bluuebunny/crossref_metadata_2025_split huggingface dataset:
A New Napthopyrone from the Root of Pleuropterus ciliinervis.
Authors: Min Byung‐Sun , Lee Jong‐Pill , Na Min‐Kyun , An Ren‐Bo , Lee Sang‐Myung , Lee Hyeong‐Kyu , Bae KiHwan , Kang Sam‐Sik 
Published: March 2004

AbstractFor Abstract see ChemInform Abstract in Full Text.
Prenylates Xanthones from Garcinia xanthochymus.
Authors: Chanmahasathien Wisinee , Li Yushan , Satake Masayuki , Oshima Yasukatsu , Ishibashi Masami , Ruangrungsi Nijsiri , Ohizumi Yasushi 
Published: March 2004

AbstractFor Abstract see ChemInform Abstract in Full Text.
The “Rebound Controversy”: An Overview and Theoretical Modeling of the Rebound Step in C—H Hydroxylation by Cytochrome P450
Authors: Shaik Sason , Cohen Shimrit , de Visser Samuel P. , Sharma Pankaz K. , Kumar Devesh , Kozuch Sebastian , Ogliaro Francois , Danovich David 
Published: March 2004

AbstractFor Abstract see ChemInform Abstract in Full Text.
Radical retropubic prostatectomy in Hispanic patients
Authors: Gomez Pablo , Manoharan Muruqesan , Sved Paul , Kim Sandy S. , Soloway Mark S. 
Published: March 2004

AbstractBACKGROUNDHispanics are the largest minority group in the U.S. Most studies assessing race as a predictor of biochemical disease recurrence after radical retropubic prostatectomy (RRP) have focused on African‐American patients. To the authors' knowledge, little has been published to date regarding radical prostatectomy in Hispanic patients. Hispanics represent 29% of the patients in the current study. The authors analyzed the presentation and outcome of Hispanic males managed with radical prostatectomy.METHODSIn the current study, 1163 RRPs were performed. Patients were categorized by ethnicity as Hispanics, white non‐Hispanics, African‐Americans, and other ethnicities. African‐American and other minority group patients were excluded from the analysis because of the small number in the current series. A comparative analysis of Hispanics and white non‐Hispanics was performed.RESULTSRRP was performed in 1163 patients. Two hundred seven Hispanic and 518 white non‐Hispanic patients met the study criteria. The mean follow‐up was 46.9 months. Twenty‐three percent of the Hispanic patients received neoadjuvant therapy. RRP Gleason scores of 2–6, 7, and 8–10 were found in 45% of patients, 38% of patients, and in 17% of patients, respectively. Lymph node metastases were present in 3%, seminal vesicle invasion in 13%, and extraprostatic extension in 23% of Hispanic patients. Adjuvant hormonal therapy was administered to 6% of the Hispanic patients. The biochemical disease recurrence rate was 12%. The mean time to biochemical disease recurrence was 29.7 months. A comparison between the Hispanic and the white non‐Hispanic groups showed no significant differences in the analyzed variables.CONCLUSIONSHispanic patients managed with radical prostatectomy for prostate carcinoma were found to have similar presentation, pathologic findings, and outcome as the white non‐Hispanic patients. Cancer 2004. © 2004 American Cancer Society.
The fragile genes FHIT and WWOX are inactivated coordinately in invasive breast carcinoma
Authors: Guler Gulnur , Uner Aysegul , Guler Nilufer , Han Shuang‐Yin , Iliopoulos Dimitrios , Hauck Walter W. , McCue Peter , Huebner Kay 
Published: March 2004

AbstractBACKGROUNDFHIT and WWOX are a tumor suppressor and a candidate suppressor that encompass the FRA3B and FRA16D fragile sites at chromosomes 3p14.2 and 16q23.3–24.1, respectively. Reduced or absent Fhit expression has been reported in two‐thirds of invasive breast tumors in association with adverse prognostic factors. Loss of 16q has been reported frequently in low‐grade, invasive breast tumors.METHODSExpression of Fhit and Wwox was evaluated by immunohistochemical staining in 97 archived breast carcinoma specimens. Expression levels were analyzed for correlations with each other, as well as with various patient and tumor characteristics.RESULTSReduced Fhit and Wwox expression in tumors was observed in 54.6% and 63.2% of specimens, respectively. Fhit and Wwox expression were correlated strongly (P = 0.001). Reduced Fhit staining was seen more frequently in premenopausal patients (P = 0.010), estrogen receptor (ER)‐negative or scantly ER‐positive tumors (P = 0.058 borderline), high‐grade tumors (P = 0.005), and tumors with metastases (P = 0.041). Reduced Wwox staining was more common in tumors with less favorable ER status (P = 0.033). Wwox expression in normal tissue was reduced in 32.9% of specimens, especially in patients with higher stage disease (P = 0.033). Severely reduced Wwox staining (extent < 10%) in normal tissue was found only in postmenopausal women, but reduced Wwox staining (11–75%) was more common in premenopausal women (P = 0.012). Tumor status, lymph node status, and intensity of Fhit expression in tumors were related independently to survival (P = 0.003, P < 0.001, and P = 0.046, respectively).CONCLUSIONSThe strong correlation observed between Fhit and Wwox expression was consistent with the common elevated susceptibility of fragile sites to DNA damage. Reduced Fhit expression is associated with adverse prognostic factors. The current results suggest that Wwox also has an important and complex association with steroid hormone expression and breast carcinogenesis. Cancer 2004. © 2004 American Cancer Society.
High‐dose methotrexate pharmacokinetics and outcome of children and young adults with osteosarcoma
Authors: Crews Kristine R. , Liu Tiebin , Rodriguez‐Galindo Carlos , Tan Ming , Meyer William H. , Panetta J. Carl , Link Michael P. , Daw Najat C. 
Published: March 2004

AbstractBACKGROUNDHigh‐dose methotrexate (HDMTX) is used frequently in combination regimens that include nephrotoxic chemotherapy. The authors evaluated the impact of factors such as age and prior nephrotoxic agents on MTX pharmacokinetics in children and young adults with osteosarcoma and examined whether MTX pharmacokinetic parameters were associated with outcome.METHODSThe authors evaluated MTX pharmacokinetics in 140 patients who were treated with 1083 courses of HDMTX on 3 consecutive studies of multiagent chemotherapy at a single institution. The influence of MTX pharmacokinetics on the outcome of 107 patients with localized disease was examined.RESULTSMean peak MTX concentrations ≥ 1000 μM were achieved in 135 patients (96%). MTX clearance was decreased after cisplatin therapy (P= 0.01), after cisplatin in combination with ifosfamide therapy (P< 0.0001), and after MTX therapy (P= 0.003). In patients with localized osteosarcoma, a higher mean MTX area under the curve, a higher mean peak concentration of MTX, a longer mean time above a threshold concentration (500 μM), and a lower mean MTX clearance were associated with lower probability of event‐free survival (EFS). Patients who had a mean peak MTX plasma concentration > 1500 μM were found to have a worse outcome (estimated 5‐year EFS, 58.5% ± 6.7%) compared with patients who had a mean peak concentration ≤ 1500 μM (estimated 5‐year EFS, 75.5% ± 6.6%;P= 0.02).CONCLUSIONSWhen HDMTX (12 g/m2) was used with multiagent therapy for patients with osteosarcoma, very high MTX exposures were associated with poorer outcome. The prospective evaluation of MTX pharmacokinetics and their relation to outcome in a large study is warranted to further substantiate the current findings and to elucidate the causative mechanism. Cancer 2004. © 2004 American Cancer Society.
Design and evaluation of a TOP100 Linux Super Cluster system
Authors: Edmundsson Niklas , Elmroth Erik , Kågström Bo , Mårtensson Markus , Nylén Mats , Sandgren Åke , Wadenstein Mattias 
Published: March 2004

AbstractThe High Performance Computing Center North (HPC2N) Super Cluster is a truly self‐made high‐performance Linux cluster with 240 AMD processors in 120 dual nodes, interconnected with a high‐bandwidth, low‐latency SCI network. This contribution describes the hardware selected for the system, the work needed to build it, important software issues and an extensive performance analysis. The performance is evaluated using a number of state‐of‐the‐art benchmarks and software, including STREAM, Pallas MPI, the Atlas DGEMM, High‐Performance Linpack and NAS Parallel benchmarks. Using these benchmarks we first determine the raw memory bandwidth and network characteristics; the practical peak performance of a single CPU, a single dual‐node and the complete 240‐processor system; and investigate the parallel performance for non‐optimized dusty‐deck Fortran applications. In summary, this $500 000 system is extremely cost‐effective and shows the performance one would expect of a large‐scale supercomputing system with distributed memory architecture. According to the TOP500 list of June 2002, this cluster was the 94th fastest computer in the world. It is now fully operational and stable as the main computing facility at HPC2N. The system's utilization figures exceed 90%, i.e. all 240 processors are on average utilized over 90% of the time, 24 hours a day, seven days a week. Copyright © 2004 John Wiley & Sons, Ltd.
A parallel algorithm for static slicing of concurrent programs
Authors: Goswami D. , Mall R. 
Published: March 2004

AbstractSlicing of concurrent programs is a compute‐intensive task. To speed up the slicing process, we have developed a parallel algorithm. For this purpose we used the concurrent control flow graph (CCFG) as the intermediate representation. We used a network of communicating processes to develop our parallel algorithm. We have implemented our parallel algorithm and the experimental results appear promising. Copyright © 2004 John Wiley & Sons, Ltd.
A cellular automata model can quickly approximate UDP and TCP network traffic
Authors: Brooks Richard R. , Griffin Christopher , Payne T. Alan 
Published: March 2004

AbstractBrooks and Orr [R.R. Brooks and N. Orr, A model for mobile code using interacting automata. IEEE Trans Mobile Computing 2002, 1(4)] present a model for analysis and simulation of mobile code systems based on cellular automata (CA) abstractions. One flaw with that article was a lack of experimental support showing that CA can model IP networks. This article presents CA models, consistent with those in the work of Brooks and Orr, that model the transport layer of IP networks. We show how these models may be generalized for more complicated network topologies. We provide quantitative results comparing the quality of our CA implementation versus the standard network modeling tool ns‐2. The results from the CA model are qualitatively similar to ns‐2, but the CA simulation runs significantly faster and scales better. © 2004 Wiley Periodicals, Inc. Complexity 9:32–40, 2004
A novel method for detection of virus‐infected cells through moving optical gradient fields using adenovirus as a model system
Authors: Soo Hoo William , Wang Mark , Kohrumel Joshua R. , Hall Jeff 
Published: March 2004

AbstractBackgroundMost methods for cellular analysis require labeling with specific antibodies or dyes and are often destructive. We have developed a technology called Optophoresis™, which measures cell physiology based on the cell's motion in a near‐infrared optical gradient. This technique does not require labels, is nondestructive, and involves minimal sample processing.MethodsWe have used Optophoresis to interrogate nonproductive and productive adenovirus‐infected cell lines. Using an adenoviral vector containing green fluorescent protein (GFP) as a secondary assay, we show that viral infection can be monitored with Optophoresis.ResultsIn HeLa cells, adenovirus infection after 24 h caused a 12% to 17% increase in optophoretic motility of the cells. In 293 cells, adenovirus infection resulted in a 40% increase in the optophoretic motility. The P values obtained were 4.5 × 10−11 between noninfected and infected HeLa cells, and 2.1 × 10−13 between noninfected and infected 293 cells. Cells infected with adenovirus lacking the GFP reporter gene gave similar shifts. In a time course, we observed an optophoretic shift after 4 h of infection, well before GFP expression.ConclusionsOptophoresis provides nondestructive, label‐free analysis of viral infection. Detection is independent of reporter gene expression and can be observed early in the infection process. © 2004 Wiley‐Liss, Inc.
Histone H1 and chromatin interactions in human fibroblast nuclei after H1 depletion and reconstitution with H1 subfractions
Authors: Kostova Nora N. , Srebreva Ljuba , Markov Dimiter V. , Rundquist Ingemar 
Published: March 2004

AbstractBackgroundLinker histones constitute a family of lysine‐rich proteins associated with nucleosome core particles and linker DNA in eukaryotic chromatin. In permeabilized cells, they can be extracted from nuclei by using salt concentration in the range of 0.3 to 0.7 M. Although other nuclear proteins are also extracted at 0.7 M salt, the remaining nucleus represents a template that is relatively intact.MethodsA cytochemical method was used to study the affinity of reconstituted linker histones for chromatin in situ in cultured human fibroblasts. We also investigated their ability to condense chromatin by using DNA‐specific osmium ammine staining for electron microscopy.ResultsPermeabilized and H1‐depleted fibroblast nuclei were suitable for the study of linker histone–chromatin interactions after reconstitution with purified linker histone subfractions. Our results showed that exogenous linker histones bind to chromatin with lower affinity than the native ones. We detected no significant differences between the main H1 and H1° histone fractions with respect to their affinity for chromatin or in their ability to condense chromatin.ConclusionsLinker histone interactions with chromatin are controlled also by mechanisms independent of linker histone subtype composition. © 2004 Wiley‐Liss, Inc.
Telomere length assessment in tissue sections by quantitative FISH: Image analysis algorithms
Authors: O'Sullivan Jacintha N. , Finley Jennifer C. , Risques Rosa‐ana , Shen Wen‐Tang. , Gollahon Katherine A. , Moskovitz Alexander H. , Gryaznov Sergei , Harley Calvin B. , Rabinovitch Peter S. 
Published: March 2004

AbstractBackgroundTelomeres are tandem repeated DNA sequences at the ends of every chromosome, which cap, stabilize, and prevent chromosome fusions and instability. Telomere regulation is an important mechanism in cellular proliferation and senescence in normal diploid and neoplastic cells. Quantitative methods to assess telomere lengths are essential to understanding how telomere dynamics play a role in these processes.MethodsTelomere lengths have been conventionally measured using terminal restriction fragment (TRF), quantitative fluorescence in situ hybridization (QFISH), and flow FISH. In this study, we have applied QFISH to measure average telomere lengths in cultured cells and human tissues of the GI tract. Importantly, this method can be used to analyze telomere lengths in sections using confocal microscopy. We describe and compare three image analysis algorithms: a simple pixel histogram calculation of background corrected fluorescence, a telomere spot‐finding method, and a background curve subtraction algorithm.ResultsUsing normal human diploid fibroblasts (NHDF) either dropped on slides or sectioned after agar embedding, similar telomere length shortening is evident with increasing population doubling levels (PDLs), using peptide nucleic acid (PNA) and an N3′‐P5′‐phosphoamidate (PA) oligonucleotide probe for all three methods. Validation of these in situ telomere quantification methods showed excellent agreement with the commonly used telomere repeat fragment‐Southern blot method. Telomere length reductions can also be demonstrated in tissue sections from histologically normal mucosa from patients with chronic ulcerative colitis (with dysplasia or cancer elsewhere in the colon), in colon adenomas, and in mucosal biopsies from patients with Barrett's esophagus. Both on slides and in tissue sections, the telomere spot‐finding method has the greatest variability, while intra‐ and inter‐biopsy variability in telomere length assessment using the other methods is relatively low.ConclusionsAccurate and reproducible telomere length measurements can be made in tissue sections using QFISH and confocal microscopy. The simplest methods proved the most reliable and make these methods readily accessible to many laboratories. The use of these methods will enhance the ability to measure telomere lengths in tissue samples and aid in the understanding of the role of telomere length in aging and disease. © 2004 Wiley‐Liss, Inc.
A single‐step, sensitive flow cytofluorometric assay for the simultaneous assessment of membrane‐bound and ingested Candida albicans in phagocytosing neutrophils
Authors: Busetto Sara , Trevisan Elisa , Patriarca Pierluigi , Menegazzi Renzo 
Published: March 2004

AbstractBackgroundDistinguishing ingested particles from those attached to the cell surface is an essential requirement when performing quantitative studies of phagocytosis. In the present report, we describe a simple, sensitive and reliable flow cytofluorometric method that achieves this goal in a Candida albicans‐human neutrophils (PMN) system.MethodsThe assay is based on the observation that the vital dye trypan blue (TB), while quenching the green fluorescence of fluorescein‐labeled C. albicans, causes them to fluoresce red. PMN were incubated with fluorescein‐labeled yeast particles for the required time. Aliquots of the incubation mixtures were then promptly diluted with an equal volume of a TB solution at pH 4.0, and subsequently analyzed by flow cytometry for green and red fluorescence.ResultsSince TB does not penetrate into the cells, ingested yeasts retain their green fluorescence, while membrane‐bound particles display a red fluorescence.ConclusionsOur fluorescence flow cytometric method enables to simultaneously distinguish, within the leukocyte population, cell subsets with attached and ingested yeast particles. Its major features are: (1) accuracy, sensitivity and reproducibility; (2) no further sample manipulations after completion of phagocytosis; (3) possibility of counting free, attached and internalized yeast particles; and (4) use of a nontoxic reagent (TB). © 2004 Wiley‐Liss, Inc.
Automated detection of immunofluorescently labeled cytomegalovirus‐infected cells in isolated peripheral blood leukocytes using decision tree analysis
Authors: Ladanyi Andras , Sher Andrew C. , Herlitz Anna , Bergsrud Danielle E. , Kraeft Stine‐Kathrein , Kepros Jane , McDaid Gizelda , Ferguson David , Landry Marie L. , Chen Lan Bo 
Published: March 2004

AbstractBackgroundCytomegalovirus (CMV) infection continues to be a major problem for immunocompromised patients. Detection of viral antigens in leukocytes (antigenemia assay) is widely used for the diagnosis of CMV infection and for guiding antiviral therapy. The antigenemia technique, contingent upon the manual microscopic analysis of rare cells, is a laborious task that is subject to human error. In this study, we combine automated microscopy with artificial intelligence for reliable detection of fluorescently labeled CMV‐infected cells.MethodsCytospin preparations of peripheral blood leukocytes were immunofluorescently labeled for the CMV lower matrix phosphoprotein (pp65) and scanned in the Rare Event Imaging System (REIS), a fully automated image cytometer. The REIS detected potential positive objects and digitally recorded 49 measured cellular features for each identified case. The measurement data of these objects were analyzed by the See5 decision tree (DT) algorithm to ascertain whether they were true‐positive detections.ResultsThe DT was built from the measurement data of 2,047 true‐ and 2,028 false‐positive detections, collected from 32 patient samples. By designating misclassifications of false‐negatives three times more costly, the 10‐fold cross‐validation sensitivity, specificity, and misclassification error of the assay was 94.3%, 56.2%, and 25%, respectively. The method was also validated using an independent test set of 21 patient samples, in which similar results were obtained.ConclusionsTo our knowledge, this study represents the first attempt to improve the accuracy of rare event image cytometry through the implementation of artificial intelligence methodology. Results suggest that cost‐sensitive decision tree analysis of digitally measured cellular features vastly improves the performance of rare event image cytometry. © 2004 Wiley‐Liss, Inc.
Stress reactivity in 15‐month‐old infants: Links with infant temperament, cognitive competence, and attachment security
Authors: van Bakel Hedwig J. A. , Riksen‐Walraven J. Marianne 
Published: March 2004

AbstractIn a sample of eighty‐five 15‐month‐old infants, salivary cortisol was obtained prior to and following a potentially stressful episode in which the child was confronted with a stranger and with a frightening robot. Infant characteristics such as anger proneness, cognitive competence, and attachment security were expected to be related to cortisol reactivity during the stressful event. The results showed higher cortisol reactivity in more anger‐prone infants and in infants with higher levels of cognitive development as assessed with the Bayley Scales of Infant Development (N. Bayley, 1969). Attachment security, assessed with the Attachment Q‐Set (AQS; E. Waters, 1995), was found to moderate the relation between cognitive level and cortisol reactivity; the positive relation between cognitive development and cortisol response was found in only infants with low AQS security scores. The findings may have important implications for research in the development of self‐regulation in humans as well as in studies with animals. © 2004 Wiley Periodicals, Inc. Dev Psychobiol 44: 157–167, 2004.
Similar and functionally typical kinematic reaching parameters in 7‐ and 15‐month‐old in utero cocaine‐exposed and unexposed infants
Authors: Tronick E. Z. , Fetters Linda , Olson Karen L. , Chen Yuping 
Published: March 2004

AbstractThis study examined the effects of intrauterine cocaine exposure on the reaches of 19 exposed and 15 unexposed infants at 7 and 15 months using kinematic measures. Infants sat at a table and reached for a rattle, a toy doll, and a chair. Videotaped reaches were digitized using the Peak Performance system. Kinematic movement variables were extracted (e.g., reach duration, peak velocity, movement units, path length) and ratios computed (e.g., path length divided by number of movement units). Regardless of exposure status, reaches of older infants were faster, more direct, had fewer movement units, and covered more distance with the first movement unit. Exposed infants covered more distance per movement unit than unexposed infants, but there were no other significant differences. Reaches of exposed and unexposed infants were essentially similar. Importantly, reach parameters for these high‐risk infants were similar to reach parameters for infants at lower social and biological risk. © 2004 Wiley Periodicals, Inc. Dev Psychobiol 44: 168–175, 2004.