bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNase II and the Chk2 DNA Damage Pathway Form a Genetic Barrier Blocking Replication of Horizontally Transferred DNA
Authors: Bergsmedh Anna , Ehnfors Jacob , Kawane Kohki , Motoyama Noboru , Nagata Shigekazu , Holmgren Lars 
Published: March 2006

Abstract
We have previously shown that DNA from dying tumor cells may be transferred to living cells via the uptake of apoptotic bodies and may contribute to tumor progression. DNA encoding H-rasV12 and c-myc oncogenes may be transferred to the nucleus of the phagocyte but will only integrate and propagate in p53- and p21-deficient mouse embryonic fibroblasts, whereas normal cells are resistant to transformation. Here, we show that this protective mechanism (activation of p53 and p21 after uptake of apoptotic bodies) is dependent on DNA fragmentation, where inhibition of the caspase-activated DNase in the apoptotic cells, in conjunction with genetic ablation of lysosomal DNase II in the phagocytes, completely blocks p53 activation and consequently allows DNA replication of transferred DNA. We, therefore, suggest that there is a causal relationship between DNA degradation during apoptosis and p53 activation. In addition, we could further show that Chk2−/− cells were capable of replicating the hygR gene taken up from engulfed apoptotic cells, suggesting involvement of the DNA damage response. These data show that the phagocytosing cell is sensing the degraded DNA within the apoptotic cell, hence preventing these genes from being replicated, probably through activation of the DNA damage response. We, therefore, hypothesize that DNase II together with the Chk2, p53, and p21 pathway form a genetic barrier blocking the replication of potentially harmful DNA introduced via apoptotic bodies, thereby preventing transformation and malignant development. (Mol Cancer Res 2006;4(3):187–95)
Passion for (the) Real? The Passion of the Christ and Its Critics
Authors: Penner Todd , Stichele Caroline Vander 
Published: March 2006

AbstractIn this article we examine Mel Gibson's controversial 2004 film The Passion of the Christ and the critical response it evoked within the American cultural context. Focusing on the modern fascination of especially Hollywood with generating "real" experiences for the viewing audience, we argue that the film and its critics are both caught up in a particular cultural debate regarding differing social and political visions and practices. Special attention is given to the spectacle of violence in the film, examining particularities of The Passion in the larger context of Gibson's cinematic work. However, rather than criticising Gibson's film for its violence or for being "unfaithful" to history and the Gospels, we explore the ideological and socio-cultural underpinnings of Gibson's cinematic work, situating it more fully within the visual context of Hollywood and the cultural and political milieu of America. In our view, The Passion has distinctive features that come together to create a uniquely "American Gospel."
The Gospel According to Judas: Myth and Parable
Authors: Walsh Richard 
Published: March 2006

AbstractJesus films improve the Judas story by adding plot connections and amplifying Judas' character, but their Judases reprise "the Gospel according to _" pattern. Like Jewison's Judas, they all are part of the adoring Christian chorus. Films' selective uses of the gospel Judas incidents intensify the gospel exclusions. Judas remains the traitorous disciple who deserves his fate. Films' visuals continue the iconography of art and create interlocking scenes associating Judas with Jesus' opponents. While some films motivate Judas traditionally, others modernize Judas' motivation in order to create a simulacrum of a modern person. Regardless, Judas remains the mythic other whose exclusion separates us from the evil that we do not wish to accept as part of our self-identity. Films' Judases define what "we" are not. We can arrange the Judases of Jesus films into four types: a traditional Judas, a modern, human Judas, a Christ-figure Judas, and a parabolic Judas. The first two Judases are clearly part of Christian myth-making. While the Christ-figure Judas may suggest an antimyth opposing the Christian myth, it ultimately supports Christian mythology as well. Only the parabolic Judas contests the continuing power of Christian discourse by telling stories alongside "the gospel" story. The parables of Arcand's Daniel and Jones's Brian suggest a view askew on Christian discourse that invites us to read other Jesus films and the gospels themselves parabolically and to find the evil lurking and the "dark night of story" within Christian mythology.
Nature in Asian Indigenous Traditions: A Survey Article
Authors: Wiles David , Witt Joseph 
Published: March 2006

AbstractThis paper surveys the recent literature available for the study of the interaction between religion and nature within indigenous Asian traditions. Anyone engaging in this course of study must consider work from a variety of scholarly fields and engage with debates concerning definitions of the term "indigenous" in different Asian contexts. While this article does not represent every indigenous group and tradition of Asia, it nonetheless attempts to identify valuable starting points in key regions. While a large amount of important work exists on the indigenous peoples of Asia, there remains a need for more work drawing together different disciplines and analyzing interactions between religion and nature. We hope that scholars from different fields will find this survey useful for further research on nature in indigenous Asian traditions.
The "Nature" of Buddhism: A Survey of Relevant Literature and Themes
Authors: Johnston Lucas 
Published: March 2006

AbstractThis paper is a review of the scholarly conversation relating Buddhism to environmental issues, primarily in the United States. Topics of particular concern include important scholarly benchmarks in the field, and the nature of Buddhist ethics. Also considered are the relationships between Buddhism and other schools of thought that have been important in thinking about nature and the environment. In particular I focus on Deep Ecology and related philosophies, Buddhism and Christianity in Process thought, and the relationship between Buddhism and the natural sciences. I outline current practices performed worldwide by people who self-identify as Buddhists that clearly demonstrate environmental consciousness, sometimes actively participating in environmental movements in efforts to resist globalization and, often, Westernization. In the end, this survey perspective illustrates that there is no monolithic Buddhist tradition, but rather a substantial number of adapted (and adapting) Buddhisms.
Chinese Traditions and Ecology: Survey Article
Authors: Snyder Samuel 
Published: March 2006

AbstractThe increasing degradation of the natural environment, and the associated dangers to all life on the planet, very well might represent the greatest challenge to humankind. In response to such projections of impending danger, scholars and activists from a variety of fields are in the midst of investigating cultural resources as a means to understand both how humans went wrong and how humans can amend the damage. Out of this inquiry has emerged a vast body of literature exploring the various intersections between Chinese traditions, such as Confucianism, Daoism, Feng-Shui and folk practice; and the natural environment, ecology, and environmental ethics. This paper is a survey of this literature, seen through the lens of religious studies and ecology. Rather than offer critical evaluation of the field, this essay is meant to offer a broad survey of the material presented in an accessible manner as a tool for those new to, but interested in pursuing, this field of study. This paper is, therefore a guide.
Hindu Traditions and Nature: Survey Article
Authors: Van Horn Gavin 
Published: March 2006

AbstractThe scholarly investigation of the convergences between Hindu traditions and the natural world is a relatively recent endeavor, having arisen in the wake of similar projects seeking to identify the intersections between religion, culture, and nature. Partly a response to present and looming environmental threats, this effort has resulted in a wide range of material, from a more general "environmental assessment" of the tradition(s) in question to specific inquiries about the social, economic, and demographic factors that impinge upon contemporary Indians' understandings of nature. This literature review provides an overview of these materials and should offer readers a sense of the topics that have received the most attention from scholars to date.
An Emerging Magisterium? The Case of the Assemblies of God
Authors: Robeck Cecil 
Published: March 2006

AbstractTradition means giving votes to the most obscure of all classes, our ancestors. It is the democracy of the dead. Tradition refuses to submit to the small and arrogant oligarchy of those who merely happen to be walking about. All democrats object to men being disqualified by the accident of birth; tradition objects to their being disqualified by the accident of death. Democracy tells us not to neglect a good man's opinion, even if he is our groom; tradition asks us not to neglect a good man's opinion, even if he is our father. I, at any rate, cannot separate the two ideas of democracy and tradition….
A Forecast Strategy for Anticipating Cold Season Mesoscale Band Formation within Eastern U.S. Cyclones
Authors: Novak David R. , Waldstreicher Jeff S. , Keyser Daniel , Bosart Lance F. 
Published: March 2006

Abstract
An ingredients-based, time- and scale-dependent forecast strategy for anticipating cold season mesoscale band formation within eastern U.S. cyclones is presented. This strategy draws on emerging conceptual models of mesoscale band development, advances in numerical weather prediction, and modern observational tools. As previous research has shown, mesoscale band development is associated with frontogenesis in the presence of weak moist symmetric stability and sufficient moisture. These three parameters—frontogenesis, weak moist symmetric stability, and moisture—are used as the ingredients for identifying mesoscale band development in this strategy. At forecast projections beyond 2 days, the strategy assesses whether cyclogenesis is expected. Within 2 days of the event, the strategy places the band ingredients in the context of the broader synoptic flow, with attention to where deformation zones are present, to assess whether banding is possible. Within 1 day of the event, the strategy focuses on assessment of the ingredients to outline when and where band formation is favored. Plan-view and cross-sectional analyses of gridded model fields in conjunction with high-resolution model guidance are used to assess the likelihood of banding and to outline the threat area. Within 12 h, short-range forecasts of the band ingredients are evaluated in concert with observations to make specific band predictions. Particular emphasis is placed on the evolution of the frontogenetic forcing and moist symmetric stability. During the event, trends in observations and short-range model forecasts are used to anticipate the movement, intensity, and dissipation of the band. The benefits and practical challenges associated with the proposed strategy are illustrated through its operational application to the 25 December 2002 northeast U.S. snowstorm, during which intense mesoscale snowband formation occurred. Forecast products from this event demonstrate how the forecast strategy can lead to heightened situational awareness, in this case resulting in accurate band forecasts. This application shows that accurate operational forecasts of mesoscale bands can be made based on our current conceptual understanding, observational tools, and modeling capabilities.
Differential Muc2 and Muc5ac secretion by stimulated guinea pig tracheal epithelial cells in vitro
Authors: Chorley Brian N , Crews Anne L , Li Yuehua , Adler Kenneth B , Minnicozzi Michael , Martin Linda D 
Published: March 2006

Abstract

Background
Mucus overproduction is a characteristic of inflammatory pulmonary diseases including asthma, chronic bronchitis, and cystic fibrosis. Expression of two mucin genes, MUC2 and MUC5AC, and their protein products (mucins), is modulated in certain disease states. Understanding the signaling mechanisms that regulate the production and secretion of these major mucus components may contribute significantly to development of effective therapies to modify their expression in inflamed airways.

Methods
To study the differential expression of Muc2 and Muc5ac, a novel monoclonal antibody recognizing guinea pig Muc2 and a commercially-available antibody against human MUC5AC were optimized for recognition of specific guinea pig mucins by enzyme-linked immunosorbent assay (ELISA), Western blot, and immunohistochemistry (IHC). These antibodies were then used to analyze expression of Muc2 and another mucin subtype (likely Muc5ac) in guinea pig tracheal epithelial (GPTE) cells stimulated with a mixture of pro-inflammatory cytokines [tumor necrosis factor-α (TNF-α), interleukin 1β (IL-1β), and interferon- γ (IFN-γ)].

Results
The anti-Muc2 (C4) and anti-MUC5AC (45M1) monoclonal antibodies specifically recognized proteins located in Muc2-dominant small intestinal and Muc5ac-dominant stomach mucosae, respectively, in both Western and ELISA experimental protocols. IHC protocols confirmed that C4 recognizes murine small intestine mucosal proteins while 45M1 does not react. C4 and 45M1 also stained specific epithelial cells in guinea pig lung sections. In the resting state, Muc2 was recognized as a highly expressed intracellular mucin in GPTE cells in vitro. Following cytokine exposure, secretion of Muc2, but not the mucin recognized by the 45M1 antibody (likely Muc5ac), was increased from the GPTE cells, with a concomitant increase in intracellular expression of both mucins.

Conclusion
Given the tissue specificity in IHC and the differential hybridization to high molecular weight proteins by Western blot, we conclude that the antibodies used in this study can recognize specific mucin subtypes in guinea pig airway epithelium and in proteins from GPTE cells. In addition, Muc2 is highly expressed constitutively, modulated by inflammation, and secreted differentially (as compared to Muc5ac) in GPTE cells. This finding contrasts with expression patterns in the airway epithelium of a variety of mammalian species in which only Muc5ac predominates.
Toll-like receptors in cellular subsets of human tonsil T cells: altered expression during recurrent tonsillitis
Authors: Mansson Anne , Adner Mikael , Cardell Lars Olaf 
Published: March 2006

AbstractBackgroundThe palatine tonsils have a pivotal role in immunological detection of airborne and ingested antigens like bacteria and viruses. They have recently been demonstrated to express Toll-like receptors (TLRs), known to recognize molecular structures on such microbes and activate innate immune responses. Their activation might also provide a link between innate and adaptive immunity. In the present study, the expression profile of TLR1-TLR10 was characterized in human tonsil T cells, focusing on differences between subsets of CD4+T helper (Th) cells and CD8+cytotoxic T lymphocytes (CTL). The study was also designed to compare the TLR expression in T cells from patients with recurrent tonsillitis and tonsillar hyperplasia.MethodsTonsils were obtained from children undergoing tonsillectomy, and classified according to the clinical diagnoses and the outcome of tonsillar core culture tests. Two groups were defined; recurrently infected tonsils and hyperplastic tonsils that served as controls. Subsets of T cells were isolated using magnetic beads. The expression of TLR transcripts in purified cells was assessed using quantitative real-time RT-PCR. The corresponding protein expression was investigated using flow cytometry and immunohistochemistry.ResultsT cells expressed a broad repertoire of TLRs, in which TLR1, TLR2, TLR5, TLR9 and TLR10 predominated. Also, a differential expression of TLRs in CD4+and CD8+T cells was obtained. TLR1 and TLR9 mRNA was expressed to a greater extent in CD4+cells, whereas expression of TLR3 mRNA and protein and TLR4 protein was higher in CD8+cells. CD8+cells from infected tonsils expressed higher levels of TLR2, TLR3 and TLR5 compared to control. In contrast, CD4+cells exhibited a down-regulated TLR9 as a consequence of infection.ConclusionThe present study demonstrates the presence of a broad repertoire of TLRs in T cells, a differential expression in CD4+and CD8+cells, along with infection-dependent alterations in TLR expression. Collectively, these results support the idea that TLRs are of importance to adaptive immune cells. It might be that TLRs have a direct role in adaptive immune reactions against infections. Thus, further functional studies of the relevance of TLR stimulation on T cells will be of importance.
Gene selection algorithms for microarray data based on least squares support vector machine
Authors: Tang E Ke , Suganthan PN , Yao Xin 
Published: March 2006

AbstractBackgroundIn discriminant analysis of microarray data, usually a small number of samples are expressed by a large number of genes. It is not only difficult but also unnecessary to conduct the discriminant analysis with all the genes. Hence, gene selection is usually performed to select important genes.ResultsA gene selection method searches for an optimal or near optimal subset of genes with respect to a given evaluation criterion. In this paper, we propose a new evaluation criterion, named the leave-one-out calculation (LOOC, A list of abbreviations appears just above the list of references) measure. A gene selection method, named leave-one-out calculation sequential forward selection (LOOCSFS) algorithm, is then presented by combining the LOOC measure with the sequential forward selection scheme. Further, a novel gene selection algorithm, the gradient-based leave-one-out gene selection (GLGS) algorithm, is also proposed. Both of the gene selection algorithms originate from an efficient and exact calculation of the leave-one-out cross-validation error of the least squares support vector machine (LS-SVM). The proposed approaches are applied to two microarray datasets and compared to other well-known gene selection methods using codes available from the second author.ConclusionThe proposed gene selection approaches can provide gene subsets leading to more accurate classification results, while their computational complexity is comparable to the existing methods. The GLGS algorithm can also better scale to datasets with a very large number of genes.
Microarray image analysis: background estimation using quantile and morphological filters
Authors: Bengtsson Anders , Bengtsson Henrik 
Published: March 2006

Abstract

Background
In a microarray experiment the difference in expression between genes on the same slide is up to 103 fold or more. At low expression, even a small error in the estimate will have great influence on the final test and reference ratios. In addition to the true spot intensity the scanned signal consists of different kinds of noise referred to as background. In order to assess the true spot intensity background must be subtracted. The standard approach to estimate background intensities is to assume they are equal to the intensity levels between spots. In the literature, morphological opening is suggested to be one of the best methods for estimating background this way.

Results
This paper examines fundamental properties of rank and quantile filters, which include morphological filters at the extremes, with focus on their ability to estimate between-spot intensity levels. The bias and variance of these filter estimates are driven by the number of background pixels used and their distributions. A new rank-filter algorithm is implemented and compared to methods available in Spot by CSIRO and GenePix Pro by Axon Instruments. Spot's morphological opening has a mean bias between -47 and -248 compared to a bias between 2 and -2 for the rank filter and the variability of the morphological opening estimate is 3 times higher than for the rank filter. The mean bias of Spot's second method, morph.close.open, is between -5 and -16 and the variability is approximately the same as for morphological opening. The variability of GenePix Pro's region-based estimate is more than ten times higher than the variability of the rank-filter estimate and with slightly more bias. The large variability is because the size of the background window changes with spot size. To overcome this, a non-adaptive region-based method is implemented. Its bias and variability are comparable to that of the rank filter.

Conclusion
The performance of more advanced rank filters is equal to the best region-based methods. However, in order to get unbiased estimates these filters have to be implemented with great care. The performance of morphological opening is in general poor with a substantial spatial-dependent bias.
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries
Authors: Côté Richard G , Jones Philip , Apweiler Rolf , Hermjakob Henning 
Published: March 2006

Abstract

Background
With the vast amounts of biomedical data being generated by high-throughput analysis methods, controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform controlled vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries.

Results
The Ontology Lookup Service (OLS) was created to integrate publicly available biomedical ontologies into a single database. All modified ontologies are updated daily. A list of currently loaded ontologies is available online. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A programmatic interface is available to query the webservice using SOAP. The service is described by a WSDL descriptor file available online. A sample Java client to connect to the webservice using SOAP is available for download from SourceForge. All OLS source code is publicly available under the open source Apache Licence.

Conclusion
The OLS provides a user-friendly single entry point for publicly available ontologies in the Open Biomedical Ontology (OBO) format. It can be accessed interactively or programmatically at http://www.ebi.ac.uk/ontology-lookup/.