bluuebunny/crossref_metadata_2025 huggingface dataset:
Stimulus Eccentricity and Spatial Frequency Interact to Determine Circular Vection
Authors: Palmisano Stephen , Gillam Barbara
Published: January 2007

While early research suggested that peripheral vision dominates the perception of self-motion, subsequent studies found little or no effect of stimulus eccentricity. In contradiction to these broad notions of ‘peripheral dominance’ and ‘eccentricity independence’, the present experiments showed that the spatial frequency of optic flow interacts with its eccentricity to determine circular vection magnitude—central stimulation producing the most compelling vection for high-spatial-frequency stimuli and peripheral stimulation producing the most compelling vection for lower-spatial-frequency stimuli. This interaction appeared to be due, in part at least, to the effect that the higher-spatial-frequency moving pattern had on subjects’ ability to organise optic flow into related motion about a single axis. For example, far-peripheral exposure to this high-spatial-frequency pattern caused many subjects to organise the optic flow into independent local regions of motion (a situation which clearly favoured the perception of object motion not self-motion). It is concluded that both high-spatial-frequency and low-spatial-frequency mechanisms are involved in the visual perception of self-motion—with their activities depending on the nature and eccentricity of the motion stimulation.
The Perception of Depth and Slant from Texture in Three-Dimensional Scenes
Authors: Andersen George J , Braunstein Myron L , Saidpour Asad
Published: January 2007

The perception of depth and slant in three-dimensional scenes specified by texture was investigated in five experiments. Subjects were presented with computer-generated scenes of a ground and ceiling plane receding in depth. Compression, convergence, and grid textures were examined. The effect of the presence or absence of a gap in the center of the display was also assessed. Under some conditions perceived slant and depth from compression were greater than those found with convergence. The relative effectiveness of compression in specifying surface slant was greater for surfaces closer to ground planes (80° slant) than for surfaces closer to frontal parallel planes (40° slant). The usefulness of compression was also observed with single-plane displays and with displays with surfaces oriented to reduce information regarding the horizon.
Recognising the Ageing Face: The Role of Age in Face Processing
Authors: George Patricia A , Hole Graham J
Published: January 2007

The effects of age-induced changes on face recognition were investigated as a means of exploring the role of age in the encoding of new facial memories. The ability of participants to recognise each of six previously learnt faces was tested with versions which were either identical to the learnt faces, the same age (but different in pose and expression), or younger or older in age. Participants were able to cope well with facial changes induced by ageing: their performance with older, but not younger, versions was comparable to that with faces which differed only in pose and expression. Since the large majority of different age versions were recognised successfully, it can be concluded that the process of recognition does not require an exact match in age characteristics between the stored representation of a face and the face currently in view. As the age-related changes explored here were those that occur during the period of growth, this in turn implies that the underlying structural physical properties of the face are (in addition to pose and facial expression) invariant to a certain extent.
A Test of the Gravity Lens Theory
Authors: Greene Ernest
Published: January 2007

Naito and Cole [1994, in Contributions to Mathematical Psychology: Psychometrics and Methodology Eds G H Fischer and D Laming (New York: Springer)] provide a configuration which they describe as the Gravity Lens illusion. In this configuration, four small dots are presented in proximity to four large disks, and one is asked to compare the slope of an imaginary line which connects one pair of dots with the slope of a line which connects the other pair. In fact the slopes are the same, ie their axes are parallel, but because of the positioning of the large disks they appear to be at different orientations. Naito and Cole propose that the perceptual bias is analogous to the effects of gravity on the metrics of physical space, such that mental projections in the vicinity of a disk (or an open circle) are distorted just as the path of light is bent as it passes a massive body such as a star. Here we provide a simple test of this concept by having subjects judge alignments of dots which lie near tangents to a circle. Subjects were asked to project straight lines through pairs of stimulus dots, selecting and marking points in open space which were collinear with each pair. As would be predicted by the Gravity Lens theory, the locations selected by subjects were displaced from straight lines. However, the error magnitudes were substantially larger for judgments of dot pairs which had an oblique alignment, as compared with dot pairs which were aligned with a cardinal axis. This differential of effect as a function of stimulus orientation is not predicted by the gravity concept.
Perceptual Learning in Visual Conjunction Search
Authors: Lobley Katy , Walsh Vincent
Published: January 2007

Perceptual learning in colour/orientation visual conjunction search was examined in five experiments. Good transfer occurred to other conjunction arrays when only one element of the conjunction (either colour or orientation) was changed. When both elements (colour and orientation) were changed, but the same feature spaces were used (ie other colours and orientations) or when a new dimension was introduced to the transfer task (shapes instead of orientation), transfer was poor. The results suggest that perceptual learning of visual conjunction search is constrained mainly by stimulus parameters rather than by changes in cognitive strategies which are common to all search tasks. Contrary to other reports we found little evidence of long-term retention of learning.
Disparity Detection in Anticorrelated Stereograms
Authors: Cumming Bruce G , Shapiro Susan E , Parker Andrew J
Published: January 2007

Recent physiological observations in which stimuli with opposite contrast signs in the two eyes have been used (anticorrelated stereograms) show that these stimuli evoke responses in primary visual cortex which are the reverse of responses to correlated stimuli. Psychophysical investigations reveal no such reversals: reversed-contrast bars with crossed disparities are seen in front of those with uncrossed disparities. For anticorrelated random-dot stereograms human subjects perceive no depth at all, except at low dot densities. However, these human studies were carried out with stimuli that differed in several ways from those used in physiological studies. We therefore reexamined psychophysical responses using stimuli similar to those used for physiological recordings. Our results confirm the previous findings: there is no evidence of a reversed depth sensation for bar stereograms (crossed disparities are never seen behind uncrossed disparities), and subjects are unable to detect depth in anticorrelated random-dot stereograms at the densities used for the physiological recordings. The discrepancy between the psychophysical data and the responses of single neurons in primary visual cortex suggests that further processing outside area V1 is necessary to provide the signals that produce the sensation of stereoscopic depth.
In Space, the past Can Be Recast but Not the Present
Authors: Sheth Bhavin R , Shimojo Shinsuke
Published: January 2007

We address the relationship between perception and spatial, working memory. Specifically, we argue that perceptual experience following the creation of a representation of target location affects it in a systematic way. We designed a motor task in which observers had to point to the initial or final position of a horizontally drifting target embedded in a vertically drifting background. The target was perceived as having an illusory motion component in a direction opposite that of the inducer dots [Duncker, 1938, Source Book of Gestalt Psychology (London: Kegan Paul, Trench, Trubner and Co)]. For both positions, there was an identical time delay before the observer could respond. Nonetheless, estimates of the initial target position were significantly biased by the illusion in a direction opposite the perceived target motion, and both bias and variability were significantly greater than those of the target's final position. In prior studies on positional accuracy with induced displacement, a delay before a pointing response led to an unbiased position estimate obtained without delay to become biased, leading investigators to argue for a long-lasting, inaccurate cognitive system that overrules an accurate, nonetheless transient, motor one (Bridgeman et al, 1997, Perceptual Psychology59 456–469). Since the same motor task with identical delay on either position yielded different outcomes, a hypothesis based on distinct motor and cognitive representations of visual space is untenable here. Instead, we argue that an online representation of the target's original position is updated in an ongoing fashion in order to reconcile the perceived illusion with the veridically perceived present (current target location).
Mirror Symmetry Opposes Splitting of Chromatically Homogeneous Surfaces
Authors: Parovel Giulia , Vezzani Stefano
Published: January 2007

Chromatically homogeneous surfaces can be seen as single figures but also as two or more overlapping figures. Local factors such as relatability have been proposed in order to explain perception of two or more figures (Kellman and Shipley, 1991 Cognitive Psychology23 141 – 221). However, even when these factors are at work, there are conditions favouring the perception of a single figure, which have not been explored so far. Here we propose that one such factor is the mirror symmetry of the surface. Three experiments were designed to test: (a) the main hypothesis, that mirror symmetry enhances perception of a single figure; (b) the role of orientation; (c) the effect of the number of axes of symmetry. The results show that (i) there is a good general correlation between mirror symmetry and perception of a single figure; (ii) vertical and horizontal axes of symmetry are the most effective; and (iii) the more axes of symmetry a surface has, the more likely is the perception of a single figure. These results suggest that mirror symmetry is an important factor in the perception of chromatically homogeneous displays. Some explanations are discussed, particularly one based on the rejection-of-coincidence principle [Rock, 1983 The Logic of Perception (Cambridge, MA: MIT Press)], and a version of the minimum principle in which the strength of the global solution depends on symmetry, whereas the strength of the splitting solution depends on the strength of local factors. In brief, global and local factors compete in determining the perceptual outcome in chromatically homogeneous surfaces.
Luminance-Induced Shift in the Apparent Direction of Gaze
Authors: Ando Shinki
Published: January 2007

Changing the luminance of one side of the sclera induces an apparent shift of the perceived direction of gaze toward the darker side of the sclera. This luminance-induced gaze shift was measured in photographic and schematic images of eyes. The effect was substantial: a moderate darkening of one side of the sclera induced an apparent shift of 8 to 10 deg of gaze; the maximum darkening induced a shift of 15 deg of gaze or more. The effect of scleral darkening was also compared to the gaze shift induced by an actual shift of the iris. The effects of the two cues were measured independently and in combination. When pitted against each other, their effects could be nulled, demonstrating that they act on a common level. Predictions of the relative strengths of the luminance and iris shift cues were developed for two simple luminance-based mechanisms: flux ratio and luminance centroid. The data showed the luminance cue was less effective than the models predicted in determining gaze direction. As an alternative source for the gaze shift, irradiation effects on apparent size could create a perceived shift in the iris position but a direct measure of the irradiation shift showed that this was far too small. The results suggest that at least one important mechanism for gaze judgment is based on low-level analysis of the luminance configuration within the eye.
Munker–White-Like Illusions without T-Junctions
Authors: Yazdanbakhsh Arash , Arabzadeh Ehsan , Babadi Baktash , Fazl Arash
Published: January 2007

Some interpretations of the Munker–White illusion were evaluated by designing new versions of this illusion devoid of T-junctions (Munker–White-like images). The magnitudes of both Munker–White and Munker–White-like illusions were then quantified by using a brightness-matching technique. The results showed the effect to persist in all proposed versions. Since the illusion still remains despite the absence of explicit T-junctions and any explanation considering transparency, mechanisms other than those proposed by these interpretations must be responsible.
Eyes Wide Apart: Overestimating Interpupillary Distance
Authors: Thompson Peter
Published: January 2007

Our ability to perceive many aspects of the human face is so acute that some would propose that we possess specialised face-processing mechanisms. One example of this exquisite performance is our ability to discriminate differences in the lateral separation of the eyes in pairs of otherwise identical faces—see Kemp et al (1990, Perception19 531–543). However, we have found that our ability to estimate our own interpupillary distance (IPD) shows no such accuracy. Subjects were asked to indicate, without undue rumination, their own IPD and, by way of control, the distance from the bridge to the tip of their own nose. Compared to the true distances, IPD was overestimated by more than 30% while nose length was underestimated by 11%. Although a plausible reason for the nose length underestimation is foreshortening of the image, the reason for the overestimation of eye separation remains obscure.
A
Medicago truncatula
phosphate transporter indispensable for the arbuscular mycorrhizal symbiosis
Authors: Javot Hélène , Penmetsa R. Varma , Terzaghi Nadia , Cook Douglas R. , Harrison Maria J.
Published: January 2007

The arbuscular mycorrhizal (AM) symbiosis is a mutualistic endosymbiosis formed by plant roots and AM fungi. Most vascular flowering plants have the ability to form these associations, which have a significant impact on plant health and consequently on ecosystem function. Nutrient exchange is a central feature of the AM symbiosis, and AM fungi obtain carbon from their plant host while assisting the plant with the acquisition of phosphorus (as phosphate) from the soil. In the AM symbiosis, the fungus delivers P
i
to the root through specialized hyphae called arbuscules. The molecular mechanisms of P
i
and carbon transfer in the symbiosis are largely unknown, as are the mechanisms by which the plant regulates the symbiosis in response to its nutrient status. Plants possess many classes of P
i
transport proteins, including a unique clade (Pht1, subfamily I), members of which are expressed only in the AM symbiosis. Here, we show that MtPT4, a
Medicago truncatula
member of subfamily I, is essential for the acquisition of P
i
delivered by the AM fungus. However, more significantly, MtPT4 function is critical for AM symbiosis. Loss of MtPT4 function leads to premature death of the arbuscules; the fungus is unable to proliferate within the root, and symbiosis is terminated. Thus, P
i
transport is not only a benefit for the plant but is also a requirement for the AM symbiosis.
β-Sheet core of human prion protein amyloid fibrils as determined by hydrogen/deuterium exchange
Authors: Lu Xiaojun , Wintrode Patrick L. , Surewicz Witold K.
Published: January 2007

Propagation of transmissible spongiform encephalopathies is associated with the conversion of normal prion protein, PrP
C
, into a misfolded, oligomeric form, PrP
Sc
. Although the high-resolution structure of the PrP
C
is well characterized, the structural properties of PrP
Sc
remain elusive. Here we used MS analysis of H/D backbone amide exchange to examine the structure of amyloid fibrils formed by the recombinant human PrP corresponding to residues 90–231 (PrP90–231), a misfolded form recently reported to be infectious in transgenic mice overexpressing PrP
C
. Analysis of H/D exchange data allowed us to map the systematically H-bonded β-sheet core of PrP amyloid to the C-terminal region (staring at residue ≈169) that in the native structure of PrP monomer corresponds to α-helix 2, a major part of α-helix 3, and the loop between these two helices. No extensive hydrogen bonding (as indicated by the lack of significant protection of amide hydrogens) was detected in the N-terminal part of PrP90–231 fibrils, arguing against the involvement of residues within this region in stable β-structure. These data provide long-sought experimentally derived constraints for high-resolution structural models of PrP amyloid fibrils.
Fibrillin-1 regulates the bioavailability of TGFβ1
Authors: Chaudhry Shazia S. , Cain Stuart A. , Morgan Amanda , Dallas Sarah L. , Shuttleworth C. Adrian , Kielty Cay M.
Published: January 2007

We have discovered that fibrillin-1, which forms extracellular microfibrils, can regulate the bioavailability of transforming growth factor (TGF) β1, a powerful cytokine that modulates cell survival and phenotype. Altered TGFβ signaling is a major contributor to the pathology of Marfan syndrome (MFS) and related diseases. In the presence of cell layer extracellular matrix, a fibrillin-1 sequence encoded by exons 44–49 releases endogenous TGFβ1, thereby stimulating TGFβ receptor–mediated Smad2 signaling. This altered TGFβ1 bioavailability does not require intact cells, proteolysis, or the altered expression of TGFβ1 or its receptors. Mass spectrometry revealed that a fibrillin-1 fragment containing the TGFβ1-releasing sequence specifically associates with full-length fibrillin-1 in cell layers. Solid-phase and BIAcore binding studies showed that this fragment interacts strongly and specifically with N-terminal fibrillin-1, thereby inhibiting the association of C-terminal latent TGFβ-binding protein 1 (a component of the large latent complex [LLC]) with N-terminal fibrillin-1. By releasing LLC from microfibrils, the fibrillin-1 sequence encoded by exons 44–49 can contribute to MFS and related diseases.
A Study of the Beam-foil Excitation Mechanism Using 60-360 keV Be+Projectiles
Authors: B Dynefors  , I Martinson  , E Veje
Published: January 2007

Beam-foil excitation functions have been measured for a number of optical transitions in Be Ia(configuration 1s22s nl), Be Ib(configuration 1s2nl n'l'), Be IIa(configuration 1s2nl), Be IIb(configuration 1s nl n'l'), and Be IIIa(configuration 1s nl) in the projectile energy range 60-360 keV. The excitation functions within one level scheme were found to be proportional. They have been converted into relative population functions and the five sets of Be population functions have been linked together by only two empirically determined parameters. Comparisons to results from earlier works, using He and Li projectiles are drawn. Relative level population measurements have been performed in Be Ia, Be Ib, Be IIaand Be IIIa, the results are compared with earlier findings, and systematical trends are found. General conclusions about the beam-foil excitation mechanism are drawn.
Two-Component Relativistic Wave Equations for Spin-½ Particles
Authors: J F Cornwell  , C G Koutroulos  , A Sudbery
Published: January 2007

A critical re-examination is made of the derivation from the Kramers equation and the Poincaré covariance of the two-component relativistic wave equations for particles of non-zero mass and spin ½ that have recently been proposed by Biedenharn, Han and van Dam.
Beam-foil Studies of Phosphorus in the Vacuum Ultraviolet
Authors: A E Livingston  , J A Kernahan  , D J G Irwin  , E H Pinnington
Published: January 2007

We have measured lifetimes for 24 terms in P I-P V using the beam-foil technique in the vacuum UV region. The results have been compared with theoretical calculations and with other experimental values. Several significant discrepancies with earlier results have been found. We present the first experimental lifetimes for 9 terms. Most of our lifetimes can be converted directly intof-values, and we discuss these in relation to trends along isoelectronic sequences. Configuration interaction is found to be important for several transitions. We also suggest a revision of the recently-determined abundance of phosphorus in interstellar clouds, based upon our newf-value for the 1 308 Å multiplet in P II.
Strengths of Analogue Resonances in (p, γ) Reactions on Sulphur Isotopes
Authors: J Keinonen  , M Riihonen  , A Anttila
Published: January 2007

Absolute strengths of theEp= 588 keV resonance in the32S(p,γ)33Cl reaction and of theEp= 1 214 keV resonance in the34S(p,γ)35Cl reaction have been determined as 0.20 ± 0.04 eV and 9.8 ± 1.0 eV, respectively. The strength of theEp= 1 542 keV resonance in the33S(p,γ)34Cl reaction and theEp= 1 887 keV resonance in the36S(p,γ)37Cl reaction have been obtained as 1.4 ± 0.2 eV and 22 ± 3 eV, respectively, by comparison with theEp= 1 214 keV resonance in the34S(p,γ)35Cl reaction. The total, proton and γ-ray widths of theJπ = 7-/2 analogue states in35Cl and37Cl atEx= 7.55 and 10.22 MeV, respectively, are given. The γ-ray decay of these isobaric analogue resonances in34,35,37Cl is discussed.
Lifetimes of Excited Levels in MgIII, CaIII, KIV–V, CaV, and Ge I
Authors: T Andersen  , A Petrakiev Petkov  , G Sørensen
Published: January 2007

Radiative lifetimes of excited levels in Mg III, Ca III, K IV, K V, Ca V, and Ge I have been measured by means of the beam-foil technique in order to test the validity of recent theoretical methods to calculate lifetimes for heavier atoms and ions. Good agreement with theoretical lifetimes is obtained.
Polarization Effects on Discrete Transitions in Light Alkali Atoms Calculated in the Linked Diagram Formalism
Authors: Sten Garpman
Published: January 2007

A multi-configurational model space is used to construct effective operators for electromagnetic radiation. The operators are constructed by means of a Rayleigh-Schrödinger perturbation expansion of the wave operator to include the effect of the non-central part of the Coulomb interaction on the model wave functions. In this way polarization effects on Restricted Hartree-Fock (RHF) wave functions could be examined and effective radial integrals for electric dipole (E1) transitions could easily be calculated. Numerical results are given for the first members of the principal seriesns→n'pand the first subsidiary series (diffuse series)np→n'''dof Li and Na. The calculation is performed in a non-relativistic scheme. Three different representations of the dipole operator are used: length, velocity and acceleration. When including polarization one could see a remarkably better agreement between the results obtained by the different representations as compared with the corresponding RHF calculation. The effect of polarization on RHF oscillator strengths increases from Li to Na, and for the higher members in the principal series of sodium the effect is large. A comparison of our calculated strengths with accurateab initiocalculations of the variational type, shows good agreement for the strengths of the sharp and diffuse series and for some intercombination lines of Li. Accurate experimental data being sparse, it is difficult to estimate the importance of correlation on the oscillator strengths. The set of values chosen indicates that correlation effects are large for the principal series (except for the resonance transition) and smaller for the sharp and diffuse series where a good agreement with experiment is obtained.
Atmospheric Solitary Waves
Authors: K B Dysthe  , L Stenflo
Published: January 2007

We show that the hydrodynamic equations which govern the propagation of acoustic gravity waves can have shock-like solutions.
Optical Constants of Epitaxial Silicon in the Region 1–3.3 eV
Authors: Rolf Hulthén
Published: January 2007

The optical constants of epitaxial silicon have been obtained in the region 1–3.3 eV (to 3.1 eV forn) by means of optical transmission and photoconductivity measurements. The silicon layers are 0.1–3 μm thick and therefore give interference spectra in both measuring modes. The values ofnobtained here fit well with those obtained from reflectance and ellipsometric measurements on bulk silicon. The absorption coefficient α is calculated from the quotientITu/IT1, whereITu(1)is the upper (lower) envelope of the transmitted intensity interference curve. The values obtained here are greater by a factor of 2 than those of Dash & Newman (1955). Literature values obtained from ellipsometric measurements at λ = 5 461 Å show a substantial spread with the values of Dash & Newman as a lower limit.
Molecular characterization of extended-spectrum beta-lactamases in Enterobacteriaceae from patients of two hospitals in Saxony, Germany
Authors: Schmitt Joachim , Jacobs Enno , Schmidt Herbert
Published: January 2007

Between January and September 2003, 39 isolates of the family Enterobacteriaceae with phenotypically positive Vitek 1 extended-spectrum beta-lactamase (ESBL) test results were collected, originating from patients of two hospitals in Saxony, Germany. Plasmid DNA was isolated and screened by PCR for the presence of genes encoding beta-lactamases of SHV, TEM and CTX-M types. To differentiate ESBL and non-ESBL among SHV and TEM genes, detailed analysis of PCR products was performed. Twenty-four strains carried SHV-2, SHV-5 or SHV-12 genes. In a further 11 strains a CTX-M gene was detected. The CTX-M genes could be affiliated to the CTX-M-1 and CTX-M-9 cluster by RFLP analysis. In the case of four Klebsiella oxytoca isolates, hyperproduction of the chromosomal beta-lactamase K1 was inferred, because genes of the above-mentioned types were not detected. The strains contained plasmid DNA between 45 and 160 kb in size. Common plasmid restriction patterns among SHV-5 producers provided evidence of horizontal spread. Twenty strains had a MIC for cefotaxime of ⩽4 mg l−1, 18 strains had the same MIC for ceftazidime, and nine strains had this MIC of >4 mg l−1 for both antibiotics. The ESBL phenotypes often coincided with ciprofloxacin or gentamicin resistance.
Polymorphisms of the pbp5 gene and correlation with ampicillin resistance in Enterococcus faecium isolates of animal origin
Authors: Poeta Patricia , Costa Daniela , Igrejas Gilberto , Sáenz Yolanda , Zarazaga Myriam , Rodrigues Jorge , Torres Carmen
Published: January 2007

The C-terminal region of the pbp5 gene was sequenced in 11 ampicillin-resistant and 5 ampicillin-susceptible Enterococcus faecium isolates of animal origin, and compared with a pbp5 reference sequence (GenBank accession no. X84860). Eight different pbp5 alleles (designated A–H) were detected when amino acid changes in the region 461–629 were considered. Three of these alleles (A–C) were detected in ampicillin-susceptible isolates (MIC range 1–8 μg ml−1), and included the changes 470H→Q, 471V→I, 487Q→L, 581I→V, 595E→A or 622E→D. The remaining five alleles (D–H) were found in ampicillin-resistant isolates (MIC range 32–256 μg ml−1); three of these alleles (F–H) presented a serine insertion at position 466′, in addition to other important amino acid changes (485M→A, 496N→K, 499A→T, 525E→D, 586V→L or 629E→V). The other two alleles presented the amino acid changes 496N→K and 629E→V (allele D), and 470H→Q (allele F). A correlation between deduced amino acid changes in PBP5 and ampicillin MICs was detected in animal E. faecium isolates.
PCR confirmation of cutaneous manifestation due to Brucella melitensis
Authors: Mutnal Manohar B. , Purwar Shashank , Metgud Sharada C. , Nagmoti Mahantesh B. , Patil Chidanand S.
Published: January 2007

Human brucellosis, a zoonotic disease, is endemic in the Belgaum district, Karnataka, India. A male patient presented with a generalized itchy rash. Blood was sent for venereal disease research laboratory testing. Screening was carried out for Brucella antibodies following hospital policy and diagnosis was confirmed by PCR.
Rapid differentiation of Staphylococcus aureus isolates harbouring egc loci with pseudogenes ψent1 and ψent2 and the selu or selu
v gene using PCR-RFLP
Authors: Collery Mark M. , Smyth Cyril J.
Published: January 2007

The egc locus of Staphylococus aureus harbours two enterotoxin genes (seg and sei) and three enterotoxin-like genes (selm, seln and selo). Between the sei and seln genes are located two pseudogenes, ψent1 and ψent2, or the selu or selu
v gene. While these two alternative sei–seln intergenic regions can be distinguished by PCR, to date, DNA sequencing has been the only confirmatory option because of the very high degree of sequence similarity between egc loci bearing the pseudogenes and the selu or selu
v gene. In silico restriction enzyme digestion of genomic regions encompassing the egc locus from the 3′ end of the sei gene through the 5′ first quarter of the seln gene allowed pseudogene- and selu- or selu
v-bearing egc loci to be distinguished by PCR-RFLP. Experimental application of these findings demonstrated that endonuclease HindIII cleaved PCR amplimers bearing pseudogenes but not those with a selu or selu
v gene, while selu- or selu
v-bearing amplimers were susceptible to cleavage by endonuclease HphI, but not by endonuclease HindIII. The restriction enzyme BccI cleaved selu- or selu
v-harbouring amplimers at a unique restriction site created by their signature 15 bp insertion compared with pseudogene-bearing amplimers, thereby allowing distinction of these egc loci. PCR-RFLP analysis using these restriction enzymes provides a rapid, easy to interpret alternative to DNA sequencing for verification of PCR findings on the nature of an egc locus type, and can also be used for the primary identification of the intergenic sei–seln egc locus type.
The enhancement of pericentromeric cohesin association by conserved kinetochore components promotes high-fidelity chromosome segregation and is sensitive to microtubule-based tension
Authors: Eckert Carrie A. , Gravdahl Daniel J. , Megee Paul C.
Published: January 2007

Sister chromatid cohesion, conferred by the evolutionarily conserved cohesin complex, is essential for proper chromosome segregation. Cohesin binds to discrete sites along chromosome arms, and is especially enriched surrounding centromeres, but past studies have not clearly defined the roles of arm and pericentromeric cohesion in chromosome segregation. To address this issue, we developed a technique that specifically reduced pericentromeric cohesin association on a single chromosome without affecting arm cohesin binding. Under these conditions, we observed more extensive stretching of centromeric chromatin and elevated frequencies of chromosome loss, suggesting that pericentromeric cohesin enrichment is essential for high-fidelity chromosome transmission. The magnitude of pericentromeric cohesin association was negatively correlated with tension between sister kinetochores, with the highest levels of association in cells lacking kinetochore–microtubule attachments. Pericentromeric cohesin recruitment required evolutionarily conserved components of the inner and central kinetochore. Together, these observations suggest that pericentromeric cohesin levels reflect the balance of opposing forces: the kinetochore-mediated enhancement of cohesin binding and the disruption of binding by mechanical tension at kinetochores. The involvement of conserved kinetochore components suggests that this pathway for pericentromeric cohesin enrichment may have been retained in higher eukaryotes to promote chromosome biorientation and accurate sister chromatid segregation.
Electrostatic screening and backbone preferences of amino acid residues in urea‐denatured ubiquitin
Authors: Avbelj Franc , Grdadolnik Simona Golic
Published: January 2007

Local structures in denatured proteins may be important in guiding a polypeptide chain during the folding and misfolding processes. Existence of local structures in chemically denatured proteins is a highly controversial issue. NMR parameters [coupling constants 3 J(Hα,HN) and chemical shifts] of chemically denatured proteins in general deviate little from their values in small peptides. These peptides were presumed to be completely unstructured; therefore, it was considered that chemically denatured proteins are random coils. But recent experimental studies show that small peptides adopt relatively stable structures in aqueous solutions. Small deviations of the NMR parameters from their values in small peptides may thus actually indicate the existence of local structures in chemically denatured proteins. Using NMR data and theoretical predictions we show here that fluctuating β‐strands exist in urea‐denatured ubiquitin (8 M urea at pH 2). Residues in such β‐strands populate more frequently the left side of the broad β region of Φ–ψ space. Urea‐denatured ubiquitin contains no detectable β‐sheet secondary structures; nevertheless, the fluctuating β‐strands in urea‐denatured ubiquitin coincide to the β‐strands in the native state. Formation of β‐strands is in accord with the electrostatic screening model of unfolded proteins. The free energy of a residue in an unfolded protein is in this model determined by the local backbone electrostatics and its screening by backbone solvation. These energy terms introduce strong electrostatic coupling between neighboring residues, which causes cooperative formation of β‐strands in denatured proteins. We propose that fluctuating β‐strands in denatured proteins may serve as initiation sites to form fibrils.
Protein fabrication automation
Authors: Cox J. Colin , Lape Janel , Sayed Mahmood A. , Hellinga Homme W.
Published: January 2007

Facile “writing” of DNA fragments that encode entire gene sequences potentially has widespread applications in biological analysis and engineering. Rapid writing of open reading frames (ORFs) for expressed proteins could transform protein engineering and production for protein design, synthetic biology, and structural analysis. Here we present a process, protein fabrication automation (PFA), which facilitates the rapid de novo construction of any desired ORF from oligonucleotides with low effort, high speed, and little human interaction. PFA comprises software for sequence design, data management, and the generation of instruction sets for liquid‐handling robotics, a liquid‐handling robot, a robust PCR scheme for gene assembly from synthetic oligonucleotides, and a genetic selection system to enrich correctly assembled full‐length synthetic ORFs. The process is robust and scalable.
The protease allergen Der p 1 cleaves cell surface DC‐SIGN and DC‐SIGNR: experimental analysis of in silico substrate identification and implications in allergic responses
Authors: Furmonaviciene R. , Ghaemmaghami A. M. , Boyd S. E. , Jones N. S. , Bailey K. , Willis A. C. , Sewell H. F. , Mitchell D. A. , Shakib F.
Published: January 2007

Background
The cysteine protease Der p 1 from the house dust mite Dermatophagoides pteronyssinus is one of the most potent allergens known. An attractive mechanism for a component of Der p 1 allergenicity lies in its ability to cleave key regulatory molecules from leucocyte surfaces, subverting cellular function and driving abnormal immunoglobulin E (IgE) responses.

Objective
Although CD23, CD25 and CD40 have already been identified as major Der p 1 targets, other significant substrates may also exist.

Methods
To investigate this, knowledge of the proteolytic properties of Der p 1 was used to perform in silico digestion of human dendritic cell surface proteins, using the prediction of protease specificity (PoPS) bioinformatics tool, in conjunction with cellular in vitro analysis and cleavage site determination.

Results
Targets identified included DC‐SIGN and DC‐SIGNR, two C‐type lectins implicated mostly in pathogen trafficking. Treatment of positively expressing cells with Der p 1 led to loss of detectable surface DC‐SIGN and DC‐SIGNR. Digestion of purified soluble recombinant DC‐SIGN and DC‐SIGNR, followed by N‐terminal sequencing and MALDI mass spectrometry, indicated in each case one major cleavage site and several minor sites, the former correlating well with Der p 1 enzymology and the folded state of the substrate proteins. Loss of DC‐SIGN from the cell surface led to reduced binding of intracellular adhesion molecule‐3, an endogenous DC‐SIGN ligand expressed on naïve T cells which is thought to be involved in T‐helper type 1 cytokine signalling.

Conclusion
These data provide evidence of lectin involvement in the initiation of the allergic response and the value of using genome‐wide in silico digestion tools.
The impact of liquid‐based oral cytology on the diagnosis of oral squamous dysplasia and carcinoma
Authors: Navone R. , Burlo P. , Pich A. , Pentenero M. , Broccoletti R. , Marsico A. , Gandolfo S.
Published: January 2007

Objective:  Even though diagnostic oral exfoliative cytology is a useful, economical and practical tool in the diagnosis of oral dysplasia and carcinoma, it is not yet extensively used. The results of conventional exfoliative and liquid‐based diagnostic cytology in oral potentially malignant lesions (PML) are herein reported and compared with the histological diagnosis.

Methods:  Either conventional (89) or liquid‐based (384) exfoliative cytology was used for the diagnosis of oral dysplasia/carcinoma in 473 subjects and the results were compared with scalpel biopsy histology. Cells were collected using a Cytobrush device for conventional smears and with a dermatological curette for the liquid‐based cytology. The ‘curette technique’ also allowed for the collection of ‘accidental’ tissue fragments, utilized as microbiopsies.

Results:  Histological diagnosis was squamous carcinoma in 96 of 473 cases, high‐grade dysplasia (oral intraepithelial neoplasia two to three) in 24 and other lesions in 353 cases. The smears in the conventional cytology group were inadequate in 12.4%, with an 85.7% sensitivity and a 95.9% specificity. There were 8.8% of inadequate specimens in the liquid‐based cytology group; sensitivity was 95.1% and specificity was 99.0%.

Conclusions:  Although conventional cytology is useful when diagnosing oral PML (better sensitivity and predictive positive value if compared with the cervical smear test with similar specificity) and can improve the accuracy of histological diagnosis, liquid‐based cytology gives better results, as it not only enhances both sensitivity and specificity, but also provides material for further investigation (AgNORs, DNA, microbiopsies, etc.).
Fine needle aspiration cytology of lung lesions: a clinicopathological and cytopathological review of 150 cases with emphasis on the relation between the number of passes and the incidence of pneumothorax
Authors: Halloush R. A. , Khasawneh F. A. , Saleh H. A. , Soubani A. O. , Piskorowski T. J. , Al‐Abbadi M. A.
Published: January 2007

Objective:  The aim of this study was to review the lung fine needle aspirations (FNA) that were done in our hospital between January 1998 and April 2004. Interobserver agreement, sample adequacy and the relation between the number of passes and the occurrence of pneumothorax are presented.

Study design:  One hundred fifty cases of lung FNA from the department of pathology files were identified and the available specimens and patient charts were reviewed. The interobserver agreement was calculated. The relation between the number of passes and the subsequent development of pneumothorax was tested using Mann–Whitney U‐test.

Results:  The material of 132 patients (88%) out of 150 were retrieved and reviewed. There were 85 cases of non‐small cell lung cancer (NSCLC) (64.4%), nine cases of small cell lung cancer (6.8%), five cases of metastatic cancer (3.8%) and 33 cases were reported negative for cancer (25%). The NSCLC included 36 cases of adenocarcinoma (27.3%), 32 cases of squamous cell carcinoma (24.2%), and 17 cases of large cell undifferentiated carcinoma (12.9%). The interobserver agreement k was 0.93, (95% CI 0.87–0.98). The majority of cases (95.5%) were considered adequate for interpretation. The charts of 138 patients (92%) were reviewed for postprocedure radiologically confirmed pneumothorax. Sixteen patients (11.6%) developed pneumothorax only three of whom (2%) required a chest tube for treatment. The number of passes was identified in 118 patients (85.5%). The number of passes did not have a statistically significant association with the development of a pneumothorax (P = 0.747).

Conclusion:  Fine needle aspirations to diagnose lung lesions is a safe procedure with a low incidence of pneumothorax. Its findings are reproducible with high interobserver agreement. Immediate adequacy evaluation and triage by a pathologist guarantees adequate sample in most instances. The number of passes was not associated with an increased incidence of pneumothorax.
Local thermal injury elicits immediate dynamic behavioural responses by corneal Langerhans cells
Authors: Ward Brant R. , Jester James V. , Nishibu Akiko , Vishwanath Mridula , Shalhevet David , Kumamoto Tadashi , Petroll W. Matthew , Cavanagh H. Dwight , Takashima Akira
Published: January 2007

Langerhans cells (LCs) represent a special subset of immature dendritic cells (DCs) that reside in epithelial tissues at the environmental interfaces. Although dynamic interactions of mature DCs with T cells have been visualized in lymph nodes, the cellular behaviours linked with the surveillance of tissues for pathogenic signals, an important function of immature DCs, remain unknown. To visualize LCs in situ, bone marrow cells from C57BL/6 mice expressing the enhanced green fluorescent protein (EGFP) transgene were transplanted into syngeneic wild‐type recipients. Motile activities of EGFP+ corneal LCs in intact organ cultures were then recorded by time lapse two‐photon microscopy. At baseline, corneal LCs exhibited a unique motion, termed dendrite surveillance extension and retraction cycling habitude (dSEARCH), characterized by rhythmic extension and retraction of their dendritic processes through intercellular spaces between epithelial cells. Upon pinpoint injury produced by infrared laser, LCs showed augmented dSEARCH and amoeba‐like lateral movement. Interleukin (IL)‐1 receptor antagonist completely abrogated both injury‐associated changes, suggesting roles for IL‐1. In the absence of injury, exogenous IL‐1 caused a transient increase in dSEARCH without provoking lateral migration, whereas tumour necrosis factor‐α induced both changes. Our results demonstrate rapid cytokine‐mediated behavioural responses by LCs to local tissue injury, providing new insights into the biology of LCs.
CXCR3‐mediated T‐cell chemotaxis involves ZAP‐70 and is regulated by signalling through the T‐cell receptor
Authors: Dar Wasim A. , Knechtle Stuart J.
Published: January 2007

The chemokine receptor CXCR3 is critical for the function of activated T cells. We studied the molecular mechanisms of CXCR3 signalling. The addition of CXCR3 ligands to normal human T cells expressing CXCR3 led to the tyrosine phosphorylation of multiple proteins. Addition of the same ligands to Jurkat T cells engineered to express CXCR3 induced tyrosine phosphorylation of proteins with molecular weights similar to those in normal cells. Immunoblotting with phosphotyrosine‐specific antibodies identified Zeta‐associated protein of 70 000 molecular weight (ZAP‐70), linker for the activation of T cells (LAT), and phospholipase‐C‐γ1 (PLCγ1) to be among the proteins that become phosphorylated upon CXCR3 activation. ZAP‐70 was phosphorylated on tyrosine 319, LAT on tyrosines 171 and 191, and PLCγ1 on tyrosine 783. The ZAP‐70 inhibitor piceatannol reduced CXCR3‐mediated tyrosine phosphorylation of ZAP‐70, LAT, PLCγ1 and mitogen‐activated protein kinase Erk and it reduced CXCL10‐mediated chemotaxis of both CXCR3‐transfected Jurkat T cells and normal T cells expressing CXCR3. These results are consistent with the involvement of ZAP‐70 in CXCR3‐mediated protein tyrosine phosphorylation and CXCR3‐induced T‐cell chemotaxis. Studies with the Lck‐deficient Jurkat T‐cell line, JCAM1.6, demonstrated that phosphorylation of ZAP‐70 after CXCR3 activation is a Lck‐dependent process. Finally, stimulating CXCR3‐expressing Jurkat T cells and normal T cells expressing CXCR3 through the T‐cell receptor attenuated CXCR3‐induced tyrosine phosphorylation and CXCR3‐mediated T‐cell migration, indicating the occurrence of cross‐talk between T‐cell receptor and CXCR3‐signalling pathways. These results shed light on the mechanisms of CXCR3 signalling. Such information could be useful when designing therapeutic strategies to regulate T‐cell function.
Murine pregnancy leads to reduced proliferation of maternal thymocytes and decreased thymic emigration
Authors: Zoller Allison L. , Schnell Frederick J. , Kersh Gilbert J.
Published: January 2007

During mammalian pregnancy the maternal thymus undergoes significant involution, and then recovers in size after birth. The mechanism behind this involution is not known, but it has been suggested that elevated levels of hormones during pregnancy induce the involution. We have recently shown that injection of 17β‐oestradiol into mice causes loss of early thymocyte precursors and inhibits proliferation of developing thymocytes. This suggests that elevated oestrogen in pregnancy may contribute to thymic involution. We have investigated this idea by examining the fate of thymocytes during mouse pregnancy in much greater detail than has been previously reported. Looking over a broad time–course, we find that pregnancy does not affect thymocyte precursor populations in the bone marrow, but induces a profound loss of early thymic progenitors in the thymus as early as day 12·5 of pregnancy. This loss is accompanied by decreased thymocyte proliferation, which returns to normal 2–4 days postpartum. No enhancement of apoptosis is detectable at any stage of pregnancy. We also find that there is a reduction in recent thymic emigrants after oestrogen treatment and at day 17·5 of pregnancy, suggesting that thymic involution during pregnancy influences the peripheral T‐cell repertoire. The similarities between oestrogen‐mediated involution and pregnancy‐mediated involution suggest that oestrogen is a significant contributor to loss of thymocyte cellularity during pregnancy, and probably functions primarily by reducing thymocyte proliferation.