bluuebunny/crossref_metadata_2025 huggingface dataset:
A Two‐Photon Fluorescence‐Correlation Study of Lectins Interacting with Carbohydrated 20 nm Beads
Authors: Pohl Wiebke H. , Hellmuth Hendrik , Hilbert Michael , Seibel Jürgen , Walla Peter J.
Published: January 2006

We present results of a two‐photon fluorescence‐correlation study carried out with glycosylated and untreated 20 nm fluorescing spheres that interacted with the carbohydrate‐binding proteins soybean agglutinin (SBA) and concanavalin A (Con A). The assay principle allows protein–carbohydrate binding interactions to be determined without protein labeling. This assay might serve as a simple model system for studying physical and chemical interactions between proteins and carbohydrates, for example, at cell or virus surfaces. In experiments with galactosylated 20 nm beads and SBA, several stages of protein–carbohydrate interactions could be clearly distinguished. Initially, only a few lectins bound to the nanospheres. At higher lectin concentrations polymerization occurred, and aggregates consisting of about 2.6×105 glycosylated nanospheres were formed. At very high lectin concentrations, the degree of polymerization dropped, and the size of single SBA‐covered nanospheres increased to ∼40 nm. When Con A was used instead of SBA, a significantly smaller degree of aggregation (4×104 spheres) was obtained. Treatment of unglycosylated 20 nm beads with SBA as a negative control sample resulted in a much lower unspecific aggregation (5×103 spheres). The assay principle can thus help to elucidate relative binding affinities.
Deciphering the Biosynthesis Pathway of the Antitumor Thiocoraline from a Marine Actinomycete and Its Expression in Two Streptomyces Species
Authors: Lombó Felipe , Velasco Ana , Castro Angelina , de la Calle Fernando , Braña Alfredo F. , Sánchez‐Puelles José M. , Méndez Carmen , Salas José A.
Published: January 2006

Thiocoraline is a thiodepsipeptide antitumor compound produced by two actinomycetes Micromonospora sp. ACM2‐092 and Micromonospora sp. ML1, isolated from two marine invertebrates (a soft coral and a mollusc) found of the Indian Ocean coast of Mozambique. By using oligoprimers derived from nonribosomal peptide synthetase (NRPS) consensus sequences, six PCR fragments containing putative NRPS adenylation domains were amplified from the chromosome of Micromonospora sp. ML1. Insertional inactivation of each adenylation domain showed that two of them generated nonproducing mutants, thereby indicating that these domains were involved in thiocoraline biosynthesis. Sequencing of a 64.6 kbp DNA region revealed the presence of 36 complete open reading frames (ORFs) and two incomplete ones. Heterologous expression of a region of about 53 kbp, containing 26 of the ORFs, in Streptomyces albus and S. lividans led to the production of thiocoraline in these streptomycetes. Surprisingly, the identified gene cluster contains more NRPS modules than expected on the basis of the number of amino acids of thiocoraline. TioR and TioS would most probably constitute the NRPS involved in the biosynthesis of the thiocoraline backbone, according to the colinearity of the respective modules. It is proposed that two other NRPSs, TioY and TioZ, could be responsible for the biosynthesis of a small peptide molecule which could be involved in regulation of the biosynthesis of thicoraline in Micromonospora sp. ML1. In addition, a pathway is proposed for the biosynthesis of the unusual starter unit, 3‐hydroxy‐quinaldic acid.
Improved Cell Viability of Linear Polyethylenimine through γ‐Cyclodextrin Inclusion for Effective Gene Delivery
Authors: Yamashita Atsushi , Choi Hak Soo , Ooya Tooru , Yui Nobuhiko , Akita Hidetaka , Kogure Kentaro , Harashima Hideyoshi
Published: January 2006

A polypseudorotaxane consisting of a linear polyethylenimine with Mn of 22 000 (LPEI22k) and γ‐cyclodextrins (γ‐CDs; LPEI22k/γ‐CD) has been examined as a gene carrier. The polyplex formation with luciferase‐encoding plasmid DNA (pDNA), intracellular trafficking of polyplex, cytotoxicity, and transfection efficiency were evaluated by various characteristic methods. LPEI22k/γ‐CD formed a pDNA polyplex at higher N/P ratios than LPEI22k; this suggests that the γ‐CD threading sterically interfered with the polyplex formation. In addition, the ζ potentials of the polyplex significantly decreased due to the reduction in charge density of LPEI22k caused by γ‐CD threading. The cellular uptake of pDNA in the LPEI22k/γ‐CD polyplex was enhanced by free γ‐CDs released from the polyplex that might accelerate the cellular uptake through enhanced membrane affinity. LPEI22k/γ‐CD significantly increased cell viability even at high N/P ratios, and the polyplex showed high transfection efficacy. The low cytotoxicity and high gene expression of LPEI22k/γ‐CD are advantageous to polyplex administration in vivo.
Free‐Energy Simulations and Experiments Reveal Long‐Range Electrostatic Interactions and Substrate‐Assisted Specificity in an Aminoacyl‐tRNA Synthetase
Authors: Thompson Damien , Plateau Pierre , Simonson Thomas
Published: January 2006

Specific recognition of their cognate amino acid substrates by the aminoacyl‐tRNA synthetase enzymes is essential for the correct translation of the genetic code. For aspartyl‐tRNA synthetase (AspRS), electrostatic interactions are expected to play an important role, since its three substrates (aspartate, ATP, tRNA) are all electrically charged. We used molecular‐dynamics free‐energy simulations and experiments to compare the binding of the substrate Asp and its electrically neutral analogue Asn to AspRS. The preference for Asp is found to be very strong, with good agreement between simulations and experiment. The simulations reveal long‐range interactions that electrostatically couple the amino acid ligand, ATP, and its associated Mg2+ cations, a histidine side chain (His448) next to the amino acid ligand and a flexible loop that closes over the active site in response to amino acid binding. Closing this loop brings a negatively charged glutamate into the active site; this causes His448 to recruit a labile proton, which interacts favorably with Asp and accounts for most of the Asp/Asn discrimination. Cobinding of the second substrate, ATP, increases specificity for Asp further and makes the system robust towards removal of His448, which is mutated to a neutral amino acid in many organisms. Thus, AspRS specificity is assisted by a labile proton and a cosubstrate, and ATP acts as a mobile discriminator for specific Asp binding to AspRS. In asparaginyl‐tRNA synthetase, a close homologue of AspRS, a few binding‐pocket differences modify the charge balance so that asparagine binding predominates.
Analytical solution for determining feasible regions of self‐modeling curve resolution (SMCR) method based on computational geometry
Authors: Rajkó Róbert , István Krisztina
Published: January 2006

During 20 years the analytical solution for determining feasible regions of self‐modeling curve resolution (SMCR) method was only slightly researched. After publishing of the famous papers of Borgen et al. in 1985 and 1986, pure generalizations have not been given and even investigated. The reason might have been that the published algorithms and descriptions have been hard to interpret (to code) and to understand respectively. In this paper, several theoretical reasoning is revised giving clearer and more general proofs for principles of SMCR, that is the normalized responses are embraced in the (N−1)‐dimensional simplex with the vertices being the N‐normalized pure profiles. For the first time in the chemometric literature, computational geometry tools are introduced instead of, for example, linear programming tools, for developing our algorithm to draw Borgen plots of any three‐component systems. Numbers of illustrations are given for the sake of clarity. As it has turned out, the highly cited and used data matrix published by Lawton and Sylwestre has not two but more components as it is presented in detail. For a simulated three‐component system, Borgen plots are drawn and some explanations are given. Copyright © 2006 John Wiley & Sons, Ltd.
Assessment of the role of sentinel lymph node biopsy for primary cutaneous desmoplastic melanoma
Authors: Pawlik Timothy M. , Ross Merrick I. , Prieto Victor G. , Ballo Matthew T. , Johnson Marcella M. , Mansfield Paul F. , Lee Jeffrey E. , Cormier Janice N. , Gershenwald Jeffrey E.
Published: January 2006

BACKGROUND

The role of sentinel lymph node biopsy (SLNB) in the treatment of desmoplastic melanoma (DM) remains undefined. The purpose of this study was to evaluate the use of SLNB for DM.

METHODS

In all, 1850 patients with cutaneous melanoma underwent wide local excision and SLNB. Patients with DM were identified and stratified as ‘pure’ DM or ‘mixed’ DM (i.e., DM associated with at least one other common histologic subtype).

RESULTS

Of the 1850 patients, 65 (3.5%) had DM. Of these, 46 (70.8%) had pure DM and 19 (29.2%) had mixed DM. Patients with pure DM had a median tumor thickness of 3.5 mm and 6.5% were ulcerated. Compared with patients with pure DM, patients with either mixed DM or non‐DM (n = 1785) had thinner primary tumors (median, 1.7 mm and 1.5 mm, respectively, each P < 0.001 vs. pure DM) that were more likely to be ulcerated (27.7% and 21.3%, respectively, each P < 0.05 vs. pure DM). Although the incidence of a positive SLN was similar in patients with mixed DM (15.8%) and non‐DM (17.5%), patients with pure DM were less likely to have a positive SLN (2.2%) (each P < 0.01 vs. non‐DM and mixed DM). At a median follow‐up of 2.9 years, no patient with pure DM had recurred.

CONCLUSIONS

Despite having thicker primary tumors, patients with pure DM have a lower incidence of positive SLNs compared with patients with non‐DM. Whereas the treatment approach for patients with mixed DM should be similar to that of other melanoma patients, patients with pure DM are unlikely to have metastatic disease in regional lymph nodes and SLNB may not be warranted. Cancer 2006. © 2006 American Cancer Society.
Comparison of the accuracy of magnetic resonance imaging and positron emission tomography/computed tomography in the presurgical detection of lymph node metastases in patients with uterine cervical carcinoma
Authors: Choi Hyuck Jae , Roh Ju Won , Seo Sang‐Soo , Lee Sun , Kim Joo‐Young , Kim Seok‐Ki , Kang Keon Wook , Lee Jong Seok , Jeong Jun Yong , Park Sang‐Yoon
Published: January 2006

BACKGROUND

The objective of the current study was to determine the accuracy of magnetic resonance imaging (MRI) and positron emission tomography/computed tomography (PET/CT) for detecting lymph node metastases in patients with uterine cervical carcinoma compared with thin‐section histopathologic results from systemic lymphadenectomy.

METHODS

Twenty‐two patients with International Federation of Obstetrics and Gynecology (FIGO) Stage IB–IVA cervical carcinoma who underwent both MRI and PET/CT before lymphadenectomy were included in this study. Lymphadenectomy involved removing all visible lymph nodes in the surgical fields. To enable region‐specific comparisons, paraaortic and pelvic lymph nodes were divided into seven regions: the paraaortic area, both common iliac areas, both external iliac areas, and both internal iliac/obturator areas. Histopathologic evaluation of lymph nodes was the diagnostic standard. Chi‐square analysis was used to compare the accuracy of MRI and PET/CT for the detection of metastatic lymph nodes. A P value ≤ 0.05 was considered statistically significant.

RESULTS

With MRI, the sensitivity, specificity, and accuracy rates for detecting metastatic lymph nodes in each lymph node group were 30.3% (10 of 33 lymph node groups), 92.6% (112 of 121 lymph node groups), and 72.7% (122 of 154 lymph node groups), respectively; with PET/CT, those rates were 57.6% (19 of 33 lymph node groups), 92.6% (112 of 121 lymph node groups), and 85.1% (131 of 154 lymph node groups), respectively. Statistical analysis showed that PET/CT was more sensitive than MRI (P = 0.026) but that there were no statistical differences noted with regard to specificity (P = 1.000) or accuracy (P = 0.180). Power analysis demonstrated that a sample size of 685 lymph node groups (98 patients) would be necessary to demonstrate that PET/CT was more accurate than MRI (α = 0.05; β = 0.80).

CONCLUSIONS

PET/CT was more sensitive than MRI for detecting lymph node metastases in patients with uterine cervical carcinoma. Cancer 2006. © 2006 American Cancer Society.
Pathologic findings from the Breast Cancer Surveillance Consortium
Authors: Weaver Donald L. , Rosenberg Robert D. , Barlow William E. , Ichikawa Laura , Carney Patricia A. , Kerlikowske Karla , Buist Diana S. M. , Geller Berta M. , Key Charles R. , Maygarden Susan J. , Ballard‐Barbash Rachel
Published: January 2006

BACKGROUND

To the authors' knowledge, a comprehensive analysis of pathology outcomes after screening mammography, as it is practiced clinically in the U.S. general population, has not been performed.

METHODS

Breast Cancer Surveillance Consortium data from 1996–2001 were used to identify pathology specimens that were obtained within 1 year of screening mammograms performed on 786,846 women ages 40–89 years. The pathology results were classified as invasive carcinoma, ductal carcinoma in situ (DCIS), or benign. The associations between overall pathology outcomes and invasive tumor size and lymph node status were analyzed by age and mammography assessment category.

RESULTS

The rates of both recommending and performing a biopsy varied little with age. The 1,664,032 screening mammograms were followed by 26,748 known biopsies (1.6%) and 8815 diagnoses of breast carcinoma (0.53%). Overall, 81% of carcinomas were invasive, and 78% of those were pathologically lymph node‐negative tumors, in contrast to the 66% prevalence observed in the Surveillance, Epidemiology, and End Results (SEER) data during the same period. Most invasive tumors measured between 0 mm and 10 mm (35%) or between 11 mm and 20 mm (36%) in greatest dimension, and 92% and 78% were lymph node‐negative tumors, respectively: Biopsy results that were classified as malignant increased with age (P < 0.0001) and were most likely to follow Breast Imaging, Reporting, and Diagnosis System Category 5 and 4 assessments, respectively. Ductal hyperplasia (19.6%), fibroadenoma (18.5%), and other benign findings (56.1%) were the most common benign diagnoses.

CONCLUSIONS

Pathologically negative lymph nodes were more prevalent in this mammographically screened population than in the overall SEER population. The prevalence of invasive carcinoma, DCIS, and benign findings presented herein establish a range of expected biopsy outcomes for women after screening mammography in the general U.S. population. Cancer 2006. © 2006 American Cancer Society.
Twenty‐five years of follow‐up in patients with operable breast carcinoma
Authors: Arriagada Rodrigo , Le Monique G. , Dunant Ariane , Tubiana Maurice , Contesso Genevieve
Published: January 2006

BACKGROUND

Some investigators have suggested a decreased prognostic value for conventional prognostic factors over time in patients with breast carcinoma. The objective of this study was to assess the effect of prognostic factors on the risk of death in patients with breast carcinoma over a long follow‐up.

METHODS

The authors assessed clinicopathologic prognostic factors in patients with early‐stage breast carcinoma over a follow‐up > 25 years and analyzed the variation of their effect on death in consecutive 5‐year follow‐up intervals. The study included 2410 women who primarily underwent complete surgical resection. Time‐dependent variables were analyzed by using different multivariate models.

RESULTS

Four factors were related strongly to the risk of death in the first 5 years: tumor size, histologic grade, the number of involved axillary lymph nodes, and age at diagnosis. After 10–15 years of follow‐up, only age at diagnosis was related to the risk of death. The effect of powerful prognostic factors, except age at diagnosis, on the risk of death was time limited, and no effects or very small effects were detectable after 10 years of follow‐up.

CONCLUSIONS

Conventional and widely accepted prognostic factors may explain a significant portion of early deaths among patients with early‐stage breast carcinoma, but they were of limited value to explain late mortality, that also may be influenced by late events, such as new primary malignancies and treatment complications. Cancer 2006. © 2006 American Cancer Society.
Randomized Phase II study of two opposite administration sequences of irinotecan and cisplatin in patients with advanced nonsmall cell lung carcinoma
Authors: Han Ji‐Youn , Lim Hyeong‐Seok , Lee Dae Ho , Ju So Young , Lee Sung Young , Kim Hyae Young , Park Yong‐Hoon , Park Chun Gun , Lee Jin Soo
Published: January 2006

BACKGROUND

Combined chemotherapy with irinotecan and cisplatin (IP) is active in patients with nonsmall cell lung carcinoma (NSCLC). However, the optimal administration schedule needs to be defined to maximize its synergic effect. The authors evaluated the efficacy, toxicity, and pharmacokinetics (PK) of IP chemotherapy given on two administration sequences in chemotherapy‐naive patients with NSCLC.

METHODS

Eighty eligible patients were assigned randomly to receive 1 of 2 irinotecan and cisplatin administration sequences on Day 1: irinotecan followed by cisplatin (I‐P) (n = 39 patients) or cisplatin followed by irinotecan (P‐I) (n = 41 patients). Treatment was comprised of irinotecan at a dose of 80 mg/m2 intravenously on Days 1 and 8 and cisplatin at a dose of 60 mg/m2 intravenously on Day 1 of a 21‐day cycle for a maximum of 6 cycles. For PK analysis, serial plasma samples were obtained on Day 1 of the first cycle.

RESULTS

In total, 77 patients were assessable for efficacy. The overall response rate was 47%, and there was a trend in favor of P‐I (54%) compared with I‐P (39%). In multivariate logistic regression analysis, the P‐I sequence and female gender were found to be significant predictors of a better response (P = 0.047 and P = 0.011, respectively). Overall toxicity profiles and PK parameters were similar in both arms.

CONCLUSIONS

IP chemotherapy showed promising activity with a favorable 1‐year survival rate. For future clinical use, the authors recommend administering cisplatin first and then irinotecan, because that sequence was associated with a higher response rate. Cancer 2006. © 2006 American Cancer Society.
Are venous thromboembolic events associated with subsequent breast and colorectal carcinoma diagnoses in the elderly?
Authors: Polite Blase N. , Lamont Elizabeth B.
Published: January 2006

BACKGROUND

Multiple epidemiologic studies have reported associations between venous thromboembolic events and subsequent cancer diagnoses, but the published results have not suggested clear cancer screening approaches.

METHODS

Using data from the National Cancer Institute's Surveillance, Epidemiology, and End Results‐Medicare Program, the authors identified patients who were diagnosed with breast and colorectal carcinoma (n = 7166 patients) and compared them with a noncancer control group (n = 126,668 patients) according to their history of hospitalization for deep vein thrombosis (DVT) or pulmonary embolism (PE) in Medicare claims files over the previous 24 months. Using logistic regression analysis, the authors calculated the odds of receiving a diagnosis of breast carcinoma or colorectal carcinoma in the 24 months after admission for DVT or PE.

RESULTS

Patients who were hospitalized for DVT or PE had nearly 3.0 times the odds of being diagnosed with colorectal carcinoma (odds ratio [OR], 2.83; 95% confidence interval [95% CI], 1.92–4.17) and > 1.5 times the odds of being diagnosed with breast carcinoma (OR, 1.78; 95% CI, 1.05–3.02) in the subsequent 24 months.

CONCLUSIONS

Because hospitalization for DVT or PE is associated with an increased risk of a breast or colorectal carcinoma diagnosis in the subsequent 2 years, physicians should be vigilant in assessing the cancer screening status of patients with new DVT and/or PE to be certain that they are up to date with recommended breast and colorectal screening guidelines. Cancer 2006. © 2006 American Cancer Society.
Prostate cancer screening in high‐risk men
Authors: Weinrich Sally P. ,   African American Hereditary Prostate Cancer Study Network
Published: January 2006

BACKGROUND

There are scant data available on prostate cancer screening among high‐risk African American men with positive family histories. It is important to determine whether or not their screening rates differ from those in the general population.

METHODS

This study computed rates of previous digital rectal examination (DRE) and prostate‐specific antigen (PSA) screening for prostate cancer in cancer‐free (unaffected) relatives age 40–69 years from African American families that had four or more men with prostate cancer. The rates for these 134 high‐risk African American men from the African American Hereditary Prostate Cancer Study (AAHPC) were compared with nationwide estimates obtained from participants in the 1998 and 2000 National Health Interview Survey (NHIS), for which the numbers of demographically comparable subjects were 5583 (4900 Caucasians, plus 683 African Americans) and 3359 (2948 Caucasians, 411 African Americans), respectively.

RESULTS

Men in the AAHPC cohort (with a strong positive family history) had significantly less screening than both African Americans and Caucasians in the NHIS cohorts. Only about one‐third (35%) of the men in the AAHPC unaffected cohort had ever had a DRE, and only about 45% of them had ever received a PSA test. These rates were much lower than those obtained for African American men in the NHIS: 45% for DRE and 65% for PSA. These discrepancies increased with age.

CONCLUSIONS

Older African American men with positive family histories report surprisingly low rates of DRE and PSA screening compared with their counterparts in the NHIS surveys. At‐risk men need to be informed of the benefits and limitations of prostate cancer screening and actively involved in decision‐making for or against prostate cancer screening. Cancer 2006. © 2006 American Cancer Society.
Role of exposure to radon and silicosis on the cell type of lung carcinoma in German uranium miners
Authors: Taeger Dirk , Fritsch Arno , Wiethege Thorsten , Johnen Georg , Eisenmenger Andreas , Wesch Horst , Ko Yon , Stier Sebastian , Michael Muller Klaus , Bruning Thomas , Pesch Beate
Published: January 2006

BACKGROUND

In East Germany, uranium mining was undertaken on a large scale from 1946 to 1990. Poor working conditions led to a high level of exposure to ionizing radiation and quartz dust. This analysis evaluates the histopathology of lung carcinoma in uranium miners in relation to radon exposure and silicosis.

METHODS

A database developed for autopsy cases ascertained in a pathological tissue repository of German uranium miners was used to estimate odds ratios for developing lung carcinoma by major cell type with regard to radon exposure and silicosis. Silicosis information was extracted from autopsy protocols. Working level months (WLM) were calculated with a job‐exposure matrix to assess lifetime radon exposure. Risk estimates were based on 3414 male miners who died from small cell lung carcinoma (SCLC, n = 1446), squamous cell carcinoma (SqCC, n = 1006), or adenocarcinoma (AC, n = 962) between 1957 and 1990.

RESULTS

SCLC and SqCC seem more likely to be associated with high radon exposure than AC. Mean cumulative radon exposure was 868 (SD 631) WLM in SCLC, 871 (SD 652) WLM in SqCC, and 743 (SD 598) WLM in AC. Silicosis prevalence was 26% in SCLC, 38% in SqCC, and 30% in AC. In silicotics, AC and SqCC had a relatively higher frequency at the expense of SCLC. SCLC occurred earlier than AC and SqCC.

CONCLUSION

High radon exposure was associated with a higher relative frequency of SCLC and SqCC than AC. Silicosis tended to increase the appearance of SqCC and AC. Cancer 2006. © 2006 American Cancer Society.
Smaller white‐matter volumes are associated with larger deficits in attention and learning among long‐term survivors of acute lymphoblastic leukemia
Authors: Reddick Wilburn E. , Shan Zuyao Y. , Glass John O. , Helton Susan , Xiong Xiaoping , Wu Shengjie , Bonner Melanie J. , Howard Scott C. , Christensen Robbin , Khan Raja B. , Pui Ching‐Hon , Mulhern Raymond K.
Published: January 2006

BACKGROUND

The primary objective of this study was to test the hypothesis that survivors of childhood acute lymphoblastic leukemia (ALL) have deficits in neurocognitive performance, and smaller white‐matter volumes are associated with these deficits.

METHODS

The patients studied included 112 ALL survivors (84 patients who had received chemotherapy only, 28 patients who had received chemotherapy and irradiation; 63 males, 49 females; mean age ± standard deviation, 4.1 yrs ± 2.6 yrs at diagnosis; mean ± standard deviation yrs since diagnosis, 6.0 ± 3.5 yrs), and 33 healthy siblings who participated as a control group. Neurocognitive tests of attention, intelligence, and academic achievement were performed; and magnetic resonance images were obtained and subsequently were segmented to yield tissue volume measurements. Comparisons of neurocognitive measures and tissue volumes between groups were performed, and the correlations between volumes and neurocognitive performance measures were assessed.

RESULTS

Most performance measures demonstrated statistically significant differences from the normative test scores, but only attention measures exceeded 1.0 standard deviation from normal. Patients who had received chemotherapy alone had significantly larger volumes of white matter than patients who had received treatment that also included cranial irradiation, but their volumes remained significantly smaller than the volumes in the control group. Smaller white‐matter volumes were associated significantly with larger deficits in attention, intelligence, and academic achievement.

CONCLUSIONS

Survivors of childhood ALL had significant deficits in attention and smaller white‐matter volumes that were associated directly with impaired neurocognitive performance. Cranial irradiation exacerbated these deficits. Cancer 2006. © 2006 American Cancer Society.
Integrating generations with advanced reference counting garbage collectors
Authors: Azatchi Hezi , Petrank Erez
Published: January 2006

We propose the use of generations with modern reference counting. A reference counting collector is well suited to collect the old generation, containing a large fraction of live objects that are modified infrequently. Such a collector can be combined with a tracing collector to collect the young generation, typically containing a small fraction of live objects. We have designed such a collector appropriate for running on a multiprocessor. As our building blocks, we used the sliding‐views on‐the‐fly collectors. We have implemented the new collector on the Jikes Research Java Virtual Machine (Jikes RVM) and compared it with the concurrent reference counting collector supplied with the Jikes RVM package. Our measurements demonstrate short pause times, retaining those of the original on‐the‐fly collectors and a gain in application throughput time. It turns out that a modern reference counting collector may benefit from the use of generations. Copyright © 2006 John Wiley & Sons, Ltd.
Multimedia vectorization of floating‐point MIN/MAX reductions
Authors: Bik Aart J. C. , Tian Xinmin , Girkar Milind B.
Published: January 2006

Finding the minimum or maximum value in an array forms an important step in a variety of applications. This paper discusses vectorization schemes that take advantage of the streaming‐SIMD‐extensions in commonly used floating‐point MIN and MAX reductions. Performance advantages are demonstrated with experimental results. Copyright © 2006 John Wiley & Sons, Ltd.
An overlapping task assignment scheme for hierarchical coarse‐grain task parallel processing
Authors: Yoshida Akimasa
Published: January 2006

This paper proposes an overlapping task assignment scheme for the hierarchical coarse‐grain task parallel processing on multiprocessor systems. In coarse‐grain task parallel processing, the compiler extracts parallelism among coarse‐grain tasks automatically and the coarse‐grain tasks are assigned to processor clusters at runtime. However, several programs may decrease the processor‐cluster utilization factor owing to lack of parallelism inside each coarse‐grain task. Therefore, in order to improve the processor‐cluster utilization factor, this paper proposes the execution scheme with overlapping task assignment whose dynamic scheduler can assign several coarse‐grain tasks to a processor cluster simultaneously. Also, the performance evaluations by simulations and executions on SMP showed that the proposed scheme could reduce the execution time remarkably. Copyright © 2006 John Wiley & Sons, Ltd.
Instruction scheduling for a clustered VLIW processor with a word‐interleaved cache
Authors: Gibert Enric , Sánchez Jesús , González Antonio
Published: January 2006

Clustering is a common technique to overcome the wire delay problem incurred by the evolution of technology. Fully distributed architectures, where the register file, the functional units and the data cache are partitioned, are particularly effective to deal with these constraints and moreover they are very scalable. In this paper, effective instruction scheduling techniques for a word‐interleaved cache clustered VLIW processor are presented. Such scheduling techniques rely on (i) loop unrolling and variable alignment to increase the fraction of local accesses, (ii) a latency assignment process to schedule memory instructions with an appropriate latency, and (iii) different heuristics to assign memory instructions to clusters. Memory consistency is guaranteed by constraining the assignment of memory instructions to clusters. In addition, the use of Attraction Buffers is also introduced. An Attraction Buffer is a hardware mechanism that allows some data replication in order to increase the number of local accesses and, in consequence, reduces stall time. Performance results for the Mediabench benchmark suite demonstrate the effectiveness of the presented techniques and mechanisms. The number of local accesses is increased by more than 25% by using the mentioned scheduling techniques, while stall time is reduced by more than 30% when Attraction Buffers are used. Finally, IPC results for such an architecture are 10% and 5% better compared to those of a clustered VLIW processor with a centralized/unified data cache depending on the scheduling heuristic, respectively. Copyright © 2006 John Wiley & Sons, Ltd.
UFS: a global trade‐off strategy for loop unrolling for VLIW architectures
Authors: Heydemann K. , Bodin F. , Knijnenburg P. M. W. , Morin L.
Published: January 2006

Embedded systems are increasingly expected to provide good performance at low cost. As the characteristics of compiled code can have an impact on the overall cost of an embedded system, a compilation strategy must be cost aware as well as achieve high performance. As one major factor for system cost is memory size, code size becomes an important issue in code generation. Thus, cost‐effective optimization strategies that are able to perform a good trade‐off between code size and performance improvement are needed. In this paper, we propose a novel method based on Integer Linear Programming for computing efficient unroll factors for collections of loop nests with control over code size and side‐effects of the transformation. We define a notion of trade‐off between code size and performance. Experiments on the Philips Trimedia show that our method achieves excellent trade‐offs. Copyright © 2006 John Wiley & Sons, Ltd.
Optimizing code‐copying JIT compilers for virtual stack machines
Authors: Gregg David , Ertl M. Anton
Published: January 2006

Just‐in‐time (JIT) compilers are widely used to implement stack‐based virtual machines, such as the Java and .NET virtual machines. One disadvantage of most JIT compilers is that they are unportable; much of the back‐end is specific to the target machine. An alternative to machine‐specific code generation methods is to define a routine in a high‐level language for each virtual machine instruction. These can be compiled to native code using a normal C compiler. The native code for these routines can then be strung together, allowing very simple, unoptimized code to be produced just in time. In this paper we present such a system based on an existing implementation of the Forth language. We present a novel system of optimizations for the system based on exploiting common sequences of virtual machine instructions. We use a small domain specific language and tool to generate stack‐optimized code for sequences of virtual machine instructions, and for choosing the most useful sequences for a code‐copying compiler. By measuring the length of the resulting executable code, we allow machine‐specific sequences to be chosen without any machine‐dependent code in our system. Experimental results show that best (average) speedups of 47.2% (15.75%) are possible on a Pentium 4 machine, and even higher an a PowerPC based machine. Furthermore, our optimizations allow the size of the generated code to be reduced by an average of 17.9% on the Pentium 4, and 20.5% on the PowerPC over a wide range of programs. Copyright © 2006 John Wiley & Sons, Ltd.
Is Morton layout competitive for large two‐dimensional arrays yet?
Authors: Thiyagalingam Jeyarajan , Beckmann Olav , Kelly Paul H. J.
Published: January 2006

Two‐dimensional arrays are generally arranged in memory in row‐major order or column‐major order. Traversing a row‐major array in column‐major order, or vice versa, leads to poor spatial locality. With large arrays the performance loss can be a factor of 10 or more. This paper explores the Morton storage layout, which has substantial spatial locality whether traversed in row‐major or column‐major order. Using a small suite of dense kernels working on two‐dimensional arrays, we have carried out an extensive study of the impact of poor array layout and of whether Morton layout can offer an attractive compromise. We show that Morton layout can lead to better performance than the worse of the two canonical layouts; however, the performance of Morton layout compared to the better choice of canonical layout is often disappointing. We further study one simple improvement of the basic Morton scheme: we show that choosing the correct alignment for the base address of an array in Morton layout can sometimes significantly improve the competitiveness of this layout. Copyright © 2006 John Wiley & Sons, Ltd.
Middleware adaptation with the Delphoi service
Authors: Maassen Jason , van Nieuwpoort Rob V. , Kielmann Thilo , Verstoep Kees , den Burger Mathijs
Published: January 2006

Grid middleware needs to adapt to changing resources for a large variety of operations. Currently, however, there is only low‐level information available about Grid resources, coming from various but functionally isolated monitoring and information systems. In this paper, we present the Delphoi service. It provides a unified interface to the necessary information, and also matches the abstraction level needed by middleware services to adapt their behavior. We describe Delphoi's architecture, the information it provides, and we evaluate the quality of its performance information. Delphoi has been developed as part of the EC‐funded GridLab project and is currently being deployed on the project's testbed for adding adaptivity to GridLab's middleware services. Copyright © 2006 John Wiley & Sons, Ltd.
Resource reservations with fuzzy requests
Authors: Röblitz T. , Schintke F. , Reinefeld A.
Published: January 2006

We present a scheme for reserving job resources with imprecise requests. Typical parameters such as the estimated runtime, the start time or the type or number of required CPUs need not be fixed at submission time but can be kept fuzzy in some aspects. Users may specify a list of preferences which guide the system in determining the best matching resources for the given job. Originally, the impetus for our work came from the need for efficient co‐reservation mechanisms in the Grid where rigid constraints on multiple job components often make it difficult to find a feasible solution. Our method for handling fuzzy reservation requests gives the users more freedom to specify the requirements and it gives the Grid Reservation Service more flexibility to find optimal solutions. In the future, we will extend our methods to process co‐reservations. We evaluated our algorithms with real workload traces from a large supercomputer site. The results indicate that our scheme greatly improves the flexibility of the solution process without having much affect on the overall workload of a site. From a user's perspective, only about 10% of the non‐reservation jobs have a longer response time, and from a site administrator's view, the makespan of the original workload is extended by only 8% in the worst case. Copyright © 2006 John Wiley & Sons, Ltd.
How to bring together fault tolerance and data consistency to enable Grid data sharing
Authors: Antoniu G. , Deverge J.‐F. , Monnet S.
Published: January 2006

This paper addresses the challenge of transparent data sharing within computing Grids built as cluster federations. On such platforms, the availability of storage resources may change in a dynamic way, often due to hardware failures. We focus on the problem of handling the consistency of replicated data in the presence of failures. We propose a software architecture which decouples consistency management from fault tolerance management. We illustrate this architecture with a case study showing how to design a consistency protocol using fault‐tolerant building blocks. As a proof of concept, we describe a prototype implementation of this protocol within JUXMEM, a software experimental platform for Grid data sharing, and we report on a preliminary experimental evaluation of the proposed approach. Copyright © 2006 John Wiley & Sons, Ltd.
Complex dynamics in one‐dimensional CNNs
Authors: Petrás István , Gilli Marco
Published: January 2006

The effect of boundary conditions on the global dynamics of cellular neural networks (CNNs) is investigated. As a case study one‐dimensional template CNNs are considered. It is shown that if the off‐diagonal template elements have opposite sign, then the boundary conditions behave as bifurcation parameters and can give rise to a very rich and complex dynamic behaviour. In particular, they determine the equilibrium point patterns, the transition from stability to instability and the occurrence of several bifurcation phenomena leading to strange and/or chaotic attractors and to the coexistence of several attractors. Then the influence of the number of cells on the global dynamics is studied, with particular reference to the occurrence of hyperchaotic behaviour. Copyright © 2006 John Wiley & Sons, Ltd.
Immune response inspired spatial–temporal target detection algorithms with CNN‐UM
Authors: Cserey György , Falus András , Roska Tamás
Published: January 2006

In this paper we show that, similar to the nervous system and the genetic system, the immune system provides a prototype for a ‘computing mechanism.’ We are presenting an immune response inspired algorithmic framework for spatial–temporal target detection applications using CNN technology (IEEE Trans. Circuits Syst. II1993;40(3):163–173;Foundations and Applications. Cambridge University Press: Cambridge, 2002). Unlike most analogic CNN algorithms (IEEE Trans. Circuits Syst.1988;35(10):1257–1290;Foundations and Applications. Cambridge University Press: Cambridge, 2002) here we will detect various targets by using a plethora of templates. These algorithms can be implemented successfully only by using a computer upon which thousands of elementary, fully parallel spatial–temporal actions can be implemented in real time. In our tests the results show a statistically complete success rate, and we are presenting a special example of recognizing dynamic objects. Results from tests in a 3D virtual world with different terrain textures are also reported to demonstrate that the system can detect unknown patterns and dynamical changes in image sequences. Applications of the system include in explorer systems for terrain surveillance. Copyright © 2006 John Wiley & Sons, Ltd.
Analog‐VLSI, array‐processor‐based, Bayesian, multi‐scale optical flow estimation
Authors: Török L. , Zarándy Á.
Published: January 2006

Optical flow (OF) estimation aims at derive a motion‐vector field that characterizes motions on a video sequence of images. In this paper, we propose a new multi‐scale (or scale‐space) algorithm that generates OF on cellular neural/non‐linear network universal machine, a general purpose analog‐VLSI hardware, at resolution of 128 × 128 with fair accuracy and working over a speed of 100 frames/s. The performance of the hardware implementation of the proposed algorithm is measured on a standard image sequence. As far as we are concerned, this is the first time when an OF estimator hardware is tested on a practical‐size standard image sequence. Copyright © 2006 John Wiley & Sons, Ltd.
Non‐linear coupled CNN models for multiscale image analysis
Authors: Corinto F. , Biey M. , Gilli M.
Published: January 2006

A CNN model of partial differential equations (PDEs) for image multiscale analysis is proposed. The model is based on a polynomial representation of the diffusivity function and defines a paradigm of polynomial CNNs, for approximating a large class of non‐linear isotropic and/or anisotropic PDEs. The global dynamics of space‐discrete polynomial CNN models is analysed and compared with the dynamic behaviour of the corresponding space‐continuous PDE models. It is shown that in the isotropic case the two models are not topologically equivalent; in particular, discrete CNN models allow one to obtain the output image without stopping the image evolution after a given time (scale). This property represents an advantage with respect to continuous PDE models and could simplify some image preprocessing algorithms. Copyright © 2006 John Wiley & Sons, Ltd.
Automated detection of a preseizure state: non‐linear EEG analysis in epilepsy by Cellular Nonlinear Networks and Volterra systems
Authors: Tetzlaff Ronald , Niederhöfer Christian , Fischer Philipp
Published: January 2006

In this paper we present our work analysing electroencephalographic (EEG) signals for the detection of seizure precursors in epilepsy. Volterra systems and Cellular Nonlinear Networks are considered for a multidimensional signal analysis which is called the feature extraction problem throughout this contribution. Recent results obtained by applying a pattern detection algorithm and a non‐linear prediction of brain electrical activity will be discussed in detail. The aim of this interdisciplinary project is the realization of an implantable seizure warning and preventing system. Copyright © 2006 John Wiley & Sons, Ltd.
Climbing obstacle in bio‐robots via CNN and adaptive attitude control
Authors: Pavone M. , Arena P. , Fortuna L. , Frasca M. , Patané L.
Published: January 2006

In this paper, we introduce a novel control system architecture for hexapod robots. Our aim is to guarantee efficient horizontal walking and obstacle climbing via suitable postural adjustments. The control scheme takes its inspiration from recent neurobiological and kinematic observations of cockroaches walking on a treadmill and climbing over barriers. Based on a hierarchical and modular approach, the control architecture is divided into two levels. In the low level two parts working in parallel are present: rhythmic movements leading to gaits are performed by a cellular neural network (CNN) playing the role of an artificial central pattern generator (CPG), while a parallel PD attitude control system modulates (with adding terms) the CNN‐CPG signals to achieve postural adjustments. The higher level, in turn, adds plasticity to the whole system; it is based on motor maps and maps sensory information in suitable attitude references for the low level PD attitude control. Tests performed with a dynamic model of hexapod have shown that after a training period the high level is able to enhance walking and climbing capabilities. Copyright © 2006 John Wiley & Sons, Ltd.
Learning of spatiotemporal behaviour in cellular neural networks
Authors: Xavier‐de‐Souza Samuel , Suykens Johan A. K. , Vandewalle Joos
Published: January 2006

In this paper the problem of learning spatiotemporal behaviour with cellular neural networks is analysed and a novel method is proposed to approach the problem. The basis for this method is found in trajectory learning with recurrent neural networks. Despite of similarities, the two learning problems have underling differences which make non‐trivial a direct mapping into the problem at hand. In order to solve the problem, a new cost function is proposed, which also assimilates time instants as parameters to be optimized. As a consequence, it does not force the desired spatiotemporal behaviour to be learned in its original speed, and thus different speed versions of the desired behaviour are allowed to be learned; hence, also providing a promising direction for increasing the speed of existing applications. Learning examples are presented for different classes of spatiotemporal dynamics including spiral autowaves. Results of simulation and on‐chip learning show that the proposed approach is able to learn these dynamics with cellular neural networks. Copyright © 2006 John Wiley & Sons, Ltd.
An eight layer cellular neural network for spatio‐temporal image filtering
Authors: Shi Bertram E.
Published: January 2006

Spatio‐temporal filters are critical components of biologically inspired or neuromorphic algorithms for image motion analysis. In this paper, we describe eight layer cellular neural network architectures that can be used to implement these filters. Despite the apparently large number of layers, we describe how these architectures can be implemented efficiently using weak inversion transistor circuits. Integrating both spatial and temporal filtering into a single network reduces hardware complexity in comparison with an architecture that cascades separate spatial and temporal filtering stages. In addition, by considering spatial and temporal filtering jointly, we can obtain filters with enhanced velocity selectivity, as well as more robust population responses to moving image input. Copyright © 2006 John Wiley & Sons, Ltd.
On the Existence of the Elusive Monomethyl Ester of Carbonic Acid [CH3OC(O)OH] at 300 K: 1H‐ and 13C NMR Measurements and DFT Calculations
Authors: Dibenedetto Angela , Aresta Michele , Giannoccaro Potenzo , Pastore Carlo , Pápai Imre , Schubert Gábor
Published: January 2006

The elusive monomethyl ester of carbonic acid [CH3OC(O)OH] has been prepared at 300 K by protonation of the sodium salt NaOC(O)OCH3 with anhydrous HCl or water and characterized by 1H‐ and 13C NMR spectroscopy. The stability of the acid and its reactivity towards hydroxo ions and methylating agents under ambient conditions are discussed. The energetics and the mechanism of the investigated reactions are examined on the basis of density functional calculations. For kinetic and thermodynamic reasons CH3OC(O)OH is unlikely to be formed by insertion of CO2 into the O–H bond of methanol. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2006)