bluuebunny/crossref_metadata_2025 huggingface dataset:
Influence of Individual Differences in Temporal Sensitivity on Timing Performance
Authors: Brown Scott W
Published: January 2007

This research was designed to examine the consistency of individual differences in timing. Subjects were tested initially on a temporal-signal-detection task. In a series of trials, subjects judged whether a stimulus figure was displayed for either 12 s or greater than 12 s. Task performance was used to classify the subjects into groups with high or low temporal sensitivity ( d'). Later, the subjects were tested on two classic time-judgment tasks. In a temporal-interference task, subjects reproduced intervals of 8 – 16 s during which they had rehearsed 0, 3, or 7 digits. Absolute error in time judgments increased linearly as a function of task demands. However, subjects with low temporal sensitivity made more error under all conditions compared with those with high sensitivity. In an isochronous-tapping task, subjects produced a series of 2-s and 5-s intervals. The low-temporal-sensitivity group produced more variable and inaccurate responses than the high-sensitivity group. The results demonstrate cross-situational consistency in timing performance across different tasks, time-judgment methods, and stimulus durations.
Light and Sight since Antiquity
Authors: Wade Nicholas J
Published: January 2007

Light and sight were not distinguished from one another until the dioptrics and the anatomy of the eye had been adequately described in the seventeenth century. A survey of early theories of light is presented, together with descriptions of developing knowledge of ocular anatomy Once the analogy between the eye and a camera had been made, the problem of accommodation was exposed, and corrections for errors of refraction could be given theoretical support. Theories of accommodation in the seventeenth and eighteenth centuries are briefly reviewed, as is the early history of eye glasses.
Illumination-Induced Apparent Shift in Orientation of Human Heads
Authors: Troje Nikolaus F , Siebeck Ulrike
Published: January 2007

Changing the position of a light source illuminating a human face induces an apparent shift of the perceived orientation of that face. The direction of this apparent shift is opposite to the shift of the light source. We demonstrated the illumination-induced apparent orientation shift (IAOS), quantified it in terms of the physical orientation shift needed to compensate for it, and evaluated the results in the context of possible mechanisms underlying orientation judgment. Results indicate that IAOS depends not only on the angle between the two light source positions, but also on the mean orientation of the face. Availability of cues coded in the visual texture of the face did not affect IAOS. The most effective cue was the location of the visible outline of the face. IAOS seems to be due to a shift of this outline when shadowed areas on the face merge with the black background. We conclude that an important mechanism for orientation judgment is based on a comparison of visible parts left and right of the profile line.
Spatial-Frequency Discrimination, Brain Lateralisation, and Acute Intake of Alcohol
Authors: Watten Reidulf G , Magnussen Svein , Greenlee Mark W
Published: January 2007

The effect of alcohol (breath-alcohol level of 0.1%) on perceptual discrimination of low (1.5 cycles deg−1) and high (8 cycles deg−1) spatial frequencies in the left and right visual field was measured in eighteen right-handed males, in a double-blind, balanced placebo design. Discrimination thresholds for briefly (180 ms) presented sinusoidal gratings were determined by two-alternative forced-choice judgments with four interleaving psychophysical staircases providing random trial-to-trial variation of reference spatial frequency and visual field, in addition to a random (±10%) jitter of reference spatial frequency. Alcohol produced overall higher discrimination thresholds but did not alter the visual-field balance: no main effect of visual field was observed, but in both placebo and alcohol conditions spatial frequency interacted with visual field in the direction predicted by the spatial-frequency hypothesis of hemispheric asymmetry in visual-information processing, with left-visual-field/right-hemisphere superiority in discrimination of low spatial frequencies and right-visual-field/left-hemisphere superiority in discrimination of high spatial frequencies.
Does Segregation by Colour/Luminance Facilitate the Detection of Structure-from-Motion in Noise?
Authors: Li Hyung-Chul O , Kingdom Frederick A A
Published: January 2007

The aim in the experiments was to examine whether the detection of structure-from-motion (SFM) in noise was facilitated when target and noise were segregated by colour and/or luminance polarity The SFM target was a rotating ‘V-shape’ structure simulated with limited-lifetime Gaussian micropatterns and embedded in random-motion noise. Threshold levels of V-shape slant were measured for stimuli in which target and noise were segregated or unsegregated by colour/luminance, and under two conditions, with and without static form cues to the SFM target. The presence or absence of static form cues to the SFM target was manipulated by varying the relative numbers of micropatterns in target and noise. In the absence of static form cues, segregation of target and noise by colour and/or luminance polarity did not facilitate target detection, even when subjects knew which micropatterns belonged to the target. On the other hand, when static form cues were present, segregation improved performance. These results imply that SFM processing is ‘form-cue invariant’ except when the target form is immediately identifiable in the static view of the stimulus. The significance of the results for understanding the role of colour vision in breaking camouflage and in ‘grouping’ is discussed.
A Computational and Perceptual Account of Motion Lines
Authors: Kim Hyungjun , Francis Gregory
Published: January 2007

To indicate motion in a static drawing, artists often include lines trailing a moving object. The use of these motion lines is notable because they do not seem to be related to anything in the optic array. The dynamic behavior of a neural-network model for contour detection is analyzed and it is shown that it generates trails of oriented responses behind moving stimuli. The properties of the oriented response trails are shown to correspond to motion lines. The model generates trails of different orientations depending on the speed and length of the movement, and thereby predicts different uses of two types of motion lines. The model further predicts that motion lines should bias real motion in some situations. An experiment relating motion lines to ambiguous motion percepts demonstrates that motion lines contribute to motion percepts.
Apparent Depth with Retinal Image Motion of Expansion and Contraction Yoked to Head Movement
Authors: Yajima Takanao , Ujike Hiroyasu , Uchikawa Keiji
Published: January 2007

The two main questions addressed in this study were (a) what effect does yoking the relative expansion and contraction (EC) of retinal images to forward and backward head movements have on the resultant magnitude and stability of perceived depth, and (b) how does this relative EC image motion interact with the depth cues of motion parallax? Relative EC image motion was produced by moving a small CCD camera toward and away from the stimulus, two random-dot surfaces separated in depth, in synchrony with the observers' forward and backward head movements. Observers viewed the stimuli monocularly, on a helmet-mounted display, while moving their heads at various velocities, including zero velocity. The results showed that (a) the magnitude of perceived depth was smaller with smaller head velocities (<10 cm s−1), including the zero-head-velocity condition, than with a larger velocity (10 cm s−1), and (b) perceived depth, when motion parallax and the EC image motion cues were simultaneously presented, is equal to the greater of the two possible perceived depths produced from either of these two cues alone. The results suggested the role of nonvisual information of self-motion on perceiving depth.
Illusory Volumes from Conformation
Authors: Tse Peter Ulric
Published: January 2007

The purpose of this paper is to offer demonstrations of ‘illusory volumes’ in the spirit of the illusory flat surfaces described by Kanizsa. These demonstrations of illusory volumes exploit a new cue to the recovery of surface curvature from ambiguous images: conformation. In assuming conformation, the visual system assumes that the surface of a volume conforms to the curvature of its neighboring, underlying, or supporting surface, in the absence of image cues to the contrary. Demonstrations that exploit the assumption of conformation provide several insights into the nature of the inferential processing that underlies contour, surface, and volume formation. In particular, these demonstrations imply that the visual system does not calculate local surface curvature, illusory contours, or occlusion relationships before it analyzes global surface relationships.
Temporal Aspects of Slant and Inclination Perception
Authors: Allison Robert S , Howard Ian P , Rogers Brian J , Bridge Holly
Published: January 2007

Linear transformations (shear or scale transformations) of either horizontal or vertical disparity give rise to the percept of slant or inclination. It has been proposed that the percept of slant induced by vertical size disparity, known as Ogle's induced-size effect, and the analogous induced-shear effect, compensate for scale and shear distortions arising from aniseikonia, eccentric viewing, and cyclodisparity. We hypothesised that these linear transformations of vertical disparity are processed more slowly than equivalent transformations of horizontal disparity (horizontal shear and size disparity). We studied the temporal properties of the stereoscopic slant and inclination percepts that arose when subjects viewed stereograms with various combinations of horizontal and vertical size or shear disparities. We found no evidence to support our hypothesis. There were no clear differences in the build-up of percepts of slant or inclination induced by step changes in horizontal size or shear disparity and those induced by step changes in vertical size or shear disparity. Perceived slant and inclination decreased in a similar manner with increasing temporal frequency for modulations of transformations of both horizontal and vertical disparity. Considerable individual differences were found and several subjects experienced slant reversal, particularly with oscillating stimuli. An interesting finding was that perceived slant induced by modulations of dilation disparity was in the direction of the vertical component. This suggests the vertical size disparity mechanism has a higher temporal bandwidth than the horizontal size disparity mechanism. However, conflicting perspective information may play a dominant role in determining the temporal properties of perceived slant and inclination.
Cues to Viewing Distance for Stereoscopic Depth Constancy
Authors: Glennerster Andrew , Rogers Brian J , Bradshaw Mark F
Published: January 2007

A veridical estimate of viewing distance is required in order to determine the metric structure of objects from binocular stereopsis. One example of a judgment of metric structure, which we used in our experiment, is the apparently circular cylinder task (E B Johnston, 1991 Vision Research31 1351 – 1360). Most studies report underconstancy in this task when the stimulus is defined purely by binocular disparities.

We examined the effect of two factors on performance: (i) the richness of the cues to viewing distance (using either a naturalistic setting with many cues to viewing distance or a condition in which the room and the monitors were obscured from view), and (ii) the range of stimulus disparities (cylinder depths) presented during an experimental run. We tested both experienced subjects (who had performed the task many times before under full-cue conditions) and naive subjects.

Depth constancy was reduced for the naïve subjects (from 62% to 46%) when the position of the monitors was obscured. Under similar conditions, the experienced subjects showed no reduction in constancy. In a second experiment, using a forced-choice method of constant stimuli, we found that depth constancy was reduced from 64% to 23% in naive subjects and from 77% to 55% in experienced subjects when the same set of images was presented at all viewing distances rather than using a set of stimulus disparities proportional to the correct setting.

One possible explanation of these results is that, under reduced-cue conditions, the range of disparities presented is used by the visual system as a cue to viewing distance.
The Missing-Fundamental Illusion at Isoluminance
Authors: Kingdom Frederick A A , Simmons David R
Published: January 2007

The missing-fundamental illusion describes how a square wave with its fundamental Fourier component removed appears as a square wave. This illusion is normally explained with reference to the bandpass nature of the luminance-contrast-sensitivity function, together with a ‘default-to-square-wave’ rule. Since the chromatic-contrast-sensitivity function is low-pass, we should not expect a missing-fundamental illusion at isoluminance. Using a simultaneous-detection-and-identification paradigm to eliminate contrast as a cue to discrimination, we nevertheless found that chromatic missing fundamentals and square waves could not be separately identified at detection threshold: just under twice the contrast required to detect the stimuli was needed to identify them. To test whether this was due to insufficiently narrow chromatic-channel band-widths, we measured detection and identification thresholds for chromatic F and 3 F sine-wave gratings. In this case identification was possible almost at detection threshold, suggesting that channel bandwidth limitations were not the critical factor. It is suggested that the weak missing-fundamental illusion observed at isoluminance probably reflects the operation of mechanisms similar to those that are responsible for the chromatic Craik – Cornsweet illusion.
Cognitively Based Apparent Motion: An Extreme Case
Authors: Parks Theodore E , Coss Richard G
Published: January 2007

An ambiguous figure is used to provide a demonstration of apparent motion in which there is no change in the retinal image or in external space.
Perceiving Binocular Depth with Reference to a Common Surface
Authors: He Zijiang J , Ooi Teng Leng
Published: January 2007

A common surface is a spatial regularity of our terrestrial environment. For instance, we walk on the common ground surface, lay a variety of objects on the table top, and display our favorite paintings on the wall. It has been proposed that the visual system utilizes this regularity as a reference frame for coding objects' distances. Presumably, by treating the common surface as such—ie an anticipated constant—the visual system can reduce its coding redundancy, and divert its resources to representing other information. For intermediate-distance space perception, it has been found that absolute distance judgment is most accurate when a common ground surface is available. Here we explored if the common surface also serves as the reference frame for the processing of binocular-disparity information, which is a predominant cue for near-distance space perception. We capitalized on an established observation where the perceived slant of a surface with linear binocular-disparity gradient is underestimated. Clearly, if the visual system utilizes this incorrectly represented slant surface as a reference frame for coding the objects' locations, the perceived depth separation between the objects will be adversely affected. Our results confirm this, by showing that the depth judgment of objects (two laterally separated vertical lines) on, or in the vicinity of, the surface is underestimated. Furthermore, we show that the impact of the common surface on perceived depth separation most likely occurs at the surface-representation level where the visual surface has been explicitly delineated, rather than at the earlier disparity-processing level.
Different Spatial-Relational Information is Used to Recognise Faces and Emotional Expressions
Authors: White Murray
Published: January 2007

In a face photo in which the two eyes have been moved up into the forehead region, configural spatial relations are altered more than categorical relations; in a photo in which only one eye is moved up, categorical relations are altered more. Matching the identities of two faces was slower when an unaltered photo was paired with a two-eyes-moved photo than when paired with a one-eye-moved photo, implicating configural relations in face identification. But matching the emotional expressions of the same faces was slower when an unaltered photo was paired with a one-eye-moved photo than when paired with a two-eyes-moved photo, showing that expression recognition uses categorically coded relations. The findings also indicate that changing spatial-relational information affects the perceptual encoding of identities and expressions rather than their memory representations.
Biplane wing planform and flight performance of the feathered dinosaur
Microraptor gui
Authors: Chatterjee Sankar , Templin R. Jack
Published: January 2007

Microraptor gui
, a four-winged dromaeosaur from the Early Cretaceous of China, provides strong evidence for an arboreal-gliding origin of avian flight. It possessed asymmetric flight feathers not only on the manus but also on the pes. A previously published reconstruction shows that the hindwing of
Microraptor
supported by a laterally extended leg would have formed a second pair of wings in tetrapteryx fashion. However, this wing design conflicts with known theropod limb joints that entail a parasagittal posture of the hindlimb. Here, we offer an alternative planform of the hindwing of
Microraptor
that is concordant with its feather orientation for producing lift and normal theropod hindlimb posture. In this reconstruction, the wings of
Microraptor
could have resembled a staggered biplane configuration during flight, where the forewing formed the dorsal wing and the metatarsal wing formed the ventral one. The contour feathers on the tibia were positioned posteriorly, oriented in a vertical plane for streamlining that would reduce the drag considerably. Leg feathers are present in many fossil dromaeosaurs, early birds, and living raptors, and they play an important role in flight during catching and carrying prey. A computer simulation of the flight performance of
Microraptor
suggests that its biplane wings were adapted for undulatory “phugoid” gliding between trees, where the horizontal feathered tail offered additional lift and stability and controlled pitch. Like the Wright 1903 Flyer,
Microraptor
, a gliding relative of early birds, took to the air with two sets of wings.
Msx2-interacting nuclear target protein (Mint) deficiency reveals negative regulation of early thymocyte differentiation by Notch/RBP-J signaling
Authors: Tsuji Masayuki , Shinkura Reiko , Kuroda Kazuki , Yabe Daisuke , Honjo Tasuku
Published: January 2007

Notch/RBP-J signaling is required for generation of early T progenitors (ETP) and promotion of double-negative (DN) 4 cells from DN3 cells in thymocyte differentiation. However, whether Notch affects other steps during thymocyte differentiation remains unknown. Msx2-interacting nuclear target protein (Mint) is an endogenous inhibitor of Notch regulation. Concordantly, by
ex vivo
analyses of embryonic thymi and
in vitro
differentiation studies of fetal liver progenitors, we find that Mint deficiency enhances generation of ETP and DN4 cells. Unexpectedly, however, Mint deficiency impairs differentiation of ETP into DN2 cells, suggesting that Notch/RBP-J signaling negatively regulates DN1–DN2 transition.
Lifetimes of Excited Levels in Ca I-Ca III
Authors: B Emmoth  , M Braun  , J Bromander  , I Martinson
Published: January 2007

The lifetimes for a number of levels in neutral and ionized calcium have been determined by the beam-foil technique. The effects of cascades were analyzed and corrected for. The experimental lifetimes mostly agree with theoretical calculations.
New Identifications and Lifetime Measurements in Ne VIII
Authors: L Barrette  , D J G Irwin  , R Drouin
Published: January 2007

Using the beam-foil technique four new identifications in Ne VIII corresponding to transitions betweenn= 4, 5 andn= 3 levels have been obtained in the spectral region 175-300 Å. The lifetimes of the fourn= 4 levels are reported and compared with other experimental and theoretical results.
Observation et Classification du Spectre d'Arc du Tellure (Te I) entre 3 678 et 11 761 cm-1
Authors: C Morillon  , J Vergès
Published: January 2007

The spectrum emitted by an electrodeless discharge tube filled with pure130Te has been investigated by Fourier transform spectroscopy. The observations have led to a list of wavenumbers and estimated intensities for 277 lines in the range 3 678 to 11 761 cm-1. Zeeman structures for 90 lines were studied. 70 levels, 65 of them being new, have been found and 170 lines have been classified. For these levels the energy is given with an accuracy equal to 0.005 cm-1. Landé factors for 46 levels have been measured with an accuracy up to 0.003 U.L. Parametric studies performed on 5s25p3-(6s+7s+5d+6d) configurations on the one hand and on 5s25p3(6p+7p) on the other hand, give a good interpretation for most of the levels; the r.m.s. deviation of the level energy between theory and experiment is equal to roughly 30 cm-1.
Asymptotic States of Massless Fields
Authors: Christin Högfors
Published: January 2007

It is shown that, within the framework of Wightman field theory, there exist uniquely determined asympotic states of a massless field provided the field is not directly self-interacting, but through a massive current. It is also shown that a massless Wightman field with an energy cut-off satisfies a weak locality condition.
The Quasi-steady Plasma-neutral Gas Balance in Magnetic Bottles
Authors: B Lehnert
Published: January 2007

Neutral gas which penetrates into a hot plasma of characteristic dimensionLb, average density n̄, and temperatureT, consists mainly of a slow and fast component of densities nns, nnfand temperaturesTns≪T,Tnf≃T, respectively. These components have the penetration lengthsLns= 1/σcsn̄ andLnf= 1σcfn̄ defining the critical densities ncs= 1/σcsLbandncf= 1σcfLbwhere 1/σcf≃ 100/σcs≃ 5×1018m-2for hydrogen in the range 106<T< 107K. Thus, hot plasmas can be divided into the classes of permeable dilute, permeable non-dilute, and impermeable systems defined by n̄ ≲ncs≪ncf,ncs≪n̄ ≲ ncfand ncs≪ncf≪n̄ respectively: (i) These classes have different equilibrium and stability properties, depending on the relative concentrations, spatial distributions, and transport processes of the neutral gas. (ii) The density of the neutral gas immersed in a quasi-steady permeable plasma becomes a measure of the plasma particle loss rate. (iii) The ratio between the neutral gas "blanket" density and the average plasma density increases when transitions are made from the permeable dilute to the permeable non-dilute state, and further to the impermeable state. (iv) The spatial distributions and relaxation times of the plasma. The pressure gradient, which acts as a driving force of instabilities, reaches a maximum value when the transition is made from a permeable to an impermeable state.
Electron–Electron Renormalization of the Electronic Heat Capacity in Simple Metals
Authors: Göran Grimvall
Published: January 2007

The electron–electron many-body renormalization of the effective electron mass in the alkali metals and A1 is discussed on the basis of a critical analysis of the measured thermal electron mass, the calculated band mass and the calculated electron–phonon mass enhancement. The mass renormalization is small and of the same order of magnitude as for a uniform electron gas but is stressed that a direct comparision between these two cases is not justified.
Appearance Potential Studies of Pr, Sm and Er
Authors: J Kanski  , P O Nilsson
Published: January 2007

Electron excited soft X-ray appearance potential spectra are reported for theM5,4andN5,4levels of Pr, Sm and Er. For Pr the photoyield has also been measured. The results are interpreted in terms of multiplet splitting and are compared with soft X-ray absorption data.
SatDNA Analyzer: a computing tool for satellite-DNA evolutionary analysis
Authors: Navajas-Pérez Rafael , Rubio-Escudero Cristina , Aznarte José Luis , Rejón Manuel Ruiz , Garrido-Ramos Manuel A.
Published: January 2007

Summary: satDNA Analyzer is a program, implemented in C++, for the analysis of the patterns of variation at each nucleotide position considered independently amongst all units of a given satellite-DNA family when comparing it between a pair of species. The program classifies each site accordingly as monomorphic or polymorphic, discriminates shared from non-shared polymorphisms and classifies each non-shared polymorphism according to the model proposed by Strachan et al. in six different stages of transition during the spread of a variant repeat unit toward its fixation. Furthermore, this program implements several other utilities for satellite-DNA analysis evolution such as the design of the average consensus sequences, the average base pair contents, the distribution of variant sites, the transition to transversion ratio and different estimates of intra-specific variation and inter-specific variation. Aprioristic hypotheses on factors influencing the molecular drive process and the rates and biases of concerted evolution can be tested with this program. Additionally, satDNA Analyzer generates an output file containing a sequence alignment without shared polymorphisms to be used for further evolutionary analysis by using different phylogenetic softwares.

Availability: satDNA Analyzer is freely available at http://satdna.sourceforge.net/. SatDNA Analyzer has been designed to operate on Windows, Linux and Mac OS X.

Contact:  rnavajas@uga.edu
Large- and very-large-scale motions in channel and boundary-layer flows
Authors: Balakumar B.J , Adrian R.J
Published: January 2007

Large-scale motions (LSMs; having wavelengths up to 2–3 pipe radii) and very-LSMs (having wavelengths more than 3 pipe radii) have been shown to carry more than half of the kinetic energy and Reynolds shear stress in a fully developed pipe flow. Studies using essentially the same methods of measurement and analysis have been extended to channel and zero-pressure-gradient boundary-layer flows to determine whether large structures appear in these canonical wall flows and how their properties compare with that of the pipe flow. The very large scales, especially those of the boundary layer, are shorter than the corresponding scales in the pipe flow, but otherwise share a common behaviour, suggesting that they arise from similar mechanism(s) aside from the modifying influences of the outer geometries. Spectra of the net force due to the Reynolds shear stress in the channel and boundary layer flows are similar to those in the pipe flow. They show that the very-large-scale and main turbulent motions act to
decelerate
the flow in the region above the maximum of the Reynolds shear stress.
Turbulent flux events in a nearly neutral atmospheric boundary layer
Authors: Narasimha Roddam , Kumar S. Rudra , Prabhu A , Kailas S.V
Published: January 2007

We propose here a novel method of analysing turbulent momentum flux signals. The data for the analysis come from a nearly neutral atmospheric boundary layer and are taken at a height of 4 m above ground corresponding to 1.1×10
5
wall units, within the log layer for the mean velocity. The method of analysis involves examining the instantaneous flux profiles that exceed a given threshold, for which an optimum value is found to be 1 s.d. of the flux signal. It is found feasible to identify normalized flux variation signatures separately for positive and negative ‘flux events’—the sign being determined by that of the flux itself. Using these signatures, the flux signal is transformed to one of events characterized by the time of occurrence, duration and intensity. It is also found that both the average duration and the average time-interval between successive events are of order 1 s, about four orders of magnitude higher than a wall unit in time. This episodic description of the turbulence flux in the time domain enables us to identify separately productive, counter-productive and idle periods (accounting, respectively, for 36, 15 and 49% of the time), taking as criterion the generation of the momentum flux. A ‘burstiness’ index of 0.72 is found for the data. Comparison with laboratory data indicates higher (/lower) ejection (/sweep) quadrant occupancy but lower (/higher) contributions to flux from the ejection (/sweep) quadrant at the high Reynolds numbers of the atmospheric boundary layer. Possible connections with the concept of active and passive motion in a turbulent boundary layer are briefly discussed.
Evaluation of routine microbiological techniques for establishing the diagnosis of catheter-related bloodstream infection caused by coagulase-negative staphylococci
Authors: Casey Anna L. , Worthington Tony , Lambert Peter A. , Elliott Tom S. J.
Published: January 2007

Microbiological diagnosis of catheter-related bloodstream infection (CR-BSI) is often based on isolation of indistinguishable micro-organisms from an explanted catheter tip and blood culture, confirmed by antibiograms. Whether phenotypic identification of coagulase-negative staphylococci (CoNS) allows an accurate diagnosis of CR-BSI to be established was evaluated. Eight patients with a diagnosis of CR-BSI had CoNS isolated from pure blood cultures and explanted catheter tips which were considered as indistinguishable strains by routine microbiological methods. For each patient, an additional three colonies of CoNS isolated from the blood and five from the catheter tip were subcultured and further characterized by antibiogram profiles, analytical profile index (API) biotyping and PFGE. PFGE distinguished more strains of CoNS compared to API biotyping or antibiograms (17, 10 and 11, respectively). By PFGE, indistinguishable micro-organisms were only isolated from pure blood and catheter tip cultures in four out of eight (50 %) patients thus supporting the diagnosis of CR-BSI. In another patient, indistinguishable micro-organisms were identified in both cultures; however, other strains of CoNS were also present. The remaining three patients had multiple strains of CoNS, none of which were indistinguishable in the tip and blood cultures, thus questioning the diagnosis of CR-BSI. Phenotypic characterization of CoNS lacked discriminatory power. Current routine methods of characterizing a limited number of pooled colonies may generate misleading results as multiple strains may be present in the cultures. Multiple colonies should be studied using a rapid genotypic characterization method to confirm or refute the diagnosis of CR-BSI.
Ciprofloxacin treatment failure in a case of typhoid fever caused by Salmonella enterica serotype Paratyphi A with reduced susceptibility to ciprofloxacin
Authors: Dimitrov Tzonyo , Udo Edet E. , Albaksami Osama , Kilani Abdul A. , Shehab El-Din M. R.
Published: January 2007

This report describes a case of ciprofloxacin treatment failure in a patient with enteric fever caused by Salmonella enterica serotype Paratyphi A. The organism was isolated from a blood culture from a patient who was treated with oral ciprofloxacin (500 mg every 12 h) for 13 days. The organism showed reduced susceptibility to ciprofloxacin (MIC 0.75 μg ml−1) and was resistant to nalidixic acid. The patient was then placed on intravenous ceftriaxone (1 g every 12 h) and responded within 3 days. The patient was discharged after 9 days on ceftriaxone with no relapse on follow-up. This case adds to the increasing incidence of treatment failures with ciprofloxacin in typhoid fever caused by typhoid salmonellae with reduced susceptibility to ciprofloxacin. It also highlights the inadequacy of current laboratory methods for fluoroquinolone susceptibility testing in adequately predicting in vivo activity of ciprofloxacin against typhoid salmonellae and supports calls for new guidelines for fluoroquinolone susceptibility testing of these organisms.
Relationship between O-antigen subtypes, bacterial surface structures and O-antigen gene clusters in Escherichia coli O123 strains carrying genes for Shiga toxins and intimin
Authors: Beutin Lothar , Wang Quan , Naumann Dieter , Han Weiqing , Krause Gladys , Leomil Luciana , Wang Lei , Feng Lu
Published: January 2007

Escherichia coliO123 strains express a broad spectrum of phenotypes, H serotypes and virulence markers and are able to colonize and to cause disease in different hosts including humans. In this study, two subtypes ofE. coliO123 antigen (group I and group II) have been identified based on their cross-reactions with otherE. coliO antigens. Investigation of the relationship between O123 group I and group II strains by O serotyping and Fourier transform infrared spectroscopy of whole bacteria revealed surface structural differences between these two groups ofE. coliO123 strains. Nucleotide sequence analysis of the O-antigen gene clusters of twoE. coliO123 strains representing O123 group I and group II revealed no change at the amino acid level. These findings indicate that the differences in the surface structures of group I and group II strains are not related to genetic heterogeneity in their O-antigen gene clusters. A PCR assay based on O123 antigen-specificwzxandwzygenes was developed and found to be suitable for reliable detection of all subtypes ofE. coliO123 strains, which bears an advantage over traditional serological detection.
The pro‐peptide of proNGF: Structure formation and intramolecular association with NGF
Authors: Kliemannel Marco , Golbik Ralph , Rudolph Rainer , Schwarz Elisabeth , Lilie Hauke
Published: January 2007

The pro‐peptide of human nerve growth factor (NGF) functions as an intramolecular chaperone during oxidative renaturation of proNGF in vitro and interacts intramolecularly with the mature part of native proNGF. Here, we analyzed the structure formation and stability of the pro‐peptide in the context of proNGF and its intramolecular interaction with the native mature part. Folding and unfolding of the NGF‐coupled pro‐peptide, as analyzed by fluorescence, were biphasic reactions with both phases depending on the interaction with the mature part. This interaction was characterized by an overall stability of ΔG = 20.9 kJ/mol that was subdivided into two reactions, native ↔ intermediate state (14.8 kJ/mol) and intermediate ↔ unfolded state (6.1 kJ/mol). An additional very fast unfolding reaction was observed using circular dichroism (CD), indicating the presence of at least two kinetically populated intermediates in the unfolding of proNGF. The part of the pro‐peptide involved in the intramolecular association with mature NGF comprised the peptide Trp−83‐Ala−63as determined by H/D exchange experiments. Spectroscopic analyses revealed that on the NGF side, a surface area around Trp21interacted with the pro‐peptide. Trp21also participates in binding to TrkA and p75 receptors. These overlapping binding sites of the pro‐peptide and the NGF receptors might explain the previously observed lower affinity of proNGF to its receptors as compared to NGF.
Analysis of ligand binding to a ribose biosensor using site‐directed mutagenesis and fluorescence spectroscopy
Authors: Vercillo Natalie C. , Herald Kaitlin J. , Fox John M. , Der Bryan S. , Dattelbaum Jonathan D.
Published: January 2007

Computational design of proteins with altered ligand specificity is an emerging method for the creation of new biosensing systems. In this work, we investigated the outcome of site‐directed mutagenesis on the Escherichia coli ribose binding protein (RBP), which is frequently used as a design scaffold for computational searches. A ribose biosensor was first constructed whereby an environmentally sensitive fluorescent probe was covalently attached to RBP at position S265C. This protein conjugate displayed a 54% decrease in emission intensity upon the addition of saturating ribose concentrations and exhibited an apparent dissociation constant (Kd) of 3.4 μM. Site‐directed mutants within the RBP binding pocket were created and examined for ribose binding ability and overall structural stability. Because as many as 12 mutations are needed to alter ligand specificity in RBP, we measured the effect of single and multiple alanine mutations on stability and signal transduction potential of the ribose biosensor. Single alanine mutations had significant impact on both stability and signaling. Mutations of N190A and F214A each produced melting temperatures >8°C below those observed for the wild‐type protein. Residue Q235, located in the hinge region of RBP, appeared to be a hot spot for global protein stability as well. Additional single alanine mutations demonstrated as much as 200‐fold increase in apparent Kd but retained overall protein stability. The data collected from this study may be incorporated into design algorithms to help create more stable biosensors and optimize signal transduction properties for a variety of important analytes.
Phenology model from surface meteorology does not capture satellite‐based greenup estimations
Authors: FISHER JEREMY I. , RICHARDSON ANDREW D. , MUSTARD JOHN F.
Published: January 2007

Seasonal temperature change in temperate forests is known to trigger the start of spring growth, and both interannual and spatial variations in spring onset have been tied to climatic variability. Satellite dates are increasingly being used in phenology studies, but to date that has been little effort to link remotely sensed phenology to surface climate records. In this research, we use a two‐parameter spring warming phenology model to explore the relationship between climate and satellite‐based phenology. We employ daily air temperature records between 2000 and 2005 for 171 National Oceanographic and Atmospheric Administration weather stations located throughout New England to construct spring warming models predicting the onset of spring, as defined by the date of half‐maximum greenness (D50) in deciduous forests as detected from Moderate Resolution Imaging Spectrometer. The best spring warming model starts accumulating temperatures after March 20th and when average daily temperatures exceed 5°C. The accumulated heat sums [heating degree day (HDD)] required to reach D50 range from 150 to 300 degree days over New England, with the highest requirements to the south and in coastal regions. We test the ability of the spring warming model to predict phenology against a null photoperiod model (average date of onset). The spring warming model offers little improvement on the null model when predicting D50. Differences between the efficacies of the two models are expressed as the ‘climate sensitivity ratio’ (CSR), which displays coherent spatial patterns. Our results suggest that northern (beech‐maple‐birch) and central (oak‐hickory) hardwood forests respond to climate differently, particularly with disparate requirements for the minimum temperature necessary to begin spring growth (3 and 6°C, respectively). We conclude that spatial location and species composition are critical factors for predicting the phenological response to climate change: satellite observations cannot be linked directly to temperature variability if species or community compositions are unknown.
Early factor VIII exposure and subsequent inhibitor development in children with severe haemophilia A
Authors: CHALMERS E. A. , BROWN S. A. , KEELING D. , LIESNER R. , RICHARDS M. , STIRLING D. , THOMAS A. , VIDLER V. , WILLIAMS M. D. , YOUNG D. ,   ON BEHALF OF THE PAEDIATRIC WORKING PARTY OF UKHCDO
Published: January 2007

Summary.  Recent reports have suggested that the incidence of inhibitors in haemophilia is the highest in those first exposed to factor VIII under 6 months of age. In this study, we investigated inhibitor development in children first exposed to FVIII as neonates and also examined the effect of other genetic and environmental variables. Three hundred and forty‐eight children with severe haemophilia A were investigated. Inhibitors developed in 68 of 348 (20%), with 34 of 348 (10%) high titre inhibitors. The incidence in relation to initial FVIII exposure was: <1 month nine of 35 (26%), 1–6 months 13 of 51 (25%), 6–12 months 27 of 130 (21%), 12–18 months 13 of 66 (20%) and >18 months six of 66 (9%). While we observed a significant difference in inhibitor development and age at first exposure across all age groups (P = 0.018), no significant difference was observed in children treated at different time points during the first year of life (P = 0.44). Similar results were obtained for high titre inhibitors. There was also no difference in the incidence of inhibitors in relation to initial FVIII exposure in a subgroup of 144 children with the intron 22 mutation. Inhibitors developed more frequently in those initially treated with recombinant when compared with plasma‐derived FVIII (P = 0.006) and in those with a major molecular defect (P = 0.009). In this study, exposure to FVIII during the neonatal period was not associated with a higher incidence of inhibitors than those treated later during the first year of life. Initial treatment with recombinant FVIII and the presence of a major molecular defect were the most important variables affecting inhibitor development.
Cells in Behaviourally Relevant Brain Regions Coexpress Nuclear Receptor Coactivators and Ovarian Steroid Receptors
Authors: Tetel M. J. , Siegal N. K. , Murphy S. D.
Published: January 2007

Oestradiol and progesterone act in the brain to elicit profound effects on behaviour and physiology. One physiological function of oestradiol is the induction of progesterone receptor (PR) expression in a variety of behaviourally relevant brain regions, including the ventromedial nucleus of the hypothalamus (VMN), the medial preoptic nucleus of the preoptic area (MPOA), the arcuate nucleus (ARC) and the medial central grey (MCG). Ligand‐dependent transcriptional activity of steroid receptors, including oestrogen receptors (ER) and PR, is dramatically influenced by nuclear receptor coactivators. In previous studies, we have found that two of these nuclear receptor coactivators, steroid receptor coactivator‐1 (SRC‐1) and CREB‐binding protein (CBP), are important in ER‐mediated induction of PR in the VMN and in steroid‐dependent behaviours. For nuclear receptor coactivators to function in hormone‐dependent transcription in the brain and regulate behaviour, both receptor and coactivator must be expressed in the same cell. In the present study, we used a dual‐label immunohistochemical technique to investigate if individual cells in behaviourally relevant brain regions coexpress nuclear receptor coactivators and steroid receptors. Confocal analysis revealed that in oestrogen‐primed rats, most of the E‐induced PR cells in the VMN (89.6%), MPOA (63%), ARC (82.6%), and many in the MCG (39%), also express SRC‐1. In addition, the majority of the cells containing E‐induced PR in the VMN (78.3%), MPOA (83.1%), ARC (83.6%), and MCG (60%) also express CBP. These results, taken together with the findings that virtually all oestradiol‐induced PR containing cells in the brain express ER, suggest that these neurones represent sites of functional interaction of nuclear receptor coactivators with ovarian steroid receptors in the brain. The present findings provide neuroanatomical evidence that nuclear receptor coactivators are integral in mediating steroid hormone action in behaviourally relevant brain regions.
Fine‐scale spatial genetic structure in mixed oak stands with different levels of hybridization
Authors: VALBUENA‐CARABAÑA M. , GONZÁLEZ‐MARTÍNEZ S. C. , HARDY O. J. , GIL L.
Published: January 2007

Oaks are model species for the study of natural introgressive hybridization. High interfertility among oak taxa might result in collective evolution, through transpecific spread of advantageous alleles, challenging the standard concept of species. Nine highly polymorphic microsatellite (nuSSR) loci were analysed in three mixed oak populations ofQuercus pyrenaicaandQuercus petraea(Montejo, Somosierra and Robregordo) with different density and hybridization rates. Both leaf morphology and molecular markers were used to assess individual admixture rates. Insights about the relative effect of density and hybridization rates on fine‐scale spatial genetic structure (SGS) were obtained from autocorrelograms andSpstatistics. Differences in SGS among populations were higher than between species. These differences cannot be attributed solely to census densities but also relate to other factors, such as the spatial configuration of the population. Hybridization was an important factor shaping within‐population spatial genetic structure, and an interspecific component of SGS was found in Somosierra. Indirect estimates of historical gene flow in Montejo were compared with actual values of gene dispersal assessed by parentage analysis in a former study. Similar values were found for current and historical gene flow in both species, which might reflect demographical stability.
Regional differences in expression of TPH‐1, SERT, 5‐HT3 and 5‐HT4 receptors in the human stomach and duodenum
Authors: Van Lelyveld N. , Ter Linde J. , Schipper M. E. I. , Samsom M.
Published: January 2007

Abstract  The aim of this study was to increase the understanding of the role of serotonergic signalling in normal gastroduodenal function at a molecular level.

Mucosal biopsy specimens were collected from the fundus, antrum and duodenum of 11 healthy subjects. Serotonin (5‐HT)‐positive cells were counted and the mRNA levels of tryptophan hydroxylase (TPH), serotonin transporter (SERT), 5‐HT4 receptor and 5‐HT3 receptor subunits were quantified by real‐time reverse transcription polymerase chain reaction.

The number of 5‐HT‐positive cells was larger in the duodenum compared with the stomach (P < 0.001). Serotonin transport protein expression was 19‐fold higher in the duodenum compared with the antrum and 457‐fold higher compared with the fundus (P < 0.001). Tryptophan hydroxylase‐1 expression was lower in the duodenum compared with the antrum and fundus (regional differences −2.3 and −3.6, respectively). The 5‐HT4 receptor and the 5‐HT3C and 5‐HT3E receptor subunits were more abundantly expressed in duodenum compared with the stomach (P < 0.001).

The larger number of 5‐HT‐positive cells, the higher expression of 5‐HT3 and 5‐HT4 receptors, and in particularly the higher uptake capacity of 5‐HT in the duodenum, point out to a more prominent role of serotonergic signalling at the mucosal level in the duodenum compared with the stomach.
The evolutionary ecology of individual phenotypic plasticity in wild populations
Authors: NUSSEY D. H. , WILSON A. J. , BROMMER J. E.
Published: January 2007

The ability of individual organisms to alter morphological and life‐history traits in response to the conditions they experience is an example of phenotypic plasticity which is fundamental to any population's ability to deal with short‐term environmental change. We currently know little about the prevalence, and evolutionary and ecological causes and consequences of variation in life history plasticity in the wild. Here we outline an analytical framework, utilizing the reaction norm concept and random regression statistical models, to assess the between‐individual variation in life history plasticity that may underlie population level responses to the environment at both phenotypic and genetic levels. We discuss applications of this framework to date in wild vertebrate populations, and illustrate how natural selection and ecological constraint may alter a population's response to the environment through their effects at the individual level. Finally, we present future directions and challenges for research into individual plasticity.