bluuebunny/crossref_metadata_2025 huggingface dataset:
Physics for Philosophers
Authors: Bourne Craig
Published: February 2007

Discusses the Galilean transformations, and the Newtonian conception of space, time, and motion, essentials for understanding the Lorentz transformations and Einstein's special theory of relativity. Discusses, with the aid of many diagrams, the properties of Minkowski space‐time, such as the relativity of simultaneity, and concludes with some reflections on their philosophical significance.
All the Time in the Worlds: Gödel's Modal Moral
Authors: Bourne Craig
Published: February 2007

I discuss Gödel's philosophical position on the nature of time. I describe Gödel's model, which contains closed time‐like curves allowing us to take a journey into our future and arrive in our past, and show how it is incompatible with presentism. I do not discuss the well‐known implications of this for time travel, but focus on Gödel's subtler ‘modal’ argument. I discuss various ways of rejecting this argument and show that the conclusion that presentists must draw is that tense is not an essential feature of it: whether time is presentist or tenseless is an entirely contingent matter. I conclude by considering the extent to which metaphysics can tell us about the nature of time as it actually is.
Conclusion
Authors: Aghion Phillippe , Banerjee Abhijit
Published: February 2007

This chapter begins with a synthesis of the topics covered in the preceding chapters. It argues that in order to explain the recent boom and bust episode in the United States, one should turn attention to models of the stock market. It sketches an approach to booms and crashes that gives a central role to technical progress and the expansion of new markets.
Understanding People
Authors: Millar Alan
Published: February 2007

This book shows that ascriptions of beliefs and intentions are normative in that they have normative implications. Since there is no more to believing something and intending something than meeting the conditions for falling under, respectively, the concepts of so believing and of so intending, it follows that there is a normative dimension to the states of believing and intending. The idea is extended to all propositional attitudes via the assumption that attitudes with conceptual content have a normative dimension. The resulting picture is applied to issues about understanding people in terms of rationalizing explanations of what they think or do. An important concern is to explain how the fact that agents’ attitudes rationalize the performance of actions or the formation of beliefs on their part can be relevant to the explanation of what they do or believe. Along the way, there are discussions of normative commitments, differences between reasons for action and reasons for belief, practices conceived as essentially rule-governed activities, simulation theory, and the limits of mentalistic explanation.
CHAPTER IIntroduction
Authors: Millar Alan
Published: February 2007

The rationality assumption is to the effect that having propositional attitudes is inextricably tied to rationality in that there are limits to how incoherent our attitudes can be, which are imposed by the contents and roles of these attitudes. It is accepted that rationalizing explanation is causal and implicates generalizations, but this leads to the problem of the explanatory relevance of rationalization, which is addressed in Chapter 7. Consideration is given to various strategies designed to play down the significance of the rationality assumption for the issues about normativity and the mind. These include: arguing against the rationality assumption; denying that rationality is in any interesting sense normative; and adopting expressivism about rationality. It is suggested that we should think of our understanding of people as inseparable from normative considerations relating to the coherence and cogency of their thinking, and to their being or not being in touch with reality.
CHAPTER 2Reasons for Belief and for Action
Authors: Millar Alan
Published: February 2007

This chapter argues that all belief calls for justification and that, accordingly, a normative reason for a belief must justify or be positively relevant to the justification of that belief. This is explained in terms of the idea that belief constitutively aims at truth. It is argued (a) that while normative reasons for action must favour or recommend the action, they may do so merely by giving an instrumental point to the action, and (b) that it is far from clear that all intentional action calls for justification in anything like the sense in which beliefs call for justification. The classical view that intentional action constitutively aims at the good is rejected on the grounds that it does not square with the possibility of deeply perverse action. The relation between motivating and normative reasons for belief or action is discussed.
CHAPTER 4Explaining Normative Import
Authors: Millar Alan
Published: February 2007

This chapter discusses how to explain the relation between ascriptions of belief and intention, and statements ascribing the corresponding implication or means-end commitments. Dispositionalism about propositional attitudes must explain the link in terms of principles connecting a non-normative attitude ascription with a normative commitment. It is argued that such explanations are unsatisfactory because they cannot do justice to the peculiar character of our relation to our own current intentions and beliefs. Under dispositionalism, it would be possible to adopt a purely contemplative attitude to our current intentions and beliefs just as it is possible to adopt such an attitude to our character traits. Such an attitude to our current beliefs and intentions is not intelligible and we can make better sense of how we stand in relation to those beliefs and intentions if we assume that ascriptions of beliefs and intentions are implicitly normative.
CHAPTER 6Meaning and Intentional Content
Authors: Millar Alan
Published: February 2007

This chapter develops the idea that there is a normative dimension to all propositional attitudes in virtue of the fact that these attitudes have conceptual content. The starting point is Kripke’s critique of dispositionalism about semantic meaning. It is argued that meaning something by a term is a matter of participating in a practice of using that term in a manner that respects its conditions of correct, in the sense of true, application. The relevant normative commitment is to using the word in this way and is to be explained in terms of general considerations about practices. In the course of discussion, much is made of a distinction between correctness as true application and correctness as keeping faith with the meaning. It is argued that possessing a concept incurs a normative commitment of a sort that is structurally analogous to that implicated by semantic meaning.
Democracy in Europe
Authors: Schmidt Vivien A.
Published: February 2007

This book focuses on the impact of European integration on national democracies. It argues that the democratic deficit is indeed a problem, but not so much at the level of the European Union per se as at the national level. This is because national leaders and publics have yet to come to terms with the institutional impact of the EU on the traditional workings of their national democracies. The book begins with a discussion of what the EU is — a new form ofregional statein which sovereignty is shared, boundaries are variable, identity composite, and democracy fragmented. But the main focus of the book is on how the EU has altered national governance practices, thereby challenging national ideas about democracy. It finds that the EU’s ‘policy without politics’ has led to ‘politics without policy’ at the national level. The book also shows that institutional ‘fit’ matters. The compound EU, in which governing activity is highly dispersed among multiple authorities, is more disruptive to simple polities like Britain and France, where governing activity has traditionally been more concentrated in a single authority, than to similarly compound polities like Germany and Italy. The book concludes that the real problem for member-states is not so much that their democratic practices have changed as that national ideas and discourse about democracy have not. The failure has been one of the communicative discourse to the general public — a problem which again has been more pronounced for simple polities, despite political leaders’ potentially greater capacity to communicate through a single voice, than for compound polities, where the coordinative discourse among policymakers predominates.
3 The European Union and National Policymaking
Authors: Schmidt Vivien A.
Published: February 2007

This chapter begins with a brief overview of the EU’s policymaking processes in comparison with national processes. It then outlines the EU’s impact on the macro patterns of its member-states’ national policymaking and its impact on the micro patterns of member-states’ sectoral policymaking. This is followed by an extensive illustration of both macro and micro patterns of policymaking in France, Britain, Germany, and Italy. Although Europeanization has been equally (although differently) disruptive to the statist patterns of policymaking of France and of Britain, Britain has had a harder time accepting EU-related changes but an easier time in influencing their formulation. Europeanization has yet again been least disruptive to Germany’s corporatist and legalistic patterns of policymaking, and most salutary to those of Italy, by reinforcing corporatism while denying clientelism.
Conclusion: The Prospects for Democracy in Europe
Authors: Schmidt Vivien A.
Published: February 2007

This concluding chapter argues that the prospects for democracy in the EU are nevertheless good so long as national leaders and national publics face up to the problems. But facing up to the problems will not be easy. For the EU level, it requires recognizing that for the time being, at least, reinforcing democracy cannot mean creating more governing by and of the people through any directly elected government. And yet more ‘democracy’ is clearly required. The difficulty is that doing more with regard to democracy butts up against the contradictions inherent in the fragmented basis of EU democracy.
LOST CHORDS
Authors: Wilson Mark
Published: February 2007

‘Where do musical or colour traits get primarily instantiated, directly in the physical world or merely within the realms of our own subjectivity?’ This chapter surveys how popular resolutions of this traditional philosophical question sometimes affect real life practical decisions in unfortunate ways. Several cases involving musical preservation are provided to illustrate this theme.
SEMANTIC MIMICRY
Authors: Wilson Mark
Published: February 2007

Distinct forms of linguistic strategy can masquerade for one another quite ably — early chapters illustrated how serious philosophical confusions often arise when a facade-structured language is mistaken for a simpler, classical usage. In this chapter, some of Hume's celebrated worries about causation are traced to several allied forms of semantic masquerade.
Pleasure and Social Utility: The Virtues of Being Epicurean
Authors: Long A. A.
Published: February 2007

The Epicurean explanation for the origin of community life and laws was the utility of these institutions in facilitating people's natural and necessary desires for a secure life. In advising his followers to ‘live quietly’, Epicurus has at least three defences to advance against the criticism that such a lifestyle is politically irresponsible and morally complacent. First, he can argue that his ethical theory provides human beings, who are natural and persistent pleasure seekers, with the strongest of reasons for the peaceful cooperation that legal systems seek to promote. Second, he can argue that contemporary societies, even if they do provide some measure of security for their members, do so inadequately; and that they compound these failings by systems of education, competitive values, religion, and other practices which do great harm to their citizens. Third, he can argue that the Epicurean way of life, which threatens no one in its scrupulous adherence to justice and is positively philanthropic in its cultivation of friendship, provides society with a model of how to live best at the present stage of human culture. This chapter develops this set of arguments from three perspectives or bodies of material: the basic ethical theory, justice and friendship, and social evolution.
Cicero's Politics inDe officiis
Authors: Long A. A.
Published: February 2007

TheDe officiis(henceforthOff.) is one of the ‘great books’, but no one today perhaps can read it with fresh eyes. Less obvious aboutOff. is the work's radical nature in its effort to reform Roman ideology. ApproachingOff., as Cicero encourages us to do via his adaptation of Panaetius, interpreters are tempted to read it as Greek philosophy in Roman dress, or — to cite Miriam Griffin — as ‘a fusion of Greek philosophical precepts with the traditional values of the great Roman statesmen of the past’. It is argued that this temptation should be resisted. It is too bland to represent Cicero's existential situation, at the time when he wrote. It is also too bland to register the problems Roman ideology had generated and Cicero's proposed solutions to them.
Philosopher‐Kings and Queens
Authors: O’Meara Dominic J.
Published: February 2007

This chapter explores the reasons why a philosopher should take an interest in political life, as these reasons were discussed by Neoplatonists: the motivation derives from sharing in the absolute Good. The question of the philosopher-king’s happiness (can it suffer from political involvement?) is also discussed, as is the Neoplatonic defence of Plato’s claim that women philosophers should also rule (philosopher-queens).
Eusebius and Augustine
Authors: O’Meara Dominic J.
Published: February 2007

This chapter discusses the extent to which Eusebius’ Christian politics of theocracy and Augustine’s rejection both of pagan political theory and of Christian theocracy (in the City of God) may relate as Christian reactions to the political philosophy reconstructed in Parts II and III of this book.
8 Conclusion
Authors: Reilly Benjamin
Published: February 2007

This concluding chapter discusses the implications of reform trends for political development in the Asia-Pacific region and for new democracies in other parts of the world. It is argued that there is indeed an emerging Asian model of democracy — but one that has little relationship with the political restrictions advocated by the region’s now-retired autocrats. Rather, in something of a grand irony, the political systems of most new Asia-Pacific democracies are not only becoming more consolidated, but in many cases are actually moving closer to the Anglo-American model of two-party democracy.
6 GERMANY: A REACTIVE AND PASSIVE COORDINATOR?
Authors: Jordan Andrew , Schout Adriaan
Published: February 2007

This chapter analyses the administrative capacities that this actor has developed to coordinate the implementation of EPI across the whole of the EU (that is, EU-EPI). In so doing, it moves on from looking at the ways in which this particular actor operates in its immediate institutional space, to gauge how all the actors coordinate together in a network or networks. This chapter is written to fit a standard analytical framework, which is outlined in Chapter 2.
2 William Hone
Authors: Larsen Timothy
Published: February 2007

This chapter explores the life of William Hone. It pays particular attention to his thought as a freethinker, parodist, and alleged blasphemer that led to his famous trials. His atheist phase was influenced by Baron d’Holbach’s System of Nature. It then goes on to explore the contours of his reconversion and his later Christian thought.
9 How Many Reconverts Were There?
Authors: Larsen Timothy
Published: February 2007

This chapter argues that the crisis of doubt in the world of popular freethought was a deep one. A significant percentage of Secularist leaders reconverted.
Objects, Names, Facts, and Propositions
Authors: McManus Denis
Published: February 2007

This chapter presents some of the crucial proposals that the Tractatus offers concerning the nature of objects, facts, propositions, names, and what he calls ‘the internal relation of depicting that holds between language and world’. It explores how Wittgenstein defends these proposals on the grounds that they free us from any commitment to there being impossibly ‘substantial’ logical truths. It sketches a possible interpretation of those proposals as articulating, nonetheless, a species of what is called ‘con-formism’ (cf. Ch.1), a species which is distinctive in being, strictly speaking, inexpressible. It goes on to argue that this interpretation is mistaken. An argument against con-formism is presented and how Wittgenstein’s sign/symbol distinction helps to articulate the confusion that con-formism embodies is explained.
The Picture Analogy
Authors: McManus Denis
Published: February 2007

This chapter presents an interpretation of Wittgenstein’s proposal that we see propositions as analogous to pictures. Thinking through this analogy in the way that Wittgenstein suggests reveals both a certain truth in his proposal that propositions and the names that make up those propositions are ‘internally related’, and a confusion in the belief that there is a substantial and philosophically interesting ‘relation’ to be found here. It is argued that the picture analogy helps us recognize ‘the illogical’ as merely the product of sign/symbol confusions, something that is not recognized by those who attempt to explain how ‘the logical’ differs from ‘the illogical’ on the basis of a substantial philosophy of thought and language.
Problem Cases for the General Form
Authors: McManus Denis
Published: February 2007

This chapter examines how Wittgenstein envisaged the analysis of some important kinds of proposition that, at least superficially, do not fit the requirements of the general form of the proposition. General propositions represent a fundamental and central case in point and an explanation is offered of how Wittgenstein might have imagined their analysis. This explanation draws on ideas set out earlier in the book concerning the articulation of how particular languages and models ‘make sense’, the character of ‘logical types’ and ‘the illogical’, and Wittgenstein’s philosophical ambitions for notational reforms.
6 Communion and Discipline
Authors: Holmes Andrew R.
Published: February 2007

The first section of this chapter examines the communal, personal, and practical preparations for communion, including a general discussion of the practice of church discipline. The last two sections explore the organization, structure, and meaning of the communion season while highlighting some of the changes and continuities in the 19th century, particularly the impact of the reforms promoted by Presbyterian evangelicals.
9 Death
Authors: Holmes Andrew R.
Published: February 2007

This chapter examines two areas of practice to illustrate how Ulster Presbyterians perceived both life and death. Section one deals with wakes, their social character, the various popular beliefs that surrounded death, and the efforts of the Presbyterian authorities to reform perceived abuses. Section two examines the rituals of the deathbed, specifically the differences and shared experiences of evangelical and liberal Presbyterians as they attempted to ‘die well’.
Gender and Justice in Multicultural Liberal States
Authors: Deveaux Monique
Published: February 2007

This book explores the challenges that culturally plural liberal states face when they hold competing political commitments to cultural rights and sexual equality, and advances an argument for resolving such dilemmas through democratic dialogue and negotiation. Exploring recent examples of gendered cultural conflicts in South Africa, Canada, and Britain, this study shows that there is an urgent need for workable strategies to mediate the antagonisms between the cultural practices and arrangements of certain ethno-cultural and religious groups, and the norms and constitutional rights endorsed by liberal states. Yet such strategies will be successful only insofar as they can resolve conflicts without either reinforcing women’s subordination within cultural communities or unjustly dismissing calls for cultural recognition and forms of self-governance. To this end, the book develops an approach to mediating cultural tensions that takes seriously the demands for justice by cultural and religious minorities in liberal democratic states. Grounded in an argument for democratic legitimacy, this approach invokes norms of political inclusion and democratic dialogue, and highlights negotiation and compromise as the best vehicles for arriving at resolutions to conflicts of cultural value. However, the book also reconceives the basis of democratic legitimacy so as to include not merely formal expressions of political consent, but also a range of informal democratic activities that occur in the private and social spheres, from acts of cultural reinvention and subversion to outright expressions of dissent and cultural refusal.
4 Democratic Deliberation: Empowering Cultural Communities
Authors: Deveaux Monique
Published: February 2007

This chapter argues that deliberative democracy theory is an invaluable resource for thinking about how liberal democracies and minority cultural groups might mediate conflicts of culture. However, it needs to be amended in important ways if it is to respond to the needs of minority cultural communities. This chapter makes the case for a deliberative democratic approach to resolving tensions between gender equality and cultural recognition, grounding it in principle of political inclusion and democratic legitimacy. This conception of democratic deliberation is open-ended with respect to outcomes, and takes its cue from an agonistic account of power and dialogue rather than the reasoned deliberation usually urged by proponents of discourse ethics, such as Jürgen Habermas, Joshua Cohen, and Seyla Benhabib. This approach to negotiating conflicts, which emphasizes negotiation and compromise, can also help to empower vulnerable members of cultural groups who dissent from prevailing cultural roles and arrangements in their communities.
The Worldview of Personalism
Authors: Bengtsson Jan Olof
Published: February 2007

The book challenges the current view that personalism is primarily an early 20th-century phenomenon. The established definitions of personalism, mainly in terms of the American school of B. P. Bowne, are shown to fit broadly the positions of much earlier continental European and Scandinavian philosophers and theologians. The beginnings of specifically personalistic thought are traced to F. H. Jacobi’s criticism of pantheism, first set forth in the 1780s, and the work of the later F. W. J. Schelling. Its development is then identified in the work of selected, representative thinkers who, throughout the 19th century, build on or develop further positions established by Jacobi and Schelling, primarily the thinkers belonging to the broad current of so-called ‘speculative theism’ in Germany and in Sweden. The development of idealistic personalism in Britain by A. S. Pringle-Pattison, J. R. Illingworth, C. C. J. Webb and others is shown to be parallel to the emergence of the American school. It is argued that these should be seen as a continuation of the earlier European movement. Both the American and the British schools drew on the work of H. Lotze, but the book points to the neglected continental European background to Lotze, the current of personalistic, partly idealistic, and theistic philosophy of which Lotze’s work was only one, late variation. Discerning the central themes of the emerging worldview of personalism, the book establishes that they developed consistently in a broad, unitary movement with a distinct historical profile from the late 18th to the early 20th centuries, the nature and importance of which has heretofore been neglected in the history of philosophy and in historical theology.
4 Personal unity‐in‐diversity
Authors: Bengtsson Jan Olof
Published: February 2007

This chapter presents a broader picture of the whole of the worldview that results from the themes introduced in earlier chapters: reality is conceived as a system of related personalities, of God and finite persons, the dynamic principle and living content of which is determined, more or less, by the reciprocity of the I-Thou-relation. The view of the society of persons is also shown to have consequences for the understanding of the moral order as personal and impersonal ethics are distinguished, and, with a terminological shift in the later personalists, for the questions of the relation of ‘values’ to the person.
De novo SVM classification of precursor microRNAs from genomic pseudo hairpins using global and intrinsic folding measures
Authors: Ng Kwang Loong Stanley , Mishra Santosh K.
Published: February 2007

Motivation: MicroRNAs (miRNAs) are small ncRNAs participating in diverse cellular and physiological processes through the post-transcriptional gene regulatory pathway. Critically associated with the miRNAs biogenesis, the hairpin structure is a necessary feature for the computational classification of novel precursor miRNAs (pre-miRs). Though many of the abundant genomic inverted repeats (pseudo hairpins) can be filtered computationally, novel species-specific pre-miRs are likely to remain elusive.

Results:  miPred is a de novo Support Vector Machine (SVM) classifier for identifying pre-miRs without relying on phylogenetic conservation. To achieve significantly higher sensitivity and specificity than existing (quasi) de novo predictors, it employs a Gaussian Radial Basis Function kernel (RBF) as a similarity measure for 29 global and intrinsic hairpin folding attributes. They characterize a pre-miR at the dinucleotide sequence, hairpin folding, non-linear statistical thermodynamics and topological levels. Trained on 200 human pre-miRs and 400 pseudo hairpins, miPred achieves 93.50% (5-fold cross-validation accuracy) and 0.9833 (ROC score). Tested on the remaining 123 human pre-miRs and 246 pseudo hairpins, it reports 84.55% (sensitivity), 97.97% (specificity) and 93.50% (accuracy). Validated onto 1918 pre-miRs across 40 non-human species and 3836 pseudo hairpins, it yields 87.65% (92.08%), 97.75% (97.42%) and 94.38% (95.64%) for the mean (overall) sensitivity, specificity and accuracy. Notably, A.mellifera, A.geoffroyi, C.familiaris, E.Barr, H.Simplex virus, H.cytomegalovirus, O.aries, P.patens, R.lymphocryptovirus, Simian virus and Z.mays are unambiguously classified with 100.00% (sensitivity) and >93.75% (specificity).

Availability: Data sets, raw statistical results and source codes are available at http://web.bii.a-star.edu.sg/~stanley/Publications

Contact: stanley@bii.a-star.edu.sg; santosh@bii.a-star.edu.sg

Supplementary information: Supplementary data are available at Bioinformatics online.
RETRACTED: Spike protein of SARS‐CoV stimulates cyclooxygenase‐2 expression via both calcium‐dependent and calcium‐independent protein kinase C pathways
Authors: Liu Mo , Yang Yongbo , Gu Chunfang , Yue Yinpu , Wu Kenneth K. , Wu Jianguo , Zhu Ying
Published: February 2007

We have previously shown that the nucleocapsid protein of SARS‐associated coronavirus (SARS‐CoV) activated cyclooxygenase‐2 (COX‐2) expression (1). In this study, we identified another viral protein, the spike of SARS‐CoV, which played an important role in virus‐stimulated COX‐2 expression after screening all genes from the SARS‐CoV genome. We found that an upstream calcium‐dependent PKC isozyme PKCα that modulates the downstream ERK/ NF‐κB pathway through an influx of extracellular Ca2+ is induced by the spike protein of SARS‐CoV. The ERK/NF‐κB was identified to be involved in the activation of COX‐2 promoter and production of COX‐2 protein in HEK293T cells. We also demonstrated that another unusual pathway, the calcium‐independent PI3K/PKCε/JNK/CREB pathway, functioned in cooperation with the calcium‐dependent pathway to induce COX‐2 expression upon stimulation by spike protein. This pathway can be blocked by PKCε‐specific, small interfering RNA, PI3K/JNK kinase‐specific inhibitors as well as dominant negative JNK. PKCε‐specific siRNA also attenuated the phosphorylation of JNK. Our results provide evidence that helps us understand the function of SRAS‐CoV spike protein in SARS pathogenesis.—Liu, M., Yang, Y., Gu, C., Yue, Y., Wu, K. K., Wu, J., Zhu, Y. Spike protein of SARS‐CoV stimulates cyclo‐oxygenase‐2 expression via both calcium‐dependent and calcium‐independent protein kinase C pathways. FASEB J. 21, 1586–1596 (2007)
Efficacy of Radiologic Screening for Distant Metastases and Second Primaries in Newly Diagnosed Patients With Head and Neck Cancer
Authors: Jäckel Martin C. , Reischl Andrea , Huppert Peter
Published: February 2007

Objectives: Detection of distant metastases and second primary tumors in newly diagnosed patients with head and neck cancer has usually a major effect on prognosis but does not always influence clinical management. This must be considered when radiologic screening investigations are used. The present study particularly evaluates how often additional neoplastic lesions detected by screening had an impact on therapy.

Study Design: The authors conducted a single‐institution retrospective analysis.

Methods: The medical records of 260 patients with newly diagnosed squamous cell carcinoma of the head and neck treated between 1999 and 2002 were retrospectively analyzed. Before therapy, all patients had undergone screening by computed tomography scan of the chest, abdominal ultrasound, and bone scintigraphy.

Results: Screening investigations identified 16 patients (6.2%) with distant metastases and six patients (2.3%) with simultaneous second primaries. Chest computed tomography scan detected 20 neoplastic lesions; abdominal ultrasound and bone scintigraphy each detected 2. Three findings of distant metastases proved to be false‐positive during follow up. Of the 22 patients with positive screening results, clinical management was affected in 13 (59.1%). Twelve were originally scheduled for curative surgery and 10 had chest abnormalities.

Conclusion: Chest computed tomography scan was the most effective screening investigation, which should be routinely used whenever curative surgery of head and neck cancer is planned. Abdominal ultrasound and bone scintigraphy may sometimes be valuable before extensive surgical treatment of far advanced disease. In patients scheduled for primary radiotherapy, radiologic screening had hardly any consequence and should be confined to conventional x‐ray of the chest.
Identification of Viruses in Patients With Postviral Olfactory Dysfunction
Authors: Suzuki Motohiko , Saito Koichi , Min Wei‐Ping , Vladau Costin , Toida Kazunori , Itoh Hirotaka , Murakami Shingo
Published: February 2007

Objective: Causative viruses of postviral olfactory dysfunction (PVOD) have not yet been identified. The aim of this study was to investigate causative viruses in patients with PVOD.

Study Design and Methods: Nasal discharge was collected from 24 patients with PVOD. We investigated the presence of 10 viruses in nasal discharge and examined the time course, with regard to changes in olfactory dysfunction and nasal obstruction in patients with PVOD, using questionnaires, acoustic rhinometry, and olfactory tests.

Results: Rhinoviruses were detected in 10 patients by electrophoresis. Rhinoviruses were also confirmed in four patients by nucleotide sequences. Viral serotypes were identified to be human rhinovirus (HRV)‐40, HRV‐75, HRV‐78, and HRV‐80. One of the four patients complained of anosmia, whereas another complained of dysosmia. Olfactory testing did not show significant improvement at 4, 8, 11, and 24 weeks after the first visit in the four patients, although results of acoustic rhinometry significantly improved. Two of the four patients complained of olfactory dysfunction even 6 months after the first visit. Coronavirus and parainfluenza virus were detected in one patient each, and Epstein‐Barr viruses were detected in three patients.

Conclusions: This study for the first time detected rhinovirus, coronavirus, parainfluenza virus, and Epstein‐Barr virus in nasal discharge of patients with PVOD. Furthermore, the present study suggests that rhinoviruses can cause olfactory dysfunction through mechanisms other than nasal obstruction and that rhinoviruses can induce various severities and different time courses of olfactory dysfunction.
Anatomic Continuity of Longitudinal Pharyngeal and Esophageal Muscles
Authors: Wang Qin , Xu Shengchun , Tu Lili , Liu Yehai , Zhang Ming
Published: February 2007

Objectives: The pharyngeal and esophageal shortenings during deglutition are attributable to longitudinal muscle contraction. The two shortenings may be independent events because the longitudinal pharyngeal and esophageal muscular insertions are believed to be separated from each other. The aim of this study was to investigate the superior attachments of the longitudinal esophageal muscle.

Study Design: Prospective.

Methods: With use of dissection, sectional anatomy, and confocal microscopy, 30 adult cadavers were examined in this study.

Results: We found that the longitudinal esophageal muscle fibers had multiple superior insertions. Some of the fibers were continuous with the longitudinal pharyngeal muscles and merged with a membrane‐like fascia that anchored the pharyngoesophageal wall to the thyroid cartilage.

Conclusions: This study demonstrates that the longitudinal pharyngeal and esophageal muscle fibers are continuous with each other and are integrated with fibrous and cartilaginous structures. Such anatomic integrity at the pharyngoesophageal junction is important for the function of the upper esophageal sphincter.
Lentibacillus kapialis sp. nov., from fermented shrimp paste in Thailand
Authors: Pakdeeto Amnat , Tanasupawat Somboon , Thawai Chitti , Moonmangmee Somporn , Kudo Takuji , Itoh Takashi
Published: February 2007

Two strains of strictly aerobic, moderately halophilic Gram-positive rods were isolated from fermented shrimp paste (‘ka-pi’) produced in Thailand. They produced a red pigment and grew optimally in the presence of 5–30 % NaCl. The diagnostic diamino acid in the cell-wall peptidoglycan wasmeso-diaminopimelic acid. The predominant menaquinone was MK-7. The major cellular fatty acid was anteiso-C15 : 0. Phosphatidylglycerol, diphosphatidylglycerol and two unidentified glycolipids were found to be the major polar lipid components. The DNA G+C content was 41.2–41.6 mol%. Comparative 16S rRNA gene sequence analyses showed that strain PN7-6Twas most closely related toLentibacillus salariusKCTC 3911Twith 96.5 % sequence similarity. On the basis of phenotypic and molecular properties, the two isolates represent a novel species of the genusLentibacillus, for which the nameLentibacillus kapialissp. nov. is proposed. The type strain is PN7-6T(=JCM 12580T=PCU 259T=TISTR 1551T).
Oceanobacillus chironomi sp. nov., a halotolerant and facultatively alkaliphilic species isolated from a chironomid egg mass
Authors: Raats Dina , Halpern Malka
Published: February 2007

Chironomids (Diptera; Chironomidae) are the most abundant insects in freshwater aquatic habitats. Females of the genus Chironomus lay egg masses containing hundreds of eggs embedded in a gelatinous matrix. A bacterial strain, designated T3944DT, was isolated from a chironomid egg mass sampled from a waste-stabilization pond in northern Israel and was found to be Gram-positive, motile by peritrichous flagella, endospore-forming, halotolerant and facultatively alkaliphilic. Comparative 16S rRNA gene sequence analysis showed that strain T3944DT belonged to the genus Oceanobacillus, exhibiting the highest levels of similarity with the sequences of Oceanobacillus oncorhynchi subsp. incaldanensis DSM 16557T (94.9 %), Oceanobacillus oncorhynchi subsp. oncorhynchi JCM 12661T (94.8 %), Oceanobacillus iheyensis JCM 11309T (94.7 %) and Oceanobacillus picturae LMG 19416 (94.5 %). Strain T3944DT grew optimally at 1–3 % NaCl, pH 8.5 and 37 °C. The major cellular fatty acids were anteiso-C15 : 0 (60.0 %) and anteiso-C17 : 0 (12.9 %) and the DNA G+C content was 38.1 mol%. On the basis of its phenotypic properties and phylogenetic distinctiveness, strain T3944DT represents a novel species in the genus Oceanobacillus, for which the name Oceanobacillus chironomi sp. nov. is proposed. The type strain is T3944DT (=LMG 23627T=DSM 18262T).
Maribius salinus gen. nov., sp. nov., isolated from a solar saltern and Maribius pelagius sp. nov., cultured from the Sargasso Sea, belonging to the Roseobacter clade
Authors: Choi Dong H. , Cho Jang-Cheon , Lanoil Brian D. , Giovannoni Stephen J. , Cho Byung C.
Published: February 2007

Two strictly aerobic, Gram-negative bacteria, designated strains CL-SP27T and B5-6T, were isolated from the hypersaline water of a solar saltern in Korea and from the surface water of the Sargasso Sea, respectively. The two strains were rod-shaped, non-motile and grew on marine agar 2216 as beige colonies. Phylogenetic analyses of 16S rRNA gene sequences revealed a clear affiliation of the novel strains to the family Rhodobacteraceae. However, the novel strains were only distantly related to members of the Roseobacter clade, forming a distinct lineage. Although the 16S rRNA gene sequence similarity between strains CL-SP27T and B5-6T was very high (99.6 %), DNA–DNA relatedness between the strains was 48.4 %, suggesting that the strains be categorized as two genospecies. Additionally, the two novel strains could be differentiated by DNA G+C contents, fatty acid profiles, carbon source utilization patterns, antibiotic susceptibilities and biochemical characteristics. Based on taxonomic data obtained in this study, strains CL-SP27T and B5-6T represent separate species within a novel genus of the family Rhodobacteraceae, for which the names Maribius salinus gen. nov., sp. nov. (type species) and Maribius pelagius sp. nov. are proposed. The type strains of Maribius salinus and Maribius pelagius are CL-SP27T (=KCCM 42113T=JCM 13037T) and B5-6T (=KCCM 42336T=JCM 14009T), respectively.
Sergeia podlipaevi gen. nov., sp. nov. (Trypanosomatidae, Kinetoplastida), a parasite of biting midges (Ceratopogonidae, Diptera)
Authors: Svobodová Milena , Zídková Lenka , Čepička Ivan , Oborník Miroslav , Lukeš Julius , Votýpka Jan
Published: February 2007

Three strains of a trypanosomatid protozoan were isolated from the midguts of two naturally infected species of biting midges [Culicoides (Oecacta) festivipennis and Culicoides (Oecacta) truncorum] and characterized by light and electron microscopy and by molecular techniques. Morphological characteristics and sequences of the 18S rRNA, 5S rRNA, spliced leader RNA and glycosomal glyceraldehyde-3-phosphate dehydrogenase genes indicate that the studied flagellates represent a novel phylogenetic lineage within the Trypanosomatidae. Based on phylogenetic analyses, the novel endosymbiont-free, monoxenous trypanosomatid was classified as Sergeia podlipaevi gen. nov., sp. nov. Interestingly, it is closely related to another trypanosomatid species that parasitizes the sand fly Lutzomyia evansi, a blood-sucking dipteran from South America. The type strain of S. podlipaevi sp. nov., ICUL/CZ/2000/CER3, was obtained from Malpighian tubes. Of 2518 females of seven species of biting midges trapped in the Czech Republic, more than 1.5 % were infected by trypanosomatid parasites. An unrelated insect species, Culicoides (Monoculicoides) nubeculosus, was experimentally infected with S. podlipaevi, demonstrating that its host range extends to different subgenera of biting midges.
Clostridium aciditolerans sp. nov., an acid-tolerant spore-forming anaerobic bacterium from constructed wetland sediment
Authors: Lee Yong-Jin , Romanek Christopher S. , Wiegel Juergen
Published: February 2007

An obligately anaerobic, spore-forming, moderately acid-tolerant bacterium, strain JW/YJL-B3T, was isolated from a sediment sample from a constructed wetland system receiving acid sulfate water. Based on 16S rRNA gene sequence analysis, the isolate belonged to the Firmicutes branch with Clostridium drakei SL1T (96.2 % gene sequence similarity) as its closest relative. The G+C content of the genomic DNA was 30.8 mol% (HPLC). Cells were straight to curved rods, 0.5–1.0 μm in diameter and 3.0–9.0 μm in length. The temperature range for growth was 20–45 °C, with an optimum around 35 °C. Growth was not detected below 18 °C or above 47 °C. The pH range for growth was broad, pH25 °C 3.8–8.9, with an optimum at 7.0–7.5. However at pH 4.5, the strain grew at 52 % of the optimal growth rate. The salinity range was 0–1.5 % NaCl (w/v). Strain JW/YJL-B3T utilized beef extract, Casamino acids, peptone, tryptone, arabinose, cellobiose, fructose, galactose, glucose, lactose, maltose, mannose, raffinose, ribose, sucrose, xylose, pyruvate, glutamate and inulin as a carbon and energy source. There were no indications of growth under aerobic or autotrophic conditions. The isolate produced acetate, butyrate and ethanol as fermentation end products from glucose. Based on these characteristics and other physiological properties, the isolate is placed into the novel taxon, Clostridium aciditolerans sp. nov., with strain JW/YJL-B3T (=DSM 17425T=ATCC BAA-1220T) as the type strain.
Lactobacillus namurensis sp. nov., isolated from a traditional Belgian sourdough
Authors: Scheirlinck Ilse , Van der Meulen Roel , Van Schoor Ann , Cleenwerck Ilse , Huys Geert , Vandamme Peter , De Vuyst Luc , Vancanneyt Marc
Published: February 2007

A biodiversity study on lactic acid bacteria (LAB) occurring in traditional Belgian sourdoughs resulted in the isolation of two Lactobacillus isolates, LMG 23583T and LMG 23584, that could not be assigned to any recognized LAB species. The two isolates were initially investigated by means of phenylalanyl-tRNA synthase (pheS) gene sequence analysis and were found to occupy a separate position relative to recognized Lactobacillus species present in the pheS database. Subsequently, their phylogenetic affiliation was determined by 16S rRNA gene sequence analysis, indicating that the two isolates belong to the Lactobacillus buchneri species group with Lactobacillus zymae, Lactobacillus acidifarinae and Lactobacillus spicheri as closest relatives. Whole-cell protein analysis (SDS-PAGE) and amplified fragment length polymorphism fingerprinting of whole genomes confirmed their separate taxonomic status. DNA–DNA hybridization experiments, DNA G+C content, growth characteristics and biochemical features demonstrated that the two isolates represent a novel Lactobacillus species, for which the name Lactobacillus namurensis sp. nov. is proposed. The type strain is LMG 23583T (=CCUG 52843T).
Sediminibacter furfurosus gen. nov., sp. nov. and Gilvibacter sediminis gen. nov., sp. nov., novel members of the family Flavobacteriaceae
Authors: Khan Shams Tabrez , Nakagawa Yasuyoshi , Harayama Shigeaki
Published: February 2007

Two Gram-negative, chemoheterotrophic, non-motile strains, Mok-1-36T and MAOS-86T, were isolated from marine-sediment samples collected from the coasts of Okinawa island and the city of Odawara in Japan, respectively. Phylogenetic studies based on 16S rRNA gene sequences indicated that Mok-1-36T and MAOS-86T were members of the family Flavobacteriaceae, clustering with members of the genera Ulvibacter and Vitellibacter, respectively. Strains Mok-1-36T and MAOS-86T shared pairwise 16S rRNA gene sequence similarities of 93.5 and 89.1 % with the type strains of Ulvibacter litoralis and Vitellibacter vladivostokensis, respectively. Phylogenetic distinctiveness and phenotypic differences from their phylogenetic neighbours indicated that these strains represent two novel species and genera within the family Flavobacteriaceae, for which the names Sediminibacter furfurosus gen. nov., sp. nov. (MAOS-86T) and Gilvibacter sediminis gen. nov., sp. nov. (Mok-1-36T) are proposed. The type strain of Sediminibacter furfurosus is MAOS-86T (=NBRC 101622T=CIP 109285T) and the type strain of Gilvibacter sediminis is Mok-1-36T (=NBRC 101626T=CIP 109286T).
Barnesiella viscericola gen. nov., sp. nov., a novel member of the family Porphyromonadaceae isolated from chicken caecum
Authors: Sakamoto Mitsuo , Lan Pham Thi Ngoc , Benno Yoshimi
Published: February 2007

Two bacterial strains isolated from chicken caecum, C46Tand C47, were characterized using a polyphasic taxonomic approach that included analysis of the phenotypic and biochemical features, cellular fatty acid profiles, menaquinone profiles and phylogenetic position (using 16S rRNA gene sequence analysis). The 16S rRNA gene sequence analysis showed that these strains belonged to the familyPorphyromonadaceae. These strains shared 100 % 16S rRNA gene sequence similarity with each other and were related toParabacteroides distasonis(showing 86 % sequence similarity). The strains were found to be obligately anaerobic, non-pigmented, non-spore-forming, non-motile, Gram-negative rods. Growth of the strains was inhibited on medium containing 20 % bile. The major menaquinones of the isolates were MK-11 and MK-12. This menaquinone composition was different from those of other genera of the familyPorphyromonadaceae, such asParabacteroides(in which the predominant menaquinones are MK-9 and MK-10),Porphyromonas(MK-9 and MK-10) andTannerella(MK-10 and MK-11). This is an important chemotaxonomic characteristic of these micro-organisms. The DNA G+C content of strain C46Tis 52.0 mol%. On the basis of these data, strains C46Tand C47 represent a novel genus and species, for which the nameBarnesiella viscericolagen. nov., sp. nov. is proposed. The type strain ofBarnesiella viscericolais C46T(=JCM 13660T=DSM 18177T).
Efficient high-resolution deletion discovery inCaenorhabditis elegansby array comparative genomic hybridization
Authors: Maydan Jason S. , Flibotte Stephane , Edgley Mark L. , Lau Joanne , Selzer Rebecca R. , Richmond Todd A. , Pofahl Nathan J. , Thomas James H. , Moerman Donald G.
Published: February 2007

We have developed array Comparative Genomic Hybridization forCaenorhabditis elegansas a means of screening for novel induced deletions in this organism. We designed three microarrays consisting of overlapping 50-mer probes to annotated exons and micro-RNAs, the first with probes to chromosomes X and II, the second with probes to chromosome II alone, and a third to the entire genome. These arrays were used to reliably detect both a large (50 kb) multigene deletion and a small (1 kb) single-gene deletion in homozygous and heterozygous samples. In one case, a deletion breakpoint was resolved to fewer than 50 bp. In an experiment designed to identify new mutations we used the X:II and II arrays to detect deletions associated with lethal mutants on chromosome II. One is an 8-kb deletion targeting theast-1gene on chromosome II and another is a 141-bp deletion in the geneC06A8.1. Others span large sections of the chromosome, up to >750 kb. As a further application of array Comparative Genomic Hybridization inC. eleganswe used the whole-genome array to detect the extensive natural gene content variation (almost 2%) between the N2 Bristol strain and the strain CB4856, a strain isolated in Hawaii and JU258, a strain isolated in Madeira.
Configuration, Column Construction, and Column Packing for a Capillary Liquid Chromatography System
Authors: Moritz Robert L.
Published: February 2007

INTRODUCTION

Capillary or microcolumn (<0.5-mm internal diameter, I.D.) high-performance liquid chromatography (HPLC) is an extremely powerful technique for separating small quantities of proteins and peptides. This protocol describes a procedure for adapting conventional HPLC systems to provide accurate low-flow rates (0.4-4 μl/min) and gradients required to operate slurry-packed capillary columns. A key component of this system is a commercial axial-beam longitudinal flow cell that can be fitted to several commercial UV detectors. Procedures are described for the fabrication of 0.32-mm I.D. polyimide-coated fused-silica columns, slurry-packed with reversed-phase chromatographic supports.