 times lower than the sensitivity threshold, a fact that precludes the perception of the signals with the stiff antennal sensilla (and Johnston organ) so far described for ants. Finally, published data and our own findings on vibrational communication in ants are summarized, clearly showing that they are highly responsive to the substrate-borne components of stridulatory signals, and insensitive to near-field sound.
Auditory detection of hollowness
Authors: Lutfi Robert A.
Published: July 2002

The airborne sounds produced by freely vibrating hollow and solid bars were synthesized according to the equations of bar motion from theoretical acoustics, and were presented to listeners over headphones. In a two-interval, forced-choice task, listeners were asked to distinguish between the hollow and solid bar sounds as bar length was varied at random from one presentation to the next. All other physical properties of the bar were held constant across trials. Listener decision strategies for detecting hollowness in iron, aluminum, and wood bars were determined from regression weights describing the relation between the listener’s response and the frequency, intensity, and decay modulus of the individual partials comprising these sounds. The obtained weights were compared to those of a hypothetical listener that bases judgments on the acoustic relations intrinsic to hollowness, as determined from the equations for motion. Results indicate that listeners adopt roughly one of two decision strategies, either basing judgments on the appropriate acoustic relations, or basing judgments predominantly on frequency alone. The decision strategy of some listeners also changed from one type to the other with a change in bar material or upon replication of the same condition. The results are interpreted in terms of the vulnerability of the intrinsic acoustic relations to small perturbations in acoustic parameters, as would be associated with listener internal noise. They demonstrate that basic limits of human sensitivity can have a profound effect on the identification of rudimentary source attributes from sound, even in conditions where acoustic variation is largely dictated by physical variation in the source.
The acoustic properties of granular materials with pore size distribution close to log-normal
Authors: Horoshenkov K. V. , Swift M. J.
Published: July 2002

The majority of realistic porous materials are composed of pores of which the shape is variable and the size of the pores normally obeys a distinctive statistical distribution. Although the variation of pore shape is less important, the statistical parameters of pore size distribution can have a considerable effect on the acoustic properties of porous media. This paper discusses the application of a simple model for the prediction of the acoustic properties of porous granular media with some assumed pore geometry and pore size distribution close to log-normal. The model is based on the rational (Padé) approximation approach [K. V. Horoshenkov, K. Attenborough, and S. N. Chandler-Wilde, J. Acoust. Soc. Am. 104, 1198–1209 (1998)] which has been developed for some simple pore geometries. It is shown that the experimentally determined pore size distribution for a representative range of granular materials is often close to log-normal. This assumption enables accurate predictions of the acoustic performance of these materials using the presented model. The water suction method is proposed to determine the parameters of the log-normal distribution, which are the mean pore size, 〈φ〉, and its standard deviation, σ. This method is nonacoustic, modelless and well-adapted to acoustic materials and, unlike the BET method [S. Brunauer, P. H. Emmett, and E. Teller, J. Am. Chem. Soc. 60, 309–319 (1938)], is easy to reproduce in any basic acoustic laboratory requiring no expensive parts or chemicals. The proposed Padé approximation is based entirely on four measurable nonacoustic parameters, the porosity, Ω, flow resistivity, Rb, tortuosity, q2 and the standard deviation of the pore size, σ. The method is successfully tested on a representative selection of consolidated and nonconsolidated porous granular materials.
Acoustic radiation force on a spherical particle in a viscous heat-conducting fluid. I. General formula
Authors: Doinikov Alexander A.
Published: July 2002

The acoustic radiation force exerted by an axisymmetric sound field on a spherical particle is calculated assuming that the surrounding fluid is viscous and heat conducting. The incident sound field pressure amplitude is supposed to be small enough such that nonlinear effects like generation of subharmonics do not occur. No restrictions are imposed on the particle size, which means that the particle can be of an arbitrary radius with respect to the sound, viscous, and thermal wavelengths in the surrounding fluid. The obtained formula for the radiation force is general in that it is applicable to first, any axisymmetric sound field, such as a plane, traveling or standing wave and a spherical wave, and, second, any of the following types of dispersed particles: a gas bubble, a liquid drop, a rigid or elastic sphere, a spherical shell, etc. The force is expressed in terms of the linear scattering coefficients to be determined by the particle type. Thus, to obtain the force on a specific particle the problem of linear scattering for that particle must be solved. Problems of this sort are known not to be mathematically difficult, but can be laborious enough if a particle at issue has a complicated internal structure. The radiation forces on particles of most interest are examined in papers that follow [J. Acoust. Soc. Am. 101, 722–740 (1997)].