bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bayesian sensitivity analysis for unmeasured confounding in observational studies
Authors: McCandless Lawrence C. , Gustafson Paul , Levy Adrian 
Published: September 2006

AbstractWe consider Bayesian sensitivity analysis for unmeasured confounding in observational studies where the association between a binary exposure, binary response, measured confounders and a single binary unmeasured confounder can be formulated using logistic regression models. A model for unmeasured confounding is presented along with a family of prior distributions that model beliefs about a possible unknown unmeasured confounder. Simulation from the posterior distribution is accomplished using Markov chain Monte Carlo. Because the model for unmeasured confounding is not identifiable, standard large‐sample theory for Bayesian analysis is not applicable. Consequently, the impact of different choices of prior distributions on the coverage probability of credible intervals is unknown. Using simulations, we investigate the coverage probability when averaged with respect to various distributions over the parameter space. The results indicate that credible intervals will have approximately nominal coverage probability, on average, when the prior distribution used for sensitivity analysis approximates the sampling distribution of model parameters in a hypothetical sequence of observational studies. We motivate the method in a study of the effectiveness of beta blocker therapy for treatment of heart failure. Copyright © 2006 John Wiley & Sons, Ltd.
Recent advances in TGFβ‐regulated transcription during carcinogenesis
Authors: Buck Anita , Ellenrieder Volker 
Published: September 2006

AbstractThe multifunctional activities of transforming growth factor‐beta (TGFβ) endow it with both tumor suppressor and tumor promoting activities, depending on the stage of carcinogenesis and the cellular activation state. In early tumor stages, TGFβ inhibits epithelial cell growth through induction of apoptosis and transcriptional regulation of cell cycle controlling genes. During tumor progression, however, many cancer cells escape from TGFβ‐induced growth inhibition and, instead, respond to TGFβ with increased malignancy. TGFβ stimulates tumor promotion particularly in those tumor cells in which Smad‐signaling remains functional and through transcriptional regulation of gene expression. Thus, loss of sensitivity to growth inhibition by TGFβ is not synonymous with complete loss of TGFβ signaling. Rather, it suggests that tumor cells gain advantage by selective inactivation of TGFβ tumor suppressor activities while retaining its tumor promoting functions. In this review we focus on novel aspects in TGFβ signaling and transcription and in particular on the role of Smad‐interacting transcription factors. We also summarize recent advances in both cytoplasmic and nuclear crosstalk mechanisms between Smad and non‐Smad signaling pathways and how this interaction results in the fine‐tuning of Smad‐mediated transcription during cancer progression. This knowledge will help to better understand the molecular mechanisms responsible for the switch of TGFβ from a tumor suppressor to a tumor promotor.
Moving on: Molecular mechanisms in TGFβ‐induced epithelial cell migration
Authors: Giehl Klaudia , Menke Andre 
Published: September 2006

AbstractTGFβ, particularly TGFβ1‐3, has been shown to promote epithelial dedifferentiation or epithelial‐mesenchymal transition (EMT). While inhibition of epithelial cell proliferation in response to TGFβ is mainly mediated by the well‐characterised Smad‐pathway and subsequent regulation of gene transcription, the molecular mechanisms leading to TGFβ‐induced migration, invasion and metastasis of epithelial tumour cells are less clear. Recent results from several groups suggest that the gain of tumourigenic activity by TGFβ includes signalling by mitogen‐activated protein kinases (MAP kinases), phosphatidylinositol 3‐kinase (PI3‐K) and Rho‐GTPases. Activation of the MAP kinases extracellular signal‐regulated kinase (ERK) 1 and 2, p38 as well as c‐jun N‐terminal kinase (JNK) has been identified as important steps in TGFβ‐induced, Smad4‐independent signal transduction in epithelial cells. A role of activated ERK and JNK and their association with focal complexes in TGFβ‐induced cell migration and actin cytoskeleton reorganisation of carcinoma cells has been identified recently. In this review we will focus on new data about the molecular mechanisms involved in the TGFβ‐induced Smad‐independent regulation of epithelial cell migration.
High‐Level Gene Expression for Recombinant Penicillin Acylase Production Using the araB Promoter System in Escherichia coli
Authors: Narayanan Niju , Xu Yali , Chou C. Perry 
Published: September 2006

AbstractThe pac gene encoding penicillin acylase (PAC) was overexpressed under the regulation of the araB promoter (ParaB, also known as PBAD) in Escherichia coli(E. coli). The current ParaB expression system exhibited minimum leaking pac expression in the absence of arabinose as well as fast and high‐level pac expression upon induction with arabinose in a wide concentration range. The production of PAC was limited by the accumulation of PAC precursors (i.e., proPAC in both soluble and insoluble forms) and various negative cellular responses, such as growth arrest and cell lysis. The culture performance could be improved by degP coexpression and the individual contribution of DegP protease and chaperone activities to the enhancement on the production of PAC was characterized. The study highlights the importance of identifying the step(s) limiting high‐level gene expression and subsequent design and construction of the host/vector system for enhancing recombinant protein production in E. coli.
High Concentration Cultivation of Bifidobacteriumbifidum in a Submerged Membrane Bioreactor
Authors: Kwon Soun‐Gyu , Son Ju‐Wan , Kim Hye‐Jung , Park Chang‐Su , Lee Jung‐Kul , Ji Geun Eog , Oh Deok‐Kun 
Published: September 2006

AbstractIn batch cultures, after 25 h, the maximum cell mass of Bifidobacterium bifidum BGN4 was 4.5 g/L, and the maximum cell count was 3.0 × 109 cfu/mL at pH 6.0 and 50 g/L sucrose. To increase the viable counts of bifidobacteria, cell retentive culture was applied using a submerged membrane bioreactor with suction and gas sparging. The maximum mass, count, and productivity of the cells after 36 h were 12.0 g/L, 2.2 × 1010 cfu/mL, and 6.1 × 108 cfu/mL·h, respectively, at the feeding (dilution) rate of 120 mL/h (0.06 h−1) in the feeding medium. The accumulated levels of organic acids and ammonium ions at the end of the cultivation were 1.5 and 1.0 g/L, respectively. The viable counts and volumetric productivity of the cells after the cell retentive culture were 7.3‐ and 5.1‐fold higher, respectively, than the values obtained during batch culture. These high viable counts and volumetric productivities were obtained by maintaining lower concentrations of organic acids and ammonium ions so that the growth of B. bifidum BGN4 was not inhibited. The submerged membrane bioreactor produced the highest viable counts of B. bifidum without membrane fouling and cell damage.
Isolation of neural crest‐derived stem cells from rat embryonic mandibular processes
Authors: Zhang Jianping , Duan Xiaoyan , Zhang Huali , Deng Zhihong , Zhou Zeyuan , Wen Ning , Smith Anthony J. , Zhao Wenming , Jin Yan 
Published: September 2006

Background information. Substantial evidence indicates the existence of NCSCs (neural crest‐derived stem cells) in embryonic mandibular processes; however, they have not been fully investigated or isolated. The aim of the present study was to isolate stem cells from mandibular process during embryonic development by MACS (magnetic‐activated cell sorting). The findings show that the cells are multipotent and self‐renewing.Results. LNGFR (low‐affinity nerve‐growth‐factor receptor)+ cells were isolated from rat embryonic mandibular processes by MACS. The cells were grown in clonal culture by limiting dilution to assess their developmental potential. Clone analysis indicated that, first, LNGFR+ cells are multipotent, being able to generate at least neurons and Schwann cells, similar to peripheral neural crest stem cells. Secondly, multipotent LNGFR+ cells generate multipotent progenies, indicating that they are capable of self‐renewal and therefore are stem cells. Thirdly, manipulation of the medium supplementation alters the fate of the isolated LNGFR+ cells.Conclusions. These results indicate that LNGFR antibodies label NCSCs with high specificity and purity, and suggest that positive selection using these antibodies may become the method of choice for obtaining multipotent cells from rat embryonic mandibular processes for tissue engineering or regenerative therapeutic use.
Identification of Rho GTPases implicated in terminal differentiation of muscle cells in ascidia
Authors: Coisy‐Quivy Marjorie , Sanguesa‐Ferrer Juan , Weill Mylène , Johnson David Scott , Donnay Jean‐Marc , Hipskind Robert , Fort Philippe , Philips Alexandre 
Published: September 2006

Background information. Members of the Rho GTPase family mediate changes in the actin cytoskeleton and are also implicated in developmental processes, including myogenesis. Nevertheless, a comprehensive analysis of these proteins during myofibrillogenesis has never been performed in any organism.Results. Using the ascidian model to identify the role of Rho GTPases on myofibrillogenesis, we show that transcripts for all Rho GTPases are detected in muscle cells of the embryo. We find that activation of RhoA, TC10 and Cdc42 (cell division cycle 42) disturbs the polarity of muscle cells, whereas that of other Rho GTPases induced cell positioning defects. Moreover, dominant negative version of five Rho GTPases, RhoA, Rac2, RCL2 (Rac‐ and Cdc42‐like 2), TC10 and WRCH (Wnt‐1 responsive Cdc42 homologue), impaired the formation of mature myofibrils.Conclusions. Taken together, our results show that several Rho GTPase‐dependent pathways are required to control the spatial localization of muscle cells in the embryo and to coordinate myofibril assembly. This stresses the importance of analysing the entire Rho family when studying a new biological process.
Origins and Legacy of the Kharijites
Authors: Kenney Jeffrey T. 
Published: September 2006

Abstract
To establish why and how modern Muslim thinkers were able to evoke and use the image of the Kharijite this chapter explores the historical, literary process by which the early Kharijites were transformed into a mythic symbol of rebellion. It argues that individuals find themselves recipients of a theology/ideology that was ordered in, and is sanctioned by, the past. However, the “givenness” with which such a tradition is received by later generations masks the fact that over time it has changed. It required interpretation and codification. In other words, the particulars of a tradition, such as those of the Kharijites in Islam, were made particular by a historical and historicizing process that is the very basis of the tradition.
The Muslim Brothers and the Neo‐Kharijite Challenge
Authors: Kenney Jeffrey T. 
Published: September 2006

AbstractThe evocation of Kharijism first occurred in connection with the activities and ideas of the Society of Muslim Brothers. On two separate occasions, in 1948 and 1954, the Muslim Brothers were accused of being Kharijite. These isolated episodes adumbrate the trend toward accusations of Kharijism that came to inform a range of political and religious rival groups in Egypt — government, official al-Azhar, conservative, Islamist, and secular. This chapter examines the first wave of accusations of Kharijism as they were applied in general to the Society of Muslim Brothers, and in particular to the writing and figure of Sayyid Qutb, a one-time literary critic who became the voice of Islamist militancy.
The New Politics of Anti‐Extremist Rhetoric
Authors: Kenney Jeffrey T. 
Published: September 2006

AbstractThis chapter explores the political discourse on extremism in the 1980s and 1990s, a time when Egyptians began to explore the causes of extremism in more critical and nuanced ways. It argues that by participating in the new anti-extremist politics and the debate over the meaning of Kharijism that accompanied it, Islamists were trying to win over the public and make a stronger case against the existing regime. But, in the process, they conceded the importance of the very middle-class demands that informed the new politics; and those demands were not for a religious transformation of Egypt — the creation of an Islamic government or the implementation of Islamic law — but rather for workable social institutions, a more open political process, and a healthy economy. In the political discourse of late-20th-century Egypt, the end of violence, the end of the problem of Kharijism, entailed a new political beginning shorn of absolutist politics of any kind.
Conclusion
Authors: Kenney Jeffrey T. 
Published: September 2006

AbstractThis chapter argues that although cultural symbols such as that provided by the Kharijites matter in Muslim societies, they are not fixed in the mind of believers compelling them to think and behave in specific ways. The meaning of such symbols may be informed by a historical tradition that weighs on individuals and the larger society, but this tradition is changed by individuals and institutions through time. In modern Egypt, the idea of Kharijism was reawakened to deal with a new environment, one driven by the modernizing forces of the nation-state and the global economy. Over time, however, this environment produced different interpretive readings of Kharijism.
Philosophical and Scientific Perspectives on Mentalizing
Authors: Goldman Alvin I. 
Published: September 2006

AbstractA brief overview and mini-history of the subject of mindreading are presented. Philosophers were the first to worry about the folk understanding of other minds and the distinctive nature of self-knowledge. They advanced the view that “folk psychology” presupposes a naive theory of mind. Empirical evidence about young children’s poor performance on false-belief tasks and about the link between autism and “mindblindness” spurred interest among developmental psychologists and psychopathologists. The central questions for a comprehensive theory of mindreading are (1) how people mindread others, (2) how they mindread themselves, (3) how they acquire their mindreading abilities, and (4) what is the content of mental-state concepts.
Conceptualizing Simulation Theory
Authors: Goldman Alvin I. 
Published: September 2006

AbstractThis chapter clarifies the notion of simulation and explores the relationship between simulating and theorizing. Generic simulation is the resemblance or imitation of one thing by another, so mental simulation is the resemblance or imitation of one mental process by another. For example, visual imagery may simulate vision by using much of the same neural machinery that vision uses. The main empirical question here is whether third-person mindreading is substantially based on attempts to simulate selected processes and states in the head of a target. The possibility of limited compatibility between simulation and theorizing undercuts arguments that mental simulation inevitably “collapses” into theorizing, and the prospects for simulation-theory hybrids are explored.
High‐Level Simulational Mindreading
Authors: Goldman Alvin I. 
Published: September 2006

AbstractSimulation is first examined in the domains of visual and motor imagery, where brain imaging confirms that many of the same regions are activated in both visual imagery and vision, and in motor imagery and motor execution. An analogous use of simulation characteristically occurs in high-level mindreading. Since an important stage of simulation for mindreading requires reflection on one’s own current states, it is confirming evidence that neuroimaging studies find loci of activation in mindreading tasks that are also found in self-reflective thought. A distinctive feature of simulation is that it invites the risk that one’s own genuine states will contaminate the process; so it is further confirming evidence that mindreading studies consistently find pronounced egocentric errors. High-level mindreading involves assignment of contentful states, and content assignment follows the procedure predicted by simulation theory, viz., default use of one’s own concepts and combinatorial operations in assigning contents to others.
The Fabric of Social Life
Authors: Goldman Alvin I. 
Published: September 2006

AbstractMany of our distinctively human social traits are interwoven with simulational propensities. A stroll through simulation-related topics includes the psychological underpinnings of social bonds, our fascination with fiction, and the relevance of simulation and empathy to moral theory. The “chameleon effect”, which involves unconscious mimicry of facial expressions, postures, and mannerisms, promotes cohesion and liking within a group. Enactment imagination and empathy lie at the core of our experience of fiction. Emotional empathy, i.e., affective contagion, is a crucial determinant of the quality of life, and high-level empathy, or perspective taking, plays a critical role in moral motivation and moral principles, especially universalization principles like the golden rule.
Introduction
Authors: Gert Bernard , Culver Charles M. , Clouser K. Danner 
Published: September 2006

AbstractThis chapter provides a preview of the rest of the book, concentrating on the concept of morality. It distinguishes between a moral system and a moral theory, and gives a preliminary account of rationality and irrationality. It discusses the content of morality, showing that the avoidance of causing harms and the preventing of harms, rather than the promoting of benefits, is central to morality. It explains why, in addition to the general moral rules and ideals, there are particular moral rules and special duties that are part of the ethics of every profession.
Morality
Authors: Gert Bernard , Culver Charles M. , Clouser K. Danner 
Published: September 2006

AbstractThis chapter distinguishes between morality, the informal public system that people use when making moral decisions, and a moral theory, which provides an explanation and justification of morality. It presents some examples of mistaken accounts of morality, shows the relation between morality and rationality, and provides an account of impartiality. It gives an account of moral rules and moral ideals, and of the morally relevant features that are used when justifying a violation of a moral rule.
Malady
Authors: Gert Bernard , Culver Charles M. , Clouser K. Danner 
Published: September 2006

AbstractThis chapter introduces the technical term “malady” as a genus term that includes as species: diseases, disorders, injuries, allergies, illnesses, etc., and can be taken as meaning that something is wrong with the person. It provides a definition of malady that includes the following features: it is a condition of the individual, it involves significantly increased risk of suffering nontrivial harms, and there is no distinct sustaining cause. The role of abnormality in the defining malady and some difficult cases such as pregnancy, short stature, old age, and various genetic conditions are discussed.
Mental Maladies
Authors: Gert Bernard , Culver Charles M. , Clouser K. Danner 
Published: September 2006

AbstractThis chapter shows that the book’s account of malady generates the objective account of mental disorders that has been included in the Diagnostic and Statistical Manual of Mental Disorders (DSM) from DSM III R to DSM IV TR. It defends this definition from the criticisms of Jerome Wakefield and others, and explains why the DSM account of the paraphilias continues to change from DSM III R to DSM IV TR. An account of volitional disabilities and a classification of actions that distinguishes between intentional, voluntary, and free actions are also provided.
Adequate Information, Competence, and Coercion
Authors: Gert Bernard , Culver Charles M. , Clouser K. Danner 
Published: September 2006

AbstractThis chapter discusses what information doctors should be morally required to give to patients, and whether it should include the new kinds of information that doctors must know. Showing that the task a patient must be competent to perform is that of making a rational decision clarifies the relationship between rationality and competence, and explains the inadequacy of all previous accounts of competence. The chapter also explains why what counts as coercion with regard to research volunteers is not the same as what counts as coercion with regard to patients.
Ecological Thinking
Authors: Code Lorraine 
Published: September 2006

AbstractArguing that ecological thinking can animate an epistemology capable of addressing feminist, multicultural, and other post-colonial concerns, this book critiques the instrumental rationality, hyperbolized autonomy, abstract individualism, and exploitation of people and places that western epistemologies of mastery have legitimated. It proposes a politics of epistemic location, sensitive to the interplay of particularity and diversity, and focused on responsible epistemic practices. Starting from an epistemological approach implicit in Rachel Carson’s scientific projects, the book draws, constructively and critically, on ecological theory and practice, on (post-Quinean) naturalized epistemology, and on feminist and post-colonial theory. Analyzing extended examples from developmental psychology, from medicine and law, and from circumstances where vulnerability, credibility, and public trust are at issue, the argument addresses the constitutive part played by an instituted social imaginary in shaping and regulating human lives. The practices and examples discussed invoke the responsibility requirements central to this text’s larger purpose of imagining, crafting, articulating a creative, innovative, instituting social imaginary, committed to interrogating entrenched hierarchical social structures, en route to enacting principles of ideal cohabitation.
NEGOTIATING EMPIRICISM
Authors: Code Lorraine 
Published: September 2006

AbstractIn this chapter, an analysis of “statements of fact” in two domains of natural knowledge-making — medicine and law — shows how they enact sedimented assumptions about women, blacks, and other so-called social minorities. Hence, judgments and diagnoses alike reproduce structures of asymmetrical social power and privilege. The analysis recommends a negotiated empiricism: an empirically based and evidence-respecting position that takes observational evidence seriously, yet contends that evidence does not speak for itself in its claims to count as evidence or in its meanings and implications. The argument shows how experiential, testimonial reports claim an enhanced, if not uncontested, credibility and authority in this approach to knowledge. The chapter concludes with a critical reading of Donna Haraway’s “situated knowledges” as a principal contributor to the conceptual apparatus that frames ecological thinking.