bluuebunny/crossref_metadata_2025 huggingface dataset:
Tissue malondialdehyde and adenosine triphosphatase level after experimental liver ischaemia–reperfusion damage
Authors: Ilhan Nevin , Halifeoglu Ihsan , Ozercan H. Ibrahim , Ilhan Necip
Published: September 2002

Functional irregularities due to damage after ischaemia–reperfusion vary depending upon the organs affected. High energy phosphates such as ATP and ADP are destroyed after ischaemia–reperfusion damage. Subsequently, protons and inorganic phosphates accumulate within the cells and the proton pumps such as adenosine triphosphatase (ATPase), which maintain intracellular ion balance are damaged. In the present study, malondialdehyde (MDA), a product of lipid peroxidation, was measured as an indicator of tissue damage. Additionally, we measured sodium‐potasium‐ATPase levels and determined the interactions between MDA and Na+‐K+ ATPase levels. A total of 31 female guinea pigs were divided into four groups: sham operated guinea pigs (group 1), ischaemia–reperfusion (group 2), ischaemia–reperfusion + superoxide dismutase (SOD) (group 3), ischaemia–reperfusion + allopurinol (group 4). Following reperfusion, the livers of guinea pigs in each group were removed for histopathological examination and the levels of MDA and Na+‐K+ ATPase were determined in homogenized tissue samples. There was a statistically significant (p < 0.05) reduction in tissue MDA levels in group 2 when compared with group 1. The level of tissue MDA in groups 3 and 4 was significantly lower than tissue MDA levels of group 2. However, there was a statistically significant (p < 0.05) reduction in tissue Na+‐K+ ATPase levels of group 2 when compared with group 1. Similiarly, the level of tissue Na+‐K+ ATPase in groups 3 and 4 was significantly higher than the tissue Na+‐K+ ATPase levels of group 2. The results of the histopathologic examination also revealed the beneficial effects of the use of SOD and allopurinol in preventing liver damage in cases of ischaemia–reperfusion. Although the levels of MDA and Na+‐K+ ATP ase in group 2 were not equal to the level in group 1, antioxidant therapy significantly improved the tendency to reverse the effects of ischaemia–reperfusion and to protect the liver from damage due to ischaemia–reperfusion. Copyright © 2001 John Wiley & Sons, Ltd.
Effects of phosphoprotein phosphatase inhibitors (phenylarsine oxide and cantharidin) on Tetrahymena
Authors: Kovács Péter , Pintér Miklós
Published: September 2002

The effects of phenylarsine oxide (PAO) (phosphotyrosine phosphatase inhibitor) and cantharidin (serine/threonine phosphatase [PP2A] inhibitor) treatments were analysed on the synthesis of phospholipids and glycolipids, and on the cytoskeletal elements (F‐actin and tubulin containing structures) of Tetrahymena pyriformis. Both phosphatase inhibitors reduced the amount of incorporated 32 of the whole phospholipid content, but the ratio of phosphatidylserine (PS) and phosphatidylcholine (PC) to the total phospholipid content increased. Both treatments influenced the phosphatidylinositol (PI) system. These inhibitors also influenced the incorporation of palmitic acid into the phospholipids: in general PAO decreased, whereas cantharidin increased the amount of incorporated palmitic acid; 1 μm cantharidin significantly increased the labelling of PE and PA. The incorporation of mannose and glucosamine was influenced differently by PAO and cantharidin treatments: the latter elevated, while PAO decreased the labelling of glycolipids with these sugars. The effects of these treatments were visible also in the case of confocal scanning laser microscopic (CSLM) images: after treatments with both inhibitors, the F‐actin containing cortical elements were destroyed, but the tubulin containing ones (longitudinal and transversal microtubules, oral apparatus and deep fibres) did not display significant alterations. The different effects of phosphatase inhibitors were visible also on the scanning electron microscopic (sEM) images: cantharidin treatments (1μm) decreased the amount of dissolved membrane lipids after chemical dehydration of the cells with 2, 2‐dimethoxy propane (DMP), but in the case of treatments with 10 μm, the surface pattern of cells was similar to the controls. On the other hand, after PAO treatments the surface pattern of Tetrahymena showed significant alterations. Both phospahatase inhibitors inhibited the phagocytotic activity of the cells. On the basis of present experiments we suppose that these treatments are able to influence signalling systems (e.g. PI) of Tetrahymena, and also the structure of the cytoskeleton and the functions (e.g. phagocytosis) which are connected with skeletal elements. Copyright © 2001 John Wiley & Sons, Ltd.
Studies on p53 and Bax protein expression in Cockayne syndrome cells after UV irradiation and interferon‐β treatment
Authors: Sugita Katsuo , Chi Xiao‐Jun , Hiwasa Takaki , Nobuo Nobuo
Published: September 2002

Human interferon (HuIFN) has a protective effect against ultraviolet (UV)‐induced killing of Cockayne syndrome (CS) and xeroderma pigmentosum (XP) cells. Irradiation with ultraviolet (UV) resulted in nuclear accumulation of p53 in normal human fibroblast cells, and this accumulation was suppressed by treatment with HuIFN‐β. On the other hand, a large amount of p53 was found in both nuclear and cytoplasmic fractions of one SV40‐transformed XP and two SV40‐transformed CS cell strains irrespective of UV irradiation. Treatment with HuIFN‐β reduced the level of pro‐apoptotic Bax protein without suppression of nuclear accumulation of p53 in the CS cells but not in the XP cells. These findings suggest that there are different mechanisms of UV‐refractoriness caused by HuIFN‐β in UV‐sensitive CS and XP cells. Copyright © 2001 John Wiley & Sons, Ltd.
Antimicrotubular and cytotoxic activity of geiparvarin analogues, alone and in combination with paclitaxel
Authors: Miglietta Antonella , Bocca Claudia , Gabriel Ludovica , Rampa Angela , Bisi Alessandra , Valenti Piero
Published: September 2002

Geiparvarin is an antiproliferative compound isolated from the leaves of Geijera parviflora, and may represent a new drug which targets tubulin. To better explore the potential use of this agent, we investigated the antimicrotubular and cytotoxic effects of new synthetic aromatic derivatives of geiparvarin. These drugs inhibited polymerization of microtubular protein, particularly when the assembly was induced by paclitaxel. The microtubular network organization of fibroblasts was altered more effectively by some drugs. Normal microtubule architecture completely disappeared when the cells were treated simultaneously with drugs and paclitaxel: microtubules depolymerized or were reorganized into bundles, in a similar but more disarrayed fashion than that observed after treatment with paclitaxel alone. Cytotoxicity studies showed a dose‐dependent effect, whereas combined administration of drugs and paclitaxel increased cytotoxicity, more effectively in paclitaxel versus derivatives administration alone. Copyright © 2001 John Wiley & Sons, Ltd.
Cytokine detection in HIV‐1/HHV‐8 co‐infected subjects
Authors: Pugliese Agostino , Torre Donato , Saini Andrea , Pagliano Gloria , Gallo Gloria , Pistono Pietro Giorgio , Paggi Gian Carlo
Published: September 2002

In a previous work we have evaluated some immunologic and haematologic parameters of HIV‐1 positive subjects co‐infected with HHV‐8. A worsening of these values were generally described in these patients as compared with those HIV‐1 positive, but negative for HHV‐8. Now we have studied the influence of HHV‐8 co‐infection of HIV‐1 positive subjects on the production of some cytokines to make clear the question of its role in the immuno‐deregulation of the above‐mentioned subjects. In particular we have analysed serum levels of IL‐4 and IL‐10, Th2 type T cells cytokines, IFN‐γ, an indirect marker of Th1 cells activation and IL‐18, a cytokine produced by monocytic‐macrophagic cells, which is able to induce IFN‐γ production and Th1 T lymphocytes activation. No significant differences were found as regards the IFN‐γ serum levels (92.1 ± 24.3 pg ml−1 in the case of HIV‐1 positive/HHV‐8 negative subjects and 96.0 ± 17.4 pg ml−1 in those HIV‐1 positive/HHV‐8 positive). In healthy subjects the mean level of this cytokine was 17.6 ± 5.2 pg ml−1 (significant difference with both the former values at p < 0.001). Moreover IL‐4 and IL‐10, which were undetectable in healthy individuals, showed the following values in HIV‐1positive/HHV‐8 negative subjects: 31.9 ± 2.7 pg ml−1 and 119.8 ± 85.1 pg ml−1 respectively and in HIV‐1 positive/HHV‐8 positive subjects: 30.4 ± 4.8 pg ml−1 and 69.4 ± 65.3 pg ml−1 (not significant differences). In contrast IL‐18 reached a mean level of 1001.2 ± 360.5 pg ml−1 in HIV‐1 positive/HHV‐8 negative subjects, but showed a significant reduction in HIV‐1 positive/HHV‐8 positive subjects (737.6 ± 284.3 pg ml−1→p < 0.05) and presented very low levels in healthy individuals (21.3 ± 30.3 pg ml−1). Moreover a significant correlation (−0.984→p < 0.001) was noticed between IL‐18 reduction in HIV‐1 positive subjects co‐infected with HHV‐8 and the degree of positivity of HHV‐8. These data suggest that HHV‐8 co‐infection has no influence on the switch Th1→ Th2 in HIV‐1 positive subjects, but is able to reduce IL‐18 production, useful for Th1 subset restoration. Copyright © 2002 John Wiley & Sons, Ltd.
Age‐related changes in the glutathione redox system
Authors: Erden‐İnal Mine , Sunal Emine , Kanbak Güngör
Published: September 2002

The effect of aging on the glutathione redox system was evaluated in this study. For this purpose, we determined reduced glutathione (GSH) and oxidized glutathione (GSSG) in whole blood, glutathione peroxidase (GPx) and glutathione reductase (GSSGR) in erythrocytes and selenium (Se) in plasma in 176 healthy individuals. We also calculated GSH/GSSG molar ratios. These subjects were divided into five groups: group 1 (n = 25; 0.2–1 years old); group 2 (n = 28; 2–11 years old); group 3 (n = 23; 12–24 years old); group 4 (n = 40; 25–40 years old); group 5 (n = 60; 41–69 years old). GSH levels in groups 1 and 5 were significantly lower than the other groups (p< 0.001). Conversely, GSSG levels were significantly high in these periods (p< 0.001). The GSH/GSSG molar ratio was found to be low both in the first year of life and in the oldest group (p< 0.001, respectively). GPx activity in group 5 was increased as compared to the other groups (p< 0.001). GSSGR activity was significantly lower in the oldest groups than in the other groups (p< 0.001). Se levels were found to be low in the oldest group (p< 0.001). Selenium levels of women in group 5 were significantly high as compared to the men (p< 0.01). We found negative correlations between age and GSH levels (r = 0.402; p< 0.001), selenium levels (r = 0.454; p< 0.001), GSH/GSSG molar ratio (r = 0.557; p< 0.001) and GSSGR activity (r = 0.556; p< 0.001). There were positive correlations between age and GPx (r = 0.538; p< 0.001) and GSSG level (r = 0.551; p< 0.001). In conclusion, our findings show that the glutathione redox system is affected by age. Oxidative stress increases during the aging process. There is no effect of aging on the glutathione redox system according to sex except for the Se level. Copyright © 2001 John Wiley & Sons, Ltd.
1α,25‐Dihydroxyvitamin D3 inhibits rat liver ultrastructural changes and the development of γ‐glutamyltranspeptidase‐positive foci in diethylnitrosamine‐initiated and streptozotocin‐induced diabetes‐promoted hepatocarcinogenesis
Authors: Saha Barun Kanti , Bhattacharya Radha , Chatterjee Malay
Published: September 2002

In the present study, the chemopreventive effect of the active metabolite of vitamin D, 1α,25‐dihydroxyvitamin D3 (VD3), against chemically‐induced and diabetes‐promoted rat liver carcinogenesis was investigated. Hepatocarcinogenesis was initiated with a single intraperitoneal (i.p.) injection of diethylnitrosamine (DEN) (125 mg kg−1 body weight) at week 4 followed by promotion with streptozotocin (STZ) (65 mg kg−1 body weight with a single i.p. injection) at week 7. With this basic experimental regimen, the effect of VD3 (0.3 μg (0.1 ml)−1 propylene glycol per os twice a week) was investigated with effect from 4 weeks prior to the exposure of DEN. The results showed that VD3 supplementation throughout the experimental period reduced the incidence, total number and multiplicity and altered the size of visible persistent nodules (PNs) in DEN‐ or DEN + STZ‐treated rats as compared with their respective controls. In these two groups, it also caused a significant decrease in the number (p < 0.002 and 0.001 respectively) and focal area (p < 0.05) of γ‐glutamyltranspeptidase (GGT)‐positive hepatic foci. Moreover, continuous supplementation of VD3 exhibits a protective effect in maintaining the normal cellular architecture of the hepatocytes in DEN‐ or DEN + STZ‐treated rats. Our results thus strongly suggest that VD3 is very effective in the inhibition of DEN‐initiated and STZ‐induced diabetes‐promoted rat liver carcinogenesis. Copyright © 2002 John Wiley & Sons, Ltd.
Azaanthraquinone inhibits respiration and in vitro growth of long slender bloodstream forms of Trypanosoma congolense
Authors: Nok Andrew Jonathan
Published: September 2002

An ethanolic extract of Mitracarpus scaber was found to possess in vitro and in vivo trypanocidal activity against Trypanosoma congolense. At a dosage of 50 mg kg−1 day−1 in normal saline for 5 days, the extract cured Balbc mice infected with T. congolense without any relapse. The isolated active component benz(g)isoquinoline 5,10 dione (Azaanthraquinone) (AQ) purified from the extract was found to inhibit glucose‐dependent cellular respiration and glycerol‐3‐phosphate‐dependent mitochondrial O2 assimilation of the long bloodstream forms of Trypanosoma congolense. On account of the pattern of inhibition, the target could be the mitochondrial electron transport system composed of glyceraldehyde 3‐phosphate dehydrogenase (G3PDH). The azaanthraquinone specifically inhibited the reduced coenzyme Q1‐dependent O2 uptake of the mitochondria with respect to ubiquinone. The susceptible site could be due to ubiquinone redox system which links the two enzyme activities. Copyright © 2002 John Wiley & Sons, Ltd.
Angiographic outcome after intracoronary X‐Sizer helical atherectomy and thrombectomy: First use in humans
Authors: Kwok On‐Hing , Prpic Ross , Gaspar Jorge , Mathey Detlef G. , Escobar A. , Goldar‐Najafi Atoussa , Reifart Nicolaus , Ischinger Thomas A. , Popma Jeffrey J.
Published: September 2002

The objective of this study was to evaluate the early angiographic outcome in the first human subjects who underwent intracoronary atherectomy and thrombectomy using the X‐Sizer helical cutting and aspiration system. Percutaneous coronary interventions in patients with thrombo‐occlusive disease or friable degenerative saphenous vein grafts are associated with considerable periprocedural morbidity and mortality, predominantly related to microscopic distal embolization. X‐Sizer catheter system is a novel atherectomy and thrombectomy device that consists of a helix cutter connected to a handheld motor drive unit and a vacuum collection chamber for aspiration of excised atheroma, thrombus, and debris. Quantitative coronary angiography was obtained in 14 patients before and after X‐Sizer extraction atherectomy with adjunctive balloon angioplasty and stenting. Thirteen native coronary arteries and one saphenous vein graft were treated. Mean preprocedural reference vessel diameter was 3.06 ± 0.66 mm. There were 71.4% AHA/ACC type B2 and C lesions. Preprocedural thrombus was present in nine patients and total occlusion in 64% of cases. Minimal luminal diameter was increased from 0.29 ± 0.47 mm to 1.32 ± 0.64 mm, a gain of 1.04 ± 0.69 mm after atherectomy. Final total gain was 1.47 ± 0.61 mm. Mean diameter stenosis was reduced from 89.3% to a final residual stenosis of 14.4%. Postatherectomy distal embolization occurred in one patient who had heavy preprocedural thrombus burden. No episodes of perforation, distal coronary spasm, abrupt closure, or slow/no‐reflow occurred. The angiographic analysis of the first cohort of human subjects suggests that X‐Sizer helical atherectomy is a feasible method of removing occlusive tissue or thrombus in coronary artery disease with a low angiographic complication rate. A large‐scale randomized phase II clinical trial is underway to determine the ultimate safety and efficacy of this device in thrombo‐occlusive native coronary arteries and saphenous vein grafts. Cathet Cardiovasc Intervent 2002;55:133–139. © 2002 Wiley‐Liss, Inc.
A protocol for prevention of radiographic contrast nephropathy during percutaneous coronary intervention: Effect of selective dopamine receptor agonist fenoldopam
Authors: Kini Annapoorna S. , Mitre Cristina A. , Kim Michael , Kamran Mazullah , Reich David , Sharma Samin K.
Published: September 2002

Radiographic contrast nephropathy (RCN), acute worsening of renal function due to contrast agents, can occur in 15%–40% of patients with baseline renal dysfunction undergoing percutaneous coronary intervention (PCI) and is associated with increased morbidity and in‐hospital mortality. The purpose of this study was to evaluate whether the selective dopamine‐1 (DA‐1) receptor agonist fenoldopam would be beneficial in patients with chronic renal insufficiency (CRI) undergoing PCI and also to design a protocol for prevention of RCN. We analyzed 150 consecutive patients with CRI [baseline serum creatinine (BSCr) ≥ 1.5% mg] who underwent PCI and received fenoldopam during and after the procedure, in addition to saline hydration. RCN, defined as > 25% increase of BSCr 48–72 hr after PCI, occurred in 4.7% (n = 7) of 150 PCI patients receiving fenoldopam and 3.5% in diabetics (n = 85) vs. 6.1% in nondiabetics (n = 65; P = NS). No patients required dialysis. The observed 4.7% incidence of RCN with fenoldopam was significantly lower than 18.8% incidence in the historical control group (P < 0.001). Our data suggest that fenoldopam is a useful adjunct in the prevention of RCN during PCI, especially in diabetics. Cathet Cardiovasc Intervent 2002;55:169–173. © 2002 Wiley‐Liss, Inc.
Late coronary stent thrombosis: Early vs. late stent thrombosis in the stent era
Authors: Wang Fenwei , Stouffer George A. , Waxman Sergio , Uretsky Barry F.
Published: September 2002

The incidence of coronary stent thrombosis is < 1%–2% in recent studies, with the highest‐risk period considered to be the first 30 days following stent implantation. Recently, stent thrombosis after 30 days has been reported in patients undergoing brachytherapy with stenting. We reviewed the incidence of stent thrombosis causing myocardial infarction in nonbrachytherapy patients at our institution between 1 January 1996 and 30 November 1999. A case control methodology was employed with a 1:3 ratio of stent thrombosis to control patients. Of 1,191 patients undergoing coronary stenting, acute (< 24 hr) plus subacute (1–30 days) stent thrombosis occurred in 0.92% (11 of 1,191 patients). A further 0.76% (9 of 1,191 patients) developed late stent thrombosis after 30 days. There were no clinical or angiographic features at the time of the initial procedure that were associated with stent thrombosis as an entire group compared with control group, but early (acute and subacute) stent thrombosis patients had a smaller final stent minimal lumen diameter and longer stent length compared with patients who had late stent thrombosis or controls. Late stent thrombosis occurs in nonbrachytherapy patients and is almost as frequent as early stent thrombosis. Further studies are required to determine whether longer‐term poststent pharmacological treatment may decrease or prevent this complication. Cathet Cardiovasc Intervent 2002;55:142–147. © 2002 Wiley‐Liss, Inc.
Simultaneous intracoronary pressure and Doppler guidewires to assess coronary stenosis: If one is enough, are two too much?
Authors: Ruiz‐Salmerón Rafael J. , Goicolea Javier , Sanmartín Marcelo , Mantilla Ramón , Sterling Juan , Romeo Daniela
Published: September 2002

We report a potential source of erroneous estimation of stenosis severity by pressure guidewire assessment. Simultaneous introduction of pressure and Doppler guidewires can lead to an overestimation of stenosis pressure gradient in the evaluation of intermediate stenosis. Cathet Cardiovasc Intervent 2002;55:255–259. © 2002 Wiley‐Liss, Inc.
Patterns of in‐stent restenosis after placement of NIR gold‐coated stents in unselected patients
Authors: Danzi Gian Battista , Capuano Cinzia , Sesana Marco , Di Blasi Alberto , Predolini Simonetta , Antoniucci David
Published: September 2002

The aim of this study was to assess the incidence and angiographic patterns of in‐stent restenosis 6 months after the implantation of NIR gold‐coated stents in an unselected patient population. One hundred and sixteen consecutive patients were treated with the implantation of 149 NIR gold‐coated stents. The majority of the patients (52%) had unstable angina or acute myocardial infarction. The baseline lesion morphology was complex in 78% of cases; the mean lesion length was 18 ± 5 mm. The procedural success rate was 97%. Subacute stent thrombosis occurred in three patients (2.6%). During the 6‐month follow‐up, there were 2 deaths and 22 subjects (19.5%) underwent target vessel revascularization. The 6‐month event‐free survival was 60%. The angiographic restenosis rate was 32%. In 83% of the cases, the morphology of the restenosis was proliferative; in the remaining 17%, it presented as total occlusion. In conclusion, the restenosis rate after NIR gold‐coated stent implantation in high‐risk patients is similar to that reported using other stent designs. However, restenosis was always diffuse, involving the overall stent length and extending beyond the margins, thus indicating a greater proliferative neointimal response to this device. Cathet Cardiovasc Intervent 2002;55:157–162. © 2002 Wiley‐Liss, Inc.
Advancing post‐genome data and system integration through machine learning
Authors: Azuaje Francisco
Published: September 2002

Research on biological data integration has traditionally focused on the
development of systems for the maintenance and interconnection of databases.
In the next few years, public and private biotechnology organisations will
expand their actions to promote the creation of a post‐genome semantic web.
It has commonly been accepted that artificial intelligence and data mining
techniques may support the interpretation of huge amounts of integrated data.
But at the same time, these research disciplines are contributing to the creation of
content markup languages and sophisticated programs able to exploit the constraints
and preferences of user domains. This paper discusses a number of issues on
intelligent systems for the integration of bioinformatic resources. Copyright
© 2001 John Wiley & Sons, Ltd.
SNP and mutation data on the Web – hidden treasures for uncovering.
Authors: Barnes Michael R
Published: September 2002

SNP data has grown exponentially over the last two years, SNP database
evolution has matched this growth, as initial development of several independent
SNP databases has given way to one central SNP database, dbSNP. Other SNP
databases have instead evolved to complement this central database by providing
gene specific focus and an increased level of curation and analysis on subsets
of data, derived from the central data set. By contrast, human mutation data,
which has been collected over many years, is still stored in disparate sources,
although moves are afoot to move to a similar central database. These developments
are timely, human mutation and polymorphism data both hold complementary keys
to a better understanding of how genes function and malfunction in disease.
The impending availability of a complete human genome presents us with an
ideal framework to integrate both these forms of data, as our understanding
of the mechanisms of disease increase, the full genomic context of variation
may become increasingly significant. Copyright © 2001 John Wiley &
Sons, Ltd.
Discovery of single nucleotide polymorphisms and mutations by Pyrosequencing
Authors: Ronaghi Mostafa , Elahi Elahe
Published: September 2002

Comparative genomics, analyzing variation among individual genomes, is
an area of intense investigation. DNA sequencing is usually employed to look
for polymorphisms and mutations. Pyrosequencing, a real‐time DNA sequencing
method, is emerging as a popular platform for comparative genomics. Here we
review the use of this technology for mutation scanning, polymorphism discovery
and chemical haplotyping. We describe the methodology and accuracy of this
technique and discuss how to reduce the cost for large‐scale analysis. Copyright © 2002 John Wiley & Sons, Ltd.
From gene regulation to gene function: regulatory networks in Bacillus subtilis
Authors: Harwood Colin R , Moszer Ivan
Published: September 2002

Bacillus subtilis is a sporulating Gram‐positive bacterium that
lives primarily in the soil and associated water sources. The publication
of the B. subtilis genome sequence and subsequent systematic functional
analysis and gene regulation programmes, together with an extensive understanding
of its biochemistry and physiology, makes this micro‐organism a prime candidate
in which to model regulatory networks in silico. In this paper we discuss
combined molecular biological and bioinformatical approaches that are being
developed to model this organism's responses to changes in its environment. Copyright © 2001 John Wiley & Sons, Ltd.
RIBDB: An SRS based infrastructure for REALIS
Authors: Rice Peter , Jassal Bijay , de Daruvar Antoine
Published: September 2002

The REALIS project is an EU‐funded consortium for the post genomic analysis
of the food pathogen Listeria monocytogenes. The data generated by
the consortium members is stored under the RIBDB database, a system built
using SRS which integrates consortium data, public databases, and applications
for analysis. RIBDB is available to all consortium members through a web server,
with the option of installing a local mirror of the main server for local
analysis. Copyright © 2001 John Wiley & Sons, Ltd.
Ontology based document enrichment in bioinformatics
Authors: Stevens Robert
Published: September 2002

Controlled vocabularies are common within bioinformatics resources. They
can be used to give a summary of the knowledge held about a particular entity.
They are also used to constrain values given for particular attributes of
an entity. This helps create a shared understanding of a domain and aids increased
precision and recall during querying of resources. Ontologies can also provide
such facilities, but can also enhance their utility. Controlled vocabularies
are often simply lists of words, but may be viewed as a kind of ontology.
Ideally ontologies are structurally enriched with relationships between terms
within the vocabulary. Use of such rich forms of vocabularies in database
annotation could enhance those resources usability by both humans and computers.
The representation of the knowledge content of biological resources in a computationally
accessible form opens the prospect of greater support for a biologist investigating
new data. Copyright © 2002 John Wiley & Sons, Ltd.
Many Genbank entries for complete microbial genomes violate the Genbank standard
Authors: Karp Peter D.
Published: September 2002

A survey of Genbank entries for complete microbial genomes reveals that the majority do not conform to the Genbank standard. Typical deviations from the Genbank standard include records with information in incorrect fields, addition of extraneous and confusing information within a field, and omission of useful fields. This situation results from two principal causes: genome centres do not submit Genbank records in the proper form and the Genbank, EMBL and DDBJ staffs do not enforce the database standards that they have defined. Copyright © 2001 John Wiley & Sons, Ltd.
Cryptosporidium parvum genome project
Authors: Abrahamsen Mitchell S.
Published: September 2002

A lack of basic understanding of parasite biology has been a limiting factor in designing effective means of treating and preventing disease caused by Cryptosporidium parvum. Since the genomic DNA sequence encodes all of the heritable information responsible for development, disease pathogenesis, virulence, species permissiveness and immune resistance, a comprehensive knowledge of the C. parvum genome will provide the necessary information required for cost‐effective and targeted research into disease prevention and treatment. With the recent advances in high‐throughput automated DNA sequencing capabilities, large‐scale genomic sequencing has become a cost‐effective and time‐efficient approach to understanding the biology of an organism. In addition, the continued development and implementation of new software tools that can scan raw sequences for signs of genes and then identify clues as to potential functions, has provided the final realization of the potential rewards of genome sequencing. To further our understanding of C. parvum biology, we have initiated a random shotgun sequencing approach to obtain the complete sequence of the IOWA isolate of C. parvum. Our progress to date has demonstrated that sequencing of the C. parvum genome will be an efficient and cost‐effective method for gene discovery of this important eukaryotic pathogen. This will allow for the identification of key metabolic and immunological features of the organism that will provide the basis for future development of safe and effective strategies for prevention and treatment of disease in AIDS patients, as well as immunocompetent hosts. Moreover, by obtaining the complete sequence of the C. parvum genome, effective methods for subspecific differentiation (strain typing) and epidemiologic surveillance (strain tracking) of this pathogen can be developed. Copyright © 2001 John Wiley & Sons, Ltd.
Performance targets and stability of placements for children long looked after away from home
Authors: Ward Harriet , Skuse Tricia
Published: September 2002

There are concerns that the performance indicators for children's services may not be adequately interpreted and used to improve service delivery for individual children. Data from a longitudinal study of 249 looked after children demonstrate that one target—improving the stability of placements—is more likely to be met if agencies can identify which children move frequently and why. While age, behavioural difficulties and the absence of mental health support may have contributed to placement breakdowns, the majority of moves were planned transitions from one temporary placement to another, suggesting that the system may ignore the needs of those children who cannot swiftly return home. Copyright © 2001 John Wiley & Sons, Ltd.
Abundant expression of the microtubule‐associated protein, ensconsin (E‐MAP‐115), alters the cellular response to Taxol
Authors: Gruber Dorota , Faire Kathleen , Bulinski J. Chloë
Published: September 2002

Correlation between expression level of a microtubule‐associated protein called ensconsin (E‐MAP‐115) and degree of Taxol sensitivity in several cultured cell lines prompted us to investigate potential cause‐and‐effect relationships between ensconsin level and Taxol action. We used human MCF‐7 or HeLa cells, which are sensitive to low Taxol concentrations (LD50 of 30–35 and 3.5 nM, respectively) to prepare stably transfected populations of cells expressing heterogeneous levels of ensconsin chimeras, either green fluorescent protein (GFP) conjugated to full‐length ensconsin (GFP‐Ensc) or to ensconsin's microtubule‐binding domain (GFP‐EMTB). Both a subjective microscopic assay, i.e., scoring fluorescence of GFP‐ensconsin chimeras following Taxol treatment, and a quantitative immunobiochemical assay, i.e., measuring level of GFP‐ensconsin chimera in cells surviving treatment with Taxol, showed that cells expressing higher levels of GFP‐ensconsin chimera were killed more readily by Taxol concentrations approaching the LD50. In contrast, in TC‐7 cells, which are relatively insensitive to Taxol (LD50 > 600 nM), high‐level expression of GFP‐EMTB conferred no significant susceptibility to killing by Taxol. However, heightening the Taxol sensitivity of GFP‐EMTB‐TC‐7 cells by pre‐incubating cells with the p‐glycoprotein inhibitor, verapamil, did result in selective killing of cells highly expressing GFP‐EMTB. Taken together, results obtained in MCF‐7, HeLa, and TC‐7 cells suggest that elevated ensconsin level bestowed a selective disadvantage upon Taxol‐sensitive cells. To probe potential mechanisms by which ensconsin could alter the Taxol response, we isolated microtubules from HeLa cells that were or were not pretreated with Taxol. In vivo Taxol treatment significantly tightened microtubule‐binding of ensconsin, suggesting that Taxol alters ensconsin's microtubule‐binding properties and may, in turn, alter the Taxol response of the microtubules. Our data support the hypothesis that Taxol works synergistically or in concert with microtubule‐binding proteins in bringing about deleterious effects on the microtubule cytoskeleton. Cell Motil. Cytoskeleton 49:115–129, 2001. © 2001 Wiley‐Liss, Inc.
Remodeling of the proximal segment of crayfish motor nerves following transection
Authors: Pearce Joanne , Govind C.K.
Published: September 2002

Transected crustacean motor axons consist of a soma‐endowed proximal segment that regenerates and a soma‐less distal segment that survives for up to a year. We report on the anatomical remodeling of the proximal segment of phasic motor nerves innervating the deep flexor muscles in the abdomen of adult crayfish following transection. The intact nerve with 10 phasic axons and its two branches with subsets of 6 and 7 of these 10 axons undergo several remodeling changes. First, the transected nerve displays many more and smaller axon profiles than the 6 and 7 axons of the intact nerve, approximately 100 and 300 profiles in the two branches of a preparation transected 8 weeks previously. Serial images of the transected nerve denote that the proliferation of profiles is due to several orders of axon sprouting primary, secondary, and tertiary branches. The greater proliferation of axon sprouts, their smaller size, and the absence of intervening glia in the one nerve branch compared with the other branch denote that sprouting is more advanced in this branch. Second, the axon sprouts are regionally differentiated; thus, although in most regions the sprouts are basically axon‐like, with a cytoskeleton of microtubules and peripheral mitochondria, in some regions they appear nerve terminal‐like and are characterized by numerous clear synaptic vesicles, a few dense‐core vesicles, and dispersed mitochondria. Both regions possess active zone dense bars with clustered synaptic vesicles found opposite other sprouts, glia, hemocytes, and connective tissue, but because the opposing membranes are not differentiated into a synaptic contact, the active zones are extrasynaptic. Third, some of the transected axons display a glial cell nucleus denoting assimilation of an adaxonal glial cell by the transected axons. Fourth, within the nerve trunk are a few myocytes and muscle fibers. These most likely originate from adjoining and intimately connected hemocytes, because such transformation occurs during muscle repair. In a crustacean nerve, however, where muscle is clearly misplaced, its presence implies an instructive role for motor nerves in muscle formation. J. Comp. Neurol. 450:61–72, 2002. © 2002 Wiley‐Liss, Inc.
Ultrastructural organization of lamprey reticulospinal synapses in three dimensions
Authors: Gustafsson Jenny S. , Birinyi András , Crum John , Ellisman Mark , Brodin Lennart , Shupliakov Oleg
Published: September 2002

The giant reticulospinal synapse in lamprey provides a unique model to study synaptic vesicle traffic. The axon permits microinjections, and the active zones are often separated from each other, which makes it possible to track vesicle cycling at individual release sites. However, the proportion of reticulospinal synapses with individual active zones (“simple synapses”) is unknown and a quantitative description of their organization is lacking. Here, we report such data obtained by serial section analysis, intermediate‐voltage electron microscopy, and electron tomography. The simple synapse was the most common type (78%). It consisted of one active zone contacting one dendritic process. The remaining synapses were “complex,” mostly containing one vesicle cluster and two to three active zones synapsing with distinct dendritic shafts. Occasional axosomatic synapses with multiple active zones forming synapses with the same cell were also observed. The vast majority of active zones in all synapse types contained both chemical and electrotonic synaptic specializations. Quantitative analysis of simple synapses showed that the majority had active zones with a diameter of 0.8–1.8 μm. The number of synaptic vesicles and the height of the vesicle cluster in middle sections of serially cut synapses correlated with the active zone length within, but not above, this size range. Electron tomography of simple synapses revealed small filaments between the clustered synaptic vesicles. A single vesicle could be in contact with up to 12 filaments. Another type of filament, also associated with synaptic vesicles, emerged from dense projections. Up to six filaments could be traced from one dense projection. J. Comp. Neurol. 450:167–182, 2002. © 2002 Wiley‐Liss, Inc.
Three‐dimensional cartography of functional territories in the human striatopallidal complex by using calbindin immunoreactivity
Authors: Karachi Carine , François Chantal , Parain Karine , Bardinet Eric , Tandé Dominique , Hirsch Etienne , Yelnik Jérôme
Published: September 2002

This anatomic study presents an analysis of the distribution of calbindin immunohistochemistry in the human striatopallidal complex. Entire brains were sectioned perpendicularly to the mid‐commissural line into 70‐μm‐thick sections. Every tenth section was immunostained for calbindin. Calbindin labeling exhibited a gradient on the basis of which three different regions were defined: poorly labeled, strongly labeled, and intermediate. Corresponding contours were traced in individual sections and reformatted as three‐dimensional structures. The poorly labeled region corresponded to the dorsal part of the striatum and to the central part of the pallidum. The strongly labeled region included the ventral part of the striatum, the subcommissural part of the external pallidum but also the adjacent portion of its suscommissural part, and the anterior pole of the internal pallidum. The intermediate region was located between the poorly and strongly labeled regions. As axonal tracing and immunohistochemical studies in monkeys show a similar pattern, poorly, intermediate, and strongly labeled regions were considered as the sensorimotor, associative, and limbic territories of the human striatopallidal complex, respectively. However, the boundaries between these territories were not sharp but formed gradients of labeling, which suggests overlapping between adjacent territories. Similarly, the ventral boundary of the striatopallidal complex was blurred, suggesting a structural intermingling with the substantia innominata. This three‐dimensional partitioning of the human striatopallidal complex could help to define functional targets for high‐frequency stimulation with greater accuracy and help to identify new stimulation sites. J. Comp. Neurol. 450:122–134, 2002. © 2002 Wiley‐Liss, Inc.
Distribution of cholecystokinin, calcitonin gene‐related peptide, neuropeptide Y, and galanin in the primary gustatory nuclei of the goldfish
Authors: Farrell William J. , Böttger Bärbel , Ahmadi Ferogh , Finger Thomas E.
Published: September 2002

Cholecystokinin (CCK), neuropeptide Y (NPY), calcitonin gene‐related peptide (CGRP), and galanin all are known to have central effects on food intake. Immunocytochemistry was used to examine the presence of these substances within the primary gustatory nuclei of the goldfish, including the vagal lobe, which is a large, laminated structure composed of discrete sensory, fiber, and motor layers. The vagal lobes receive primary afferent input from the gustatory portion of the vagus nerve and contain reflex circuitry involved in the ingestion or rejection of potential food items. Immunohistochemistry indicates a heavy concentration of CCK‐, CGRP‐, NPY‐, and galanin‐immunoreactive fibers in the capsular fiber layer as well as in deeper sensory layers of the vagal lobe. CGRP immunoreactivity throughout the sensory layers and capsular immunoreactivity for CCK are greatly reduced 1–2 weeks following vagus nerve transection, indicating that the majority of these fibers are primary sensory afferents. In contrast, NPY and galanin immunoreactivity in the capsular fiber layer and reactivity for CCK, NPY, and galanin in the deeper sensory and fiber layers are relatively unaffected by vagus transection. CCK‐, NPY‐, and galanin‐immunoreactive fibers and puncta also were present in the motor layers, as were CGRP‐immunoreactive motor somata. CCK‐immunoreactive cell bodies are present in layer III and layer VII/VIII of the vagal lobe and in the superficial granular layer of the lateral subnucleus of the commissural nucleus of Cajal, which is caudally contiguous with the vagal lobe. J. Comp. Neurol. 450:103–114, 2002. © 2002 Wiley‐Liss, Inc.
Imposition of essential boundary conditions by displacement constraint equations in meshless methods
Authors: Zhang Xiong , Liu Xin , Lu Ming‐Wan , Chen Yong
Published: September 2002

One of major difficulties in the implementation of meshless methods is the imposition of essential boundary conditions as the approximations do not pass through the nodal parameter values. As a consequence, the imposition of essential boundary conditions in meshless methods is quite awkward. In this paper, a displacement constraint equations method (DCEM) is proposed for the imposition of the essential boundary conditions, in which the essential boundary conditions is treated as a constraint to the discrete equations obtained from the Galerkin methods. Instead of using the methods of Lagrange multipliers and the penalty method, a procedure is proposed in which unknowns are partitioned into two subvectors, one consisting of unknowns on boundary Γu, and one consisting of the remaining unknowns. A simplified displacement constraint equations method (SDCEM) is also proposed, which results in a efficient scheme with sufficient accuracy for the imposition of the essential boundary conditions in meshless methods. The present method results in a symmetric, positive and banded stiffness matrix. Numerical results show that the accuracy of the present method is higher than that of the modified variational principles. The present method is a exact method for imposing essential boundary conditions in meshless methods, and can be used in Galerkin‐based meshless method, such as element‐free Galerkin methods, reproducing kernel particle method, meshless local Petrov–Galerkin method. Copyright © 2001 John Wiley & Sons, Ltd.
A variational theory of the Hessian equation
Authors: Chou Kai‐Seng , Wang Xu‐Jia
Published: September 2002

By studying a negative gradient flow of certain Hessian functionals we establish the existence of critical points of the functionals and consequently the existence of ground states to a class of nonhomogenous Hessian equations. To achieve this we derive uniform, first‐ and second‐order a priori estimates for the elliptic and parabolic Hessian equations. Our results generalize well‐known results for semilinear elliptic equations and the Monge‐Ampère equation. © 2001 John Wiley & Sons, Inc.
Which paradigm should I use? An analytical comparison of the client–server, remote evaluation and mobile agent paradigms
Authors: Puliafito Antonio , Riccobene Salvatore , Scarpa Marco
Published: September 2002

In this paper we deal with the study of the actual convenience of using the agent programming paradigm for accesssing distributed service. We try to point out the benefits of such a communication paradigm, by providing an analytical study of its basic features in comparison with the client–server approach and remote evaluation. The aim of the paper is to show how the Petri net analysis technique can be used for deciding whether to use traditional client/server, remote evaluation or mobile agents paradigm in designing a particular evaluation. So, we present several models of non‐Markovian Petri nets, which have been solved through the WebSPN tool, and we provide a close comparison between the agents technique, the client‐server and the remote evaluation communication paradigm. The results that we have obtained show how agents must not always be considered the only solution to any communication issue, since in several cases their use might even reveal a drawback. We also focus out attention on providing some practical remarks, which can help the developer during the design in order to select the communication paradigm which best suits the features of the application that has to be developed. Copyright © 2001 John Wiley & Sons, Ltd.
Emmerald: a fast matrix–matrix multiply using Intel's SSE instructions
Authors: Aberdeen Douglas , Baxter Jonathan
Published: September 2002

Generalized matrix–matrix multiplication forms the kernel of many mathematical algorithms, hence a faster matrix–matrix multiply immediately benefits these algorithms. In this paper we implement efficient matrix multiplication for large matrices using the Intel Pentium single instruction multiple data (SIMD) floating point architecture. The main difficulty with the Pentium and other commodity processors is the need to efficiently utilize the cache hierarchy, particularly given the growing gap between main‐memory and CPU clock speeds. We give a detailed description of the register allocation, Level 1 and Level 2 cache blocking strategies that yield the best performance for the Pentium III family. Our results demonstrate an average performance of 2.09 times faster than the leading public domain matrix–matrix multiply routines and comparable performance with Intel's SIMD small matrix–matrix multiply routines. Copyright © 2001 John Wiley & Sons, Ltd.
Simulating asynchronous hardware on multiprocessor platforms: the case of AMULET1
Authors: Theodoropoulos Georgios K.
Published: September 2002

Synchronous VLSI design is approaching a critical point, with clock distribution becoming an increasingly costly and complicated issue and power consumption rapidly emerging as a major concern. Hence, recently, there has been a resurgence of interest in asynchronous digital design techniques which promise to liberate digital design from the inherent problems of synchronous systems. This activity has revealed a need for modelling and simulation techniques suitable for the asynchronous design style. The concurrent process algebra communicating sequential processes (CSP) and its executable counterpart, occam, are increasingly advocated as particularly suitable for this purpose. This paper focuses on issues related to the execution of CSP/occam models of asynchronous hardware on multiprocessor machines, including I/O, monitoring and debugging, partition, mapping and load balancing. These issues are addressed in the context of occarm, an occam simulation model of the AMULET1 asynchronous microprocessor; however, the solutions devised are more general and may be applied to other systems too. Copyright © 2001 John Wiley & Sons, Ltd.