CiteULike: Tag experiment

Regulatory Pathway Analysis by High-Throughput In Situ Hybridization

Axel Visel — 2007-10-22T06:21:30-00:00

PLoS Genetics, Vol. 3, No. 10. (1 October 2007), e178.

Automated in situ hybridization enables the construction of comprehensive atlases of gene expression patterns in mammals. Such atlases can become Web-searchable digital expression maps of individual genes and thus offer an entryway to elucidate genetic interactions and signaling pathways. Towards this end, an atlas housing ∼1,000 spatial gene expression patterns of the midgestation mouse embryo was generated. Patterns were textually annotated using a controlled vocabulary comprising >90 anatomical features. Hierarchical clustering of annotations was carried out using distance scores calculated from the similarity between pairs of patterns across all anatomical structures. This process ordered hundreds of complex expression patterns into a matrix that reflects the embryonic architecture and the relatedness of patterns of expression. Clustering yielded 12 distinct groups of expression patterns. Because of the similarity of expression patterns within a group, members of each group may be components of regulatory cascades. We focused on the group containing Pax6, an evolutionary conserved transcriptional master mediator of development. Seventeen of the 82 genes in this group showed a change of expression in the developing neocortex of Pax6-deficient embryos. Electromobility shift assays were used to test for the presence of Pax6-paired domain binding sites. This led to the identification of 12 genes not previously known as potential targets of Pax6 regulation. These findings suggest that cluster analysis of annotated gene expression patterns obtained by automated in situ hybridization is a novel approach for identifying components of signaling cascades.

Principles of Genome Evolution in the Drosophila melanogaster Species Group

José Ranz — 2007-06-14T01:02:58-00:00

PLoS Biology, Vol. 5, No. 6. (1 June 2007), e152.

That closely related species often differ by chromosomal inversions was discovered by Sturtevant and Plunkett in 1926. Our knowledge of how these inversions originate is still very limited, although a prevailing view is that they are facilitated by ectopic recombination events between inverted repetitive sequences. The availability of genome sequences of related species now allows us to study in detail the mechanisms that generate interspecific inversions. We have analyzed the breakpoint regions of the 29 inversions that differentiate the chromosomes of Drosophila melanogaster and two closely related species, D. simulans and D. yakuba, and reconstructed the molecular events that underlie their origin. Experimental and computational analysis revealed that the breakpoint regions of 59% of the inversions (17/29) are associated with inverted duplications of genes or other nonrepetitive sequences. In only two cases do we find evidence for inverted repetitive sequences in inversion breakpoints. We propose that the presence of inverted duplications associated with inversion breakpoint regions is the result of staggered breaks, either isochromatid or chromatid, and that this, rather than ectopic exchange between inverted repetitive sequences, is the prevalent mechanism for the generation of inversions in the melanogaster species group. Outgroup analysis also revealed evidence for widespread breakpoint recycling. Lastly, we have found that expression domains in D. melanogaster may be disrupted in D. yakuba, bringing into question their potential adaptive significance.

Experimental Characterization of Cis-Acting Elements Important for Translation and Transcription in Halophilic Archaea

Mariam Brenneis — 2008-01-02T10:44:59-00:00

PLoS Genetics, Vol. 3, No. 12. (1 December 2007), e229.

The basal transcription apparatus of archaea is well characterized. However, much less is known about the mechanisms of transcription termination and translation initation. Recently, experimental determination of the 5′-ends of ten transcripts from Pyrobaculum aerophilum revealed that these are devoid of a 5′-UTR. Bioinformatic analysis indicated that many transcripts of other archaeal species might also be leaderless. The 5′-ends and 3′-ends of 40 transcripts of two haloarchaeal species, Halobacterium salinarum and Haloferax volcanii, have been determined. They were used to characterize the lengths of 5′-UTRs and 3′-UTRs and to deduce consensus sequence-elements for transcription and translation. The experimental approach was complemented with a bioinformatics analysis of the H. salinarum genome sequence. Furthermore, the influence of selected 5′-UTRs and 3′-UTRs on transcript stability and translational efficiency in vivo was characterized using a newly established reporter gene system, gene fusions, and real-time PCR. Consensus sequences for basal promoter elements could be refined and a novel element was discovered. A consensus motif probably important for transcriptional termination was established. All 40 haloarchaeal transcripts analyzed had a 3′-UTR (average size 57 nt), and their 3′-ends were not posttranscriptionally modified. Experimental data and genome analyses revealed that the majority of haloarchaeal transcripts are leaderless, indicating that this is the predominant mode for translation initiation in haloarchaea. Surprisingly, the 5′-UTRs of most leadered transcripts did not contain a Shine-Dalgarno (SD) sequence. A genome analysis indicated that less than 10% of all genes are preceded by a SD sequence and even most proximal genes in operons lack a SD sequence. Seven different leadered transcripts devoid of a SD sequence were efficiently translated in vivo, including artificial 5′-UTRs of random sequences. Thus, an interaction of the 5′-UTRs of these leadered transcripts with the 16S rRNA could be excluded. Taken together, either a scanning mechanism similar to the mechanism of translation initiation operating in eukaryotes or a novel mechanism must operate on most leadered haloarchaeal transcripts.

Noise characteristics and prior expectations in human visual speed perception

Alan Stocker — 2006-03-27T16:11:32-00:00

Nature Neuroscience, Vol. 9, No. 4. (19 March 2006), pp. 578-585.

The environment of graphene probed by electrostatic force microscopy

J Moser — 2008-05-02T01:05:10-00:00

Applied Physics Letters, Vol. 92, No. 12. (2008)

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Spatially Resolved Raman Spectroscopy of Single- and Few-Layer Graphene

D Graf — 2008-02-29T13:28:32-00:00

Nano Lett., Vol. 7, No. 2. (14 February 2007), pp. 238-242.

Abstract: We present Raman spectroscopy measurements on single- and few-layer graphene flakes. By using a scanning confocal approach, we collect spectral data with spatial resolution, which allows us to directly compare Raman images with scanning force micrographs. Single-layer graphene can be distinguished from double- and few-layer by the width of the D' line: the single peak for single-layer graphene splits into different peaks for the double-layer. These findings are explained using the double-resonant Raman model based on ab initio calculations of the electronic structure and of the phonon dispersion. We investigate the D line intensity and find no defects within the flake. A finite D line response originating from the edges can be attributed either to defects or to the breakdown of translational symmetry.

Mechanical integrity of transparent conductive oxide films for flexible polymer-based displays

Y Leterrier — 2007-01-16T18:33:20-00:00

Thin Solid Films, Vol. 460, No. 1-2. (22 July 2004), pp. 156-166.

The mechanical integrity of tin-doped indium oxide (ITO) thin films sputtered onto a high temperature aromatic polyester developed for flexible display applications was investigated by means of tensile experiments equipped with electrical measurement, and carried out in-situ in an optical microscope. Attention was paid to the influence of ITO thickness, composition and crystalline microstructure, internal stress, annealing, and polymer substrate. It was observed that process-induced internal stresses were systematically compressive, and that tensile cracks in the ITO always initiated at pin-hole defect sites. A transition from stable to unstable crack growth was detected when crack length was several 100 times coating thickness. The occurrence of such a transition, which corresponded to an increase in electrical resistance equal to approximately 10%, indicated that crack propagation controlled the loss of functional performance of the device. It was moreover found that an improved surface quality of the polymer substrate, such as that obtained with planarization hard coats, was a major factor to increase the cohesive properties of ITO thin films. It was also observed that the intrinsic crack onset strain followed classic fracture mechanics scaling, in inverse proportion to the square root of ITO thickness.

Large-area ultrathin films of reduced graphene oxide as a transparent and flexible electronic material

Goki Eda — 2008-07-15T19:19:39-00:00

Nat Nano, Vol. 3, No. 5. (May 2008), pp. 270-274.

Atomic structure of graphene on SiO2.

M Ishigami — 2008-06-30T15:46:56-00:00

Nano letters, Vol. 7, No. 6. (June 2007), pp. 1643-1648.

We employ scanning probe microscopy to reveal atomic structures and nanoscale morphology of graphene-based electronic devices (i.e., a graphene sheet supported by an insulating silicon dioxide substrate) for the first time. Atomic resolution scanning tunneling microscopy images reveal the presence of a strong spatially dependent perturbation, which breaks the hexagonal lattice symmetry of the graphitic lattice. Structural corrugations of the graphene sheet partially conform to the underlying silicon oxide substrate. These effects are obscured or modified on graphene devices processed with normal lithographic methods, as they are covered with a layer of photoresist residue. We enable our experiments by a novel cleaning process to produce atomically clean graphene sheets.

High-resolution scanning tunneling microscopy imaging of mesoscopic graphene sheets on an insulating surface.

E Stolyarova — 2007-06-07T20:02:36-00:00

Proc Natl Acad Sci U S A, Vol. 104, No. 22. (29 May 2007), pp. 9209-9212.

We present scanning tunneling microscopy (STM) images of single-layer graphene crystals examined under ultrahigh vacuum conditions. The samples, with lateral dimensions on the micrometer scale, were prepared on a silicon dioxide surface by direct exfoliation of crystalline graphite. The single-layer films were identified by using Raman spectroscopy. Topographic images of single-layer samples display the honeycomb structure expected for the full hexagonal symmetry of an isolated graphene monolayer. The absence of observable defects in the STM images is indicative of the high quality of these films. Crystals composed of a few layers of graphene also were examined. They exhibited dramatically different STM topography, displaying the reduced threefold symmetry characteristic of the surface of bulk graphite.

Electric Field Effect in Atomically Thin Carbon Films

KS Novoselov — 2007-07-27T21:44:51-00:00

Science, Vol. 306, No. 5696. (22 October 2004), pp. 666-669.

We describe monocrystalline graphitic films, which are a few atoms thick but are nonetheless stable under ambient conditions, metallic, and of remarkably high quality. The films are found to be a two-dimensional semimetal with a tiny overlap between valence and conductance bands, and they exhibit a strong ambipolar electric field effect such that electrons and holes in concentrations up to 1013 per square centimeter and with room-temperature mobilities of [~]10,000 square centimeters per volt-second can be induced by applying gate voltage. 10.1126/science.1102896

The structure of suspended graphene sheets

Jannik Meyer — 2007-03-02T05:22:46-00:00

Nature, Vol. 446, No. 7131., pp. 60-63.

Morphology and flexibility of graphene and few-layer graphene on various substrates

U Stöberl — 2008-06-27T12:42:39-00:00

(25 Jun 2008)

We report on detailed microscopy studies of graphene and few-layer-graphene produced by mechanical exfoliation on various semi-conducting substrates. We demonstrate the possibility to prepare and analyze graphene on (001)-GaAs, manganese p-doped (001)-GaAs and InGaAs substrates. The morphology of graphene on these substrates was investigated by scanning electron and atomic force microscopy and compared to layers on silicon oxide. It was found that graphene sheets strongly follow the texture of the sustaining substrates independent on doping, polarity or roughness. Furthermore resist residues exist on top of graphene after a lithographic step. The obtained results provide the opportunity to research the graphene-substrate interactions.

Atomic and electronic structure of few-layer graphene on SiC(0001) studied with scanning tunneling microscopy and spectroscopy

P Lauffer — 2008-07-07T20:36:08-00:00

Physical Review B (Condensed Matter and Materials Physics), Vol. 77, No. 15. (2008)

Epitaxial growth of graphene on SiC surfaces by solid state graphitization is a promising route for future development of graphene based electronics. In the present work, we have studied the morphology, atomic scale structure, and electronic structure of thin films of few-layer graphene (FLG) on SiC(0001) by scanning tunneling microscopy and spectroscopy (STS). We show that a quantitative evaluation of the roughness induced by the interface is a tool for determining the layer thickness of FLG. We present and interpret thickness dependent tunneling spectra, which can serve as an additional fingerprint for the determination of the layer thickness. By performing spatially resolved STS, we find evidence that the charge distribution in bilayer graphene is inhomogeneous.

Think different: increasing online community participation using uniqueness and group dissimilarity

Pamela Ludford — 2005-07-27T16:06:28-00:00

(2004), pp. 631-638.

Cooperation and Punishment in Public Goods Experiments

Ernst Fehr — 2006-03-27T19:14:25-00:00

The American Economic Review, Vol. 90, No. 4. (2000), pp. 980-994.

A meta-analytic review of experiments examining the effects of extrinsic rewards on intrinsic motivation.

EL Deci — 2006-12-28T22:25:01-00:00

Psychol Bull, Vol. 125, No. 6. (November 1999)

A meta-analysis of 128 studies examined the effects of extrinsic rewards on intrinsic motivation. As predicted, engagement-contingent, completion-contingent, and performance-contingent rewards significantly undermined free-choice intrinsic motivation (d = -0.40, -0.36, and -0.28, respectively), as did all rewards, all tangible rewards, and all expected rewards. Engagement-contingent and completion-contingent rewards also significantly undermined self-reported interest (d = -0.15, and -0.17), as did all tangible rewards and all expected rewards. Positive feedback enhanced both free-choice behavior (d = 0.33) and self-reported interest (d = 0.31). Tangible rewards tended to be more detrimental for children than college students, and verbal rewards tended to be less enhancing for children than college students. The authors review 4 previous meta-analyses of this literature and detail how this study's methods, analyses, and results differed from the previous ones.

Magnetic characterization of the frustrated three-leg ladder compound [(CuCl[sub 2]tachH)[sub 3]Cl]Cl[sub 2]

Jurgen Schnack — 2006-09-21T17:35:55-00:00

Physical Review B (Condensed Matter and Materials Physics), Vol. 70, No. 17. (2004)

We report the magnetic features of a one-dimensional stack of antiferromagnetically coupled equilateral copper(II) triangles. High-field magnetization measurements show that the interaction between the copper triangles is of the same order of magnitude as the intratriangle exchange although only coupled via hydrogen bonds. The infinite chain turns out to be an interesting example of a frustrated cylindrical three-leg ladder with competing intra- and inter-triangle interactions. We demonstrate that the ground state is a spin singlet which is gaped from the triplet excitation.

Predicting How People Play Games: Reinforcement Learning in Experimental Games with Unique, Mixed Strategy Equilibria

Ido Erev — 2005-11-22T17:57:12-00:00

The American Economic Review, Vol. 88, No. 4. (1998), pp. 848-881.

We examine learning in all experiments we could locate involving 100 periods or more of games with a unique equilibrium in mixed strategies, and in a new experiment. We study both the ex post ("best fit") descriptive power of learning models, and their ex ante predictive power, by simulating each experiment using parameters estimated from the other experiments. Even a one-parameter reinforcement learning model robustly outperforms the equilibrium predictions. Predictive power is improved by adding "forgetting" and "experimentation," or by allowing greater rationality as in probabilistic fictitious play. Implications for developing a low-rationality, cognitive game theory are discussed.

A Pattern Language: Towns, Buildings, Construction (Center for Environmental Structure Series)

Christopher Alexander — 2005-08-28T12:42:33-00:00

(17 August 1977)

The second of three books published by the Center for Environmental Structure to provide a "working alternative to our present ideas about architecture, building, and planning," <I>A Pattern Language</I> offers a practical language for building and planning based on natural considerations. The reader is given an overview of some 250 patterns that are the units of this language, each consisting of a design problem, discussion, illustration, and solution. By understanding recurrent design problems in our environment, readers can identify extant patterns in their own design projects and use these patterns to create a language of their own. Extraordinarily thorough, coherent, and accessible, this book has become a bible for homebuilders, contractors, and developers who care about creating healthy, high-level design. "Brilliant....Here's how to design or redesign any space you're living or working in--from metropolis to room. Consider what you want to happen in the space, and then page through this book. Its radically conservative observations will spark, enhance, organize your best ideas, and a wondrous home, workplace, town will result"--San Francisco Chronicle. A handbook designed for the layman which aims to present a language which people can use to express themselves in their own communities or homes, and to better communicate with each other.

What kind of creature is a design experiment?

Stephen Gorard — 2006-01-24T11:46:34-00:00

British Educational Research Journal, Vol. 30, No. 4. (2004), pp. 577-590.

This article considers the emerging method of design experimentation, and its developing use in educational research. It considers the extent to which design experiments are different from other, more established, methods and the extent to which elements of established methods can be adapted for use in conjunction with them. One major issue to be addressed before the metaphors and methods of design experiments can be fully accepted is that they assume the combination of different forms of data from different sources. How this combination takes place is, as yet, unresolved. The article, therefore, looks at similar problems also faced in `new' political arithmetic, research syntheses and field trials to see how lessons learned in these approaches could help in the development of the design field.

Infrared spectroscopic study of thiophene adsorbed on zeolites

BA De Angelis — 2006-04-19T12:23:40-00:00

Journal of Colloid and Interface Science, Vol. 53, No. 1. (October 1975), pp. 14-19.

The infrared spectra of thiophene adsorbed on NaY, 13X and HY zeolites were investigated. It was shown that the presence of Bronsted acidic sites is the key factor in determining the behavior of thiophene on zeolites. While on NaY and 13X only small perturbations on the spectrum were noticed, the drastic changes observed on HY indicated a cleavage of the C-S bond and the formation of SH groups. These are revealed by the presence of a strong band at 2380 cm-1, which is also given by ethanethiol adsorbed on HY. It is suggested that protonic acidity may play a role also in the reaction mechanism of thiophene hydrodesulfurization on molybdenum-based catalysts.

Hydrogen bonding of sulfur containing compounds adsorbed on zeolite HZSM5

Cristina Garcia — 2006-04-19T12:20:17-00:00

Journal of Molecular Structure, Vol. 293 (March 1993), pp. 235-238.

The interaction of H2S, ethanethiol and thiophene with H-ZSM5 were studied in situ by means of quantitative FTIR spectroscopy and gravimetry. Hydrogen bonding through the sulfur atom to the SiOHAl groups of the zeolite was concluded to be the primary type of interaction. The larger size of the sulfur atoms induced adsorption structures not observed with the corresponding oxygen compounds. In the case of thiophene adsorption at coverages higher than one molecule per acid site, hydrogen bonding was accompanied by the breakdown of the aromatic ring promoted by the strong acidity of HZSM5.

Telepathy: Origins of Randomization in Experimental Design

Ian Hacking — 2005-06-06T18:37:56-00:00

Isis, Vol. 79, No. 3. (1988), pp. 427-451.

Quantum mysteries revisited

David Mermin — 2008-03-10T18:49:43-00:00

American Journal of Physics, Vol. 58, No. 8. (1990), pp. 731-734.

A gedanken gadget is described, based on an idea of Greenberger, Horne, and Zeilinger, that provides a more powerful demonstration of quantum nonlocality than Bell's analysis of the Einstein–Podolsky–Rosen experiment. ©1990 American Association of Physics Teachers

Glass Transition in Liquids: Two versus Three-Dimensional Confinement

G Barut — 2007-09-24T14:27:46-00:00

Physical Review Letters, Vol. 80, No. 16. (20 April 1998), pp. 3543-3546.

The molecular dynamics of glass-forming liquids is strongly affected by nm-scale confinements. Our dielectric data provide strong evidence both for the “cooperativity” concept and for the existence of two states (interfacial layer and volume liquid). With decreasing size of confinement the orientational relaxation associated with the glass transition becomes faster; and the glass transition temperature is lowered. These effects are stronger for 3D confined droplets than for 2D confined pores. However; the radius at which size effects cease; i.e.; the cooperativity length; does not depend on the dimensionality of the confinement.

How the choice of experimental organism matters: epistemological reflections on an aspect of biological practice.

RM Burian — 2007-03-15T21:48:10-00:00

J Hist Biol, Vol. 26, No. 2. (1993), pp. 351-367.

The Uses of Experiment: Studies in the Natural Sciences

2007-03-31T13:35:38-00:00

(01 December 1989)

Experiment is widely regarded as the most distinctive feature of natural science and essential to the way scientists find out about the world. Yet there has been little study of the way scientists actually make and use experiments. The Uses of Experiment fills this gap in our knowledge about how science is practised. Presenting 14 original case studies of important and often famous experiments, the book asks the questions: What tools do experimenters use? How do scientists argue from experiments? What happens when an experiment is challenged? How do scientists check that their experiments are working? Are there differences between experiments in the physical sciences and technology? Leading scholars in the fields of history, sociology and philosophy of science consider topics such as the interaction of experiment; instruments and theory; accuracy and reliability as hallmarks of experiment in science and technology; realising new phenomena; the believability of experiments and the sort of knowledge they produce; and the wider contexts on which experimentalists draw to develop and win support for their work. Drawing on examples as diverse as Galilean mechanics, Victorian experiments on electricity, experiments on cloud formation, and testing of nuclear missiles, a new view of experiment emerges. This view emphasises that experiments always involve choice, tactics and strategy in persuading audiences that Nature resembles the picture experimenters create.

The Philosophy Of Scientific Experimentation

Hans Radder — 2007-03-31T13:34:34-00:00

(23 February 2003)

<div>Since the late 1980s, the neglect of experiment by philosophers and historians of science has been replaced by a keen interest in the subject. In this volume, a number of prominent philosophers of experiment directly address basic theoretical questions, develop existing philosophical accounts, and offer novel perspectives on the subject, rather than rely exclusively on historical cases of experimental practice.<br> Each essay examines one or more of six interconnected themes that run throughout the collection: the philosophical implications of actively and intentionally interfering with the material world while conducting experiments; issues of interpretation regarding causality; the link between science and technology; the role of theory in experimentation involving material and causal intervention; the impact of modeling and computer simulation on experimentation; and the philosophical implications of the design, operation, and use of scientific instruments.<br></div>

Randomized experiments as the bronze standard

Richard Berk — 2007-04-13T15:13:43-00:00

Journal of Experimental Criminology, Vol. 1, No. 4. (24 December 2005), pp. 417-433.

Error and the Growth of Experimental Knowledge (Science and Its Conceptual Foundations series)

Deborah Mayo — 2007-03-31T13:16:41-00:00

(15 August 1996)

<div>We may learn from our mistakes, but Deborah Mayo argues that, where experimental knowledge is concerned, we haven't begun to learn enough. <i>Error and the Growth of Experimental Knowledge</i> launches a vigorous critique of the subjective Bayesian view of statistical inference, and proposes Mayo's own error-statistical approach as a more robust framework for the epistemology of experiment. Mayo genuinely addresses the needs of researchers who work with statistical analysis, and simultaneously engages the basic philosophical problems of objectivity and rationality.<br><br>Mayo has long argued for an account of learning from error that goes far beyond detecting logical inconsistencies. In this book, she presents her complete program for how we learn about the world by being "shrewd inquisitors of error, white gloves off." Her tough, practical approach will be important to philosophers, historians, and sociologists of science, and will be welcomed by researchers in the physical, biological, and social sciences whose work depends upon statistical analysis.<br><br></div>

We should be designing better experiments.

MF Festing — 2007-07-09T11:46:01-00:00

Vet Anaesth Analg, Vol. 30, No. 2. (April 2003), pp. 59-61.

Guidelines for the design and statistical analysis of experiments using laboratory animals.

MF Festing — 2007-07-09T11:34:32-00:00

ILAR J, Vol. 43, No. 4. (2002), pp. 244-258.

For ethical and economic reasons, it is important to design animal experiments well, to analyze the data correctly, and to use the minimum number of animals necessary to achieve the scientific objectives---but not so few as to miss biologically important effects or require unnecessary repetition of experiments. Investigators are urged to consult a statistician at the design stage and are reminded that no experiment should ever be started without a clear idea of how the resulting data are to be analyzed. These guidelines are provided to help biomedical research workers perform their experiments efficiently and analyze their results so that they can extract all useful information from the resulting data. Among the topics discussed are the varying purposes of experiments (e.g., exploratory vs. confirmatory); the experimental unit; the necessity of recording full experimental details (e.g., species, sex, age, microbiological status, strain and source of animals, and husbandry conditions); assigning experimental units to treatments using randomization; other aspects of the experiment (e.g., timing of measurements); using formal experimental designs (e.g., completely randomized and randomized block); estimating the size of the experiment using power and sample size calculations; screening raw data for obvious errors; using the t-test or analysis of variance for parametric analysis; and effective design of graphical data.

Science as experiment; science as observation

Eliza Chakravarty — 2006-12-19T14:25:10-00:00

Nat Clin Pract Rheum, Vol. 2, No. 6. (June 2006), pp. 286-287.

Direct Experimental Evidence of a Growing Length Scale Accompanying the Glass Transition

L Berthier — 2006-02-06T23:09:02-00:00

Science, Vol. 310, No. 5755. (16 December 2005), pp. 1797-1800.

Understanding glass formation is a challenge, because the existence of a true glass state, distinct from liquid and solid, remains elusive: Glasses are liquids that have become too viscous to flow. An old idea, as yet unproven experimentally, is that the dynamics becomes sluggish as the glass transition approaches, because increasingly larger regions of the material have to move simultaneously to allow flow. We introduce new multipoint dynamical susceptibilities to estimate quantitatively the size of these regions and provide direct experimental evidence that the glass formation of molecular liquids and colloidal suspensions is accompanied by growing dynamic correlation length scales.

Survival value of chemotaxis in mixed cultures.

WK Pilgram — 2008-04-16T13:04:28-00:00

Canadian journal of microbiology, Vol. 22, No. 12. (December 1976), pp. 1771-1773.

A motile, chemotactic strain of Proteus mirabilis outgrew a motile, non-chemotactic mutant in a semisolid, amino acid medium, although the two strains grew equally well in broth.

Role of Chemotaxis in the Ecology of Denitrifiers.

Michael J Kennedy — 2008-04-16T13:00:01-00:00

Applied and environmental microbiology, Vol. 49, No. 1. (January 1985), pp. 109-114.

A modification of the Adler capillary assay was used to evaluate the chemotactic responses of several denitrifiers to nitrate and nitrite. Strong positive chemotaxis was observed to NO(3) and NO(2) by soil isolates of Pseudomonas aeruginosa, Pseudomonas fluorescens, and Pseudomonas stutzeri, with the peak response occurring at 10 M for both attractants. In addition, a strong chemoattraction to serine (peak response at 10 M), tryptone, and a soil extract, but not to NH(4), was observed for all denitrifiers tested. Chemotaxis was not dependent on a previous growth on NO(3), NO(2), or a soil extract, and the chemoattraction to NO(3) occurred when the bacteria were grown aerobically or anaerobically. However, the best response to NO(3) was usually observed when the cells were grown aerobically with 10 mM NO(3) in the growth medium. Capillary tubes containing 103 M NO(3) submerged into soil-water mixtures elicited a significant chemotactic response to NO(3) by the indigenous soil microflora, the majority of which were Pseudomonas spp. A chemotactic strain of P. fluorescens also was shown to survive significantly better in aerobic and anaerobic soils than was a nonmotile strain of the same species. Both strains had equal growth rates in liquid cultures. Thus, chemotaxis may be one mechanism by which denitrifiers successfully compete for available NO(3) and NO(2), and which may facilitate the survival of naturally occurring populations of some denitrifiers.

Adhesion and chemotaxis as determinants of bacterial association with mucosal surfaces.

R Freter — 2008-04-16T12:56:43-00:00

Advances in experimental medicine and biology, Vol. 107 (1978), pp. 429-437.

1) Chemotaxis of cholera vibrios facilitates the association of these bacteria with the mucosal surface. 2) Mucosal extracts can block the chemotactic receptors on the bacterial surface and thereby retard the association of chemotactic bacteria with the mucosal surface. 3) Chemotactic cholera vibrios grow more efficiently than non-chemotactic mutants in germfree mice and in isolated intestinal loops of rabbits. Conversely, non-chemotactic mutants grow more efficiently in infant mice. 4) Chemotaxis is therefore of considerable importance to the in vivo growth of cholera vibrios. The various mechanisms, including those of local immunity, by which bacterial chemotaxis can be exploited for the benefit of the host deserve further exploration.

X-Ray Reflectivity from the Surface of a Liquid Crystal: Surface Structure and Absolute Value of Critical Fluctuations

PS Pershan — 2007-07-19T02:15:03-00:00

Physical Review Letters, Vol. 52, No. 9. (27 February 1984), 759.

X-ray reflectivity from the surface of a nematic liquid crystal is interpreted as the coherent superposition of Fresnel reflection from the surface and Bragg reflection from smectic order induced by the surface. Angular dependence of the Fresnel effect yields information on surface structure. Measurement of the intensity of diffuse critical scattering relative to the Fresnel reflection yields the absolute value of the critical part of the density-density correlation function.

Smectic-A Order at the Surface of a Nematic Liquid Crystal: Synchrotron X-Ray Diffraction

J Als-Nielsen — 2007-07-19T02:10:35-00:00

Physical Review Letters, Vol. 48, No. 16. (19 April 1982), 1107.

A novel geometry in which it is possible to do x-ray diffraction from a horizontal surface of fluids is applied to liquid crystals. A large-diameter drop of octyloxycyanobiphenyl (8OCB) on a glass plate treated for homeotropic alignment yields perfect alignment of the smectic- A layers at the top surface over an area of several square millimeters. The surface in the bulk nematic as well as in the isotropic phase was found to consist of smectic- A layers with a penetration depth equal to the longitudinal smectic- A correlation length ξ ∥ ∼( T - T NA ) -ν ∥ determined previously.

Surface Roughness of Water Measured by X-Ray Reflectivity

A Braslau — 2007-07-19T02:04:31-00:00

Physical Review Letters, Vol. 54, No. 2. (14 January 1985), 114.

The roughness of the liquid-vapor interface for pure water was measured by a technique of x-ray reflectivity. With synchrotron radiation (λ∼1.5 ÅA); the angular dependence of the x-ray reflectivity was measured from grazing incidence (∼0.0021 rad); where the reflectivity was greater than 0.96; to an incident angle of ∼0.05 rad; where the reflectivity was ∼7×10 -8 . A fit to the data by a theory with only one adjustable parameter obtains 3.2 ÅA for the root-mean-square roughness of the water surface.

Wall-Induced Pretransitional Birefringence: A New Tool to Study Boundary Aligning Forces in Liquid Crystals

K Miyano — 2007-07-19T02:02:40-00:00

Physical Review Letters, Vol. 43, No. 1. (2 July 1979), 51.

A wall-induced birefringence in a nematic liquid crystal above the nematic-isotropic phase transition point has been observed for the first time. It is expected that this phenomenon will provide a useful tool to study the nature of aligning forces at liquid-crystal-solid interfaces.

X-Ray Studies of Tilted Hexatic Phases in Thin Liquid-Crystal Films

EB Sirota — 2008-01-17T04:22:34-00:00

Physical Review Letters, Vol. 55, No. 19. (4 November 1985), 2039.

X-ray-diffraction studies of the structures and phase transitions of the tilted hexatic phases (smectic F and smectic I in thin liquid-crystal films of 4- n -heptyloxybenzylidene-4-n- n -heptylaniline (70.7) are reported. The measured correlation lengths were strongly anisotropic in both phases. The smectic- I to smectic- F transition is first order as expected from the symmetry change. The smectic- F to smectic- G transition is first order with strong pretransition effects and becomes nearly second order as the film thickness is decreased.

X-ray and optical studies of the thickness dependence of the phase diagram of liquid-crystal films

EB Sirota — 2008-01-17T04:13:00-00:00

Physical Review A, Vol. 36, No. 6. (1987), 2890.

A comprehensive study of the thickness dependence of the phase diagram of freely suspended films of the liquid crystal 4- n -heptyloxybenzylidene-4- n -heptylaniline (7O.7) between 50 and 69 ° C is reported. In thick films (thicker than about 300 layers and characteristic of bulk samples) there is a low-temperature crystalline- G phase followed by five crystalline- B phases with different stacking arrangements at higher temperatures. In thinner films there are two additional crystalline- B phases and two tilted hexatic phases; smectic- F and smectic- I ; which do not appear in bulk samples. The in-plane and interlayer correlations in the tilted hexatic phases are anisotropic with a clear dependence on the molecular tilt direction; the in-plane correlations are more developed (longer range) perpendicular to the molecular tilt direction and the interlayer correlations are more developed parallel to the tilt direction.

Quantized layer growth at liquid-crystal surfaces

BM Ocko — 2007-07-11T06:41:16-00:00

Physical Review Letters, Vol. 57, No. 1. (7 July 1986), 94.

We report x-ray reflectivity measurements on the free surface of dodecylcyanobiphenyl (12CB) at the isotropic to smectic- A phase transition. At about 10?deC above T IA ; smectic- A -like ordering develops at the surface while the bulk phase remains isotropic. The angular dependence of the specular reflectivity is consistent with a sinusoidal density modulation; starting at the surface and terminating abruptly; after an integral number of bilayers. As the transition is approached the number of layers increases in quantized steps from zero to five before the bulk undergoes a first-order transition to the smectic- A phase.

Free-standing films above the bulk smectic-nematic-isotropic transitions

VK Dolganov — 2006-07-24T04:39:49-00:00

Physics Letters A, Vol. 220, No. 4-5. (9 September 1996), pp. 242-246.

Optical reflectivity of free-standing films in the temperature interval of the smectic phases and above the bulk smectic-nematic transition temperature has been studied. Melting phenomena have been found to be dependent on the film thickness. For thick films, nematic-like droplets and an unstable state over the entire film have been observed above the bulk smectic-nematic transition temperature. These droplets and the unstable state of the film look like the “quasi-smectic” phase predicted by Mirantsev.

Role of molecular weight and phase sequence in the temperature variation of film tension above the bulk isotropic transition in freestanding liquid-crystal films

M Veum — 2006-07-24T04:27:57-00:00

Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 74, No. 1. (2006)

Building upon our previous report [Veum et al., Phys. Rev. E 17, 020701(R) (2005)] involving two compounds, we have performed a systematic study of the temperature variation of film tension above the bulk isotropic transition in freestanding films to include a total of six smectic liquid-crystal compounds. Consistent with the previous results, the tension increases sharply with temperature above the transition, the tension-temperature slope is proportional to the film's thickness, and the data can be interpreted in the context of theoretical models for layer thinning. Our data suggest that both molecular weight and bulk phase appearing below its isotropic phase play important roles in the slope values.

Optical determination of smectic A layer spacing in freely suspended thin films

Charles Rosenblatt — 2006-09-07T09:10:07-00:00

Applied Physics Letters, Vol. 36, No. 6. (1980), pp. 432-434.

Optical measurements of smectic A layer spacings in freely suspended thin films of three liquid crystals are reported. Although the measured spacings are close to those reported for the bulk, some anomalous behavior is noted. In addition, we report that the smectic A phase in the film can exist at unusually high temperatures.

Temperature variation of film tension above the bulk smectic-A--isotropic transition in freestanding liquid-crystal films

M Veum — 2007-03-12T01:03:30-00:00

Physical Review E (Statistical, Nonlinear, and Soft Matter Physics), Vol. 71, No. 2. (2005), 020701(R).

We have measured the temperature variation of film tension above the bulk smectic-A–isotropic transition in freestanding films of two liquid-crystal compounds. Above the transition, the tension increases sharply with temperature, and the slope is proportional to the film's thickness regardless of whether or not the compound exhibits regular layer-by-layer thinning. The data can be interpreted in the context of theoretical models for layer thinning.

Thinning transitions in free-standing liquid-crystal films as the successive formation of dislocation loops

S Pankratz — 2007-08-29T09:04:43-00:00

Physical Review E, Vol. 60, No. 3. (1999), R2456.

We describe a model for the layer-thinning transition in free-standing liquid-crystal films based on the successive; spontaneous formation of dislocation loops. As the film temperature increases and the smectic order and layer compressional modulus decrease; the condition for creating a dislocation loop of critical radius is met and a thinning is nucleated. The resulting equation for N ; the number of smectic layers; as a function of temperature yields good fitting results to the thinning transitions obtained from several fluorinated compounds.