bluuebunny/crossref_metadata_2025 huggingface dataset:
The First Year of Family‐ and Couple‐initiated Marriages of a Turkish Sample: A Longitudinal Investigation
Authors: Hortaçsu Nuran
Published: July 2002

One hundred and thirty Turkish couples were interviewed twice during the first year of marriage. One fifth of the couples were involved in traditional family‐initiated marriages and the rest were involved in Western‐style couple‐initiated marriages. The interviews included questions related to demographic measures, marital functioning, and relationships with social network. Analyses revealed earlier parenthood, greater decision power of women for housework‐related decisions, and less frequent interaction with wife's than husband's family during the first months of marriage for family‐ than for couple‐initiated marriages. Similarities such as gender stereotypic division of labour and marital decision making, high degrees of reported emotional involvement with spouse, reports of close feelings for and almost weekly contacts with the families of origin were also found. It was seen that, with time, husbands contributed more to traditional male duties and that the reported frequency of interaction with families and friends decreased. There was some evidence, with respect to interaction with social network, of convergence between the two types of marriage within the first year. The results were discussed in relation to interplay of marital typologies with time and culture.
Party system change and electoral platforms: A study of the 1996 Italian election
Authors: Campus Donatella
Published: July 2002

Comparative research suggests that parties regularly campaign by emphasizing issues on which they are advantaged and by ignoring topics that are traditionally associated with other parties. Focusing on the 1996 Italian elections, this article discusses whether such a generalization holds when the party system is affected by radical changes such as those that occurred in Italy in the mid-1990s. Moreover, the analysis of the party electoral platforms highlights some basic features of the new parties, and identifies either innovations or continuities with the past. I present evidence that in 1996 the Italian parties mostly competed on a similar range of issues. Especially regarding economic policy, there was not a polarized ideological debate: also the centre-left parties converged on a moderate position by playing down typical socialist themes such as state intervention and the expansion of social services. I also analyse the degree of internal programmatic cohesion of the two main coalitions, the Ulivo (Olive Tree) and the Polo delle Libertà (Freedom Pole) and relate it to the stability of the Italian political system.
Two Separate Signals Act Independently to Localize a Yeast Late Golgi Membrane Protein through a Combination of Retrieval and Retention
Authors: Bryant Nia J. , Stevens Tom H.
Published: July 2002

The localization of proteins to late-Golgi membranes (TGN) of Saccharomyces cerevisiae is conferred by targeting motifs containing aromatic residues in the cytosolic domains of these proteins. These signals could act by directing retrieval from a post-Golgi compartment or by preventing exit from the TGN. To investigate the mechanism of localization of yeast TGN proteins, we used the heterologous protein A-ALP (consisting of the cytosolic domain of dipeptidyl aminopeptidase A [DPAP A] fused to the transmembrane and luminal domains of the vacuolar protein alkaline phosphatase [ALP]), which localizes to the yeast TGN. Insertion of the aromatic residue–based TGN localization motif (FXFXD) of DPAP A into the cytosolic domain of ALP results in a protein that resides in the TGN. We demonstrate that the FXFXD motif confers Golgi localization through retrieval from a post-Golgi compartment by detecting a post-Golgi processed form of this protein in the TGN. We present an assay that uncouples retrieval-mediated Golgi localization from static retention-based localization, allowing measurement of the rate at which proteins exit the yeast TGN. We also demonstrate that the cytosolic domain of DPAP A contains additional information, separate from the retrieval motif, that slows exit from the TGN. We propose a model for DPAP A localization that involves two distinct mechanisms: one in which the FXFXD motif directs retrieval from a post-Golgi compartment, and a second that slows the rate at which DPAP A exits the TGN.
Redundant and Distinct Functions for Dynamin-1 and Dynamin-2 Isoforms
Authors: Altschuler Yoram , Barbas Shana M. , Terlecky Laura J. , Tang Kitty , Hardy Stephen , Mostov Keith E. , Schmid Sandra L.
Published: July 2002

A role for dynamin in clathrin-mediated endocytosis is now well established. However, mammals express three closely related, tissue-specific dynamin isoforms, each with multiple splice variants. Thus, an important question is whether these isoforms and splice variants function in vesicle formation from distinct intracellular organelles. There are conflicting data as to a role for dynamin-2 in vesicle budding from the TGN. To resolve this issue, we compared the effects of overexpression of dominant-negative mutants of dynamin-1 (the neuronal isoform) and dynamin-2 (the ubiquitously expressed isoform) on endocytic and biosynthetic membrane trafficking in HeLa cells and polarized MDCK cells. Both dyn1(K44A) and dyn2(K44A) were potent inhibitors of receptor-mediated endocytosis; however neither mutant directly affected other membrane trafficking events, including transport mediated by four distinct classes of vesicles budding from the TGN. Dyn2(K44A) more potently inhibited receptor-mediated endocytosis than dyn1(K44A) in HeLa cells and at the basolateral surface of MDCK cells. In contrast, dyn1(K44A) more potently inhibited endocytosis at the apical surface of MDCK cells. The two dynamin isoforms have redundant functions in endocytic vesicle formation, but can be targeted to and function differentially at subdomains of the plasma membrane.
Cytoplasmic Dynein Is Required for Distinct Aspects of Mtoc Positioning, Including Centrosome Separation, in the One Cell Stage Caenorhabditis elegans Embryo
Authors: Gönczy Pierre , Pichler Silke , Kirkham Matthew , Hyman Anthony A.
Published: July 2002

We have investigated the role of cytoplasmic dynein in microtubule organizing center (MTOC) positioning using RNA-mediated interference (RNAi) in Caenorhabditis elegans to deplete the product of the dynein heavy chain gene dhc-1. Analysis with time-lapse differential interference contrast microscopy and indirect immunofluorescence revealed that pronuclear migration and centrosome separation failed in one cell stage dhc-1 (RNAi) embryos. These phenotypes were also observed when the dynactin components p50/dynamitin or p150Glued were depleted with RNAi. Moreover, in 15% of dhc-1 (RNAi) embryos, centrosomes failed to remain in proximity of the male pronucleus. When dynein heavy chain function was diminished only partially with RNAi, centrosome separation took place, but orientation of the mitotic spindle was defective. Therefore, cytoplasmic dynein is required for multiple aspects of MTOC positioning in the one cell stage C. elegans embryo. In conjunction with our observation of cytoplasmic dynein distribution at the periphery of nuclei, these results lead us to propose a mechanism in which cytoplasmic dynein anchored on the nucleus drives centrosome separation.
A Selective Transport Route from Golgi to Late Endosomes That Requires the Yeast Gga Proteins
Authors: Black Michael W. , Pelham Hugh R.B.
Published: July 2002

Pep12p is a yeast syntaxin located primarily in late endosomes. Using mutagenesis of a green fluorescent protein chimera we have identified a sorting signal FSDSPEF, which is required for transport of Pep12p from the exocytic pathway to late endosomes, from which it can, when overexpressed, reach the vacuole. When this signal is mutated, Pep12p instead passes to early endosomes, a step that is determined by its transmembrane domain. Surprisingly, Pep12p is then specifically retained in early endosomes and does not go on to late endosomes.

By testing appropriate chimeras in mutant strains, we found that FSDSPEF-dependent sorting was abolished in strains lacking Gga1p and Gga2p, Golgi-associated coat proteins with homology to gamma adaptin. In the gga1 gga2 double mutant endogenous Pep12p cofractionated with the early endosome marker Tlg1p, and recycling of Snc1p through early endosomes was defective. Pep12p sorting was also defective in cells lacking the clathrin heavy or light chain. We suggest that specific and direct delivery of proteins to early and late endosomes is required to maintain the functional heterogeneity of the endocytic pathway and that the GGA proteins, probably in association with clathrin, help create vesicles destined for late endosomes.
Myosin V exhibits a high duty cycle and large unitary displacement
Authors: Moore Jeffrey R. , Krementsova Elena B. , Trybus Kathleen M. , Warshaw David M.
Published: July 2002

Myosin V is a double-headed unconventional myosin that has been implicated in organelle transport. To perform this role, myosin V may have a high duty cycle. To test this hypothesis and understand the properties of this molecule at the molecular level, we used the laser trap and in vitro motility assay to characterize the mechanics of heavy meromyosin–like fragments of myosin V (M5HMM) expressed in the Baculovirus system. The relationship between actin filament velocity and the number of interacting M5HMM molecules indicates a duty cycle of ≥50%. This high duty cycle would allow actin filament translocation and thus organelle transport by a few M5HMM molecules. Single molecule displacement data showed predominantly single step events of 20 nm and an occasional second step to 37 nm. The 20-nm unitary step represents the myosin V working stroke and is independent of the mode of M5HMM attachment to the motility surface or light chain content. The large M5HMM working stroke is consistent with the myosin V neck acting as a mechanical lever. The second step is characterized by an increased displacement variance, suggesting a model for how the two heads of myosin V function in processive motion.
A role for cofilin and LIM kinase inListeria-induced phagocytosis
Authors: Bierne Hélène , Gouin Edith , Roux Pascal , Caroni Pico , Yin Helen L. , Cossart Pascale
Published: July 2002

The pathogenic bacterium Listeria monocytogenes is able to invade nonphagocytic cells, an essential feature for its pathogenicity. This induced phagocytosis process requires tightly regulated steps of actin polymerization and depolymerization. Here, we investigated how interactions of the invasion protein InlB with mammalian cells control the cytoskeleton during Listeria internalization. By fluorescence microscopy and transfection experiments, we show that the actin-nucleating Arp2/3 complex, the GTPase Rac, LIM kinase (LIMK), and cofilin are key proteins in InlB-induced phagocytosis. Overexpression of LIMK1, which has been shown to phosphorylate and inactivate cofilin, induces accumulation of F-actin beneath entering particles and inhibits internalization. Conversely, inhibition of LIMK's activity by expressing a dominant negative construct, LIMK1−, or expression of the constitutively active S3A cofilin mutant induces loss of actin filaments at the phagocytic cup and also inhibits phagocytosis. Interestingly, those constructs similarly affect other actin-based phenomenons, such as InlB-induced membrane ruffling or Listeria comet tail formations. Thus, our data provide evidence for a control of phagocytosis by both activation and deactivation of cofilin. We propose a model in which cofilin is involved in the formation and disruption of the phagocytic cup as a result of its local progressive enrichment.
Scleroderma Autoantigens Are Uniquely Fragmented by Metal-catalyzed Oxidation Reactions: Implications for Pathogenesis
Authors: Casciola-Rosen Livia , Wigley Fredrick , Rosen Antony
Published: July 2002

The observation that revelation of immunocryptic epitopes in self antigens may initiate the autoimmune response has prompted the search for processes which induce novel fragmentation of autoantigens as potential initiators of autoimmunity. The reversible ischemia reperfusion which characterizes scleroderma has focused attention on reactive oxygen species as molecules which might induce autoantigen fragmentation. We demonstrate that several of the autoantigens targeted in diffuse scleroderma are uniquely susceptible to cleavage by reactive oxygen species, in a metal-dependent manner. Multiple features of the fragmentation reaction and its inhibition indicate that these autoantigens possess metal-binding sites, which focus metal-catalyzed oxidation reactions (and consequent fragmentation) to specific regions of the antigens. These data suggest that the autoantibody response in scleroderma is the immune marker of unique protein fragmentation, induced by ischemia reperfusion in the presence of appropriate metals, and focus attention on abnormal metal status as a potential pathogenic principle in this disease.
The Nasal-associated Lymphoid Tissue of Adult Mice Acts as an Entry Site for the Mouse Mammary Tumor Retrovirus
Authors: Velin Dominique , Fotopoulos Grigorios , Luthi Frédéric , Kraehenbuhl Jean-Pierre
Published: July 2002

Mouse mammary tumor virus (MMTV) is a B type retrovirus transmitted to the suckling offspring through milk. MMTV crosses the intestinal barrier of neonates, initially infects the lymphoid cells of the Peyer's patches, and later spreads to all lymphoid organs and to the mammary gland. Adult mice can be infected systemically, but not by oral MMTV administration. In this study, we show that nasal administration of infected milk induces the infection of adult mice. Nasal MMTV infection shared the main features of systemic and neonatal intestinal MMTV infections: deletion of the superantigen (SAg)-reactive T cell subset from the peripheral T cell population, presence of viral DNA in lymphoid cells, and transmission of MMTV from mother to offspring. Viral DNA was restricted to the lungs and nasal-associated lymphoid tissue (NALT) 6 d after nasal infection. Furthermore, SAg-induced T cell proliferation was only detected in NALT. These results demonstrate that MMTV crosses the intact epithelium of the upper respiratory tract of adult mice and infects the lymphoid follicles associated with these structures.
Ku70 Is Required for Late B Cell Development and Immunoglobulin Heavy Chain Class Switching
Authors: Manis John P. , Gu Yansong , Lansford Rusty , Sonoda Eiichiro , Ferrini Roger , Davidson Laurie , Rajewsky Klaus , Alt Frederick W.
Published: July 2002

Immunoglobulin (Ig) heavy chain (HC) class switch recombination (CSR) is a late B cell process that involves intrachromosomal DNA rearrangement. Ku70 and Ku80 form a DNA end-binding complex required for DNA double strand break repair and V(D)J recombination. Ku70−/− (K70T) mice, like recombination activating gene (RAG)-1– or RAG-2–deficient (R1T or R2T) mice, have impaired B and T cell development at an early progenitor stage, which is thought to result at least in part from defective V(D)J recombination (Gu, Y., K.J. Seidl, G.A. Rathbun, C. Zhu, J.P. Manis, N. van der Stoep, L. Davidson, H.L. Cheng, J.M. Sekiguchi, K. Frank, et al. 1997. Immunity. 7:653–665; Ouyang, H., A. Nussenzweig, A. Kurimasa, V.C. Soares, X. Li, C. Cordon-Cardo, W. Li, N. Cheong, M. Nussenzweig, G. Iliakis, et al. 1997. J. Exp. Med. 186:921–929). Therefore, to examine the potential role of Ku70 in CSR, we generated K70T mice that carry a germline Ig HC locus in which the JH region was replaced with a functionally rearranged VH(D)JH and Ig λ light chain transgene (referred to as K70T/HL mice). Previously, we have shown that B cells from R1T or R2T mice carrying these rearranged Ig genes (R1T/HL or R2T/HL mice) can undergo CSR to IgG isotypes (Lansford, R., J. Manis, E. Sonoda, K. Rajewsky, and F. Alt. 1998. Int. Immunol. 10:325–332). K70T/HL mice had significant numbers of peripheral surface IgM+ B cells, which generated serum IgM levels similar to those of R2T/HL mice. However, in contrast to R2T/HL mice, K70T/HL mice had no detectable serum IgG isotypes. In vitro culture of K70T/HL B cells with agents that induce CSR in normal or R2T/HL B cells did lead to the induction of germline CH transcripts, indicating that initial signaling pathways for CSR were intact in K70T/HL cells. However, treatment with such agents did not lead to detectable CSR by K70T/HL B cells, and instead, led to cell death within 72 h. We conclude that Ku70 is required for the generation of B cells that have undergone Ig HC class switching. Potential roles for Ku70 in the CSR process are discussed.
A Natural Immunological Adjuvant Enhances T Cell Clonal Expansion through a CD28-dependent, Interleukin (IL)-2–independent Mechanism
Authors: Khoruts Alexander , Mondino Anna , Pape Kathryn A. , Reiner Steven L. , Jenkins Marc K.
Published: July 2002

The adoptive transfer of naive CD4+ T cell receptor (TCR) transgenic T cells was used to investigate the mechanisms by which the adjuvant lipopolysaccharide (LPS) enhance T cell clonal expansion in vivo. Subcutaneous administration of soluble antigen (Ag) resulted in rapid and transient accumulation of the Ag-specific T cells in the draining lymph nodes (LNs), which was preceded by the production of interleukin (IL)-2. CD28-deficient, Ag-specific T cells produced only small amounts of IL-2 in response to soluble Ag and did not accumulate in the LN to the same extent as wild-type T cells. Injection of Ag and LPS, a natural immunological adjuvant, enhanced IL-2 production and LN accumulation of wild-type, Ag-specific T cells but had no significant effect on CD28-deficient, Ag-specific T cells. Therefore, CD28 is critical for Ag-driven IL-2 production and T cell proliferation in vivo, and is essential for the LPS-mediated enhancement of these events. However, enhancement of IL-2 production could not explain the LPS-dependent increase of T cell accumulation because IL-2–deficient, Ag-specific T cells accumulated to a greater extent in the LN than wild-type T cells in response to Ag plus LPS. These results indicate that adjuvants improve T cell proliferation in vivo via a CD28-dependent signal that can operate in the absence of IL-2.
αdβ2 Integrin Is Expressed on Human Eosinophils and Functions as an Alternative Ligand for Vascular Cell Adhesion Molecule 1 (VCAM-1)
Authors: Grayson Mitchell H. , Van der Vieren Monica , Sterbinsky Sherry A. , Michael Gallatin W. , Hoffman Patricia A. , Staunton Donald E. , Bochner Bruce S.
Published: July 2002

The β2 family of integrins, CD11a, CD11b, CD11c, and αd, are expressed on most leukocytes. We show that the newest member of this family, αd, is expressed on human eosinophils in peripheral blood, and surface expression can be upregulated within minutes by phorbol ester or calcium ionophore A23187. Culture of eosinophils with interleukin 5 (IL-5) leads to a two- to fourfold increase in αd levels by 3–7 d without a change in α4 integrin expression. Eosinophils isolated from late phase bronchoalveolar lavage fluids express αd at levels similar to that seen after 3 d of IL-5 culture. Regarding αdβ2 ligands, in both freshly isolated and IL-5–cultured eosinophils, as well as αdβ2-transfected Chinese hamster ovary cells, αdβ2 can function as a ligand for vascular cell adhesion molecule 1 (VCAM-1). This conclusion is based on the ability of monoclonal antibodies to αd, β2, or VCAM-1 to block cell attachment in static adhesion assays. In experiments with eosinophils, the relative contribution of αdβ2 integrin– mediated adhesion is enhanced after IL-5 culture. These experiments demonstrate that αdβ2 is an alternative ligand for VCAM-1, and this integrin may play a role in eosinophil adhesion to VCAM-1 in states of chronic inflammation.
Loss of Precursor B Cell Expansion but Not Allelic Exclusion in VpreB1/VpreB2 Double-Deficient Mice
Authors: Mundt Cornelia , Licence Steve , Shimizu Takeyuki , Melchers Fritz , Mårtensson Inga-Lill
Published: July 2002

The pre-B cell receptor consists of immunoglobulin (Ig) μ heavy chains and surrogate light chain, i.e., the VpreB and λ5 proteins. To analyze the role of the two VpreB proteins, mice lacking the VpreB1 and VpreB2 genes were generated. VpreB1−/−VpreB2−/− mice were impaired in their B cell development at the transition from pre-BI to large pre-BII cells. Pre-BII cells did not expand by proliferation, consequently 40-fold less small pre-BII and immature B cells were found in bone marrow, and the generation of immature and mature conventional B cells in spleen appeared reduced. In addition, only low numbers of B-1a cells were detected in the peritoneum. Surprisingly, Ig heavy chain allelic exclusion was still active, apparently ruling out a signaling role of a VpreB1/VpreB2–containing receptor in this process.
Most α/β T Cell Receptor Diversity Is Due to Terminal Deoxynucleotidyl Transferase
Authors: Cabaniols Jean-Pierre , Fazilleau Nicolas , Casrouge Armanda , Kourilsky Philippe , Kanellopoulos Jean M.
Published: July 2002

The contribution of template-independent nucleotide addition to antigen receptor diversity is unknown. We therefore determined the size of the T cell receptor (TCR)α/β repertoire in mice bearing a null mutation on both alleles of the terminal deoxynucleotidyl transferase (Tdt) gene. We used a method based upon polymerase chain reaction amplification and exhaustive sequencing of various AV-AJ and BV-BJ combinations. In both wild-type and Tdt°/° mice, TCRAV diversity is one order of magnitude lower than the TCRBV diversity. In Tdt°/° animals, TCRBV chain diversity is reduced 10-fold compared with wild-type mice. In addition, in Tdt°/° mice, one BV chain can associate with three to four AV chains as in wild-type mice. The α/β repertoire size in Tdt°/° mice is estimated to be 105 distinct receptors, ∼5–10% of that calculated for wild-type mice. Thus, while Tdt activity is not involved in the combinatorial diversity resulting from α/β pairing, it contributes to at least 90% of TCRα/β diversity.
Rapid Induction of Tumor-specific Type 1 T Helper Cells in Metastatic Melanoma Patients by Vaccination with Mature, Cryopreserved, Peptide-loaded Monocyte-derived Dendritic Cells
Authors: Schuler-Thurner Beatrice , Schultz Erwin S. , Berger Thomas G. , Weinlich Georg , Ebner Susanne , Woerl Petra , Bender Armin , Feuerstein Bernadette , Fritsch Peter O. , Romani Nikolaus , Schuler Gerold
Published: July 2002

There is consensus that an optimized cancer vaccine will have to induce not only CD8+ cytotoxic but also CD4+ T helper (Th) cells, particularly interferon (IFN)-γ–producing, type 1 Th cells. The induction of strong, ex vivo detectable type 1 Th cell responses has not been reported to date. We demonstrate now that the subcutaneous injection of cryopreserved, mature, antigen-loaded, monocyte-derived dendritic cells (DCs) rapidly induces unequivocal Th1 responses (ex vivo detectable IFN-γ–producing effectors as well as proliferating precursors) both to the control antigen KLH and to major histocompatibility complex (MHC) class II–restricted tumor peptides (melanoma-antigen [Mage]-3.DP4 and Mage-3.DR13) in the majority of 16 evaluable patients with metastatic melanoma. These Th1 cells recognized not only peptides, but also DCs loaded with Mage-3 protein, and in case of Mage-3DP4–specific Th1 cells IFN-γ was released even after direct recognition of viable, Mage-3–expressing HLA-DP4+ melanoma cells. The capacity of DCs to rapidly induce Th1 cells should be valuable to evaluate whether Th1 cells are instrumental in targeting human cancer and chronic infections.
Phosphoinositides Decrease Atp Sensitivity of the Cardiac Atp-Sensitive K+ Channel
Authors: Fan Zheng , Makielski Jonathan C.
Published: July 2002

Anionic phospholipids modulate the activity of inwardly rectifying potassium channels (Fan, Z., and J.C. Makielski. 1997. J. Biol. Chem. 272:5388–5395). The effect of phosphoinositides on adenosine triphosphate (ATP) inhibition of ATP-sensitive potassium channel (KATP) currents was investigated using the inside-out patch clamp technique in cardiac myocytes and in COS-1 cells in which the cardiac isoform of the sulfonylurea receptor, SUR2, was coexpressed with the inwardly rectifying channel Kir6.2. Phosphoinositides (1 mg/ml) increased the open probability of KATP in low [ATP] (1 μM) within 30 s. Phosphoinositides desensitized ATP inhibition with a longer onset period (>3 min), activating channels inhibited by ATP (1 mM). Phosphoinositides treatment for 10 min shifted the half-inhibitory [ATP] (Ki) from 35 μM to 16 mM. At the single-channel level, increased [ATP] caused a shorter mean open time and a longer mean closed time. Phosphoinositides prolonged the mean open time, shortened the mean closed time, and weakened the [ATP] dependence of these parameters resulting in a higher open probability at any given [ATP]. The apparent rate constants for ATP binding were estimated to be 0.8 and 0.02 mM−1 ms−1 before and after 5-min treatment with phosphoinositides, which corresponds to a Ki of 35 μM and 5.8 mM, respectively. Phosphoinositides failed to desensitize adenosine inhibition of KATP. In the presence of SUR2, phosphoinositides attenuated MgATP antagonism of ATP inhibition. Kir6.2ΔC35, a truncated Kir6.2 that functions without SUR2, also exhibited phosphoinositide desensitization of ATP inhibition. These data suggest that (a) phosphoinositides strongly compete with ATP at a binding site residing on Kir6.2; (b) electrostatic interaction is a characteristic property of this competition; and (c) in conjunction with SUR2, phosphoinositides render additional, complex effects on ATP inhibition. We propose a model of the ATP binding site involving positively charged residues on the COOH-terminus of Kir6.2, with which phosphoinositides interact to desensitize ATP inhibition.
Intrinsic Cone Adaptation Modulates Feedback Efficiency from Horizontal Cells to Cones
Authors: Fahrenfort I. , Habets R.L. , Spekreijse H. , Kamermans M.
Published: July 2002

Processing of visual stimuli by the retina changes strongly during light/dark adaptation. These changes are due to both local photoreceptor-based processes and to changes in the retinal network. The feedback pathway from horizontal cells to cones is known to be one of the pathways that is modulated strongly during adaptation. Although this phenomenon is well described, the mechanism for this change is poorly characterized. The aim of this paper is to describe the mechanism for the increase in efficiency of the feedback synapse from horizontal cells to cones. We show that a train of flashes can increase the feedback response from the horizontal cells, as measured in the cones, up to threefold. This process has a time constant of ∼3 s and can be attributed to processes intrinsic to the cones. It does not require dopamine, is not the result of changes in the kinetics of the cone light response and is not due to changes in horizontal cells themselves. During a flash train, cones adapt to the mean light intensity, resulting in a slight (4 mV) depolarization of the cones. The time constant of this depolarization is ∼3 s. We will show that at this depolarized membrane potential, a light-induced change of the cone membrane potential induces a larger change in the calcium current than in the unadapted condition. Furthermore, we will show that negative feedback from horizontal cells to cones can modulate the calcium current more efficiently at this depolarized cone membrane potential. The change in horizontal cell response properties during the train of flashes can be fully attributed to these changes in the synaptic efficiency. Since feedback has major consequences for the dynamic, spatial, and spectral processing, the described mechanism might be very important to optimize the retina for ambient light conditions.
Semiclassical analysis of general second order elliptic operators on bounded domains
Authors: Dancer E. , López-Gómez J.
Published: July 2002

In this work we ascertain the semiclassical behavior of the fundamental energy and the ground state of an arbitrary second order elliptic operator, not necessarily selfadjoint, on a bounded domain. Our analysis provides us with substantial improvements of many previous results found in the context of quantum mechanics forC∞C^\inftyperturbations of the Laplacian.
Removing redundancy in SWISS-PROT and TrEMBL.
Authors: O'Donovan C , Martin M J , Glemet E , Codani J J , Apweiler R
Published: July 2002

SUMMARY: One of the distinguishing criteria of the SWISS-PROT protein sequence data bank is minimal redundancy. The introduction of TrEMBL as a supplementary database ensured the comprehensiveness of SWISS-PROT and TrEMBL but introduced some degree of redundancy. We developed a strategy to identify the redundancy present within and between SWISS-PROT and TrEMBL and its subsequent removal. AVAILABILITY: The tools mentioned in this paper are available on request.
Making sense of microarray data distributions
Authors: Hoyle David C. , Rattray Magnus , Jupp Ray , Brass Andrew
Published: July 2002

Motivation: Typical analysis of microarray data has focusedon spot by spot comparisons within a single organism. Less analysis has been done on the comparison of the entire distribution of spot intensities between experiments and between organisms.

Results: Here we show that mRNA transcription data from a wide range of organisms and measured with a range of experimental platforms show close agreement with Benford’s law (Benford, Proc. Am. Phil. Soc. , 78, 551–572, 1938) and Zipf’s law (Zipf, The Psycho-biology of Language: an Introduction to Dynamic Philology , 1936 and Human Behaviour and the Principle of Least Effort , 1949). The distribution of the bulk of microarray spot intensities is well approximated by a log-normal with the tail of the distribution being closer to power law. The variance, σ2, of log spot intensity shows a positive correlation with genome size (in terms of number of genes) and is therefore relatively fixed within some range for a given organism. The measured value of σ2 can be significantly smaller than the expected value if the mRNA is extracted from a sample of mixed cell types. Our research demonstrates that useful biological findings may result from analyzing microarray data at the level of entire intensity distributions.

Contact: david.c.hoyle@man.ac.uk

* To whom correspondence should be addressed.
Roles of Eph receptors and ephrins in segmental patterning
Authors: Xu Qiling , Mellitzer Georg , Wilkinson David G.
Published: July 2002

Eph receptor tyrosine kinases and their membrane–bound ligands, ephrins, have key roles in patterning and morphogenesis. Interactions between these molecules are promiscuous, but largely fall into two groups: EphA receptors bind to glycosylphosphatidyl inositol–anchored ephrin–A ligands, and EphB receptors bind to transmembrane ephrin–B proteins. Ephrin–B proteins transduce signals, such that bidirectional signalling can occur upon interaction with the Eph receptor. In many tissues, there are complementary and overlapping expression domains of interacting Eph receptors and ephrins. An important role of Eph receptors and ephrins is to mediate cell contact–dependent repulsion, and this has been implicated in the pathfinding of axons and neural crest cells, and the restriction of cell intermingling between hindbrain segments. Studies in anin vitrosystem show that bidirectional activation is required to prevent intermingling between cell populations, whereas unidirectional activation can restrict cell communication via gap junctions. Recent work indicates that Eph receptors can also upregulate cell adhesion, but the biochemical basis of repulsion versus adhesion responses is unclear. Eph receptors and ephrins have thus emerged as key regulators that, in parallel with cell adhesion molecules, underlie the establishment and maintenance of patterns of cellular organization.
TRAIL-induced apoptosis requires Bax-dependent mitochondrial release of Smac/DIABLO
Authors: Deng Yibin , Lin Yahong , Wu Xiangwei
Published: July 2002

Recent reports suggest that a cross-talk exists between apoptosis pathways mediated by mitochondria and cell death receptors. In the present study, we report that mitochondrial events are required for apoptosis induced by the cell death ligand TRAIL (TNF-relatedapoptosis-inducing ligand) in human cancer cells. We show that the Bax null cancer cells are resistant to TRAIL-induced apoptosis. Bax deficiency has no effect on TRAIL-induced caspase-8 activation and subsequent cleavage of Bid; however, it results in an incomplete caspase-3 processing because of inhibition by XIAP. Release of Smac/DIABLO from mitochondria through the TRAIL–caspase-8–tBid–Bax cascade is required to remove the inhibitory effect of XIAP and allow apoptosis to proceed. Inhibition of caspase-9 activity has no effect on TRAIL-induced caspase-3 activation and cell death, whereas expression of the active form of Smac/DIABLO in the cytosol is sufficient to reconstitute TRAIL sensitivity in Bax-deficient cells. Our results show for the first time that Bax-dependent release of Smac/DIABLO, not cytochrome c, from mitochondria mediates the contribution of the mitochondrial pathway to death receptor-mediated apoptosis.
Numerical analysis for nonlinear resonant oscillations of gas in axisymmetric closed tubes
Authors: Chun Young-Doo , Kim Yang-Hann
Published: July 2002

A numerical investigation on nonlinear oscillations of gas in an axisymmetric closed tube is presented. When the tube is oscillated at a resonant frequency of the interior acoustic field, it is well known that acoustic variables such as density, velocity, and pressure undergo very large perturbation, often described as nonlinear oscillation. One-dimensional nonlinear governing equations, which explicitly include attenuation terms related to viscosity, were derived. Then, the equations were solved numerically by using the higher-order finite difference scheme, which divided into two parts of spatial differentiation and time evolution. Numerical simulations were accomplished to study the effect of the tube shape on the maximum pressure we can obtain. The tubes of cylindrical, conical, and cosine shape, which have the same volume and length, were investigated. Results show that the resonant frequency and patterns of pressure waves strongly depend on not only the tube shape but also the amplitude of driving acceleration. The degree of nonlinearity of wave patterns was also measured by the newly defined nonlinear energy ratio of the pressure signals. It was found that the 12 cosine-shape tube is more suitable to induce high compression ratio than other shapes.
Fine structure of the 2 f1−f2 acoustic distortion product: Effects of primary level and frequency ratios
Authors: He Ning-ji , Schmiedt Richard A.
Published: July 2002

The fine structure of the 2 f1−f2 acoustic distortion product (ADP) was measured in humans with different primary level (L1/L2) and frequency (f2/f1,f2>f1) ratios. The (L1/L2) ratio was varied under two conditions. In the first condition L1 was fixed at 50 dB SPL while L2 was varied from 30 to 75 dB SPL in 5-dB steps. An upward frequency shift was observed in the ADP fine structure as L2 was increased. In the second condition, L2 was fixed at 50 dB SPL and L1 varied, and a downward frequency shift was observed. These opposing frequency shifts are predicted by a vector-sum model [Sun et al., J. Acoust., Soc. Am. 96, 2166–2174, 2175–2183 (1994)] and support the hypothesis that the ADP fine structure largely reflects place features of the area of overlap of the primary traveling waves. The mechanisms underlying the shifts in fine structure were further investigated by using three primary f2/f1 ratios: 1.11, 1.2, and 1.33. An orderly difference in the rate of fine-structure shift with level was observed as a function of f2/f1 ratio, with the largest rate of shift associated with the smallest frequency ratio. This observation, along with the fact that downward frequency shift (with L1 varied) is always at a larger rate than the upward shift (with L2 varied), suggests that ADP levels and fine structure are strongly influenced by the nonlinear compression present in the mechanics of the basilar membrane in the region of overlap between the primary traveling waves.
Spontaneous otoacoustic emission frequency is modulated by heartbeat
Authors: Long Glenis R. , Talmadge Carrick L.
Published: July 2002

Detailed analysis of spontaneous otoacoustic emissions (SOAEs) in human subjects revealed that all stable SOAEs sufficiently above the noise floor to permit appropriate analysis have sidebands at multiples of approximately 1 Hz. This is consistent with the hypothesis that SOAEs are modulated by heartbeat. Simultaneous measurement of the rate of blood flow to the thumb and the separation of the spectral sidebands demonstrated that they covary (r=0.982, p<5×10−10). An adaptive least-squares fit (LSF) paradigm was developed to facilitate the measurement of the instantaneous frequency and amplitude of the signals. A combination of traditional spectral analyses and new LSF analyses showed that the sideband generation stems from frequency modulation of the emissions. If there is any amplitude modulation correlated with the blood flow, it is below the noise floor of the analysis. The frequency of the emission was at a minimum when the blood flow was maximal. Examination of alternative mechanisms using computer simulations suggests that these changes stem from changes of 10–100 ppm in the mass of the basilar membrane.
The measurement of coupling loss factors using the structural intensity technique
Authors: Ming Ruisen
Published: July 2002

The structural intensity technique can directly measure and distinguish power transmissions between different structural wavetypes across a joint, and its applications are numerous in practical engineering. In this paper, a new method is proposed for the measurement of coupling loss factors (CLFs) using the structural intensity technique. An outline of the method’s theory is also given. Theoretically the proposed method gives an approximate estimation of CLFs. The approximate error depends on the ratios of the effective modal overlap factor of the receiving subsystem to the modal overlap factors of the subsystems coupled through the joint of interest. If the effective modal overlap factor of the receiving subsystem is large compared with the modal overlap factors of the coupled subsystems, the approximate error is small and negligible. A series of measurements were carried out to verify the outlined theory. The results measured on the joints with two subsystems showed that this proposed method can be used to accurately measure CLFs when the modal overlap factor of the receiving subsystem is larger than that of the source subsystem. The approximate error decreases with increasing frequency and the modal overlap factor ratio of the receiving subsystem to the source subsystem.
On the multiple microphone method for measuring in-duct acoustic properties in the presence of mean flow
Authors: Jang Seung-Ho , Ih Jeong-Guon
Published: July 2002

Nowadays, the two-microphone method is accepted as the standard as specified in ASTM E1050-90 for measuring in-duct acoustic properties. However, research results on using the least square method with multiple measurement points and broadband excitation have been reported for enhancing the frequency response of the two-microphone method. In this paper, the effects of varying the relative measurement positions on errors in the estimation of the acoustic quantities is studied for the multiple microphone method. Both the theoretical and experimental results show that, among possible sensor positioning configurations, the equidistant positioning of sensors yields the smallest error within the effective measurement frequency range. In addition, it is noted that the measurement accuracy can be increased and the effective frequency range can be widened by increasing the number of equidistant sensors. Measurement examples are shown and the results support the findings.
Basilar-membrane responses to clicks at the base of the chinchilla cochlea
Authors: Recio Alberto , Rich Nola C. , Narayan S. Shyamla , Ruggero Mario A.
Published: July 2002

Basilar-membrane responses to clicks were measured, using laser velocimetry, at a site of the chinchilla cochlea located about 3.5 mm from the oval window (characteristic frequency or CF: typically 8–10 kHz). They consisted of relatively undamped oscillations with instantaneous frequency that increased rapidly (time constant: 200 μs) from a few kHz to CF. Such frequency modulation was evident regardless of stimulus level and was also present post-mortem. Responses grew linearly at low stimulus levels, but exhibited a compressive nonlinearity at higher levels. Velocity-intensity functions were almost linear near response onset but became nonlinear within 100 μs. Slopes could be as low as 0.1–0.2 dB/dB at later times. Hence, the response envelopes became increasingly skewed at higher stimulus levels, with their center of gravity shifting to earlier times. The phases of near-CF response components changed by nearly 180 degrees as a function of time. At high stimulus levels, this generated cancellation notches and phase jumps in the frequency spectra. With increases in click level, sharpness of tuning deteriorated and the spectral maximum shifted to lower frequencies. Response phases also changed as a function of increasing stimulus intensity, exhibiting relative lags and leads at frequencies somewhat lower and higher than CF, respectively. In most respects, the magnitude and phase frequency spectra of responses to clicks closely resembled those of responses to tones. Post-mortem responses were similar to in vivo responses to very intense clicks.
Directivity measurement of a singer
Authors: Kob Malte , Jers Harald
Published: July 2002

The convenient method of using broadband excitation for fast and accurate evaluation of narrow-band directivity cannot be applied to the human vocal tract. If the voice itself is used as the excitation, the variable properties of the vocal tract change with each differently pronounced phoneme, and therefore a vowel does not yield the same directivity as a consonant. Additionally, the nonstationary character of the voice does not allow for simple measurements with one scanning microphone. In the method described here, the singer stands on a turntable and sings a glissandolike vowel through at least one octave. The sound-pressure level is recorded with two microphones, one as a reference attached to the singer’s nose and the other at a 2-m distance. The spectra of both signals are calculated with a sufficiently long FFT, and the levels are subtracted. For each position of the turntable and every angle of elevation, the spectra are stored on disk and postprocessed within a matlab environment. Measured directivity plots of several human singers are compared with those of an artificial singer that has been built to reproduce the singing voice accurately.
Modeling otoacoustic emissions by active nonlinear oscillators
Authors: Sisto R. , Moleti A.
Published: July 2002

The phenomenology of spontaneous otoacoustic emissions (OAEs) is compared to theoretical predictions given by models in which they are produced by active nonlinear oscillators. Along with the well-known Van der Pol oscillator, a new active oscillator model is proposed and analyzed here. Numerical simulations and multi-scale analytical computation results are compared to experimental data of neonatal spontaneous and evoked OAEs. A simple analysis technique is proposed, in which the time evolution after a click stimulus of the amplitude of each spectral line corresponding to a spontaneous OAE is studied. Apart from a few stationary lines, an approximately exponential decay law, with characteristic damping coefficients in the 20–200 Hz range, was found to fit the data. These results are not compatible with a Van der Pol oscillator model, and show that some important aspects of the OAE phenomenology can be better explained by the proposed oscillator. Other interesting features of the spontaneous end evoked OAE phenomenology, such as spontaneous OAE suppression by external tones and the following recovery, as well as stimulus/response curves in the linear and nonlinear mode of acquisition, are also well reproduced by the proposed model.
Rheological behavior of hydrophobically modified hydroxyethyl cellulose solutions: A linear viscoelastic model
Authors: Maestro A. , González C. , Gutiérrez J. M.
Published: July 2002

The rheological behavior of hydrophobically modified hydroxyethyl cellulose (HMHEC), an associative thickener, was studied and compared with that of hydrophobically modified ethoxylated urethanes (HEURs) and nonassociative celluloses. In contrast to HEURs, a simple Maxwell model does not fit the linear viscoelastic behavior of HMHEC. Differences are attributed to the stiffness and comb structure of HMHEC. A generalized Maxwell model with a logarithmic distribution of relaxation times is proposed, and another parameter that includes Rouse-like relaxation is added to fit behavior at high frequencies. Four parameters are needed to describe HMHEC viscoelasticity: a mean relaxation time, λM; its corresponding standard deviation, σ; a plateau modulus, GN; and a viscosity at infinite frequency, η∞. Satisfactory fitting is obtained for all concentrations and temperatures in the range of frequencies studied. The sharp increase of GN with concentration indicates loop-to-bridge transitions. Temperature does not influence GN, since the reduction in the number density of elastically effective chains caused by Brownian motion masks the direct effect of temperature. The dependence of λM on temperature follows the Arrhenius equation, as does the relaxation time of HEURs, but it does not change with concentration, presumably because the comb structure of HMHEC prevents the formation of long superchains.
Rate-Dependent Relaxation Spectra and Their Determination
Authors: Yamamoto Misazo
Published: July 2002

Stress overshoot at the start of a flow, stress relaxation after the stoppage of a flow, and superposition of a small oscillation upon a steady shear flow are treated by the use of the concept of a deformation rate-dependent relaxation spectra. These analyses are used as the basis of methods to determine the spectrum of relaxation times. Although the treatment is restricted to specific types of constitutive equations in which the response function depends on the rate of deformation invariants, it is not necessary to specify any functional form of the response function. Experimental determination of the rate-dependent spectrum may play an important role in the discussion of the relative applicability of different forms of constitutive equations recently proposed in the literature.
Structural network models for molten plastics evaluated in large amplitude oscillatory shear
Authors: Giacomin A. J. , Oakley J. G.
Published: July 2002

The kinetic rate equation proposed by Mewis and Denn (1983) for their structural network model is found to predict accurately the large amplitude oscillatory shear behavior of molten low density polyethylene IUPAC X. Spectral analysis is used to compare the predictions of several kinetic rate equations. Frequency versus strain amplitude maps are constructed to examine each harmonic of the shear stress response predicted by the Mewis–Denn model. A Pipkin diagram is calculated for this model using contours for the amplitude of the third harmonic.