bluuebunny/crossref_metadata_2025_split huggingface dataset:
On the conditions necessary for removing abstraction penalties in OOLALA
Authors: Luján Mikel , Freeman T. L. , Gurd John R. 
Published: February 2005

AbstractOOLALA is an object‐oriented linear algebra library designed to reduce the effort of software development and maintenance. In contrast with traditional (Fortran‐based) libraries, it provides two high abstraction levels that significantly reduce the number of implementations necessary for particular linear algebra operations. Initial performance evaluations of a Java implementation of OOLALA show that the two high abstraction levels are not competitive with the low abstraction level of traditional libraries. These initial performance results motivate the present contribution—the characterization of a set of storage formats (data structures) and matrix properties (special features) for which implementations at the two high abstraction levels can be transformed into implementations at the low (more efficient) abstraction level. Copyright © 2005 John Wiley & Sons, Ltd.
Ibis: a flexible and efficient Java‐based Grid programming environment
Authors: van Nieuwpoort Rob V. , Maassen Jason , Wrzesińska Gosia , Hofman Rutger F. H. , Jacobs Ceriel J. H. , Kielmann Thilo , Bal Henri E. 
Published: February 2005

AbstractIn computational Grids, performance‐hungry applications need to simultaneously tap the computational power of multiple, dynamically available sites. The crux of designing Grid programming environments stems exactly from the dynamic availability of compute cycles: Grid programming environments (a) need to beportableto run on as many sites as possible, (b) they need to beflexibleto cope with different network protocols and dynamically changing groups of compute nodes, while (c) they need to provideefficient(local) communication that enables high‐performance computing in the first place. Existing programming environments are either portable (Java), or flexible (Jini, Java Remote Method Invocation or (RMI)), or they are highly efficient (Message Passing Interface). No system combines all three properties that are necessary for Grid computing. In this paper, we present Ibis, a new programming environment that combines Java's ‘run everywhere’ portability both with flexible treatment of dynamically available networks and processor pools, and with highly efficient, object‐based communication. Ibis can transfer Java objects very efficiently by combining streaming object serialization with a zero‐copy protocol. Using RMI as a simple test case, we show that Ibis outperforms existing RMI implementations, achieving up to nine times higher throughputs with trees of objects. Copyright © 2005 John Wiley & Sons, Ltd.
Identification of B and T cells in human spleen sections by infrared microspectroscopic imaging
Authors: Krafft Christoph , Salzer Reiner , Soff Gerhard , Meyer‐Hermann Michael 
Published: February 2005

AbstractBackgroundInfrared spectroscopy probes the chemical composition and molecular structure of complex systems such as tissue and cells. Infrared spectroscopic imaging combines this spectral information with lateral resolution near the single‐cell level. We analyzed whether this method is competitive with classic immunohistochemical methods for immunologic tissue and cells.MethodsWe recorded infrared microspectroscopic mapping datasets with a 90‐ × 90‐μm2 aperture from a 3‐ × 3‐mm2 unstained tissue area of human spleen. A secondary follicle containing a germinal center and a T zone were studied in more detail by infrared microspectroscopic imaging with lateral resolution near 5 μm. The results were compared with consecutive sections stained by immunoglobulin D antibodies. T and B lymphocytes were extracted from human blood and served as independent test samples.ResultsCluster analysis of infrared datasets produced images that distinguished anatomical features such as primary and secondary follicles, T zones, arteries, and spleen red pulp. The assignments could be confirmed in consecutive sections by immunohistochemical staining. Main spectral variances between T and B lymphocytes in high‐resolution measurements were attributed to specific spectral contributions of DNA and cytosol.ConclusionsSensitivity and specificity of the infrared based methods are comparable to those of standard staining procedures for identification of B and T cells. However, infrared spectroscopic imaging can offer advantages in velocity, data throughput, and standardization because of minimal sample preparation. The results emphasize the potential of infrared spectroscopy as an innovative tool for the distinction of cell types, in particular in immunologic tissue. © 2005 Wiley‐Liss, Inc.
Synthesis of the Salicylihalamide Core Structure from Epichlorohydrin– Laying the Foundation to Macrolactone Collections
Authors: Herb Christian , Dettner Frank , Maier Martin E. 
Published: February 2005

AbstractStarting from (R)‐epichlorohydrin, two successive carbon–carbon bond formations, one with acetylide and the other with cyanide, led to the 3‐hydroxynitrile 20. This compound was further elaborated to the enynol 29 via an Evans aldol reaction of the derived aldehyde 22 with the pentenoyloxazolidinone 23 and conversion of the carboxyl to a methyl group after the aldol reaction. Mitsunobu esterification of the enynol 29 with the benzoic acid 5 gave rise to the ester 30 with two double bonds and one triple bond. After protection of the terminal triple bond with a TIPS group, the ring closing metathesis proceeded in good yield. The macrolactone E‐33 was converted into the vinyl iodide 34 and the pyridin containing salicylihalamide analog 36. The described sequence, the two‐sided elongation of epichlorohydrin appears as a general route to secondary alcohols that can be further elaborated to functionalized macrolactones. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005)
Clear cell hidradenoma of the skin—a third tumor type with a t(11;19)‐associated TORC1–MAML2 gene fusion
Authors: Behboudi Afrouz , Winnes Marta , Gorunova Ludmila , van den Oord Joost J. , Mertens Fredrik , Enlund Fredrik , Stenman Göran 
Published: February 2005

AbstractRecent studies have shown that the t(11;19)(q21;p13) translocation in mucoepidermoid carcinomas and benign Warthin's tumors results in a fusion of the N‐terminal CREB‐binding domain of the cAMP coactivator TORC1 (a.k.a. MECT1 and WAMTP1) to the Notch coactivator MAML2. Here we show that a third tumor type, clear cell hidradenoma of the skin, also expresses this gene fusion. RT‐PCR analysis of a clear cell hidradenoma with a t(11;19)(q21;p13) translocation revealed expression of a TORC1–MAML2 fusion transcript consisting of exon 1 of TORC1 fused to exons 2–5 of MAML2. Because the fusion was only detected in a single case, the frequency of this aberration in clear cell hidradenomas remains unknown. These results demonstrate that the t(11;19) in mucoepidermoid carcinoma, Warthin's tumor, and clear cell hidradenoma targets the same genes and results in identical gene fusions, indicating that at least subgroups of these glandular tumors evolve through activation of the same molecular pathways. © 2005 Wiley‐Liss, Inc.
The analysis of incomplete cost data due to dropout
Authors: Oostenbrink Jan B. , Al Maiwenn J. 
Published: February 2005

AbstractIncomplete data due to premature withdrawal (dropout) constitute a serious problem in prospective economic evaluations that has received only little attention to date. The aim of this simulation study was to investigate how standard methods for dealing with incomplete data perform when applied to cost data with various distributions and various types of dropout. Selected methods included the product‐limit estimator of Linet al. the expectation maximisation (EM‐) algorithm, several types of multiple imputation (MI) and various simple methods like complete case analysis and mean imputation. Almost all methods were unbiased in the case of dropout completely at random (DCAR), but only the product‐limit estimator, the EM‐algorithm and the MI approaches provided adequate estimates of the standard error (SE). The best estimates of the mean and SE for dropout at random (DAR) were provided by the bootstrap EM‐algorithm, MI regression and MI Monte Carlo Markov chain. These methods were able to deal with skewed cost data in combination with DAR and only became biased when costs also included the costs of expensive events. None of the methods were able to deal adequately with informative dropout. In conclusion, the EM‐algorithm with bootstrap, MI regression and MI MCMC are robust to the multivariate normal assumption and are the preferred methods for the analysis of incomplete cost data when the assumption of DCAR is not justified. Copyright © 2005 John Wiley & Sons, Ltd.
Development of the vasculature in “pushing‐type” liver metastases of an experimental colorectal cancer
Authors: Paku Sándor , Kopper László , Nagy Péter 
Published: February 2005

AbstractA mechanism for stroma formation (development of vasculature and supportive connective tissue) is suggested in an experimental “pushing‐type” colorectal carcinoma liver metastasis model. The key element is the appearance of smooth muscle actin (SMA)‐positive cells and the sinusoidal lakes at the border of the metastases. These lakes are the consequence of the disappearance (‘stepping back’ of hepatocytes from the border zone, resulting in the fusion of partially capillarized sinusoids. The growing tumor incorporates SMA‐expressing cells and sinusoidal lakes. SMA‐positive cells produce collagenous matrix, whereas the lakes become the central vessels within the connective tissue columns. Formation of these columns within the tumor is a consequence of the compression atrophy of the base of the incorporated liver tissue, leading to partial separation of the innermost part of the invagination containing functional vessel(s) from the surrounding liver. © 2005 Wiley‐Liss, Inc.
XPC polymorphisms and lung cancer risk
Authors: Lee Ga Young , Jang Jin‐Sung , Lee Sin Yeob , Jeon Hyo‐Sung , Kim Kyung Mee , Choi Jin Eun , Park Jung Min , Chae Myung Hwa , Lee Won Kee , Kam Sin , Kim In‐San , Lee Jae‐Tae , Jung Tae Hoon , Park Jae Yong 
Published: February 2005

AbstractPolymorphisms in DNA repair genes may be associated with differences in the capacity to repair DNA damage and thereby influence an individual's susceptibility to smoking‐related cancer. To test this hypothesis, we investigated the potential association of 7 XPC polymorphisms (–449G→C, –371G→A, –27G→C, Val499Arg, PAT–/+, IVS11‐5C→A and Lys939Gln) and their haplotypes with lung cancer risk in a Korean population. XPC genotypes were determined in 432 lung cancer patients and 432 healthy controls frequency‐matched for age and sex. XPC haplotypes were predicted using a Bayesian algorithm in the Phase program. The combined –27CG+CC genotype was associated with a significantly increased risk for overall lung cancer compared to the –27GG genotype (adjusted OR = 1.97, 95% CI 1.22–3.17, p = 0.005). The other 6 polymorphisms were not significantly associated with overall risk of lung cancer. When lung cancer cases were categorized by tumor histology, the –371AA genotype was associated with a significantly increased risk of squamous cell carcinoma compared to the combined –371GG and GA genotype (adjusted OR = 2.08, 95% CI 1.09–4.00, p = 0.03). The PAT–/+, IVS11‐5C→A and Lys939Gln polymorphisms were associated with a significantly decreased risk of small cell carcinoma (SM) under a dominant model for the polymorphic allele (adjusted OR = 0.49, 95% CI 0.29–0.82, p = 0.006; adjusted OR = 0.60, 95% CI 0.36–1.00, p = 0.05; and adjusted OR = 0.58, 95% CI 0.35–0.97, p = 0.04, respectively). Consistent with genotyping analyses, haplotype 4 (1112222) containing the PAT+/IVS11‐5A/939Gln alleles was associated with a significantly decreased risk of SM (adjusted OR = 0.56, 95% CI 0.37–0.85, p = 0.007 and Bonferroni‐corrected p = 0.049), whereas haplotype 5 (1122111) containing the –27C allele was associated with a significantly increased risk of SM (adjusted OR = 2.88, 95% CI 1.41–5.87, p = 0.004 and Bonferroni‐corrected p = 0.028). These results suggest that XPC polymorphisms/haplotypes may contribute to genetic susceptibility for lung cancer. © 2005 Wiley‐Liss, Inc.
Expression of cell cycle markers and human papillomavirus infection in oral squamous cell carcinoma: Use of fuzzy neural networks
Authors: Muzio Lorenzo Lo , D'Angelo Matteo , Procaccini Maurizio , Bambini Fabrizio , Calvino Francesco , Florena Ada Maria , Franco Vito , Giovannelli Lucia , Ammatuna Pietro , Campisi Giuseppina 
Published: February 2005

AbstractOur aim was to evaluate in oral squamous cell carcinoma (OSCC) the relationship between some cell cycle markers and HPV infection, conditionally to age, gender and certain habits of patients, and to assess the ability of fuzzy neural networks (FNNs) in building up an adequate predictive model based on logic inference rules. Eighteen cases of OSCC were examined by immunohistochemistry for MIB‐1, PCNA and survivin expression; presence of HPV DNA was investigated in exfoliated oral mucosa cells by nested PCR (nPCR, MY09‐MY11/GP5‐GP6), and HPV genotype was determined by direct DNA sequencing. Data were analyzed by traditional statistics (TS) and FNNs. HPV DNA was found in 9/18 OSCCs (50.0 %) without any significant higher risk of HPV infection with respect to the sociodemographic variables considered (p > 0.2), apart from tobacco smoking, reported in 44.4% of OSCC HPV‐positive vs. 100% HPV‐negative subjects (p = 0.029). Regarding cell cycle markers, TS and FNN revealed that survivin was expressed significantly more in HPV‐negative than in HPV‐positive OSCC [root mean‐square error (RMSE) = 5.89 × 10–6, % predicted 100.0]; furthermore, smoking played a protective role for survivin expression in HPV‐positive cases (OR = 0.019, 95%CI 0.001–0.723, RMSE = 0.20, % of prevision 94.4). FNN, although on a small sample size, allowed us to confirm data by TS and to hypothesize a different cell cycle pattern for HPV‐positive vs. HPV‐negative OSCC. In the latter cases, the relevance of apoptotic vs. proliferative markers suggested that they may be related to the different supposed outcome of HPV‐negative OSCC and that HPV may have a protective role in the expression level of survivin, especially in tobacco smokers. © 2005 Wiley‐Liss, Inc.
Responses of human T cells to peptides flanking the tandem repeat and overlapping the signal sequence of MUC1
Authors: Correa Isabel , Plunkett Timothy , Coleman Julia , Galani Eleni , Windmill Elisabeth , Burchell Joy M. , Taylor‐Papdimitriou Joyce 
Published: February 2005

AbstractThe epithelial mucin MUC1 is one of the few tumour‐associated antigens identified for breast cancer. Several MUC1‐derived peptides binding HLA‐A*0201 molecules have been identified that correspond to sequences outside the tandem repeat. Immunisation with some of these peptides induces protective antitumour immunity in mice. Another HLA‐A*0201‐binding peptide has been identified in a human system. We have evaluated the CD8+ T‐cell responses to all these peptides using peripheral blood lymphocytes from breast cancer patients and normal donors. Specific CD8+ T‐cell responses could be generated in vitro against some of these peptides but only after several rounds of in vitro restimulation, and they did not recognise human cells endogenously expressing the antigen. Nevertheless, T cells recognised by HLA‐A*0201 tetramers carrying a peptide from the signal sequence (LLLLTVLTV) could be detected in the peripheral blood of some HLA‐A*0201+ breast cancer patients but not in healthy adults. This peptide is the only one of those tested which was identified in the human system, and the results emphasize the potential problems involved in translation of data from laboratory animal models to the human system. © 2005 Wiley‐Liss, Inc.
Achieving strategy with scorecarding
Authors: Lawson Raef , Stratton William , Hatch Toby 
Published: February 2005

AbstractThere are four key factors to achieving strategy through implementation of a scorecarding system. The first of these is clear communication of strategy to employees. Second is tracking results and providing visual feedback, such as through scorecards with traffic lights, trend indicators, benchmarks, and scores. Third is having people with the right skills doing the things necessary to push the strategy forward. Fourth is having a strategy champion to keep the scorecard system initiative visible and to encourage communication. © 2005 Wiley Periodicals, Inc.
A personal computer based implementation of the maximum‐likelihood method of analysis of electron microscope autoradiographs
Authors: Roysam Badrinath , Maffitt David R. , Miller Michael I. , Saffitz Jeffrey E. , Thomas Lewis J. 
Published: February 2005

AbstractThe maximum‐likelihood (ML) method for the quantitative analysis of electron‐microscopic autoradiographs has been shown to be substantially superior to the conventional crossfire (CF) method. It can generate reliable and accurate tracer concentration estimates with far fewer micrographs and produce valid estimates even at counts low enough to preclude the use of the crossfire method while eliminating the need for special ad hoc treatment of narrow membranous structures as well as the secondary verification of the tracer concentration estimates.Despite these significant advantages, the large computational requirements of the ML method has to date hampered its widespread use. In this paper, we present a new line‐integration method that allows us to reduce the computational requirements of the ML method to a point where it becomes feasible to implement it on a small computer system of the type typically available to a laboratory user of EM autoradiography. We present the complete line‐integration method for the particular case of EM autoradiography with tritium, and show how it can be adapted to other isotopes.We have constructed a software package that implements the complete maximum‐likelihood method on the IBM PC class of machines using our line‐integration method. Features of this software package which are of particular importance to the research community are device independence, which makes it usable with a large variety of currently available laboratory equipment, and easy portability of the software and data between different computer systems.
A temperature‐jump device for time‐resolved cryo‐transmission electron microscopy
Authors: Chestnut M. H. , Siegel D. P. , Burns J. L. , Talmon Y. 
Published: February 2005

AbstractWe describe a temperature‐jump device that permits time‐resolved studies of thin cryo‐transmission electron microscopy specimens. The specimen is rapidly heated to induce a change in microstructure just prior to cryo‐fixation. The apparatus consists of a xenon arc lamp equipped with a shutter controlled by timing circuitry, used in conjunction with an environmental specimen preparation chamber. The specimen is heated by exposure to focused light from the lamp, and then plunged into cryogen. Using a thermocouple constructed from an electron microscope grid, we show that temperature jumps of 30–60 K are achieved with exposure times of 150–450 milliseconds. Micrographs of dimyristoyl phosphatidylcholine (DMPC) vesicles and n‐docosane films, subjected to these exposures, shew that the specimens are still at least 20–30 K above their initial temperature when they contact the cryogen. This method could be applied to a variety of biological and chemical systems which undergo structural changes activated by a rise in temperature.
Utilization of electron microscopic techniques in the in vitro study of adenohypophysial function and regulation
Authors: Asa Sylvia L. , Kovacs Kalman 
Published: February 2005

AbstractMorphologic studies of human adenohypophysial cells using immunocytochemistry and electron microscopy have characterized the hormone‐producing cell types of the normal gland and pituitary adenomas. The classifications which have emerged allow more accurate clinicopathologic correlations than ever before, but have also raised new questions concerning cytogenesis, pathogenesis, and structure‐function correlations. We report the results of studies which marry the conventional morphologic techniques of light microscopy, immunohistochemistry, electron microscopy, and ultrastructural immunocytology with functional analyses using tissue culture and radioimmunoassay of hormones released into culture media. The hormone secretory activity of nontumorous and adenomatous pituitary cells is correlated with their structural features; their secretory responses to several adenohypophysiotropic factors are compared with morphologic alterations which are characterized at the light and electron microscopic levels by morphometric analysis. These studies have shown that hypothalamic stimulating hormones increase hormone release by their target cells and alter the ultrastructural appearance of the affected cells by increasing organelles involved in hormone synthesis. Inhibitory drugs and adrenal and gonadal steroids are capable of suppressing hormone release by some tumors and also give rise to morphologic changes which correlate with the functional inhibition. Hormone release by clinically nonfunctioning adenomas has been characterized and the behavior of these tumor cells in vitro sheds some light on the reasons for lack of clinical symptomatology. The plurihormonal nature of several nontumorous and adenomatous pituitary cell types has been characterized in vitro. The results of these studies provide the basis for more accurate structure‐function correlations which can be used to study the hormonal milieu in vivo, to predict the role of pathogenetic factors in pituitary tumorigenesis, and to assess the therapeutic value of stimulating or inhibiting hormones and drugs.
Cytoskeletal elements in mammalian spermiogenesis and spermatozoa
Authors: Camatini Marina , Colombo Anita , Bonfanti Patrizia 
Published: February 2005

AbstractIdentification of the cytoskeletal elements and their role in the formation as well as the maintenance of head membrane compartmentalization is a much debated issue in mammalian spermatozoa. Data which have emerged during the last ten years are summarized. Those which have converged in a common opinion, such as the distribution of actin in mammalian spermiogenesis, are distinguished from those which have to be confirmed, such as the role of actin related proteins and actin in mature spermatozoa.
Recent studies of surface dynamic processes by reflection electron microscopy
Authors: Yagi Katsumichi , Yamanaka Akira , Homma Itsuro 
Published: February 2005

AbstractReflection electron microscope studies of surface dynamic processes are reviewed and illustrated with recent new observations. They include: surface electromigration and current dependent structures of Si surfaces; surface etching by oxidation of Si surface; and growth of two dimensional alloyed adsorbate by co‐deposition of metals on Si surface. The observations revealed details of the surface dynamic processes, which are difficult to obtain with other surface analysis techniques.