bluuebunny/crossref_metadata_2025_split huggingface dataset:
Time trends in the incidence of myocardial infarction among professional drivers in Stockholm 1977–96
Authors: Bigert C , Klerdal K , Hammar N , Hallqvist J , Gustavsson P 
Published: November 2004

Aims:To investigate time trends in the incidence of first myocardial infarction (MI) among bus, taxi, and lorry drivers in Stockholm.Methods:In this population based case-control study, all first events of acute MI among men aged 40–69 in Stockholm County 1977–96 were identified using registers of hospital discharges and deaths. Controls were selected randomly from the general population. National censuses were used for information on occupational titles. A total of 20 364 cases and 136 342 controls were included in the study. Among these, 1183 cases and 6072 controls had worked as drivers.Results:During 1977–84 the MI incidence was higher in all three driver groups than among other manual workers. There was a decline in MI incidence among drivers as well as in the general population during the study period. The decline was greater among drivers than among other manual workers. During 1985–96 the relative risk remained increased compared to other manual workers among taxi and lorry drivers, but not among bus drivers.Conclusions:Despite a reduced MI incidence for professional drivers in recent years, preventive measures to reduce the risk of MI in these occupational groups, and in particular among taxi and lorry drivers, continue to be of importance.
Customizing adaptive software to object-oriented software using grammars
Authors: Lieberherr Karl J. , Xiao Cun 
Published: November 2004

Although numerous researchers have pointed out that object-oriented software is easier to extend than software that is not written in an object-oriented style, object-oriented software is still rigid to adapt and maintain. This paper builds on an extension of object-oriented programming which is called adaptive programming. Adaptive programming allows the programmer to write more extensible software called adaptive software without committing to a specific input language. After writing an adaptive program, the programmer selects a specific input language and partially evaluates the program into an executable program. This paper formally studies class dictionaries and informally describes how adaptive programs are partially evaluated by freezing class dictionaries. A class dictionary is mapped into classes of an object-oriented programming language, for example, C++, CLOS etc. A class dictionary defines both a set of objects and a set of sentences (a language). We derive a set of restrictions on class dictionaries which permit a simple printing algorithm and its inverse, a parsing algorithm, to be bijection functions between objects and sentences of the same class. We review propagation patterns for describing adaptive object-oriented software at a higher level of abstraction than the one used by today’s object-oriented programming languages. A propagation pattern is an adaptive program which defines a family of programs. From the family, we can select a member by choosing a class dictionary. The theory presented in this paper has been successfully implemented and used in the Demeter Tools/C++. The system consists of a set of tools that facilitate software evolution.
A KOREAN LARGE VOCABULARY SPEECH RECOGNITION SYSTEM FOR AUTOMATIC TELEPHONE NUMBER QUERY SERVICE
Authors: KOO J.M. , KIM H.S. , UN C.K. 
Published: November 2004

In this paper, we introduce a Korean large vocabulary speech recognition system. This system recognizes sentence utterances with a vocabulary size of 1160 words, and is designed for an automatic telephone number query service. The system consists of four subsystems. The first is an acoustic processor recognizing words in an input sentence by a Hidden Markov Model (HMM) based speech recognition algorithm. The second subsystem is a linguistic processor which estimates input sentences from the results of the acoustic processor and determines the following words using syntactic information. The third is a time reduction processor reducing recognition time by limiting the number of candidate words to be computed by the acoustic processor. The time reduction processor uses linguistic information and acoustic information contained in the input sentence. The last subsystem is a speaker adaptation processor which quickly adapts parameters of the speech recognition system to new speakers. This subsystem uses VQ adaptation and HMM parameter adaptation based on spectral mapping. We also present our recent work on improving the performance of the large vocabulary speech recognition system. These works focused on the enhancement of the acoustic processor and the time reduction processor for speaker-independent speech recognition. A new approach for speaker adaptation is also described.
APPLYING CONVENTIONAL UNIT TESTING TECHNIQUES TO ABSTRACT DATA TYPE OPERATIONS
Authors: PARRISH ALLEN , CORDES DAVID 
Published: November 2004

Abstract data types (ADTs) represent the fundamental building blocks of object-oriented software development. There have been a variety of techniques in the literature for testing ADT modules. Virtually all of the proposed techniques have involved testing sequences of ADT operations (e.g., for a stack ADT, test the sequence PUSH; PUSH; POP) to discover defects in their interactions. However, the operations inside an ADT module are really nothing more than conventional procedures and functions. Consequently, it is conceivable that conventional subprogram unit testing techniques can be adapted to test ADT operations. To support such testing techniques, test cases are best designed and expressed in terms of data values. When test cases are integers, for example, expressing a test case is trivial (e.g., ‘253’). However, when test cases are data abstractions (such as stacks), this problem is much more difficult due to the variety of different formats in which a single data abstraction can be legitimately viewed. In this paper, we provide a conceptual framework for applying classical white-box and black-box unit testing techniques to ADT operations. We then use this framework to develop a collection of guidelines for determining the best format for test case design, given different module characteristics and testing techniques.
Remarks on Braid Theory and the characterisation of periodic orbits
Authors: Natiello Mario A. , Solari Hernán G. 
Published: November 2004

The relationship between Braid Theory and the organisation of periodic orbits of dynamical systems is considered. It is shown that for some (physically relevant) 3-d flows the characterisation of periodic orbits by means of Braid Theory can be done on the Poincaré surface in an efficient way. The result is a thread-less graphical presentation of a braid class. We discuss extensions of this approach to (adequate) dynamical systems of dimension higher than three, using results from Central Manifold Theory.
Galileo and the Mountains of the Moon: Analogical Reasoning, Models and Metaphors in Scientific Discovery
Authors: Spranzi Marta 
Published: November 2004

AbstractThis paper is about the use of analogical reasoning, models and metaphors in Galileo's discovery of the mountains of the moon, which he describes in the Starry Messenger, a short but groundbreaking treatise published in 1610. On the basis of the observations of the Moon he has made with the newly invented telescope, Galileo shows that the Moon has mountains and that therefore it shares the same solid, opaque and rugged nature of the Earth. I will first reconstruct Galileo's reasoning, and illustrate the counterintuitive and quasi-circular way in which discovery depends on analogy: in order for analogical reasoning to succeed in bridging ontological gaps and thus serve as a discovery tool, a certain similarity between what are considered as radically different domains has to be presupposed. More particularly, in order for analogical reasoning to lead to genuine discoveries, salient features have to be selected in the source domain that will be mapped onto the target domain. There is disagreement as to how this mapping is successfully carried out: the syntactical (Dedre Gentner), pragmatic (Paul Thagard) and ontological-categorical (Rom Harré) approaches, all illuminate some features of this selection in the mapping process. On the basis of an analysis of Galileo's discovery, I will argue that we need a different "bootstrapping" approach which involves the construction of an imaginary temporary model encompassing both the source and the target domains, and which is occasionally strengthened by metaphors which serve as incomplete transitional models.
What Has History to Do with Cognition? Interactive Methods for Studying Research Laboratories
Authors: Kurz-Milcke Elke , Nersessian Nancy , Newstetter Wendy 
Published: November 2004

Abstract
We have been studying cognition and learning in research laboratories in the field of biomedical engineering (Nersessian, Kurz-Milcke, Newstetter & Davies 2003; Newstetter, Kurz-Milcke & Nersessian, in press[a]). Through our combining of ethnography and cognitive-historical analysis in studying these settings we have been led to understand these labs as comprising evolving distributed cognitive systems and as furnishing agentive learning environments. For this paper we develop the theme of 'models-in-action,' a variant of what Knorr Cetina (1999) has called 'knowledge-in-action.' Among the epistemically most salient objects in these labs are so called "model systems," which are designs that blend engineering with the study and use of biological systems for purposes of simulative model-based reasoning. We portray the prevalent design-orientation in this engineering specialty and how the prevailing activity of cell-culturing in these labs transitions into a design activity for the bio-medical engineers, leading them to work with 'wet' devices. We discuss how devices, 'wet' and 'dry,' situate model-based understandings and how they participate in model systems in these labs. Models tend to come in clusters or configurations, and the model systems in these labs are epistemically salient junctures of interlocking models. Model systems in these labs evolve thereby consolidating what we want to call a 'fabric of interlocking models,' which functions as point of stability and departure in these labs. We convey a taste of such a 'fabric' for a tissue-engineering lab. We conjecture that through this 'fabric' extended developments in technology and methodology have a 'situated' presence in the workings of these labs.
Putative chemical signals of leopard
Authors: Poddar-Sarkar Mousumi , Brahmachary  
Published: November 2004

Abstract
A study of marking fluid (MF) of Indian male leopard has been undertaken as a continuation of the earlier work on tiger and cheetah pheromones. The behavioural observations reveal that MF is presumably the primary means of communication in leopard. The chemical analyses reveal the presence of acetic, propionic, isobutyric, butyric, isovarleric, valeric, isohexanoic, hexanoic, isoheptanoic, heptanoic, isooctanoic, octanoic and nonanoic acid in the acidic fraction of steam distillate of MF. Amines like etylenediamine, putrescine, cadaverine and phenylethylamine, dimethylamine and trimethylamine were also detected in the basic fraction of MF. The amount of lipid extracted from MF is 1.15 mg/ml.
Rituximab plus infusional cyclophosphamide, doxorubicin, and etoposide in HIV-associated non-Hodgkin lymphoma: pooled results from 3 phase 2 trials
Authors: Spina Michele , Jaeger Ulrich , Sparano Joseph A. , Talamini Renato , Simonelli Cecilia , Michieli Mariagrazia , Rossi Giuseppe , Nigra Ezio , Berretta Massimiliano , Cattaneo Chiara , Rieger Armin C. , Vaccher Emanuela , Tirelli Umberto 
Published: November 2004

Abstract
Evidence suggests that infusional therapy is a more effective means for administering cytotoxic therapy than intravenous bolus therapy for lymphoma and offers greater potential for therapeutic synergy with rituximab, which has a long half-life. We pooled the results of 3 prospective phase 2 trials evaluating rituximab in combination with 96-hour infusion of cyclophosphamide (187.5-200 mg/m2 per day), doxorubicin (12.5 mg/m2 per day), and etoposide (60 mg/m2 per day) (R-CDE) plus granulocyte–colony-stimulating factor (G-CSF) in 74 patients with HIV-associated, B-cell non-Hodgkin lymphoma, of whom 56 (76%) patients received concurrent highly active antiretroviral therapy (HAART). The complete remission (CR) rate was 70% (95% confidence interval [CI], 59%-81%), and the estimated 2-year failure-free survival and overall survival rates were 59% (95% CI, 47%-71%) and 64% (95% CI, 52%-76%), respectively. Ten (14%) patients had opportunistic infections during or within 3 months of the end of R-CDE, and 17 (23%) patients developed nonopportunistic infections after that time. Six (8%) patients died because of infection; 2 (3%) of those infections were bacterial sepsis during R-CDE, and 4 (5%) were opportunistic infections that occurred between 2 and 8 months after the completion of R-CDE. R-CDE produced a 70% CR rate and a 59% 2-year failure-free survival rate in patients with HIV-associated lymphoma. Consistent with other reports, adding rituximab to cytotoxic therapy in this population may increase the risk for life-threatening infection. Further studies evaluating rituximab in combination with infusional chemotherapy are warranted, but caution is advised.
Calibration and assessment of channel-specific biases in microarray data with extended dynamical range
Authors: Bengtsson Henrik , Jönsson Göran , Vallon-Christersson Johan 
Published: November 2004

Abstract
Background
Non-linearities in observed log-ratios of gene expressions, also known as intensity dependent log-ratios, can often be accounted for by global biases in the two channels being compared. Any step in a microarray process may introduce such offsets and in this article we study the biases introduced by the microarray scanner and the image analysis software.

Results
By scanning the same spotted oligonucleotide microarray at different photomultiplier tube (PMT) gains, we have identified a channel-specific bias present in two-channel microarray data. For the scanners analyzed it was in the range of 15–25 (out of 65,535). The observed bias was very stable between subsequent scans of the same array although the PMT gain was greatly adjusted. This indicates that the bias does not originate from a step preceding the scanner detector parts. The bias varies slightly between arrays. When comparing estimates based on data from the same array, but from different scanners, we have found that different scanners introduce different amounts of bias. So do various image analysis methods. We propose a scanning protocol and a constrained affine model that allows us to identify and estimate the bias in each channel. Backward transformation removes the bias and brings the channels to the same scale. The result is that systematic effects such as intensity dependent log-ratios are removed, but also that signal densities become much more similar. The average scan, which has a larger dynamical range and greater signal-to-noise ratio than individual scans, can then be obtained.

Conclusions
The study shows that microarray scanners may introduce a significant bias in each channel. Such biases have to be calibrated for, otherwise systematic effects such as intensity dependent log-ratios will be observed. The proposed scanning protocol and calibration method is simple to use and is useful for evaluating scanner biases or for obtaining calibrated measurements with extended dynamical range and better precision. The cross-platform R package aroma, which implements all described methods, is available for free from http://www.maths.lth.se/bioinformatics/.
Density-dependence and within-host competition in a semelparous parasite of leaf-cutting ants
Authors: Hughes William OH , Petersen Klaus S , Ugelvig Line V , Pedersen Dorthe , Thomsen Lene , Poulsen Michael , Boomsma Jacobus J 
Published: November 2004

Abstract
Background
Parasite heterogeneity and within-host competition are thought to be important factors influencing the dynamics of host-parasite relationships. Yet, while there have been many theoretical investigations of how these factors may act, empirical data is more limited. We investigated the effects of parasite density and heterogeneity on parasite virulence and fitness using four strains of the entomopathogenic fungus, Metarhizium anisopliae var. anisopliae, and its leaf-cutting ant host Acromyrmex echinatior as the model system.

Results
The relationship between parasite density and infection was sigmoidal, with there being an invasion threshold for an infection to occur (an Allee effect). Although spore production was positively density-dependent, parasite fitness decreased with increasing parasite density, indicating within-host scramble competition. The dynamics differed little between the four strains tested. In mixed infections of three strains the infection-growth dynamics were unaffected by parasite heterogeneity.

Conclusions
The strength of within-host competition makes dispersal the best strategy for the parasite. Parasite heterogeneity may not have effected virulence or the infection dynamics either because the most virulent strain outcompeted the others, or because the interaction involved scramble competition that was impervious to parasite heterogeneity. The dynamics observed may be common for virulent parasites, such as Metarhizium, that produce aggregated transmission stages. Such parasites make useful models for investigating infection dynamics and the impact of parasite competition.
Identification of a panel of tumor-associated antigens from breast carcinoma cell lines, solid tumors and testis cDNA libraries displayed on lambda phage
Authors: Pavoni Emiliano , Vaccaro Paola , Pucci Andrea , Monteriù Giorgia , Beghetto Elisa , Barca Stefano , Dupuis Maria Luisa , De Pasquale Ceratti Adolfo , Lugini Antonio , Cianfriglia Maurizio , Cortesi Enrico , Felici Franco , Minenkova Olga 
Published: November 2004

Abstract
Background
Tumor-associated antigens recognized by humoral effectors of the immune system are a very attractive target for human cancer diagnostics and therapy. Recent advances in molecular techniques have led to molecular definition of immunogenic tumor proteins based on their reactivity with autologous patient sera (SEREX).

Methods
Several high complexity phage-displayed cDNA libraries from breast carcinomas, human testis and breast carcinoma cell lines MCF-7, MDA-MB-468 were constructed. The cDNAs were expressed in the libraries as fusion to bacteriophage lambda protein D. Lambda-displayed libraries were efficiently screened with sera from patients with breast cancer.

Results
A panel of 21 clones representing 18 different antigens, including eight proteins of unknown function, was identified. Three of these antigens (T7-1, T11-3 and T11-9) were found to be overexpressed in tumors as compared to normal breast. A serological analysis of the 21 different antigens revealed a strong cancer-related profile for at least five clones (T6-2, T6-7, T7-1, T9-21 and T9-27).

Conclusions
Preliminary results indicate that patient serum reactivity against five of the antigens is associated with tumor disease. The novel T7-1 antigen, which is overexpressed in breast tumors and recognized specifically by breast cancer patient sera, is potentially useful in cancer diagnosis.
Neuroblastoma and pre-B lymphoma cells share expression of key transcription factors but display tissue restricted target gene expression
Authors: Lagergren Anna , Manetopoulos Christina , Axelson Håkan , Sigvardsson Mikael 
Published: November 2004

Abstract
Background
Transcription factors are frequently involved in the process of cellular transformation, and many malignancies are characterized by a distinct genetic event affecting a specific transcription factor. This probably reflects a tissue specific ability of transcription factors to contribute to the generation of cancer but very little is known about the precise mechanisms that governs these restricted effects.

Methods
To investigate this selectivity in target gene activation we compared the overall gene expression patterns by micro-array analysis and expression of target genes for the transcription factor EBF in lymphoma and neuroblastoma cells by RT-PCR. The presence of transcription factors in the different model cell lines was further investigated by EMSA analysis.

Results
In pre-B cells mb-1 and CD19 are regulate by EBF-1 in collaboration with Pax-5 and E-proteins. We here show that neuroblastoma cells express these three, for B cell development crucial transcription factors, but nevertheless fail to express detectable levels of their known target genes. Expression of mb-1 could, however, be induced in neuroblastoma cells after disruption of the chromatin structure by treatment with 5-azacytidine and Trichostatin A.

Conclusion
These data suggest that transcription factors are able to selectively activate target genes in different tissues and that chromatin structure plays a key role in the regulation of this activity.
Direct visualization of electroporation-assisted in vivo gene delivery to tumors using intravital microscopy – spatial and time dependent distribution
Authors: Cemazar Maja , Wilson Ian , Dachs Gabi U , Tozer Gillian M , Sersa Gregor 
Published: November 2004

Abstract
Background
Electroporation is currently receiving much attention as a way to increase drug and DNA delivery. Recent studies demonstrated the feasibility of electrogene therapy using a range of therapeutic genes for the treatment of experimental tumors. However, the transfection efficiency of electroporation-assisted DNA delivery is still low compared to viral methods and there is a clear need to optimize this approach. In order to optimize treatment, knowledge about spatial and time dependency of gene expression following delivery is of utmost importance in order to improve gene delivery. Intravital microscopy of tumors growing in dorsal skin fold window chambers is a useful method for monitoring gene transfection, since it allows non-invasive dynamic monitoring of gene expression in tumors in a live animal.

Methods
Intravital microscopy was used to monitor real time spatial distribution of the green fluorescent protein (GFP) and time dependence of transfection efficiency in syngeneic P22 rat tumor model. DNA alone, liposome-DNA complexes and electroporation-assisted DNA delivery using two different sets of electric pulse parameters were compared.

Results
Electroporation-assisted DNA delivery using 8 pulses, 600 V/cm, 5 ms, 1 Hz was superior to other methods and resulted in 22% increase in fluorescence intensity in the tumors up to 6 days post-transfection, compared to the non-transfected area in granulation tissue. Functional GFP was detected within 5 h after transfection. Cells expressing GFP were detected throughout the tumor, but not in the surrounding tissue that was not exposed to electric pulses.

Conclusions
Intravital microscopy was demonstrated to be a suitable method for monitoring time and spatial distribution of gene expression in experimental tumors and provided evidence that electroporation-assisted gene delivery using 8 pulses, 600 V/cm, 5 ms, 1 Hz is an effective method, resulting in early onset and homogenous distribution of gene expression in the syngeneic P22 rat tumor model.