bluuebunny/crossref_metadata_2025 huggingface dataset:
Differential inhibitory effects of carbon tetrachloride on the hepatic plasma membrane, mitochondrial and endoplasmic reticular calcium transport systems: implications to hepatotoxicity
Authors: Hemmings Susan J. , Pulga Vivian B. , Tran Sam T. , Uwiera Richard R.E.
Published: September 2002

Mitochondrial, endoplasmic reticular and plasma membrane fractions were isolated by a new method from control male Fischer 344 rats and rats given CCl4 by gavage. After 1 h of CCl4 treatment, rats were in glucose and pancreatic hormone balance but plasma levels of T3 and T4 were decreased 29 and 22%, respectively. After 24 hours of CCl4 treatment, rats were: hypoglycaemic and insulin and glucagon levels were increased 33‐ and 35‐fold, respectively; total T4 levels were decreased 62%; while total T3 levels were normalized. In liver fractions from CCI4‐treated rats, 1 h after CCl4 administration: (i) calcium binding was decreased 65% in the mitochondrial fraction, 66% in the endoplasmic reticular fraction and 46% in the plasma membrane fraction; (ii) calcium uptake was decreased 59% in the mitochondrial fraction, 46% in the endoplasmic reticular fraction and 37% in the plasma membrane fraction. After 24 h of CCl4 administration: (i) calcium binding was decreased 57% in the mitochondrial fraction, 50% in the endoplasmic reticular fraction and 71% in the plasma membrane fraction; (ii). calcium uptake was decreased 55% in the mitochondrial fraction, 17% in the endoplasmic reticular fraction and 53% in the plasma membrane fraction. In vitro studies indicated the plasma membrane calcium transport system to be rapidly (within a minute) and strongly (>90%) inhibited by CCl4. We conclude that CCl4 produces a differential inhibitory effect on the hepatoctye calcium pumps that are implicated with hepatocellular damage. Copyright © 2001 John Wiley & Sons, Ltd.
Cervico‐vaginal dysplasia—papillomavirus‐induced and HIV‐1 infection: role of correlated markers for prognostic evaluation
Authors: Pugliese A. , Andronico L. , Gennero L. , Pagliano G. , Gallo G. , Torre D.
Published: September 2002

Sexually‐transmitted diseases (STD) can facilitate the progression of HIV‐1 infection. Among them, as we have previously demonstrated, cervico‐vaginal dysplasia—papillomavirus (HPV)‐induced, together with HSV‐2 co‐infection, seems to be correlated with a more evident immunodepression in HIV‐positive women, compared with other sexually transmitted diseases. Here we have analysed some of the main correlated markers of HIV‐1 infection progression: CD4 + T lymphocyte concentration, CD4 +/CD8 + T cells ratio, HIV‐1 RNA loads and haemoglobin (Hb) concentration in 30 HIV‐1 positive women co‐infected with HPV, and suffering from cervico‐vaginal dysplasia, in different stages. In particular, we noticed a positive correlation, evaluated by Spearman's test, between the degree of progression of dysplastic stages (CIN1→3) until invasive carcinoma (IC) and HIV‐1 RNA loads (Cs = +0.78; p < 0.001), and in contrast, a negative correlation between the same stages of progression and respectively CD4+ T cell concentration (Cs = −0.54; p = 0.01), ratio (Cs =− 0.63; p = 0.002) and Hb concentration (Cs = −0.85; p < 0.001). In conclusion, it is important to underline that low levels of Hb generally paralleled the degree of immunodepression. In fact CD4 + T cell levels and ratio positively correlated with Hb concentrations respectively, with Cs = +0.83; p < 0.001 and Cs = +0.90; p < 0.001. Finally, the most efficacious antiretroviral combined therapy (HAART = Highly Active Antiretroviral Therapy) can improve the above described laboratory parameters in HIV‐1/HPV co‐infected women and seems to prevent the progression of CIN1 to the following stages of the dysplastic disease. Copyright © 2002 John Wiley & Sons, Ltd.
Transcriptional activation of the human insulin receptor gene by 1,25‐dihydroxyvitamin D3
Authors: Maestro B. , Molero S. , Bajo S. , Dávila N. , Calle C.
Published: September 2002

Treatment with 10−8 m 1,25‐dihydroxyvitamin D3 for 24 h causes transcriptional activation of the human insulin receptor gene in U‐937 human promonocytic cells. The activation seems to potentiate the response to insulin in terms of glucose oxidation. Wortmannin, a phosphatidylinositol 3‐kinase inhibitor, causes a greater inhibition of insulin‐stimulated glucose oxidation in 1,25‐dihydroxyvitamin D3‐treated cells than in untreated cells. This suggests a stimulation of phosphatidylinositol 3‐kinase activity by 1,25‐dihydroxyvitamin D3, which could mediate, at least in part, the potentiation of the insulin response. Copyright © 2002 John Wiley & Sons, Ltd.
Melatonin in the unicellular Tetrahymena pyriformis: effects of different lighting conditions
Authors: Köhidai L. , Vakkuri O. , Keresztesi M. , Leppäluoto J. , Csaba G.
Published: September 2002

Melatonin content in the cellular fraction and medium of Tetrahymena pyriformis GL cultures was measured at different time points of light and dark exposures. Tetrahymena produced, stored and secreted immunoreactive melatonin, which in displacement and HPLC studies, behaved like synthetic melatonin. There was not a continuous secretion of melatonin produced by the cells. In contrast to this, storage of melatonin was observed, which was more expressed in dark conditions. Prolonged light exposure suppressed melatonin production and secretion alike, however it did not block it completely. Copyright © 2002 John Wiley & Sons, Ltd.
Transcatheter closure of patent foramen ovale in patients with paradoxical embolism: Intermediate‐term risk of recurrent neurological events
Authors: Du Zhong‐Dong , Cao Qi‐Ling , Joseph Annette , Koenig Peter , Heischmidt Mary , Waight David J. , Rhodes Jonathan , Brorson James , Hijazi Ziyad M.
Published: September 2002

Closure of patent foramen ovale (PFO) has been proposed as an alternative to anticoagulation in patients with presumed paradoxical emboli. We report our preliminary intermediate results of patients who underwent transcatheter PFO closure for paradoxical embolism using DAS‐Angel Wings occluder or Amplatzer devices. Eighteen patients (8 male/10 female) underwent catheter closure of their PFOs at a median age of 42 years. The complete closure rate was 67% immediately after the procedure and 100% at a mean follow‐up interval of 2.2 ± 1.8 years. The mean fluoroscopy time and procedure time in the Amplatzer group were 8.5 ± 3.2 min and 65 ± 21 min, respectively, which were significantly shorter than those of DAS‐Angel Wings group (18.9 ± 4.7 min and 137 ± 28 min, respectively). There were no recurrent embolic neurological events following device placement in this subset of patients. No complications were encountered either during or after the closure procedure. In conclusion, transcatheter closure of PFO seems to be an effective alternative therapy in the prevention of presumed paradoxical emboli. Further study is needed to identify patients most likely to benefit from this intervention. Cathet Cardiovasc Intervent 2002;55:189–194. © 2002 Wiley‐Liss, Inc.
New stent design for autologous venous graft–covered stent preparation: First human application for sealing of a coronary aneurysm
Authors: Stefanadis Christodoulos , Toutouzas Konstantinos , Tsiamis Eleftherios , Toutouzas Pavlos
Published: September 2002

In this case report, we present the first clinical application of a new stent design for autologous venous graft–covered stent preparation. This stent consists of a main body, resembling the configuration of conventional stents, and two connecting arms at the edges of the stent for the stabilization of the venous graft on the external surface of the stent. This new stent design was applied in a patient with an aneurysm in a stented segment in the right coronary artery. The immediate and long‐term angiographic evaluation after the covered stent implantation showed complete sealing of the aneurysm without restenosis. Cathet Cardiovasc Intervent 2002;55:222–227. © 2002 Wiley‐Liss, Inc.
Expression profiling of all protein‐coding genes in wild‐type and three DNA repair‐deficient substrains of Escherichia coli K‐12
Authors: Salmelin Camilla , Vilpo Juhani
Published: September 2002

Gene chips or cDNA arrays of the entire set of Escherichia coli (E.
coli) K12 genes were used to measure the expression, at the mRNA level,
of all 4290 protein‐coding genes in wild‐type (WT) and three DNA repair‐deficient
derivative strains: (i) AB1157 (WT), (ii) LR39 (ada, ogt), (iii)
MV1932 (alkA1, tag‐1) and (iv) GM5555 (mutS). The aim
was to investigate whether disruption of a single gene would result in significant
deviation in the expression of other genes in these organisms. We describe
here a simple approach for a stringent statistical evaluation of cDNA array
data. This includes: (i) determination of intra‐ and interassay variation
coefficients for different expression levels, (ii) rejection of biased duplicates,
(iii) mathematical background determination, and (iv) comparison of expression
levels of identical copies of a gene. The results demonstrated a highly significant
correlation of gene expression when the mutants were individually compared
with the wild‐type. Altogether, 81 deviations of the expression of 59 genes
were noted, out of 12,870, when 3‐fold or greater up‐ or down‐regulation was
used as a criterion of differential expression. In the light of current knowledge
of E. coli biology, the differential expression did not follow any
logical pattern. In fact, the deviations may simply represent inter‐assay
variation. The results obtained here with a simple model organism are different
from those obtained with most mammalian knockouts: disruption of the function
of a single gene does not, under good growth conditions, necessarily result
in great changes in the expression of other genes. Copyright ©
2002 John Wiley & Sons, Ltd.
Website Review: Cancer and the web
Authors: Robert Albertella Mark
Published: September 2002

The applications of functional genomics, proteomics and informatics to cancer research have yielded a tremendous amount of information, which is growing all the time. Much of this information is available publicly on the Internet and ranges from general information about different cancers from a patient or clinical viewpoint, through to databases suitable for cancer researchers of all backgrounds, to very specific sites dedicated to individual genes or molecules. A simple search for ‘cancer’ from a typical Web browser search engine yields more than half a million hits; an even more specific search for ‘leukaemia’ (>40 000 hits) or ‘p53’ (>5700 hits) yields far too many hits to allow one to identify particular sites of interest. This review aims to provide a brief guide to some of the resources and databases that can be used as springboards to home in rapidly on information relevant to many fields of cancer research. As such, this article will not focus on a single website but hopes to illustrate some of the ways that postgenomic biology is revolutionizing cancer research. It will cover genomics and proteomics approaches that have been applied to studying global expression patterns in cancers, in addition to providing links ranging from general information about cancer to specific cancer gene mutation databases. Copyright © 2001 John Wiley & Sons, Ltd.
From genome to function: systematic analysis of the soil bacterium Bacillus subtilis
Authors: Harwood Colin R. , Crawshaw Samuel G. , Wipat Anil
Published: September 2002

Bacillus subtilis is a sporulating Gram‐positive bacterium that lives primarily in the soil and associated water sources. Whilst this bacterium has been studied extensively in the laboratory, relatively few studies have been undertaken to study its activity in natural environments. The publication of the B. subtilis genome sequence and subsequent systematic functional analysis programme have provided an opportunity to develop tools for analysing the role and expression of Bacillus genes in situ. In this paper we discuss analytical approaches that are being developed to relate genes to function in environments such as the rhizosphere. Copyright © 2001 John Wiley & Sons, Ltd.
Featured Organism: Reductive evolution in bacteria: Buchnera sp., Rickettsia prowazekii and Mycobacterium leprae
Authors: Wixon Jo
Published: September 2002

Obligate intracellular bacteria commonly have much reduced genome sizes compared to their nearest free‐living relatives. One reason for this is reductive evolution: the loss of genes rendered non‐essential due to the intracellular habitat. This can occur because of the presence of orthologous genes in the host, combined with the ability of the bacteria to import the protein or metabolite products of the host genes. In this article we take a look at three such bacteria whose genomes have been fully sequenced. Buchnera is an endosymbiont of the pea aphid, Acyrthosiphon pisum, the relationship between these two organisms being so essential that neither can reproduce in the absence of the other. Rickettsia prowazekii is the causative agent of louse‐borne typhus in humans and Mycobacterium leprae infection of humans leads to leprosy. Both of these human pathogens have fastidious growth requirements, which has made them very difficult to study. Copyright © 2001 John Wiley & Sons, Ltd.
Vascular smooth muscle cell phenotypic modulation in culture is associated with reorganisation of contractile and cytoskeletal proteins
Authors: Worth Nathalie F. , Rolfe Barbara E. , Song Jian , Campbell Gordon R.
Published: September 2002

Smooth muscle cells (SMC) exhibit a functional plasticity, modulating from the mature phenotype in which the primary function is contraction, to a less differentiated state with increased capacities for motility, protein synthesis, and proliferation. The present study determined, using Western analysis, double‐label immunofluorescence and confocal microscopy, whether changes in phenotypic expression of rabbit aortic SMC in culture could be correlated with alterations in expression and distribution of structural proteins. “Contractile” state SMC (days 1 and 3 of primary culture) showed distinct sorting of proteins into subcellular domains, consistent with the theory that the SMC structural machinery is compartmentalised within the cell. Proteins specialised for contraction (α‐SM actin, SM‐MHC, and calponin) were highly expressed in these cells and concentrated in the upper central region of the cell. Vimentin was confined to the body of the cell, providing support for the contractile apparatus but not co‐localising with it. In line with its role in cell attachment and motility, β‐NM actin was localised to the cell periphery and basal cortex. The dense body protein α‐actinin was concentrated at the cell periphery, possibly stabilising both contractile and motile apparatus. Vinculin‐containing focal adhesions were well developed, indicating the cells' strong adhesion to substrate. In “synthetic” state SMC (passages 2–3 of culture), there was decreased expression of contractile and adhesion (vinculin) proteins with a concomitant increase in cytoskeletal proteins (β‐non‐muscle [NM] actin and vimentin). These quantitative changes in structural proteins were associated with dramatic changes in their distribution. The distinct compartmentalisation of structural proteins observed in “contractile” state SMC was no longer obvious, with proteins more evenly distributed throughout the cytoplasm to accommodate altered cell function. Thus, SMC phenotypic modulation involves not only quantitative changes in contractile and cytoskeletal proteins, but also reorganisation of these proteins. Since the cytoskeleton acts as a spatial regulator of intracellular signalling, reorganisation of the cytoskeleton may lead to realignment of signalling molecules, which, in turn, may mediate the changes in function associated with SMC phenotypic modulation. Cell Motil. Cytoskeleton 49:130–145, 2001. © 2001 Wiley‐Liss, Inc.
Recovery of flagellar dynein function in a Chlamydomonas actin/dynein‐deficient mutant upon introduction of muscle actin by electroporation
Authors: Hayashi Masahito , Hirono Masafumi , Kamiya Ritsu
Published: September 2002

Flagellar and ciliary inner‐arm dyneins contain actin as a subunit; however, the function of this actin subunit remains unknown. As a first step toward experimental manipulation of actin in dynein, we developed a method for introducing exogenous actin into Chlamydomonas cells by electroporation. A non‐motile mutant, ida5oda1, lacking inner‐arm dyneins due to the absence of conventional actin, was electroporated in the presence of rabbit skeletal muscle actin. About 20% of the electroporated cells recovered motility under optimal conditions. In addition, by taking advantage of their phototactic behavior, the rescued cells could be concentrated. Motility was also recovered with fluorescently labeled actin; in this case, axonemes became fluorescent after electroporation, suggesting that actin was in fact incorporated as a dynein subunit. The feasibility of incorporating a substantial amount of macromolecules by electroporation will be useful not only for studying actin function, but also for a variety of studies using Chlamydomonas in which no efficient methods have been developed for expressing or introducing foreign proteins and other macromolecules. Cell Motil. Cytoskeleton 49:146–153, 2001. © 2001 Wiley‐Liss, Inc.
Elastic extension and jump of the flagellar nexin links: A theoretical mechanical cycle
Authors: Cibert C.
Published: September 2002

The functions of the nexin links of a flagellar axoneme have not been clearly demonstrated. Taking into account both the elastic (Hookean) characteristics and the possible jump of the nexin links, we calculated the sliding to bending conversion of a theoretical model in a tip‐ward direction step by step, according to the essential principles proposed by the geometric clutch hypothesis [Lindemann, 1994: J Theoret Biol 168:175–189]: the activity of the dynein arms depends on the transverse forces induced by the axonemal curvature. In our calculations, however, the transverse forces that are involved in the regulation of the activities of the dynein arms were due to the extension of the nexin links located upstream of a given abscissa. This allowed us to define a bent segment as the axonemal portion at whose proximal and distal ends the nexin links were relaxed, and as fully extended as possible, respectively. The model creates an apparent disorder in the orientation of the nexin links as already observed [Bozkurt and Wooley, 1993: Cell Motil Cytoskeleton 24:109–118; Wooley, 1997: J Cell Sci 110:85–94]. We propose that the nexin links are involved in a mechanical cycle, whose 3 stages are (1) rapid extension, (2) slow relaxation, and (3) stand‐by. The rapid extension is compatible with the mechanical interactions between the nexin links and the inner dynein arms with which they form the dynein regulatory complex. This was correlated with the oscillating properties of the nexin links along the axoneme that allow them to be one of the regulatory elements of the local ATPase activity of the dynein arms. Cell Motil. Cytoskeleton 49:161–175, 2001. © 2001 Wiley‐Liss, Inc.
Organization of the honey bee mushroom body: Representation of the calyx within the vertical and gamma lobes
Authors: Strausfeld Nicholas J.
Published: September 2002

Studies of the mushroom bodies of Drosophila melanogaster have suggested that their gamma lobes specifically support short‐term memory, whereas their vertical lobes are essential for long‐term memory. Developmental studies have demonstrated that the Drosophila gamma lobe, like its equivalent in the cockroach Periplaneta americana, is supplied by a special class of intrinsic neuron—the clawed Kenyon cells—that are the first to differentiate during early development. To date, however, no account identifies a corresponding lobe in the honey bee, another taxon used extensively for learning and memory research. Received opinion is that, in this taxon, each of the mushroom body lobes comprises three parallel divisions representing one of three concentric zones of the calyces, called the lip, collar, and basal ring. The present account shows that, although these zones are represented in the lobes, they occupy only two thirds of the vertical lobe. Its lowermost third receives the axons of the clawed class II Kenyon cells, which are the first to differentiate during early development and which represent the whole calyx. This component of the lobe is anatomically and developmentally equivalent to the gamma lobe of Drosophila and has been here named the gamma lobe of the honey bee. A new class of intrinsic neurons, originating from perikarya distant from the mushroom body, provides a second system of parallel fibers from the calyx to the gamma lobe. A region immediately beneath the calyces, called the neck, is invaded by these neurons as well as by a third class of intrinsic cell that provides connections within the neck of the pedunculus and the basal ring of the calyces. In the honey bee, the gamma lobe is extensively supplied by afferents from the protocerebrum and gives rise to a distinctive class of efferent neurons. The terminals of these efferents target protocerebral neuropils that are distinct from those receiving efferents from divisions of the vertical lobe that represent the lip, collar, and basal ring. The identification of a gamma lobe unites the mushroom bodies of evolutionarily divergent taxa. The present findings suggest the need for critical reinterpretation of studies that have been predicated on early descriptions of the mushroom body's lobes. J. Comp. Neurol. 450:4–33, 2002. © 2002 Wiley‐Liss, Inc.
Immunohistochemical localization and biochemical characterization of ghrelin in the brain and stomach of the frog Rana esculenta
Authors: Galas Ludovic , Chartrel Nicolas , Kojima Masayasu , Kangawa Kenji , Vaudry Hubert
Published: September 2002

Ghrelin is a 28‐amino acid n‐octanoylated peptide recently isolated from the rat stomach as an endogenous ligand of the growth hormone secretagogue receptor. So far, the occurrence of ghrelin has not been investigated in submammalian vertebrates. In the present work, we have studied the anatomic distribution and biochemical characterization of ghrelin‐like immunoreactivity in the brain and stomach of the frog Rana esculenta by using two distinct antisera directed against rat ghrelin. In the brain, sparse ghrelin‐positive cells were detected in three nuclei of the diencephalon, namely the suprachiasmatic nucleus and the posterior tuberculum in the hypothalamus, and the posterodorsal aspect of the lateral nucleus in the thalamus. A few ghrelin‐immunoreactive neurons were also found in the mesencephalon, i.e., in the pretoral gray and the anterodorsal tegmental nucleus. Ghrelin‐containing fibers were widely distributed in the frog brain. In particular, diffuse networks of immunoreactive processes were observed in various regions of the telencephalon, including the medial pallium, the striatum, the nucleus of the diagonal band of Broca, the nucleus accumbens, and the amygdala. In the diencephalon, the magnocellular nucleus, the suprachiasmatic nucleus, the posterior tuberculum, and the ventrolateral and lateral thalamic nuclei were moderately to densely innervated with ghrelin‐containing fibers. A moderate density of positive fibers was also found in different areas of the mesencephalon such as the nucleus of the medial longitudinal fasciculus, the pretoral gray, and the tegmentum. In the stomach, a few brightly immunofluorescent cells were detected in the mucosa. The distribution pattern and morphologic characteristics of ghrelin‐containing cells in the stomach suggest that they correspond to endocrine cells. Reversed‐phase high performance liquid chromatography analysis of frog brain and stomach extracts, combined with RIA detection, revealed that ghrelin‐immunoreactive material eluted as a single peak with a retention time slightly shorter than that of synthetic rat ghrelin. The present data provide the first evidence that a ghrelin‐related peptide is present in submammalian vertebrates. The occurrence of ghrelin‐containing cells in the hypothalamus and the stomach mucosa suggests that, in amphibians, ghrelin may exert both neuroendocrine and endocrine activities. J. Comp. Neurol. 450:34–44, 2002. © 2002 Wiley‐Liss, Inc.
Antagonism of vasoactive intestinal peptide mRNA in the suprachiasmatic nucleus disrupts the rhythm of FRAs expression in neuroendocrine dopaminergic neurons
Authors: Gerhold Lynnette M. , Sellix Michael T. , Freeman Marc E.
Published: September 2002

This study was designed to determine whether there is a functional relationship between cfos expression in vasoactive intestinal peptide (VIP) ‐containing neurons of the suprachiasmatic nucleus (SCN) and Fos‐related antigens (FRAs) expression in neuroendocrine dopaminergic neurons of the arcuate (ARN) and periventricular (PeVN) nuclei of the hypothalamus. Brains were obtained from ovariectomized (OVX) female rats killed at 12:00 AM, 7:00 AM, 9:00 AM, 12:00 PM, and 7:00 PM (12 hours illumination beginning 6:00 AM). Antibodies against FRAs and tyrosine hydroxylase (TH) identified activated neuroendocrine dopaminergic neurons. Antibodies against cfos and VIP identified activated VIP‐immunoreactive (IR) neurons in the SCN. The proportion of neuroendocrine dopaminergic neurons in the ARN and PeVN expressing FRAs was greatest and equivalent at 7:00 AM, 9:00 AM, 12:00 PM, and 12:00 AM. At 7:00 PM, the proportion of neuroendocrine dopaminergic neurons expressing FRAs was significantly lower than all other time points. In the SCN, a subpopulation of VIP‐IR neurons maximally expressed cfos at 7:00 AM, which decreased through 9:00 AM. cFos was not expressed at 7:00 PM and 12:00 AM in VIP‐IR neurons. Antisense VIP oligonucleotides were injected into the SCN to determine whether attenuation of VIP expression disturbs rhythms in neuroendocrine dopaminergic neuronal activity. OVX rats were infused with either antisense VIP oligonucleotides or scrambled sequence oligonucleotides bilaterally (0.5 μg in 0.5 μl of saline per side) in the SCN. Animals were killed 34 hours (7:00 PM) and 46 hours (7:00 AM) after receiving infusions, and brains were recovered. Administration of antisense VIP oligonucleotides decreased VIP protein expression in the SCN and prevented the decrease in the percentage of neuroendocrine dopaminergic neurons expressing FRAs at 7:00 PM but did not affect FRAs expression at 7:00 AM when compared with animals receiving scrambled oligonucleotides. These data suggest that VIP fibers from the SCN may relay time‐of‐day information to neuroendocrine dopaminergic neurons to inhibit their activity and, thus, initiate prolactin release in the evening. J. Comp. Neurol. 450:135–143, 2002. © 2002 Wiley‐Liss, Inc.
BEM‐analysis of interaction of elastic waves with unilateral interface crack
Authors: Bing‐Zheng Gai , Qingcai Chen
Published: September 2002

In this paper, to solve the problems of the interaction between the unilateral interface cracks and elastic wave, a new numerical method based on boundary element method (BEM) has been proposed. In this method, an iterating–correcting process of the solution in frequency domain and the correction in time domain has been designed to eliminate the mutual interference between the time and frequency domain. As an illustration to the algorithm, an interface crack between two half‐planes under the attack of harmonic plane elastic wave has been analysed in detail. The contact configurations and stress field at the crack surface, and dynamic stress intensity factor (DSIF) at the crack tip have been given. Copyright © 2001 John Wiley & Sons, Ltd.
The non‐linear analysis of flexibly connected space frames
Authors: Erdem Hakan , Aksogan Orhan , Arslan H. Murat
Published: September 2002

This study considers the effect of the non‐linear behaviour of connections and geometric non‐linearity on the behaviour of space frames. The Richard model (Comput. Struct. 1993; 46: 55) has been used for the non‐linear moment–rotation relation of the connections and the behaviour of the material is assumed to be linearly elastic. The tangent stiffness matrix has been obtained from the solution of the pertinent linear differential equation that governs the moment–curvature relation of a prismatic member, including the above‐mentioned non‐linear effects. The non‐linear equilibrium equations that show up are solved iteratively using an incremental loading procedure. The iterative procedure is repeated until the unbalanced forces are less than a predefined tolerance. Consequently, the errors emerging due to the linearization of the non‐linear analysis can be made as small as desired. An example problem is solved using the computer program written to implement the proposed analysis and the results are in good agreement with those in the literature. Copyright © 2002 John Wiley & Sons, Ltd.
Experiences from integrating algorithmic and systemic load balancing strategies
Authors: Banicescu Ioana , Ghafoor Sheikh , Velusamy Vijay , Russ Samuel H. , Bilderback Mark
Published: September 2002

Load balancing increases the efficient use of existing resources for parallel and distributed applications. At a coarse level of granularity, advances in runtime systems for parallel programs have been proposed in order to control available resources as efficiently as possible by utilizing idle resources and using task migration. Simultaneously, at a finer granularity level, advances in algorithmic strategies for dynamically balancing computational loads by data redistribution have been proposed in order to respond to variations in processor performance during the execution of a given parallel application. Combining strategies from each level of granularity can result in a system which delivers advantages of both. The resulting integration is systemic in nature and transfers the responsibility of efficient resource utilization from the application programmer to the runtime system. This paper presents the design and implementation of a system that combines an algorithmic fine‐grained data parallel load balancing strategy with a systemic coarse‐grained task‐parallel load balancing strategy, and reports on recent experimental results of running a computationally intensive scientific application under this integrated system. The experimental results indicate that a distributed runtime environment which combines both task and data migration can provide performance advantages with little overhead. It also presents proposals for performance enhancements of the implementation, as well as future explorations for effective resource management. Copyright © 2001 John Wiley & Sons, Ltd.
Analysis and measurement of the effect of kernel locks in SMP systems
Authors: Kaieda Akihiro , Nakayama Yasuichi , Tanaka Atsuhiro , Horikawa Takashi , Kurasugi Toshiyasu , Kino Issei
Published: September 2002

This article reports the use of case studies to evaluate the performance degradation caused by the kernel‐level lock. We define the lock ratio as a ratio of the execution time for critical sections to the total execution time of a parallel program. The kernel‐level lock ratio determines how effective programs work on symmetric multiprocessor (SMP) systems. We have measured the lock ratios and the performance of three types of parallel programs on SMP systems with Linux 2.0: matrix multiplication, parallel make, and WWW server programs. Experimental results show that the higher the lock ratio of parallel programs, the worse their performance becomes. Copyright © 2001 John Wiley & Sons, Ltd.
Code generator for the HPF Library and Fortran 95 transformational functions
Authors: van Waveren Matthijs , Addison Cliff , Harrison Peter , Orange Dave , Brown Norman , Iwashita Hidetoshi
Published: September 2002

One of the language features of the core language of HPF 2.0 (High Performance Fortran) is the HPF Library. The HPF Library consists of 55 generic functions. The implementation of this library presents the challenge that all data types, data kinds, array ranks and input distributions need to be supported. For instance, more than 2 billion separate functions are required to support COPY_SCATTER fully. The efficient support of these billions of specific functions is one of the outstanding problems of HPF. We have solved this problem by developing a library generator which utilizes the mechanism of parameterized templates. This mechanism allows the procedures to be instantiated at compile time for arguments with a specific type, kind, rank and distribution over a specific processor array. We describe the algorithms used in the different library functions. The implementation gives the ease of generating a large number of library routines from a single template. The templates can be extended with special code for specific combinations of the input arguments. We describe in detail the implementation and performance of the matrix multiplication template for the Fujitsu VPP5000 platform. Copyright © 2002 John Wiley & Sons, Ltd.
Implementation and evaluation of HPF/SX V2
Authors: Murai Hitoshi , Araki Takuya , Hayashi Yasuharu , Suehiro Kenji , Seo Yoshiki
Published: September 2002

We are developing HPF/SX V2, a High Performance Fortran (HPF) compiler for vector parallel machines. It provides some unique extensions as well as the features of HPF 2.0 and HPF/JA. In particular, this paper describes four of them: (1) the ON directive of HPF 2.0; (2) the REFLECT and LOCAL directives of HPF/JA; (3) vectorization directives; and (4) automatic parallelization. We evaluate these features through some benchmark programs on NEC SX‐5. The results show that each of them achieved a 5–8 times speedup in 8‐CPU parallel execution and the four features are useful for vector parallel execution. We also evaluate the overall performance of HPF/SX V2 by using over 30 well‐known benchmark programs from HPFBench, APR Benchmarks, GENESIS Benchmarks, and NAS Parallel Benchmarks. About half of the programs showed good performance, while the other half suggest weakness of the compiler, especially on its runtimes. It is necessary to improve them to put the compiler to practical use. Copyright © 2002 John Wiley & Sons, Ltd.
Optimization of element‐by‐element FEM in HPF 1.1
Authors: Okuda Hiroshi , Anan Norihisa
Published: September 2002

In this study, Poisson's equation is numerically evaluated by the element‐by‐element (EBE) finite‐element method in a parallel environment using HPF 1.1 (High‐Performance Fortran). In order to achieve high parallel efficiency, the data structures have been altered to node‐based data instead of mixtures of node‐ and element‐based data, representing a node‐based EBE finite‐element scheme (nEBE). The parallel machine used in this study was the NEC SX‐4, and experiments were performed on a single node having 32 processors sharing common memory. The HPF compiler used in the experiments is HPF/SX Rev 2.0 released in 1997 (unofficial), which supports HPF 1.1. Models containing approximately 200 000 and 1 500 000 degrees of freedom were analyzed in order to evaluate the method. The calculation time, parallel efficiency, and memory used were compared. The performance of HPF in the conjugate gradient solver for the large model, using the NEC SX‐4 compiler option ‐noshrunk, was about 85% that of the message passing interface. Copyright © 2002 John Wiley & Sons, Ltd.
High‐performance numerical pricing methods
Authors: Moritsch Hans , Benkner Siegfried
Published: September 2002

The pricing of financial derivatives is an important field in finance and constitutes a major component of financial management applications. The uncertainty of future events often makes analytic approaches infeasible and, hence, time‐consuming numerical simulations are required. In the Aurora Financial Management System, pricing is performed on the basis of lattice representations of stochastic multidimensional scenario processes using the Monte Carlo simulation and Backward Induction methods, the latter allowing for the exploitation of shared‐memory parallelism. We present the parallelization of a Backward Induction numerical pricing kernel on a cluster of SMPs using HPF+, an extended version of High‐Performance Fortran. Based on language extensions for specifying a hierarchical mapping of data onto an SMP cluster, the compiler generates a hybrid‐parallel program combining distributed‐memory and shared‐memory parallelism. We outline the parallelization strategy adopted by the VFC compiler and present an experimental evaluation of the pricing kernel on an NEC SX‐5 vector supercomputer and a Linux SMP cluster, comparing a pure MPI version to a hybrid‐parallel MPI/OpenMP version. Copyright © 2002 John Wiley & Sons, Ltd.
Achieving performance under OpenMP on ccNUMA and software distributed shared memory systems
Authors: Chapman B. , Bregier F. , Patil A. , Prabhakar A.
Published: September 2002

OpenMP is emerging as a viable high‐level programming model for shared memory parallel systems. It was conceived to enable easy, portable application development on this range of systems, and it has also been implemented on cache‐coherent Non‐Uniform Memory Access (ccNUMA) architectures. Unfortunately, it is hard to obtain high performance on the latter architecture, particularly when large numbers of threads are involved. In this paper, we discuss the difficulties faced when writing OpenMP programs for ccNUMA systems, and explain how the vendors have attempted to overcome them. We focus on one such system, the SGI Origin 2000, and perform a variety of experiments designed to illustrate the impact of the vendor's efforts. We compare codes written in a standard, loop‐level parallel style under OpenMP with alternative versions written in a Single Program Multiple Data (SPMD) fashion, also realized via OpenMP, and show that the latter consistently provides superior performance. A carefully chosen set of language extensions can help us translate programs from the former style to the latter (or to compile directly, but in a similar manner). Syntax for these extensions can be borrowed from HPF, and some aspects of HPF compiler technology can help the translation process. It is our expectation that an extended language, if well compiled, would improve the attractiveness of OpenMP as a language for high‐performance computation on an important class of modern architectures. Copyright © 2002 John Wiley & Sons, Ltd.
Efficient parallel programming on scalable shared memory systems with High Performance Fortran
Authors: Benkner Siegfried , Brandes Thomas
Published: September 2002

OpenMP offers a high‐level interface for parallel programming on scalable shared memory (SMP) architectures. It provides the user with simple work‐sharing directives while it relies on the compiler to generate parallel programs based on thread parallelism. However, the lack of language features for exploiting data locality often results in poor performance since the non‐uniform memory access times on scalable SMP machines cannot be neglected. High Performance Fortran (HPF), the de‐facto standard for data parallel programming, offers a rich set of data distribution directives in order to exploit data locality, but it has been mainly targeted towards distributed memory machines.

In this paper we describe an optimized execution model for HPF programs on SMP machines that avails itself with mechanisms provided by OpenMP for work sharing and thread parallelism, while exploiting data locality based on user‐specified distribution directives. Data locality does not only ensure that most memory accesses are close to the executing threads and are therefore faster, but it also minimizes synchronization overheads, especially in the case of unstructured reductions. The proposed shared memory execution model for HPF relies on a small set of language extensions, which resemble the OpenMP work‐sharing features. These extensions, together with an optimized shared memory parallelization and execution model, have been implemented in the ADAPTOR HPF compilation system and experimental results verify the efficiency of the chosen approach. Copyright © 2002 John Wiley & Sons, Ltd.
The personality structure questionnaire (PSQ): a measure of the multiple self states model of identity disturbance in cognitive analytic therapy
Authors: Pollock Philip H. , Broadbent Matthew , Clarke Sue , Dorrian Angela , Ryle Anthony
Published: September 2002

The Multiple Self‐States Model (MSSM) of Cognitive Analytic Therapy (CAT) conceptualizes identity disturbances in personality, particularly borderline personality disorder. The Personality Structure Questionnaire (PSQ) has been devised to measure deficits in personality integrity and represent an assessment measure of the MSSM. A spectrum of multiplicity in the self and dissociation is implied within the MSSM with gradation from borderline personality to dissociative identity disorder. The construction, psychometric properties, reliability, validity and clinical utility of the PSQ as a measure of the MSSM are described based on data from the present study and that of Broadbent, Clarke and Ryle (The Personality Structure Questionnaire: a brief self‐report measure of personality integration. Unpublished manuscript) and its relationship to psychological constructs of identity integrity is investigated. A series of non‐clinical and clinical groups of participants were administered the PSQ and other standardized measures. The PSQ was shown to be a reliable self‐report measure and factor analysis revealed it to be unidimensional and to correlate convergently with multiplicity, dissociation and constructs related to identity disturbance. Regression analysis indicated the PSQ to be predicted by greater multiplicity. The PSQ, in combination with other constructs, also discriminated between diagnosed clinical groups (psychotherapy patients, borderline personality disorder and dissociative identity disorder). The PSQ is shown to be a brief, psychometrically sound self‐report measure of identity disturbance as conceptualized by the MSSM in CAT. The applicability of the PSQ and its relevance to the concepts of multiplicity and dissociation within the MSSM of CAT are discussed. Copyright © 2001 John Wiley & Sons, Ltd.
Chalcones as potent antiplatelet agents and calcium channel blockers
Authors: Lin Chun‐Nan , Hsieh Hsin‐Kaw , Ko Horng‐Huey , Hsu Mei‐Feng , Lin Hsien‐Cheng , Chang Ya‐Ling , Chung Mei‐Ing , Kang Jaw‐Jou , Wang Jih‐Pyang , Teng Che‐Ming
Published: September 2002

In an effort to continually develop potent antiplatelet agents with vasorelaxing and antiinflammatory actions, a novel series of antiinflammatory chalcones was continually screened to evaluate their antiplatelet and vasorelaxing effects. Their structure–activity relationships and mode of action were discussed and characterized. A novel series of antiinflammatory chalcones was studied on antiplatelet effect in rabbit washed platelets and human platelet‐rich plasma (PRP) and vasorelaxing effect in rat thoracic aorta. Arachidonic acid‐induced platelet aggregation was potently inhibited by almost all the chalcone derivatives and 13–15 also had a potent inhibitory effect on cyclooxygenase. The selective chalcones 12–16 tested in human PRP significantly inhibited secondary aggregation induced by adrenaline. In rat thoracic aorta, most of chalcones at high concentration significantly depressed the contractions induced by Ca2+ (1.9 mM) in high K+ (80 mM) medium and the phasic and tonic contractions caused by norepinephrine (3 μM). In the rat thoracic aorta, the phenylephrine‐ and high K+‐induced 45Ca2+ influx were both inhibited by a selective chalcone derivative, 14. These results indicate that the antiplatelet actions of chalcones are mainly mediated through the suppression of cyclooxygenase activity and reduced thromboxane formation and their inhibitory effects on the contractile response caused by high K+ and norepinephrine in rat thoracic aorta are mainly due to inhibition of Ca2+ influx through both voltage‐dependent and receptor‐operated Ca2+ channels. Drug Dev. Res. 53:9–14, 2001. © 2001 Wiley‐Liss, Inc.
Characterization and expression of ATP P2X4 receptor from embryonic chick skeletal muscle
Authors: Bo Xuenong , Liu Min , Schoepfer Ralf , Burnstock Geoffrey
Published: September 2002

Previous pharmacological experiments have indicated the existence of ATP P2X receptors in chick embryonic skeletal muscles. In this study we cloned a P2X4‐like cDNA encoding a protein of 385 amino acids, which shares 75% and 76% identity with rat and human P2X4 receptors, respectively. Functional studies of this cP2X4 receptor expressed in Xenopus oocytes showed that ATP induced a fast inward current, which was partially desensitized upon prolonged application of ATP. The ATP‐induced currents were concentration‐dependent, with an EC50 of 9.5 μM. Adenosine 5′‐O‐(thio)triphosphate and 2‐methylthioATP very weak agonists. α,β‐methyleneATP was almost inactive. In contrast to their potentiating effects on recombinant rat P2X4 receptors, both suramin and pyridoxalphosphate‐6‐azophenyl‐2′,4′‐disulfonic acid partially blocked ATP‐induced currents. TrinitrophenylATP was able to block ATP‐induced response completely, with an IC50 of 4.7 μM. Northern blot and RT‐PCR analysis showed that cP2X4 mRNAs were mainly expressed in skeletal muscle, brain, and gizzard of day 10 chick embryos. Lower levels of expression were also detected in liver, heart, and retina. Whole‐mount in situ hybridization showed that cP2X4 mRNAs were expressed in the brain, spinal cord, notochord, gizzard, and skeletal muscle. The physiological functions of cP2X4 receptors in embryonic skeletal muscle remain unclear at present. Drug Dev. Res. 53:22–28, 2001. © 2001 Wiley‐Liss, Inc.
Annexin expressions are temporally and spatially regulated during rat hepatocyte differentiation
Authors: Della Gaspera Bruno , Braut‐Boucher Françoise , Bomsel Morgane , Chatelet Françoise , Guguen‐Guillouzo Christiane , Font Jacqueline , Weinman Jacqueline , Weinman Serge
Published: September 2002

Annexin (Anx) 1, 2, 5, and 6 expressions were determined at the transcriptional and translational levels in the rat hepatocytes from gestational day 15 to postnatal day 17. Dramatic shifts were observed in Anx 1 and 2 levels, which peaked at day 1 and gestational day 20, respectively, and reached low levels thereafter. However, Anx 5 and 6 rates were more constant. Prenatal administration of dexamethasone (dex) resulted in a decrease of Anx 1 mRNA levels, and a strong increase in Anx 2 mRNA contents. In adult hepatocytes cultured in the presence of EGF or HGF, Anx 1 and 2 expressions resumed. By immunohistochemistry, Anx 1 was detected only in the cytoplasm of hepatocytes of 1‐ to 3‐day‐old rats, Anx 2 and 6 both exhibited a redistribution from the cytoplasm toward the plasma membrane, and Anx 5 was present in the nucleus, cytoplasm, and plasma membrane. Thus, Anx 1, 2, 5, and 6 have individual modes of expression and localization in the differentiating hepatocytes, where they might play unique roles at well defined phases of liver ontogeny. © 2001 Wiley‐Liss, Inc.