bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel photocurable multifunctional acrylate monomers containing perfluorinated aromatic units and their copolymers for photonic applications
Authors: Song Bok Ju , Park Jin Kyu , Kim Hwan Kyu 
Published: November 2004

AbstractWe designed and synthesized novel UV‐curable multifunctional acrylate monomers with perfluorinated aromatic units and their copolymers. The UV‐curable multifunctional acrylate monomers with perfluorinated aromatic units were synthesized as follows. Perfluorinated aromatic methylmethane derivatives were prepared through the reaction of pentaerythritol with hexafluorobenzene and decafluorobiphenyl in the presence of sodium hydride. They were sequentially substituted with 2,2,3,3,4,4,5,5‐octafluoro‐6‐(tetrahydropyran‐2‐yloxy)‐hexan‐1‐ol, and this yielded hydroxy‐functional compounds after tetrahydropyran deprotection. Finally, the reaction of the resultant hydroxy compounds with acryloyl chloride generated the perfluorinated multifunctional acrylate monomers in high yields of greater than 85%. The novel photocrosslinked and perfluorinated copolyacrylates, obtained after the UV and thermal curing of these monomers, satisfied the material requirements for photonic devices. Most of these copolymers were thermally stable over 370 °C, and their glass‐transition temperatures were not detected because of their highly crosslinked nature. The refractive indices of the copolymers ranged from 1.410 to 1.441. The refractive indices of the photocrosslinked and perfluorinated copolyacrylates were easily tuned by the variation of the copolymer composition. Some of these copolymers exhibited a birefringence of less than 0.0003. This was much lower than the birefringence of fluorinated polyacrylate‐based materials. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 6375–6383, 2004
The diet of sperm whales (Physeter macrocephalus) in southern Australian waters
Authors: Evans Karen , Hindell Mark A. 
Published: November 2004

AbstractStomach contents were collected from 36 sperm whales (Physeter macrocephalus) involved in two mass stranding events during February 1998 along the west coastline of Tasmania, Australia. Contents were dominated by oceanic cephalopods, with a total of 101 883 cephalopod beaks representing 48 species from 14 families of Teuthids, two species from two families of Octopods, and a single Vampyromorph species identified. Species diversity was higher in these animals than other sperm whales studied in the southern hemisphere, with samples containing an average of (±s.d.) 28.4 ± 11.1 species per sample. Diet samples were dominated by subtropical and muscular cephalopod species. Members of the family Histioteuthidae were the most important numerically, and were also important in terms of estimated reconstituted mass, although members of the Onychoteuthidae were the most dominant species in samples in terms of estimated reconstituted mass. Other families numerically important to species composition included the cranchiid, lepidoteuthid, onychoteuthid, and pholidoteuthid families, while the architeuthid, pholidoteuthid, and ommastrephid families were also important in terms of reconstituted mass. Cephalopod species composition varied with stranding site and with sex, but not with age. However, differences did not represent systemic variation with groups marked by high individual variability. Lower rostral lengths of all cephalopod species ranged from 1.3 to 40.7 mm. Calculated dorsal mantle lengths from all species ranged from 10.7 to 2640.7 mm (mean ± s.d. = 233.7 ± 215.7 mm) and estimated wet weights of cephalopod prey ranged from 2.7 to 110 233.1 g (mean ± s.d. = 828.3 ± 3073.6 g). While there were differences in the size of some cephalopod species between stranding sites and with age, this was marked by high individual variability. Differences in diet composition and prey size between sperm whales reflect individual variability in foraging success and perhaps also foraging groups related to the social structure of this species.
Symptoms and referral of women with epithelial ovarian tumors
Authors: Paulsen T. , Kærn J. , Kjærheim K. , Tropé C. , Tretli S. 
Published: November 2004

AbstractObjective: To study referral to hospital units and the clinical characteristics of women with epithelial ovarian tumors in a prospective, population‐based study. Methods: Clinical information on all women diagnosed with epithelial invasive (n=486) and borderline ovarian tumors (n=137) in Norway during 2002 was derived from notifications to the Cancer Registry of Norway and medical, surgical and histopathological records. Results: Sixty‐one percent of women with invasive ovarian tumors were initially referred to gynecology units. The 38% of women referred to surgical and medical units were more likely to have symptoms as ‘bowel irregularity’, ‘pain outside the abdominal cavity’, ‘persisting fatigue’ and ‘respiratory difficulties’. These women were older, had lower performance status and had a delay in treatment of 20 and 24 days respectively compared to 11 at gynecology units. Conclusion: Greater awareness of the symptoms of ovarian cancer might lead to earlier diagnosis and treatment and thus possibly improve survival.
ESTminer: a suite of programs for gene and allele identification
Authors: Nelson Rex T. , Grant David , Shoemaker Randy C. 
Published: November 2004

AbstractSummary: ESTminer is a collection of programs that use expressed sequence tag (EST) data from inbred genomes to identify unique genes within gene families. The algorithm utilizes Cap3 to perform an initial clustering of related EST sequences to produce a consensus sequence of a gene family. These consensus sequences are then used to collect all ESTs in the original EST library that are related using BLAST. A redundancy based criterion is applied to each EST to identify reliable unique gene-sequences. Using a highly inbred genome as a source of ESTs eliminates the necessity of computing covariance on each polymorphism to identify alleles of the same gene, thus making this algorithm more streamlined than other alternatives which must computationally attempt to distinguish genes from alleles.Availability: The programs were written in PERL and are freely available at http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.htmlContact: nelsonrt@iastate.eduSupplementary information: Figures and dataset can be obtained from: http://www.soybase.org/publication_data/Nelson/ESTminer/ESTminer.html
In silicogene function prediction using ontology-based pattern identification
Authors: Zhou Yingyao , Young Jason A. , Santrosyan Andrey , Chen Kaisheng , Yan S. Frank , Winzeler Elizabeth A. 
Published: November 2004

AbstractMotivation: With the emergence of genome-wide expression profiling data sets, the guilt by association (GBA) principle has been a cornerstone for deriving gene functional interpretations in silico. Given the limited success of traditional methods for producing clusters of genes with great amounts of functional similarity, new data-mining algorithms are required to fully exploit the potential of high-throughput genomic approaches.Results: Ontology-based pattern identification (OPI) is a novel data-mining algorithm that systematically identifies expression patterns that best represent existing knowledge of gene function. Instead of relying on a universal threshold of expression similarity to define functionally related groups of genes, OPI finds the optimal analysis settings that yield gene expression patterns and gene lists that best predict gene function using the principle of GBA. We applied OPI to a publicly available gene expression data set on the life cycle of the malarial parasite Plasmodium falciparum and systematically annotated genes for 320 functional categories based on current Gene Ontology annotations. An ontology-based hierarchical tree of the 320 categories provided a systems-wide biological view of this important malarial parasite.Availability: A web accessible P. falciparum e-annotation database containing the results of this study can be accessed online at http://carrier.gnf.org/publications/OPIContact: zhou@gnf.org
CGH-Explorer: a program for analysis of array-CGH data
Authors: Lingjærde Ole Christian , Baumbusch Lars O. , Liestøl Knut , Glad Ingrid K. , Børresen-Dale Anne-Lise 
Published: November 2004

Abstract
Summary: CGH-Explorer is a program for visualization and statistical analysis of microarray-based comparative genomic hybridization (array-CGH) data. The program has preprocessing facilities, tools for graphical exploration of individual arrays or groups of arrays, and tools for statistical identification of regions of amplification and deletion.
Availability: The program is available as Java class files that runs on any platform with the Java 2 runtime environment (J2SE JRE) installed, and as a Windows executable. Java source files are also available. See http://www.ifi.uio.no/bioinf/Papers/CGH/
Contact: ole@ifi.uio.no
The MIPS mammalian protein–protein interaction database
Authors: Pagel Philipp , Kovac Stefan , Oesterheld Matthias , Brauner Barbara , Dunger-Kaltenbach Irmtraud , Frishman Goar , Montrone Corinna , Mark Pekka , Stümpflen Volker , Mewes Hans-Werner , Ruepp Andreas , Frishman Dmitrij 
Published: November 2004

Abstract
Summary: The MIPS mammalian protein–protein interaction database (MPPI) is a new resource of high-quality experimental protein interaction data in mammals. The content is based on published experimental evidence that has been processed by human expert curators. We provide the full dataset for download and a flexible and powerful web interface for users with various requirements.
Availability: The MPPI database is located at http://mips.gsf.de/proj/ppi/
Contact: d.frishman@wzw.tum.de
Accurate identification of alternatively spliced exons using support vector machine
Authors: Dror Gideon , Sorek Rotem , Shamir Ron 
Published: November 2004

Abstract
Motivation: Alternative splicing is a major component of the regulatory action on mammalian transcriptomes. It is estimated that over half of all human genes have more than one splice variant. Previous studies have shown that alternatively spliced exons possess several features that distinguish them from constitutively spliced ones. Recently, we have demonstrated that such features can be used to distinguish alternative from constitutive exons. In the current study, we used advanced machine learning methods to generate robust classifier of alternative exons.
Results: We extracted several hundred local sequence features of constitutive as well as alternative exons. Using feature selection methods we find seven attributes that are dominant for the task of classification. Several less informative features help to slightly increase the performance of the classifier. The classifier achieves a true positive rate of 50% for a false positive rate of 0.5%. This result enables one to reliably identify alternatively spliced exons in exon databases that are believed to be dominated by constitutive exons.
Availability: Upon request from the authors.
Contact: gideon@mta.ac.il
AUG codons at the beginning of protein coding sequences are frequent in eukaryotic mRNAs with a suboptimal start codon context
Authors: Kochetov Alex V. 
Published: November 2004

Abstract
Motivation: The translation start site plays an important role in the control of translation efficiency of eukaryotic mRNAs. However, mRNAs with a suboptimal context of start AUG codon are relatively abundant. It is likely that at least some mRNAs with suboptimal start codon context contain the other signals providing additional information for efficient AUG recognition.
Results: Frequency of AUG codons at the beginning of the coding part of eukaryotic mRNAs was analyzed in relation to the context of translation start codon. It was found that the observed downstream AUG content in the mRNAs with optimal start codon context was close to the expected value, whereas it was significantly higher in the mRNAs with a suboptimal context. It is likely that downstream AUG codons can often be utilized as additional start sites to increase translation rate of mRNAs with a suboptimal context of the annotated start codon and many eukaryotic proteins can be characterized by some N-end heterogeneity.
Contact: ak@bionet.nsc.ru
ISYMOD: a knowledge warehouse for the identification, assembly and analysis of bacterial integrated systems
Authors: Chabalier Julie , Capponi Cécile , Quentin Yves , Fichant Gwennaele 
Published: November 2004

AbstractMotivation: Complex biological functions emerge from interactions between proteins in stable supra-molecular assemblies and/or through transitory contacts. Most of the time protein partners of the assemblies are composed of one or several domains which exhibit different biochemical functions. Thus the study of cellular process requires the identification of different functional units and their integration in an interaction network; such complexes are referred to as integrated systems. In order to exploit with optimum efficiency the increased release of data, automated bioinformatics strategies are needed to identify, reconstruct and model such systems. For that purpose, we have developed a knowledge warehouse dedicated to the representation and acquisition of bacterial integrated systems involved in the exchange of the bacterial cell with its environment.Results: ISYMOD is a knowledge warehouse that consistently integrates in the same environment the data and the methods used for their acquisition. This is achieved through the construction of (1) a domain knowledge base (DKB) devoted to the storage of the knowledge about the systems, their functional specificities, their partners and how they are related and (2) a methodological knowledge base (MKB) which depicts the task layout used to identify and reconstruct functional integrated systems. Instantiation of the DKB is obtained by solving the tasks of the MKB, whereas some tasks need instances of the DKB to be solved. AROM, an object-based knowledge representation system, has been used to design the DKB, and its task manager, AROMTasks, for developing the MKB. In this study two integrated systems, ABC transporters and two component systems, both involved in adaptation processes of a bacterial cell to its biotope, have been used to evaluate the feasibility of the approach.Contact: julie.chabalier@ibsm.cnrs-mrs.fr
Uninterrupted Dialogue: Between Two Infinities, the Poem
Authors: Derrida Jacques 
Published: November 2004

With the attempt to express my feeling of admiration for Hans-Georg Gadamer an ageless melancholy mingles. This melancholy begins as of the friends' lifetime. A
cogito
of the farewell signs the breathing of their dialogues. One of the two will have been doomed, from the beginning, to carry alone both the dialogue that he must pursue beyond the interruption, and the memory of the first interruption. To carry the world of the other, to carry both the other and his world, the other and the world that have disappeared, in a world without world. That shall be one of the ways to let resound within ourselves the line of poetry by Paul Celan, "
Die Welt ist fort, ich muss dich tragen
."
Gadamer, Aesthetic Modernism, and the Rehabilitation of Allegory: The Relevance of Paul Klee
Authors: Watson Stephen 
Published: November 2004

Paul Klee's art found broad impact upon philosophers of varying commitments, including Hans-Georg Gadamer. Moreover, Klee himself was not only one of the most important artists of aesthetic modernism but one of its leading theoreticians, and much in his work, as in Gadamer's, originated in post-Kantian literary theory's explications of symbol and allegory. Indeed at one point in
Truth and Method
, Gadamer associates his project for a general "theory of hermeneutic experience" not only with Goethe's metaphysical account of the symbolic but equally with a "rehabilitation" of allegory. In this paper, I examine this position and Gadamer's own use of it in his analysis of Klee's work, contrasting it with that of Walter Benjamin's account of allegory, equally indebted to Goethe and this archive. Finally, I contrast the resulting interpretations of Klee, discussing the implications that evolve for understanding both Gadamer and Benjamin— but equally for understanding Klee's work and, provisionally, the work of art, thus construed, for philosophy.
On Hölderlin's "Andenken": Heidegger, Gadamer and Henrich—a Decision?
Authors: Freydberg Bernard 
Published: November 2004

Often, respectable scholars attack the soundness of Heidegger's "violent" interpretations of Hölderlin (and others). In this case, Dieter Henrich offers a particularly harsh assessment of Heidegger's interpretation of "
Andenken
." Hans-Georg Gadamer, student of Heidegger and teacher of Henrich, attempts to bring harmony where none seems possible. A study of the three interpretations indicates that scholarship alone is sufficient to reach a decision on the strength of the interpretations.
The p53-dependent apoptotic pathway of breast cancer cells (BC-M1) induced by the bis-type bioreductive compound aziridinylnaphthoquinone
Authors: Yang Yu-Ping , Kuo Hsien-Shou , Tsai Hsin-Da , Peng Yi-Chen , Lin Yuh-Ling 
Published: November 2004

Abstract
Introduction
Several aziridinylbenzoquinone drugs have undergone clinical trials as potential antitumor drugs. These bioreductive compounds are designed to kill cells preferentially within the hypoxia tumor microenvironment. The bioreductive compound of bis-type naphthoquinone synthesized in our laboratory, 2-aziridin-1-yl-3-[(2-{2-[(3-aziridin-1-yl-1,4-dioxo-1,4-dihydronaphthalen-2-yl)thio]ethoxy}ethyl)thio]naphthoquinone (AZ-1), had the most potent death effect on the breast cancer cells BC-M1 in our previous screening. In the present study, we determined that the mechanism of the death effect of BC-M1 cells induced by AZ-1 was mediated by the apoptosis pathway.

Methods
We evaluated the cytotoxicity of AZ-1 and the anti-breast cancer drugs tamoxifen and paclitaxel to BC-M1 cells and MCF-7 cells by the MTT assay and measured the apoptosis phenomena by Hoechst 33258 staining for apoptotic bodies. We also quantified the sub-G1 peak area and the ratio of the CH2/CH3 peak area of the cell membrane in BC-M1 cells by flow cytometry and 1H-NMR spectra, respectively.
The apoptosis-related protein expressions, including p53, p21, the RNA-relating protein T-cell restricted intracellular antigen-related protein, cyclin-dependent kinase 2 (cell cycle regulating kinase) and pro-caspase 3, were detected by western blot, and the caspase-3 enzyme activity was also quantified by an assay kit.

Results
AZ-1 induced two of the breast cancer cell lines, with IC50 = 0.51 μM in BC-M1 cells and with IC50= 0.57 μM in MCF-7 cells, and showed less cytotoxicity to normal fibroblast cells (skin fibroblasts) with IC50= 5.6 μM. There was a 10-fold difference between two breast cancer cell lines and normal fibroblasts. Of the two anti-breast cancer drugs, tamoxifen showed IC50= 0.12 μM to BC-M1 cells and paclitaxel had much less sensitivity than AZ-1. The expression of p53 protein increased from 0.5 to 1.0 μM AZ-1 and decreased at 2.0 μM AZ-1. The p21 protein increased from 0.5 μM AZ-1, with the highest at 2 μM AZ-1. Regarding the AZ-1 compound-induced BC-M1 cells mediating the apoptosis pathway, the apoptotic body formation, the sub-G1 peak area, the ratio of CH2/CH3 of phospholipids in the cell membrane and the enzyme activity of caspase-3 were all in direct proportion with the dose-dependent increase of the concentration of AZ-1. The death effect-related proteins, including T-cell restricted intracellular antigen-related protein, cyclin-dependent kinase 2, and pro-caspase-3, all dose-dependently decreased with AZ-1 concentration.

Conclusions
The AZ-1-induced cell death of BC-M1 cells mediating the apoptosis pathway might be associated with p53 protein expression, and AZ-1 could have the chance to be a candidate drug for anti-breast cancer following more experimental evidence, such as animal models.
In silico evaluation of two mass spectrometry-based approaches for the identification of novel human leukocyte cell-surface proteins
Authors: Nicholson I C , Ayhan M , Hoogenraad N J , Zola H 
Published: November 2004

Abstract
The identification and quantitation of cell-surface proteins expressed by leukocytes currently use the wide availability of monoclonal antibodies (mAb) in immunohistochemical and flow cytometric assays. Presently, ∼400 such proteins have been characterized; however, analysis of the completed human genome sequence indicates that it may contain several thousand as-yet unidentified molecules, which may be expressed on the leukocyte cell surface. Recent advances in protein isolation and analysis using mass spectrometry illustrate that it is now feasible to identify the protein composition of a complex sample such as a plasma membrane extract. Such an approach may be useful for the identification of the cell-surface proteins that have not been identified using mAb techniques. Here, we detail the results of an in silico evaluation of the peptides isolated using two methods used to label plasma membrane proteins to determine whether these methods are suitable for the identification of known leukocyte cell-surface proteins by mass spectrometry. The labeling of cell-surface proteins before isolation and characterization is a valuable means of differentiating between plasma membrane and internal membrane proteins The results indicate that although the majority of cell-surface proteins can be identified using either of the approaches, others known to be important diagnostically and/or therapeutically would not be identified using either approach. The implication of this for the use of these techniques in the discovery of new leukocyte cell-surface proteins is discussed.
Flow structure and turbulence characteristics of the daytime atmosphere in a steep and narrow Alpine valley
Authors: Weigel Andreas P. , Rotach Mathias W. 
Published: November 2004

AbstractAircraft measurements, radio soundings and sonic data—obtained during the MAP‐Riviera field campaign in autumn 1999 in southern Switzerland—are used to investigate the flow structure, temperature profiles and turbulence characteristics of the atmosphere in a steep and narrow Alpine valley under convective conditions. On all predominantly sunny days of the intensive observation periods, a pronounced valley‐wind system develops. In the southern half of the valley, the daily up‐valley winds have a jet‐like structure and are shifted towards the eastern slope. These up‐valley winds advect potentially colder air, a process which appears to be balanced by vertical warm air advection from above. The profiles of potential temperature show that, with the onset of up‐valley winds, the mixed layer consistently stops growing or—on days with very strong up‐valley winds—even stabilizes almost throughout the entire valley atmosphere. This is probably due to a pronounced secondary circulation in the southern part of the valley, which induces advection of warm air from above. The secondary circulation appears to be a consequence of sharp curvature in the along‐valley topography.Turbulence variables are calculated from flight legs in the along‐valley direction. Turbulent kinetic energy (TKE) scales surprisingly well (i) if a TKE criterion (TKE >0.5 m2s−2) is employed as a definition of the boundary layer height and (ii) if the ‘surface fluxes’—which exhibit a substantial spatial variability—from the slope sites are used rather than those from directly beneath the profile considered. Significant site‐to‐site differences in incoming solar radiation seem to be the reason for this characteristic behaviour. Profiles of momentum flux—scaled with a surface friction velocity—reveal more scatter than the TKE profiles, but still show a consistent behaviour. A surprisingly strong shear in the cross‐valley direction can be observed and is probably a result of the secondary circulation. Copyright © 2004 Royal Meteorological Society