bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic Stokes shift in green fluorescent protein variants
Authors: Abbyad Paul , Childs William , Shi Xinghua , Boxer Steven G.
Published: December 2007

Solvent reorganization around the excited state of a chromophore leads to an emission shift to longer wavelengths during the excited-state lifetime. This solvation response is absent in wild-type green fluorescent protein, and this has been attributed to rigidity in the chromophore's environment necessary to exclude nonradiative transitions to the ground state. The fluorescent protein mPlum was developed via directed evolution by selection for red emission, and we use time-resolved fluorescence to study the dynamic Stokes shift through its evolutionary history. The far-red emission of mPlum is attributed to a picosecond solvation response that is observed at all temperatures above the glass transition. This time-dependent shift in emission is not observed in its evolutionary ancestors, suggesting that selective pressure has produced a chromophore environment that allows solvent reorganization. The evolutionary pathway and structures of related fluorescent proteins suggest the role of a single residue in close proximity to the chromophore as the primary cause of the solvation response.
The power of species sorting: Local factors drive bacterial community composition over a wide range of spatial scales
Authors: Van der Gucht Katleen , Cottenie Karl , Muylaert Koenraad , Vloemans Nele , Cousin Sylvie , Declerck Steven , Jeppesen Erik , Conde-Porcuna Jose-Maria , Schwenk Klaus , Zwart Gabriel , Degans Hanne , Vyverman Wim , De Meester Luc
Published: December 2007

There is a vivid debate on the relative importance of local and regional factors in shaping microbial communities, and on whether microbial organisms show a biogeographic signature in their distribution. Taking a metacommunity approach, spatial factors can become important either through dispersal limitation (compare large spatial scales) or mass effects (in case of strongly connected systems). We here analyze two datasets on bacterial communities [characterized by community fingerprinting through denaturing gradient gel electrophoresis (DGGE)] in meso- to eutrophic shallow lakes to investigate the importance of spatial factors at three contrasting scales. Variation partitioning on datasets of both the bacterial communities of 11 shallow lakes that are part of a strongly interconnected and densely packed pond system <1 km apart, three groups of shallow lakes ≈100 km apart, as well as these three groups of shallow lakes combined that span a large part of a North-South gradient in Europe (>2,500 km) shows a strong impact of local environmental factors on bacterial community composition, with a marginal impact of spatial distance. Our results indicate that dispersal is not strongly limiting even at large spatial scales, and that mass effects do not have a strong impact on bacterial communities even in physically connected systems. We suggest that the fast population growth rates of bacteria facilitate efficient species sorting along environmental gradients in bacterial communities over a very broad range of dispersal rates.
A coactivator trap identifies NONO (p54
nrb
) as a component of the cAMP-signaling pathway
Authors: Amelio Antonio L. , Miraglia Loren J. , Conkright Juliana J. , Mercer Becky A. , Batalov Serge , Cavett Valerie , Orth Anthony P. , Busby Jennifer , Hogenesch John B. , Conkright Michael D.
Published: December 2007

Signal transduction pathways often use a transcriptional component to mediate adaptive cellular responses. Coactivator proteins function prominently in these pathways as the conduit to the basic transcriptional machinery. Here we present a high-throughput cell-based screening strategy, termed the “coactivator trap,” to study the functional interactions of coactivators with transcription factors. We applied this strategy to the cAMP signaling pathway, which utilizes two families of coactivators, the cAMP response element binding protein (CREB) binding protein (CBP)/p300 family and the recently identified transducers of regulated CREB activity family (TORCs1–3). In addition to identifying numerous known interactions of these coactivators, this analysis identified NONO (p54
nrb
) as a TORC-interacting protein. RNA interference experiments demonstrate that NONO is necessary for cAMP-dependent activation of CREB target genes
in vivo
. Furthermore, TORC2 and NONO complex on cAMP-responsive promoters, and NONO acts as a bridge between the CREB/TORC complex and RNA polymerase II. These data demonstrate the utility of the coactivator trap by identification of a component of cAMP-mediated transcription.
Water-like solvation thermodynamics in a spherically symmetric solvent model with two characteristic lengths
Authors: Buldyrev Sergey V. , Kumar Pradeep , Debenedetti Pablo G. , Rossky Peter J. , Stanley H. Eugene
Published: December 2007

We examine by molecular dynamics simulation the solubility of small apolar solutes in a solvent whose particles interact via the Jagla potential, a spherically symmetric ramp potential with two characteristic lengths: an impenetrable hard core and a penetrable soft core. The Jagla fluid has been recently shown to possess water-like structural, dynamic, and thermodynamic anomalies. We find that the solubility exhibits a minimum with respect to temperature at fixed pressure and thereby show that the Jagla fluid also displays water-like solvation thermodynamics. We further find low-temperature swelling of a hard-sphere chain dissolved in the Jagla fluid and relate this phenomenon to cold unfolding of globular proteins. Our results are consistent with the possibility that the presence of two characteristic lengths in the Jagla potential is a key feature of water-like solvation thermodynamics. The penetrable core becomes increasingly important at low temperatures, which favors the formation of low-density, open structures in the Jagla solvent.
Perceiving the avidity of T cell activation can be translated into peripheral T cell regulation
Authors: Chen Weiling , Zhang Linging , Liang Bitao , Saenger Yvonne , Li Jianfeng , Chess Leonard , Jiang Hong
Published: December 2007

The structure recognized by regulatory T cells that enables them to discriminate self from nonself in the periphery is one of the central issues of regulatory T cell biology. A link between immunoregulation and self–nonself discrimination has emerged from experiments showing that Qa-1-restricted CD8+T cells selectively down-regulate target T cells activated by the intermediate avidity of their own T cell antigen receptor–ligand interactions. Because the peripheral self-reactive T cell repertoire is devoid of high-avidity T cells compared with the foreign-reactive repertoire, as a result of thymic negative selection, the selective down-regulation of intermediate but not high-avidity T cells enables the immune system to suppress autoimmunity without damaging the ongoing immune response to foreign pathogens. However, the molecular mechanism delineating how avidity of T cell activation is perceived by the regulatory T cells has not been elucidated. Here we show that a heat shock peptide (Hsp60sp), coupled with the MHC class Ib molecule Qa-1, is a surrogate target structure that is preferentially expressed at a higher level on the intermediate avidity T cells and specifically recognized by the Qa-1-restricted CD8+T cells. The biological significance of this observation was confirmed by the ability of Hsp60sp-loaded relevant dendritic cells to induce a Qa-1-restricted CD8+T cell-mediated protection from autoimmune encephalopathy in the experimental allergic encephalomyelitis model. Thus, perceiving the avidity of T cell activation can be translated into peripheral T cell regulation to discriminate self from nonself in the periphery to maintain self-tolerance.
A learning program that ensures prompt and versatile vocal imitation
Authors: Liu Wan-chun , Nottebohm Fernando
Published: December 2007

Here we show how a migratory songbird, the chipping sparrow (
Spizella passerina
), achieves prompt and precise vocal imitation. Juvenile chipping sparrow males develop five to seven potential precursor songs; the normal development of these songs requires intact hearing but not imitation from external models. The potential precursor songs conform with general species-typical song parameters but differ from the song of wild, adult territorial males. As chipping sparrow males return from migration to start their first breeding season, they settle close to an older adult. The young male then stops producing all but one of its precursor songs, retaining the one that most resembles that of its neighbor. This single song then becomes more variable and, in a matter of days, is altered to closely match the neighbor's song. This elegant solution ensures species specificity and promptness of imitation.
Deep Plasticity: The Encoding Approach to Perceptual Change
Authors: Rollins Mark
Published: December 2007

The basic problem of perceptual change is how to account for both variation and constancy in perceiving the world. Is order learned? How deep does plasticity go in that respect? I argue that different kinds of perceptual plasticity have been confused in recent debates, notably between J. Fodor and P. M. Churchland. By focusing on changes in theuseof concepts, the issues in the Fodor-Churchland debate can be resolved. Beyond that debate, I propose a generalized encoding approach to perception as a way of accounting for a significant form of perceptual change.
Does the Bohm Theory Solve the Measurement Problem?
Authors: Stone Abraham D.
Published: December 2007

When classical mechanics is seen as the short-wavelength limit of quantum mechanics (i.e., as the limit of geometrical optics), it becomes clear just how serious and all-pervasive the measurement problem is. This formulation also leads us into the Bohm theory. But this theory has drawbacks: its nonuniqueness, in particular, and its nonlocality. I argue that these both reflect an underlying problem concerning information, which is actually a deeper version of the measurement problem itself.
A New Twist in the Conventionality of Simultaneity Debate
Authors: Zangari Mark
Published: December 2007

To date, both sides in the conventionality of simultaneity debate grant that transformations from “standard” to “nonstandard” coordinates are possible without any empirically significant effects. However, it is argued here that the very possibility of defining nonstandard coordinates vanishes if one represents special relativity, not by real four-vectors (as has been the case so far in the debate), but by complex spinors as used in the representation of half-integer spin. Thus, in the topologically simplest representation of the Lorentz group, the transformation over which the debate has been fought does not exist and one of the most basic foundations of the conventionalist thesis is challenged.
Reason, Judgement and Bayes's Law
Authors: Brown Harold I.
Published: December 2007

This paper argues that when used judiciously Bayes's law has a role to play in the evaluation of scientific hypotheses. Several examples are presented in which a rational response to evidence requires a judgement whether to apply Bayes's law or whether, for example, to redistribute prior probabilities. The paper concludes that reflection on Bayes's law illustrates how an adequate account of the rational evaluation of hypotheses requires an account of judgement—a point which several philosophers have noted despite few attempts to develop an adequate theory of judgement.
A Content-Independent Explanation of Science's Effectiveness
Authors: Quillian M. Ross
Published: December 2007

This paper proposes an explanation in terms of three kinds of freedom, first for the special efficacy of science in general and then for why such efficacy has been more impressive in the natural than the social sciences. This explanation thus complements “post-positivist” interpretations of science which argue that science's effectiveness cannot be accounted for by fundamental epistemic differences from other kinds of discourse. My explanation tries to say what is responsible for science's effectiveness, in purely nonepistemic, sociological terms. All of the three kinds of freedom have so far been denied to most other forums, including in particular nations' populations taken overall. And one of these freedoms, while now allowed to the natural sciences, is still denied to the social sciences.
Duhem, Quine, and the Multiplicity of Scientific Tests
Authors: Balashov Yuri
Published: December 2007

Duhem's and Quine's holistic theses, when properly understood, allow methodologically responsible ways of resolving a conflict between a theoretical system and experience; they only deny the possibility of doing it in an epistemically persuasive way. By developing a “string” model of scientific tests I argue that the pattern of interaction between the elements of a theoretical system arising in response to multiple adverse data can be helpful in locating a “weak spot” in it. Combining this model with antiholistic arguments of Popper, Greenwood, and Lakatos significantly reinforces their joint power.
Feminist Epistemology: Implications for Philosophy of Science
Authors: Pinnick Cassandra L.
Published: December 2007

This article examines the best contemporary arguments for a feminist epistemology of scientific knowledge as found in recent works by S. Harding. I argue that no feminist epistemology of science is worthy of the name, because such an epistemology fails to escape well-known vicissitudes of epistemic relativism. But feminist epistemology merits attention from philosophers of science because it is part of a larger relativist turn in the social sciences and humanities that now aims to extend its critique to science, and Harding's “standpoint feminism” is the best-developed case. She attempts to make new use of discredited philosophical ideas concerning underdetermination, Planck's Hypothesis, and the role of counterfactuals in historical studies of science.
Construction by Reduction
Authors: Ramsey Jeffry L.
Published: December 2007

Scientists employ a variety of procedures to eliminate degrees of freedom from computationally and/or analytically intractable equations. In the process, they often construct new models and discover new concepts, laws and functional relations. 1 argue these procedures embody a central notion of reduction, namely, the containment of one structure within another. However, their inclusion in the philosophical concept of reduction necessitates a reevaluation of many standard assumptions about the ontological, epistemological and functional features of a reduction. On the basis of the reevaluation, 1 advocate a continuum of reduction which proceeds from the eliminative to the constructive. The metaphysical aspects of theory use in constructive reductions are sketched.
The Metaphoric Origins of Objectivity, Subjectivity, and Consciousness in The Direct Perception of Reality
Authors: Mulaik Stanley A.
Published: December 2007

This paper utilizes the theories of metaphor of George Lakoff, Mark Johnson and Julian Jaynes to extend Jaynes' metaphor theory of consciousness by treating consciousness as an operator that works with ‘covert behavior’ so that humans can integrate temporally discontinuous percepts with concepts based on metaphoric extensions of the embodied schemas of direct and immediate perception and thereby transcend the limitations of direct perception. A theory of first-person expressions and covert behavior to account for self-conscious awareness as language-based is advanced. Subjectivity and objectivity are metaphors based on schemas of perception.
Causality and Conserved Quantities: A Reply to Salmon
Authors: Dowe Phil
Published: December 2007

In a recent paper (1994) Wesley Salmon has replied to criticisms (e.g., Dowe 1992c, Kitcher 1989) of his (1984) theory of causality, and has offered a revised theory which, he argues, is not open to those criticisms. The key change concerns the characterization of causal processes, where Salmon has traded “the capacity for mark transmission” for “the transmission of an invariant quantity.” Salmon argues against the view presented in Dowe (1992c), namely that the concept of “possession of a conserved quantity” is sufficient to account for the difference between causal and pseudo processes. Here that view is defended, and important questions are raised about the notion of transmission and about gerrymandered aggregates.
A Heuristic for Conceptual Change
Authors: Arntzenius Frank
Published: December 2007

One of our more fundamental beliefs is that causal chains are continuous in time: we believe that every influence from the past upon the future runs through the present. I argue that this tenet, given certain data, can force conceptual changes upon us. I attempt to formulate a heuristic for discovery, based as explicitly as possible upon this tenet, and illustrate it by means of several examples, one of which is Mendel's discovery of genes.
Two Cheers for Reductionism: Or, the Dim Prospects for Non-Reductive Materialism
Authors: Melnyk Andrew
Published: December 2007

I argue that a certain version of physicalism, which is viewed by both its admirers and its detractors as non-reductionist, in fact entails two claims which, though not reductionist in the currently most popular sense of ‘reductionist’, conform to the spirit of reductionism sufficiently closely to compromise its claim to be acomprehensivelynon-reductionist version of physicalism. Putatively non-reductionist versions of physicalism in general, I suggest, are likely to be non-reductionist only in some senses, but not in others, and hence to disappoint those who wish to be physicalists but still to remain soft and cuddly non-reductionists.
S. S. Stevens and the Origins of Operationism
Authors: Hardcastle Gary L.
Published: December 2007

Despite influencing the social sciences since the 1930s, S. S. Stevens' “operationist” philosophy of science has yet to be adequately understood. I reconstruct Stevens' operationism from his early work and assess the influence of various views (logical positivism, behaviorism and the “operational viewpoint” of P. W. Bridgman, among others) on Stevens. Stevens' operationism emerges, on my reconstruction, as a naturalistic methodological directive aimed at agreement, founded in turn on the belief that agreement is constitutive of science, the scientific community, and objectivity. Further, I show that operationism is historically and philosophically independent of the views mentioned above.
log[P(h/eb)/P(h/b)] Is the One True Measure of Confirmation
Authors: Milne Peter
Published: December 2007

Plausibly, when we adopt a probabilistic standpoint any measure Cb(h, e) of the degree to which evidence e confirms (or is evidentially relevant to) hypothesis (or theory) h relative to background knowledge b should meet these five desiderata:

(1) Cb(h,e) > 0 when P(h/eb) > P(h/b; Cb(h,e) < 0 when P(h/eb) < P(h/b); Cb(h,e) = 0 when P(h/eb) = P(h/b).

(2) Cb(h,e) is some function of the values P(·/b) and P(·/·b) assume on the at most sixteen truth-functional combinations of e and h.

(3) If P(e/hb) < P(f/hb) and P(e/b) = P(f/b) then Cb(h,e) ≤ Cb(h,f); if P(e/hb) = P(f/hb) and P(e/b) < P(f/b) then Cb(h,e) ≥ Cb(h,f).

(4) Cb(h,ef) – Cb(h,eg) is fully determined by Cb(h,e) and Cbe(h,f) – Cbe(h,g); if Cb(h,ef) = 0 then Cb(h,e) + Cbe(h,f) = 0.

(5) If P(e/hb) = P(e/tb) then Cb(h,e) = Cb(t,e).
A Note on the ‘Quantum Eraser’
Authors: Seager William
Published: December 2007

This note aims to make more familiar to philosophers yet another bizarre quantum mechanical effect with disturbing metaphysical implications. It is possible to modify the classic double-slit experiment so that one can register the path of a particle to determine which slit it passes through, and then erase this registered information so that the interference effects which would normally disappear upon registration of the “which path” information are reconstituted. Thus the “trajectory” of particles can be effected by temporally and spatially distant operations on the slit detectors. Nonetheless, no untoward effects (such as superluminal signalling) can result from the operation of the eraser.
Life, “Artificial Life,” and Scientific Explanation
Authors: Lange Marc
Published: December 2007

Recently, biologists and computer scientists who advocate the “strong thesis of artificial life” have argued that the distinction between life and nonlife is important and that certain computer software entities could be alive in the same sense as biological entities. These arguments have been challenged by Sober (1991). I address some of the questions about the rational reconstruction of biology that are suggested by these arguments: What is the relation between life and the “signs of life”? What work (if any) might the concept of “life” (over and above the “signs of life”) perform in biology? What turns on scientific disputes over the utility of this concept? To defend my answers to these questions, I compare “life” to certain other concepts used in science, and I examine historical episodes in which an entity's vitality was invoked to explain certain phenomena. I try to understand how these explanations could be illuminating even though they are not accompanied by any reductive definition of “life.”
Discussion: Thoughts on Maher's Predictivism
Authors: Barnes Eric
Published: December 2007

Predictivism asserts that where evidence E confirms theory T, E provides stronger support for T when E is predicted on the basis of T and then confirmed than when E is known before T's construction and ‘used’, in some sense, in the construction of T. Among the most interesting attempts to argue that predictivism is a true thesis (under certain conditions) is that of Patrick Maher (1988, 1990, 1993). The purpose of this paper is to investigate the nature of predictivism using Maher's analysis as a starting point. I briefly summarize Maher's primary argument and expand upon it; I explore related issues pertaining to the causal structure of empirical domains and the logic of discovery.
Fitness Made Physical: The Supervenience of Biological Concepts Revisited
Authors: Weber Marcel
Published: December 2007

The supervenience and multiple realizability of biological properties have been invoked to support a disunified picture of the biological sciences. I argue that supervenience does not capture the relation between fitness and an organism's physical properties. The actual relation is one of causal dependence and is, therefore, amenable to causal explanation. A case from optimality theory is presented and interpreted as a microreductive explanation of fitness difference. Such micro-reductions can have considerable scope. Implications are discussed for reductive physicalism in evolutionary biology and for the unity of science.
Child's Play
Authors: Nersessian Nancy J.
Published: December 2007

Although most philosophers are not aware of it, research in cognitive development and in learning in the last decade has made considerable use of the characterizations of the nature and development of scientific knowledge proffered by philosophers of science. In a “reflexive” move, Alison Gopnik proposes philosophers of science can profit from the research of psychologists investigating cognitive development-specifically from that group of researchers who advocate the “theory theory.”
On Becoming, Relativity, and Nonseparability
Authors: Dorato Mauro
Published: December 2007

In a reply to Nicholas Maxwell, Stein has proved that Minkowski spacetime can leave room for the kind of indeterminateness required both by certain interpretations of quantum mechanics and by objective becoming. By examining the consequences of outcome dependence in Bell-type experiments for the co-determinateness of spacelike-related events, I argue that the only becoming relation that is compatible with both causal and noncausal readings of the quantum correlations is the universal relation. This result might also undermine interpretations of quantum mechanics requiring non-epistemically indeterminate states before measurement and hyperplane-dependent wave collapse.
Empirical Evaluations of Theoretical Explanations of Psychotherapeutic Efficacy: A Reply to John D. Greenwood
Authors: Grünbaum Adolf
Published: December 2007

Using Grünbaum 1984 and 1993 as a springboard, Greenwood (this issue) claims to have offered several methodologically salubrious and exegetically illuminating theses on empirical evaluations of theoretical explanations of psychotherapeutic efficacy. According to his exegesis of Grünbaum's construction (1984, Ch. 2, Section C; 1993, 184–204) of Freud's “Tally Argument,” that argument bespeaks a rife neglect of the epistemologically-significant distinction between empirical evaluations of the efficacy of psychotherapy and evaluations of theoretical explanations of that efficacy. Greenwood presents a defense of a qualified version of Popper's critique of psychoanalysis against Grünbaum's objections to it (1984, Ch. 1B). Finally, Greenwood offers a clarification of the concept of a “placebo control” investigation, taking issue with Grünbaum's 1993 (84–87, 91–93).

In the present paper, it is argued contra Greenwood that: (1) his purportedly “best” reading of Freud's Tally Argument and of its import founders, (2) the distinction that Greenwood bemoans as being neglected by mental health researchers actually is a commonplace in the literature on treatment-process and therapeutic outcome, (3) Greenwood's defense of Popper's critique of psychoanalysis is an anachronism, and (4) Greenwood's conceptual analysis of placebo controls is nebulous and misconceived.
Wayne, Horwich, and Evidential Diversity
Authors: Fitelson Branden
Published: December 2007

In a recent article, Wayne (1995) offers a critique of Horwich's (1982) Bayesian explication of the confirmational significance of evidential diversity. Presently, I argue that Wayne's reconstruction of Horwich's account is not faithful to Horwich's original presentation. Because Wayne's reconstruction is uncharitable, his criticisms turn out to be off the mark. I try to provide a more faithful and charitable rendition of Horwich's account. Unfortunately, even this more charitable reconstruction of Horwich's position seems—at best—to provide an incomplete explication of the confirmational significance of evidential diversity.
Human herpesvirus 6B U19 protein is a PML-regulated transcriptional activator that localizes to nuclear foci in a PML-independent manner
Authors: Kofod-Olsen Emil , Ross-Hansen Katrine , Mikkelsen Jacob Giehm , Höllsberg Per
Published: December 2007

Human herpesvirus 6B (HHV-6B) contains anIE-Bdomain spanning open reading framesU16/17–U19, based on homology with human cytomegalovirus. Here, the protein product, U19, of the HHV-6BU19gene is identified as a 47 kDa transcriptional activator. HHV-6B infection or overexpression of U19 transactivated the RANTES promoter. Mutational analysis of the promoter indicated that transactivation was not critically dependent on the promoter sites CRE, NF-κB, ISRE or NF-IL6. ND10 are nuclear substructures that are involved in several cellular regulatory pathways, including those controlling gene expression. HHV-6B infection resulted in a reduced number of ND10 structures, but with a concomitantly increased level of promyelocytic leukaemia (PML) protein expression and mRNA induction. The U19 protein co-located to ND10 with PML and heterochromatin protein 1 (HP1), but whilst PML formed a ring structure, U19 also localized to the centre of ND10. Knockdown of PML by small interfering RNA did not prevent U19 localization to ND10-like foci, but instead led to a fourfold increase in U19-induced transcription from the RANTES promoter. Generation of four truncated U19 proteins indicated that the N-terminal portion of the protein contains a sequence responsible for nuclear localization; a domain in the N-terminal half of U19 is responsible for its ND10 localization, whereas the C-terminal portion contains the transactivation domain. None of the truncated proteins retained full transactivating ability on the RANTES promoter. Thus, U19 is a transcriptional activator that co-localizes with PML and localizes to ND10-like foci independently of PML, yet is regulated negatively by PML or its associated proteins.
A cell line infectible by prion strains from different species
Authors: Courageot M.-P. , Daude N. , Nonno R. , Paquet S. , Di Bari M. A. , Le Dur A. , Chapuis J. , Hill A. F. , Agrimi U. , Laude H. , Vilette D.
Published: December 2007

It has been shown previously that ovine prion protein (PrPC) renders rabbit epithelial RK13 cells permissive to the multiplication of ovine prions, thus providing evidence that species barriers can be crossed in cultured cells through the expression of a relevant PrPC. The present study significantly extended this observation by showing that mouse and bank vole prions can be propagated in RK13 cells that express the corresponding PrPC. Importantly, the respective molecular patterns of abnormal PrP (PrPres) and, where examined, the neuropathological features of the infecting strains appeared to be maintained during the propagation in cell culture. These findings indicate that RK13 cells can be genetically engineered to replicate prion strains faithfully from different species. Such an approach may facilitate investigations of the molecular basis of strain identity and prion diversity.
Dynamic creation of electrostatic fields
Authors: Berman P. R.
Published: December 2007

To illustrate the concept of the dynamic creation of static fields, the fields associated with the creation of a static point charge and a static point dipole between times t=0 and t=τ are calculated. For the former the field is that of a static charge in all space once t>τ. For the static point dipole the field pattern consists of three zones once t>τ: An expanding sphere of radius r=c(t−τ) in which the field is that of a static dipole, a shell defined by c(t−τ)<rct, for which the fields vanish. Despite the fact that the electric field occupies an increasing volume in space with increasing time, the energy in the field is constant once the dipole has been created. This result is established explicitly for an arbitrary creation of the static dipole.
Sadi Carnot’s contribution to the second law of thermodynamics
Authors: Lemons Don S. , Penner Margaret K.
Published: December 2007

We identify an operative principle in Sadi Carnot’s only publication that is closely related to a distinct version of the second law of thermodynamics. Although Carnot did not propose the second law of thermodynamics, he assumed its equivalent in proving Carnot’s theorem. We show that, in the absence of the first law, Carnot’s assumption is equivalent to Clausius’ version of the second law. Both Carnot’s assumption and Clausius’ version, in the absence of the first law, are more restrictive than Kelvin’s statement of the second law.
A simplified treatment of the Landau theory of phase transitions for thin ferroelectric films
Authors: Wong C. K. , Shin F. G.
Published: December 2007

A simple analytical approximation based on Landau-Ginzburg theory is developed for ferroelectric thin films with continuous and first-order phase transitions. We show that the polarization profile can be conveniently modeled by a power series expansion that allows us to re-express the Landau-Ginzburg free energy as an effective Landau-Devonshire free energy. Simple expressions are obtained for the properties of ferroelectric films. It is found that the calculated properties based on our effective Landau-Devonshire theory are consistent with numerical results from the Landau-Ginzburg theory.
Proapoptotic Bcl-2 Family Member Bim Promotes Persistent Infection and Limits Protective Immunity
Authors: Reckling Stacie , Divanovic Senad , Karp Christopher L. , Wojciechowski Sara , Belkaid Yasmine , Hildeman David
Published: December 2007

Following the peak of the T-cell response, most of the activated effector T cells die by apoptosis driven by the proapoptotic Bcl-2 family member Bim (Bcl-2-interactingmediator of death). Whether the absence of Bim-mediated T-cell apoptosis can affect protective immunity remains unclear. Here, we used a mouse model ofLeishmania majorinfection, in which parasite persistence and protective immunity are controlled by an equilibrium reached between parasite-specific gamma interferon (IFN-γ)-producing effector T cells and interleukin-10 (IL-10)-producing CD4+CD25+T regulatory cells. To further understand the role of Bim-mediated apoptosis in persistent infection and protective immunity, we infectedBim−/−mice withL. major. We found that the initial parasite growth and lesion development were similar inBim−/−and wild-type mice after primaryL. majorinfection. However, at later times after infection,Bim−/−mice had significantly increasedL. major-specific CD4+T-cell responses and were resistant to persistent infection. Interestingly, despite their resistance to primaryL. majorinfection,Bim−/−mice displayed significantly enhanced protection against challenge withL. major. Increased resistance to challenge inBim−/−mice was associated with a significant increase in the number ofL. major-specific IFN-γ-producing CD4+T cells and a lack of IL-10 production at the challenge site. Taken together, these data suggest that Bim limits protective immunity and that the absence of Bim allows the host to bypass antigen persistence for maintenance of immunity against reinfection.
Cytological changes induced by wheat streak mosaic virus in cereal leaf tissues
Authors: Gao Jian-Guo , Nassuth Annette
Published: December 2007

Cytological changes induced by wheat streak mosaic virus in cereal leaf tissues were studied at the light microscope level. Starting 4–5 days after inoculating the first leaves, a number of cylindrical inclusions were present in the dense cytoplasm of the second wheat leaf epidermal cells. Amorphous inclusions could also be identified in the epidermal cells at late infection stages (from 10 days post inoculation), often associated with deformed nuclei. In mesophyll cells of wheat, barley, and triticale, virus infection induced dense cytoplasm around enlarged nuclei and cytopathie structures within these nuclei. Pyknotic nuclei could be observed at late infection stages. Nuclei and chloroplasts became degraded as the infection progressed. In addition, the cell wall composition was changed and included deposits that were most likely phenolic compounds and lignin. At late infection stages the infected mesophyll cells had collapsed. This was not observed in either senesced virus-free mesophyll cells, or virus-infected epidermal cells. Key words: wheat streak mosaic virus, virus infection, host – virus interaction, cereals, cytological changes, cell wall deposit.
Resistance to RPV barley yellow dwarf virus in the genus Bromus
Authors: Beuve Monique , Lapierre Hervé
Published: December 2007

Susceptibility to barley yellow dwarf RPV (BYD – RPV) relative to BYD – PAV has been studied for 21 species of the genus Bromus. The following species belonging to sections Bromus (B. arvensis L., B. commutatus Shrad, B. danthoniae Trin., B. grossus Desf. ex DC. B. hordeaceus L., B. lanceolatus Roth., B. scoparius L.), Stenobromus (B. diandrus Roth., B. madritensis L., B. sterilis L., B. rubens L., B. tectorum L.), and Neobromus (B. trinii Desvaux) are all susceptible to BYD–RPV. Of the three species of the Pnigma section, B. erectus Hudson is susceptible to BYD–RPV, although the percentage of infected plants is low; B. setifolius Presl. is resistant to BYD–RPV; and the two biotypes of B. inermis Leyss. that were tested are both resistant to BYD–RPV. Most biotypes of the species in section Ceratochloa are resistant to BYD–RPV and susceptible to BYD–PAV. In B. catharticus Vahl. a few biotypes are also susceptible to both viruses. The resistance to BYD–RPV in different biotypes of Ceratochloa and in one biotype of B. setifolius cannot be explained by the resistance to the vector Rhopalosiphum padi L., as BYD – PAV is efficiently transmitted to these biotypes by the same aphid species. These results show that most biotypes of the species in section Ceratochloa are probably immune to BYD–RPV and that the virus has a restricted host range in the genus Bromus compared with BYD –PAV. Key words: BYDV, RPV, PAV, Bromus genus.
Biochemical changes in cell walls and cellular responses of tobacco leaves related to systemic resistance to blue mold (Peronospora tabacina) induced by tobacco mosaic virus
Authors: Ye X. S. , Järlfors U. , Tuzun S. , Pan S. Q. , Kuc J.
Published: December 2007

Inoculation of lower leaves of tobacco cultivar Ky 14, which carries the N gene for resistance to tobacco mosaic virus, with tobacco mosaic virus induced systemic resistance to Peronospora tabacina and a systemic accumulation of cell wall hydroxyproline. Hydroxyproline increased significantly 12 days after induction with tobacco mosaic virus, and more so after challenge with P. tabacina. During this period, hydroxyproline levels in the control plants remained unchanged. Four salt-soluble cell wall proteins were systemically induced. These proteins were not β-1,3-glucanases, chitinases, or hydroxyproline-rich glycoproteins. Light microscopy showed that blue mold development in the induced plants was severely restricted 2 days after challenge; some fungal hyphae were disorganized near the center of infection sites, and adjacent host cells were plasmolyzed and a few collapsed 3 days after challenge. All infection sites in the induced plants were associated with necrotic cells 5–6 days after challenge. Electron microscopy revealed that damage to fungal hyphae, plasmolysis and shrinking of infected cells, and more electron-opaque host cell walls and wall appositions were characteristics of induced resistance. Key words: induced systemic resistance, Nicotiana tabacum, blue mold (Peronospora tabacina).
Vesicular – arbuscular mycorrhizae in disturbed and revegetated sites from La Gran Sabana, Venezuela
Authors: Cuenca Gisela , Lovera Milagros
Published: December 2007

Savannas growing on stony, old and nutrient-poor soils of southern Venezuela were severely disturbed by removal of the soil organic layers with bulldozers for road building. Introduced species Brachiaria decumbens, Brachiaria humidicola, Pueraria phaseoloides, and Calopogonium sp. were sown. The substrate was fertilized and limed. Plant cover, vesicular – arbuscular mycorrhizae colonization, spore number, and most probable number of propagulels in undisturbed savanna, disturbed nonrevegetated savanna, and six revegetated savannas were assessed. The perturbation reduced the mycorrhizal propagule number in comparison with the undisturbed savanna. In the nonrevegetated areas the mean percent ground cover 2 years after disturbance was low (0.04%). In revegetated areas an increase in mycorrhizal propagule number occurred and the mycorrhizal colonization of the sown species was high. In restored areas there was an increase in species of nonmycotrophic Amaranthaceae. The results support other predictions on the mycorrhizae in successional biomes, because in the extremely nutrient-poor soils studied the colonizing species were mainly mycotrophic. The reclamation program applied in disturbed areas was useful because it has allowed the recovery of vesicular – arbuscular mycorrhizal inoculum and there was an increase in the recolonization of native plants. Key words: disturbance, endomycorrhizae, revegetation, savanna, vesicular – arbuscular mycorrhizae.
New litter-inhabiting hyphomycetes from Malaysia: Isthmophragmospora verruculosa, Iyengarina asymmetrica, and Iyengarina furcata
Authors: Kuthubutheen A. J. , Nawawi A.
Published: December 2007

New dematiaceous litter-inhabiting hyphomycetes Isthmophragmospora verruculosa anam. gen. et sp.nov., Iyengarina asymmetrica anam. sp.nov., and Iyengarina furcata anam. sp.nov. isolated from decaying twigs submerged in freshwater streams in Malaysia are described and compared with related taxa. Key words: Isthmophragmospora, Iyengarina, hyphomycetes, new taxa.
The Colletotrichum trifolii – Medicago sativa interface, in culture: a cytological analysis
Authors: Mould Michael J. R. , Robb Jane
Published: December 2007

Light and electron microscopy were used to investigate the interactions between the fungus Colletotrichum trifolii Bain and Essary and callus cultures derived from anthracnose resistant or susceptible alfalfa plants (Medicago sativa L.). Race 1 and race 2 of the pathogen completely overgrew both callus types at the same rate of colonization. Comparisons with the responses observed in planta showed some similarities. In both cases the plant cells proximal to the approaching pathogen underwent vacuolar fragmentation and secreted extracellular materials that were histochemically similar when stained with Toluidine blue O and Sudan black B and that appeared to be lignin- or suberin-like in composition. However, in cultures these responses took place in many cells and began while the hyphal front was 0.5 to 1.0 cm distant from the callus edge. In the intact plants the responses were localized initially to one or two epidermal cells and did not begin until the pathogen had penetrated into the cuticle. Further differences were found in the failure of callus cells to form papillae and in their premature death, prior to completion of the defense response and prior to fungal contact. The observations suggested that perhaps the absence of a cuticle in callus tissue contributes to the development of an uncontrolled defence response in which subsequent permeability barriers are incompletely formed. Such factors could contribute to the observed failure of race-specific resistance. Key words: Colletotrichum trifolii, Medicago sativa, callus cultures, cytology.
Impacts of seeding depth on emergence and seedling structure in eight perennial grasses
Authors: Redmann R. E. , Qi M. Q.
Published: December 2007

The effects of seeding depth (1.5, 3, or 6 cm) on seedling emergence, morphology, and anatomy were examined in cool-season (Agropyron dasystachyum, Agropyron desertorwn, Agropyron smithii, Elymus angustus, and Elymus junceus) and warm-season (Andropogon scoparius, Bouteloua curtipendula, and Bouteloua gracilis) perennial grasses. Caryopsis weights ranged from 0.5 mg in Bouteloua spp. to 4.7 mg in E. angustus. Prominent elongation of the subcoleoptile internode at greater seeding depths and short coleoptiles were observed in And. scoparius, B. curtipendula, and B. gracilis (type A seedlings). The remaining species had relatively long coleoptiles and no subcoleoptile internode elongation (type B seedlings). Up to 40% of the seedlings in the Agropyron species had intracoleoptile internode elongation when seeded at 3- and 6-cm depths. Relative emergence from 6 cm compared with 1.5 cm was best in Agr. dasystachyum and Agr. smithii and poorest in the type A species and in E. junceus. Diameters of xylem vessels in the subcoleoptile and intracoleoptile internodes remained relatively constant, but numbers of vesels decreased with depth of seeding, especially in the type A species. Decreases in hydraulic conductance with depth of seeding were greater in type A than in type B seedlings, mainly because of longer subcoleoptile internodes and smaller effective vessel radii in the former. Key words: grass seedling emergence, hydraulic conductance, morphology, seeding depth, seed weight, xylem dimensions.
Treatment of a single plant cell with chemicals
Authors: Toyoda Kazuhiro , Shiraishi Tomonori , Kobayashi Issei , Yamaoka Naoto , Kunoh Hitoshi
Published: December 2007

A technique to treat a single plant cell with chemicals was devised using gel beads and epidermal cells of barley coleoptile. Acridine orange (a fluorescent dye) and cytochalasin A (an inhibitor of cytoplasmic streaming) were separately infiltrated into gel beads that were then individually transferred onto a single cell of the coleoptile using a micromanipulator. Coleoptile cells on which a gel bead infiltrated with acridine orange had been placed gave a characteristic greenish fluorescence when observed with a fluorescence microscope 24 h after the onset of incubation. These results indicate that acridine orange diffused from the gel bead and permeated into the coleoptile cell. When coleoptile cells were treated with gel beads infiltrated with cytochalasin A, cytoplasmic streaming ceased in more than 90% of the cells by 6 h after the onset of treatment. These results demonstrate that cytochalasin A diffused from the gel bead and permeated into the symplast of the target cells. The technique could be applied to test physiological effects of fungal products on a single plant cell. Key words: single cell chemical treatment, cytoplasmic streaming, barley coleoptile, cytochalasin A, acridine orange.
BLACK HOLE ENTROPY FOR ANTI DE SITTER AND DE SITTER DILATONIC SPACETIME USING BRICK WALL METHOD
Authors: GHOSH TANWI
Published: December 2007

The entropy of a scalar field in the background of a dilatonic black hole both in anti de Sitter and de Sitter spacetime has been calculated using brick wall method. The form of divergent contributions to the entropy is in agreement with the previous calculations in the literature. The semiclassical approach used here is straightforward and produces finite result apart from an ambiguity in logarithmic terms.
ILLUSTRATIVE MODEL FOR PARITY DOUBLING OF ENERGY LEVELS
Authors: AFONIN S. S.
Published: December 2007

A one-dimensional quantum mechanical model possessing mass-gap, a gapless excitation, and an approximate parity doubling of energy levels is constructed based on heuristic QCD-inspired arguments. The model may serve for illustrative purposes when considering the related dynamical phenomena in particle and nuclear physics.
PLANAR HOMOLOGICAL MIRROR SYMMETRY
Authors: KONISHI EIJI
Published: December 2007

In this paper, we formulate a planar limited version of the B-side in homological mirror symmetry that formularizes Chern–Simons-type topological open string field theory using homotopy associative algebra (A∞ algebra). This formulation is based on the works by Dijkgraaf and Vafa. We show that our formularization includes gravity/gauge theory correspondence which originates in the AdS/CFT duality of Dijkgraaf–Vafa theory.
LINEAR AND NONLINEAR EFFECTS ON THE NEWTONIAN GRAVITATIONAL CONSTANT AS DEDUCED FROM THE TORSION BALANCE
Authors: ROSSI M. , ZANINETTI L.
Published: December 2007

The Newtonian gravitational constant has still 150 parts per million of uncertainty. This paper examines the linear and nonlinear equations governing the rotational dynamics of the torsion gravitational balance. A nonlinear effect modifying the oscillation period of the torsion gravitational balance is carefully explored.
SUPERSYMMETRIC FIELD THEORY BASED ON GENERALIZED UNCERTAINTY PRINCIPLE
Authors: SHIBUSA YUUICHIROU
Published: December 2007

We construct a quantum theory of free fermion field based on the deformed Heisenberg algebra [Formula: see text] where β is a deformation parameter using supersymmetry as a guiding principle. A supersymmetric field theory with a real scalar field and a Majorana fermion field is given explicitly and we also find that the supersymmetry algebra is deformed from an usual one.
FINAL STARE INTERACTION ENHANCEMENT EFFECT ON THE NEAR THRESHOLD $p\bar p$ SYSTEM IN $B^\pm\to p\bar p \pi^\pm$ DECAY
Authors: LAPORTA VINCENZO
Published: December 2007

We discuss the low-mass enhancement effect in the baryon–antibaryon invariant mass in three-body baryonic B decays using final state interactions in the framework of Regge theory. We show that the rescattering between baryonic pair can reproduce the observed mass spectrum.