bluuebunny/crossref_metadata_2025 huggingface dataset:
How Do Reliability and Timing Influence Cue-Combinations for Shading and Stereo-Disparity?
Authors: Lovell P G , Bloj M , Harris J M
Published: June 2011

Cue-conflict studies have been used with considerable success to examine the mechanisms underlying the integration of different sensory cues. Our recent studies have used these methods to examine the combination of stereo-disparity and shading cues in realistically rendered stimuli. The stimuli featured circular convexities with cyclopean shading and a stereo-cue based upon a densely dotted surface texture—other cues (shape outline and surface texture gradient) were controlled for. In our first experiment observers made depth discriminations while disparity noise was manipulated; we were able to demonstrate that for most observers cues are combined optimally—ie, PSEs and response variances shifted towards the more reliable channel. In a follow-on study we have examined how these cue-combinations are affected by presentation timing—with forwards and backwards masking. For most observers the adage that shading provides a quick and dirty mechanism for making depth judgements seems to be supported. Observers can make reliable depth judgements based upon shading when the difference in depth is relatively fine. However, for fine discriminations more time is required, and by this time the more accurate information from the stereo-channel has become available and is used.
Comparing and Contrasting View-Based and 3D Models of Navigation
Authors: Glennerster A , Pickup L C , Fitzgibbon A W , Gilson S J
Published: June 2011

What does it mean to store a 3D location and hence to navigate towards it? Participants in our experiment carried out a homing task on the scale of a room (ie, 3-4m square) in an immersive virtual reality environment. In interval one, they were shown three very long coloured vertical poles from one viewing location with some head movement permitted. The poles were easily distinguishable and designed to have constant angular width irrespective of viewing distance. Participants were then transported (virtually) to another location in the scene, and in interval two they tried to navigate to the initial viewing point relative to the poles. The distributions of end-point errors on the ground plane differed significantly in shape and extent depending on pole configuration and goal location. We compared the ability of two types of models to predict these variations in the distribution of errors: (i) view-based models, based on simple features such as angles between poles from the cyclopean point, ratios of these angles, or various disparity measures and (ii) Cartesian models based on a probabilistic 3D reconstruction of the scene geometry. For our data, we find that view-based models capture important characteristics of the end-point distributions very well whereas 3D-based models fare less well. In some ways, a Cartesian model is a very particular case of a view-based model: the two are not as different from one another as they first appear.
Inhibition of Return: Retinotopic, but Not Reflexive
Authors: Krueger H M , Hunt A R
Published: June 2011

Inhibition of return (IOR) is the term used to describe slower responses to a recently cued location. IOR has long been claimed to be reflexive, although the question of whether it is predominantly a functional process in visual search or an artefact of suppressing a motor response has been the subject of some debate. Here we show IOR is retinotopic across saccades in contrast with other studies that have suggested that the reference frame of IOR is spatiotopic. Although the existence of retinotopic IOR is consistent with a motor-artefact account, we also find that IOR depends on the predictability in the visual environment and as such suggests that IOR is strategically applied. The implications of these contradicting findings will be discussed in reference to the literature concerning the function and reference frame of IOR.
Searching for IOR: Review and Results
Authors: MacInnes J , Hunt A R , Hilchey M , Klein R
Published: June 2011

Inhibition of return (IOR) has been proposed as an attentional mechanism which facilitates visual search by inhibiting reorienting to previously attended spatial locations. IOR is typically measured following the removal of attention from a spatial location. Early facilitation of responses to this location at early stimulus-onset asynchrony (SOA of ∼100 – 300ms) is replaced with a later and long-lasting inhibition (SOA of ∼300 – 3000ms). This inhibition has been proposed to be used by the oculomotor system to tag previously fixated locations in visual search to favour new locations over old (yet still salient) locations. Indeed, slower responses to probes presented in recently fixated locations has since been demonstrated in a variety of visual search tasks, and this form of IOR has been related to the reduced likelihood of refixating the previous or penultimate search location during natural search (MacInnes and Klein, 2003). However, recent research has challenged this interpretation by suggesting that saccadic momentum facilitates forward saccades as opposed to IOR suppressing return saccades. For instance, Smith and Henderson (2010) replicated Klein and MacInnes (1999) by finding IOR in a Where's Waldo © search task, but they reanalyzed the probability distribution of saccades to provide evidence for a saccadic momentum account. This talk will provide a review of recent research outlining the evidence for IOR and saccadic momentum in natural search patterns and present new data on the distribution of saccades in complex search tasks. [Supported by BBSRC]
Remote Interactions in Contour Detection
Authors: O'Kane L , Watt R , Ledgeway T , Goutcher R
Published: June 2011

A series of experiments were carried out examining factors influencing the ability to detect contour structure within noise. In each experiment the observers' task was to detect a target embedded in a field of 900 random gabors. The target was defined as one or more pairs of aligned gabors separated by a small distance. When the pairs are placed randomly in the image, but with the same orientation, detection is poor, requiring 20 pairs to be present for performance to be good. When the pairs are aligned to be consistent with a single straight contour, detection is very good even for just 3 or 4 pairs. This effect occurs despite the distance between the pairs being considerably larger than the average distance between the elements in the background and background gabors filling the gaps along the line. To examine potential cues to the grouping process underlying the enhancement in performance, the relationships between the elements within a pair and between the pairs in the image were manipulated. The effect of changing the similarity of orientation, contrast, and disparity of the gabors within each pair and between pairs was measured. Results suggest that detection is optimal only for targets that are in a straight line. Performance is relatively unaffected by contrast, although having the same contrast within a pair is better than opposite contrast. There is no effect of contrast difference between pairs. There is small evidence of disparity differences affecting performance.
Combining Motion-Induced Blindness with Binocular Rivalry
Authors: Jaworska K , Lages M
Published: June 2011

Motion-induced blindness (MIB) and binocular rivalry (BR) are examples of multistable phenomena in which our perception varies despite constant retinal input. It has been suggested that both phenomena are related and share a common underlying mechanism. We tried to determine whether experimental manipulations of the target dot and the mask systematically affect MIB and BR in an experimental paradigm that can elicit both phenomena. Eighteen observers fixated the center of a split-screen stereo display that consisted of a distracter mask and a superimposed target dot with different colour (isoluminant Red/Green) in corresponding peripheral areas of the left and right eye. Observers reported perceived colour and disappearance of the target dot by pressing and releasing corresponding keys. In a within-subjects design the mask was presented in rivalry or not—with orthogonal drift in the left and right eye or with the same drift in both eyes. In control conditions the mask remained stationary. In addition, the size of the target dot was varied (small, medium, and large). Our results suggest that MIB measured by normalized frequency and duration of target disappearance and BR measured by normalized frequency and duration of colour reversals of the target were both affected by motion in the mask. Surprisingly, binocular rivalry in the mask had only a small effect on BR of the target and virtually no effect on MIB. The overall pattern of normalized MIB and BR measures, however, differed across experimental conditions. In conclusion, the results show some degree of dissociation between MIB and BR. Further analyses will inform whether or not the two phenomena occur independently of each other.
Internal Noise for Choosing Items is Affected by Their Number and Spatial Arrangement
Authors: Hasan B A S , Neri P
Published: June 2011

We studied whether, when choosing an item out of n items, the internal noise associated with making this choice is affected by the number of items and/or their spatial arrangement. Each item is represented by a patch of Gabor segments with different orientations; the task is to identify the patch with vertical orientation. The patches are positioned around the clock, and some spatial jitter is applied to each patch. We found an increase in internal noise with the number of patches. Jitter causes higher internal noise compared with no jitter, but different jitter configurations do not affect internal noise.
Similar Symmetries and the Effect of Scale
Authors: Clarke A D F , Green P R , Chantler M J
Published: June 2011

Tilings and symmetries are striking visual properties that have been used decoratively around the world throughout human history. Tiled patterns can be mathematically classified into 1 of 17 different wallpaper groups, and while computational models have been developed which can extract an image's symmetry group, very little work has been done on how humans perceive these patterns. We will give an overview of the results from two experiments which investigate the role wallpaper groups of two-dimensional patterns have on their perceived similarity. The first experiment involved participants grouping a set of 85 tiled patterns into subsets based on perceptual similarity. We find that patterns with the same wallpaper group are classified as similar more frequently than would be expected by chance and patterns with similar numbers of symmetries are viewed as similar. However, a simple linear-regression model fails to account for most of the variance. The second experiment looks at the interaction between scale (tile size) and wallpaper group and how they influence perceptual similarity. The empirical data are then compared with a computational model.
Biological Motion Perception in Autism
Authors: Cusack J , Williams J , Neri P
Published: June 2011

Typically developing adults can readily recognize human actions, even when conveyed to them via point-like markers placed on the body of the actor (Johansson, 1973). Previous research has suggested that children affected by autism spectrum disorder (ASD) are not equally sensitive to this type of visual information (Blake et al, 2003), but it remains unknown why ASD would impact the ability to perceive biological motion. We present evidence which looks at how adolescents and adults with autism are affected by specific factors which are important in biological motion perception, such as (eg, inter-agent synchronicity, upright/inverted, etc).
Perceiving Conspecifics is Not Purely Visual: “Body Gestalt” Completion is Influenced by the Body Posture of the Observer
Authors: Kessler K , Miellet S , Hoogenboom N
Published: June 2011

When we perceive other people in our everyday encounters their bodies are often partially occluded. High-level visual areas are known to automatically complete partially occluded objects, as revealed by the classic “gestalt” phenomena. However, here we set out to investigate if “body gestalt” completion is “embodied” and not purely visual. Human observers might intuitively map their own body knowledge onto partially occluded others and thereby complete their “body gestalt” by means of posture and/or motor resonance. To this end we developed new stimuli showing a face and two hands that could either form a “body gestalt” or not. Our most important finding across five behavioural experiments was that body gestalt completion was not solely based on visual features like the classic gestalt phenomena. Responses were significantly faster when the observer's posture matched the configuration of face and hands shown on screen then. In this sense body gestalt completion is an embodied process, where humans intuitively use their own body knowledge to ‘fill in the gaps’ in a body stimulus. We further conclude that in our particular paradigm posture resonance was apparently more important for body gestalt completion than motor resonance—with the former being most likely mediated by proprioceptive body schema representations, while the latter by the mirror neuron system. Finally, we will also present preliminary analysis of MEG data. Our findings elucidate the mechanisms of how humans perceive others holistically and how they might implicitly align themselves in everyday social interactions to facilitate an optimal co-representation of each other.
How Does Your Brain See “Living” Circles: A Study of Animacy and Intention Using fMRI
Authors: McAleer P , Becirspahic M , Love S
Published: June 2011

It is widely reported that the perception of animacy can occur from simple displays of moving shapes with participants attributing such qualities as goals, beliefs, and intentions. Furthermore, via neuroimaging studies, a network of brain areas, including regions of the temporal and frontal lobes, has been shown to process the percept. However, problems exist that prevent the bridging of fMRI studies on the perception of animacy and intention in shapes to the same percept of human movement. First, the issue of prior displays being poorly controlled in terms of low-level visual cues blurs the actual root of the effect. Second, the general use of synthetically generated displays and their relationship to actual human movement: a problem previously addressed in behavioural studies via a systematic reduction of live visual footage of human actors. Therefore, we propose experiments that incorporate both synthetically generated animacy stimuli and displays derived from human motion. Following the classic Tremoulet and Feldman displays, stimuli are created that allow for manipulation of animacy and intent whilst controlling low-level visual cues. These displays are then used in a whole-brain fMRI study to locate neural regions sensitive to the perception of animacy and intention. Finally, within these regions, a region-of-interest analysis is performed to examine the change in brain activation from viewing animacy displays derived from human movement with varying intent (eg, chasing or following). This study develops the relationship between previous animacy literature and the real-world perception of intent.
The Importance of Facial Features and Their Spatial Organization for Attractiveness is Modulated by Gender
Authors: Gill D
Published: June 2011

Many studies suggest that facial attractiveness signals mate quality. Fewer studies argue that the preference criteria emerge as a by-product of cortical processes. One way or the other, preference criteria should not be necessarily identical between female and male observers because either their preferences may have different evolutionary roles or they may even be due to known differences in visiospatial skills and brain function lateralization (ie, advantages favoring males' inability to determine spatial relations despite distracting information). The goal of this study was to assess sex differences in face attractiveness judgments by estimating the importance of facial features and their spatial organization. To this end, semipartial correlations were measured between intact-face preferences and preferences based on specific facial parts (eyes, nose, mouth, and hairstyle) or preferences based more on configuration (as reflected by low spatial frequency images). The results show strategy modulations by both observers' and faces' genders. In general, the association between intact-face preferences and parts-based preferences was significantly higher for female compared with male participants. For female faces, males' preferences were more strongly associated with their low spatial frequency preferences than were those of females. The two genders' strategies were more similar when judging male faces, and males performed more criteria modifications across face gender. The similarities between sexes regarding male faces are in line with previous studies that showed higher assignment of importance among men to attractiveness. Moreover, the results may suggest that men adjust their strategy to assess the danger of other males as potential rivals for mates.
Eye Contricks
Authors: Wade N
Published: June 2011

Icons are eye-cons: they provide a distillation of a complex object or idea into a simple pictorial shape. They create the impression of representing that which cannot be presented. Even at the level of the photograph, the links between icon and object are tenuous. The dimension of distance or depth is missing from the icon, and this alone introduces all manner of potential ambiguities. The history of art can be considered as an exploration of the missing link between icon and object. Eye-cons are more honest—they are tricks of vision so that what is seen does not necessarily correspond to what is presented. They are visual allusions rather than visual illusions, although they can display illusory effects. At its broadest, icon can be equated with image. The concept of image has thrived on its vagueness, and so attempts have been made to refine it. An icon corresponds to an optical image: it shares some of the projective characteristics of the object represented. Written words are also icons but they do not resemble the objects they represent—they are stylised or conventional rather than spatialised and projective. Words and images were set in delightful opposition by René Magritte (1898-1967) in a series of pipe paintings, and he also played on the theme of the arbitrariness of the verbal labels assigned to objects. What is surprising is that Magritte did not apply his painterly skills to transforming the word shapes he used. A similar reluctance to transform the typefaces pervades visual poetry. My interests are in the visual rather than the poetic dimension, and I will present a range of my own eye contricks which play with letter and word shapes in a variety of ways.
Genome-wide profiling of diel and circadian gene expression in the malaria vector
Anopheles gambiae
Authors: Rund Samuel S. C. , Hou Tim Y. , Ward Sarah M. , Collins Frank H. , Duffield Giles E.
Published: June 2011

Anopheles gambiae
, the primary African vector of malaria parasites, exhibits numerous rhythmic behaviors including flight activity, swarming, mating, host seeking, egg laying, and sugar feeding. However, little work has been performed to elucidate the molecular basis for these daily rhythms. To study how gene expression is regulated globally by diel and circadian mechanisms, we have undertaken a DNA microarray analysis of
An. gambiae
under light/dark cycle (LD) and constant dark (DD) conditions. Adult mated, non–blood-fed female mosquitoes were collected every 4 h for 48 h, and samples were processed with DNA microarrays. Using a cosine wave-fitting algorithm, we identified 1,293 and 600 rhythmic genes with a period length of 20–28 h in the head and body, respectively, under LD conditions, representing 9.7 and 4.5% of the
An. gambiae
gene set. A majority of these genes was specific to heads or bodies. Examination of mosquitoes under DD conditions revealed that rhythmic programming of the transcriptome is dependent on an interaction between the endogenous clock and extrinsic regulation by the LD cycle. A subset of genes, including the canonical clock components, was expressed rhythmically under both environmental conditions. A majority of genes had peak expression clustered around the day/night transitions, anticipating dawn and dusk. Genes cover diverse biological processes such as transcription/translation, metabolism, detoxification, olfaction, vision, cuticle regulation, and immunity, and include rate-limiting steps in the pathways. This study highlights the fundamental roles that both the circadian clock and light play in the physiology of this important insect vector and suggests targets for intervention.
Seeing protein monolayers with naked eye through plasmonic Fano resonances
Authors: Yanik Ahmet A. , Cetin Arif E. , Huang Min , Artar Alp , Mousavi S. Hossein , Khanikaev Alexander , Connor John H. , Shvets Gennady , Altug Hatice
Published: June 2011

We introduce an ultrasensitive label-free detection technique based on asymmetric Fano resonances in plasmonic nanoholes with far reaching implications for point-of-care diagnostics. By exploiting extraordinary light transmission phenomena through high-quality factor (
Q
solution
 ∼ 200) subradiant dark modes, we experimentally demonstrate record high figures of merits (FOMs as high as 162) for intrinsic detection limits surpassing that of the gold standard prism coupled surface-plasmon sensors (Kretschmann configuration). Our experimental record high sensitivities are attributed to the nearly complete suppression of the radiative losses that are made possible by the high structural quality of the fabricated devices as well as the subradiant nature of the resonances. Steep dispersion of the plasmonic Fano resonance profiles in high-quality plasmonic sensors exhibit dramatic light intensity changes to the slightest perturbations within their local environment. As a spectacular demonstration of the extraordinary sensitivity and the quality of the fabricated biosensors, we show direct detection of a single monolayer of biomolecules with naked eye using these Fano resonances and the associated Wood’s anomalies. To fabricate high optical-quality sensors, we introduce a high-throughput lift-off free evaporation fabrication technique with extremely uniform and precisely controlled nanofeatures over large areas, leading to resonance line-widths comparable to that of the ideally uniform structures as confirmed by our time-domain simulations. The demonstrated label-free sensing platform offers unique opportunities for point-of-care diagnostics in resource poor settings by eliminating the need for fluorescent labeling and optical detection instrumentation (camera, spectrometer, etc.) as well as mechanical and light isolation.
ELM pacing and the ITER operating window: mutual constraints
Authors: Pacher G.W. , Pacher H.D. , Kukushkin A.S. , Pitts R.A.
Published: June 2011

On ITER, one of the methods foreseen to reduce the energy loading due to edge localized modes (ELMs) on the divertor targets is the use of pellet injection to control the ELM frequency and amplitude of the energy losses at each ELM. However, the use of such pellet pacing introduces additional fuel throughput. This may constrict the burning plasma operating window through its influence on divertor plasma detachment, thus reducing the attainable alpha power. Consistent modelling of core, scrape-off layer, and divertor is used to document this effect. The result is a determination of the maximum attainable alpha power at the nominal pumping speed as a function of pacing pellet size and the maximum allowable pellet size as a function of ELM loss power fraction for which the reference operating window is not reduced.
Using a PC and external media to quantitatively investigate electromagnetic
induction
Authors: Bonanno A , Bozzo G , Camarca M , Sapia P
Published: June 2011

In this article we describe an experimental learning path about electromagnetic induction
which uses an Atwood machine where one of the two hanging bodies is a cylindrical magnet
falling through a plexiglass guide, surrounded either by a coil or by a copper pipe. The first
configuration (magnet falling across a coil) allows students to quantitatively study the
Faraday–Neumann–Lenz law, while the second configuration (falling through a copper
pipe) permits learners to investigate the complex phenomena of induction by
quantifying the amount of electric power dissipated through the pipe as a result of
Foucault eddy currents, when the magnet travels through the pipe. The magnet’s fall
acceleration can be set by adjusting the counterweight of the Atwood machine so
that both the kinematic quantities associated with it and the electromotive force
induced within the coil are continuously and quantitatively monitored (respectively,
by a common personal computer (PC) equipped with a webcam and by freely
available software that makes it possible to use the audio card to convert the PC
into an oscilloscope). Measurements carried out when the various experimental
parameters are changed provide a useful framework for a thorough understanding and
clarification of the conceptual nodes related to electromagnetic induction. The proposed
learning path is under evaluation in various high schools participating in the
project ‘Lauree Scientifiche’ promoted by the Italian Department of Education.
THE QUaD GALACTIC PLANE SURVEY. II. A COMPACT SOURCE
CATALOG
Authors: Culverhouse T. , Ade P. , Bock J. , Bowden M. , Brown M. L. , Cahill G. , Castro P. G. , Church S. , Friedman R. , Ganga K. , Gear W. K. , Gupta S. , Hinderks J. , Kovac J. , Lange A. E. , Leitch E. , Melhuish S. J. , Memari Y. , Murphy J. A. , Orlando A. , Pryke C. , Schwarz R. , O'Sullivan C. , Piccirillo L. , Rajguru N. , Rusholme B. , Taylor A. N. , Thompson K. L. , Turner A. H. , Wu E. Y. S. , Zemcov M.
Published: June 2011

We present a catalog of compact sources derived from the QUaD Galactic Plane
Survey. The survey covers ∼800 deg2 of the inner galaxy
(|b| < 4°) in Stokes I,
Q, and U parameters at 100 and 150 GHz,
with angular resolutions of 5 and 3.5 arcmin, respectively. Five hundred and
twenty-six unique sources are identified in I, of which 239 are
spatially matched between frequency bands, with 53 (234) detected at 100 (150)
GHz alone; 170 sources are identified as ultracompact H ii regions.
Approximating the distribution of total intensity source fluxes as a power law,
we find a slope of γ
S, 100 = −1.8 ± 0.4 at 100 GHz
and γ
S, 150 = −2.2 ± 0.4 at 150 GHz. Similarly, the
power-law index of the source two-point angular correlation function is γθ,
100 = −1.21 ± 0.04 and γθ, 150 = −1.25 ± 0.04. The total
intensity spectral index distribution peaks at α
I
∼
0.25, indicating that dust emission is not the only source of radiation produced
by these objects between 100 and 150 GHz; free–free radiation is likely
significant in the 100 GHz band. Four sources are detected in polarized
intensity P, of which three have matching counterparts in
I. Three of the polarized sources lie close to the Galactic
center, Sagittarius A*, Sagittarius B2, and the Galactic Radio Arc, while the
fourth is RCW 49, a bright H ii region. An extended polarized source,
undetected by the source extraction algorithm on account of its ∼0.°5 size, is
identified visually, and is an isolated example of large-scale polarized
emission oriented distinctly from the bulk Galactic dust polarization.
Improving the prediction of disulfide bonds in Eukaryotes with machine learning methods and protein subcellular localization
Authors: Savojardo Castrense , Fariselli Piero , Alhamdoosh Monther , Martelli Pier Luigi , Pierleoni Andrea , Casadio Rita
Published: June 2011

Motivation: Disulfide bonds stabilize protein structures and play relevant roles in their functions. Their formation requires an oxidizing environment and their stability is consequently depending on the redox ambient potential, which may differ according to the subcellular compartment. Several methods are available to predict cysteine-bonding state and connectivity patterns. However, none of them takes into consideration the relevance of protein subcellular localization.

Results: Here we develop DISLOCATE, a two-step method based on machine learning models for predicting both the bonding state and the connectivity patterns of cysteine residues in a protein chain. We find that the inclusion of protein subcellular localization improves the performance of these predictive steps by 3 and 2 percentage points, respectively. When compared with previously developed methods for predicting disulfide bonds from sequence, DISLOCATE improves the overall performance by more than 10 percentage points.

Availability: The method and the dataset are available at the Web page http://www.biocomp.unibo.it/savojard/Dislocate.html. GRHCRF code is available at http://www.biocomp.unibo.it/savojard/biocrf.html.

Contact:  piero.fariselli@unibo.it
Influence without Bribes: A Noncontracting Model of Campaign Giving and Policymaking
Authors: Fox Justin , Rothenberg Lawrence
Published: June 2011

Efforts to find empirical evidence that campaign money impacts policymaking choices have offered scant support for interest group influence. A possible explanation is that the hypothesis that those receiving campaign monies should adjust their policy choices to favor their donor requires the untenable assumption that interest groups and legislators can implement contracts. We develop a new, alternative, model in which legislators and interest groups cannot engage in any form of contracting, and legislators care about both the policy and fundraising implications of their policy choices. In our model, an interest group gives only to those it believes shares its policy preferences. Nonetheless, we show that the group's giving impacts incumbent policy choices. Importantly, when groups ideologically match, the relationship between actual contributions and bias is not straightforward. As long as a group is uncertain about a member's primitive policy preference, it can influence her policymaking even when it contributes to her challenger or abstains from giving altogether.
Molecular Analysis of Turfgrass Rusts Reveals the Widespread Distribution of Puccinia coronata as a Pathogen of Kentucky Bluegrass in the United States
Authors: Beirn Lisa A. , Moy Melinda , Meyer William A. , Clarke Bruce B. , Crouch Jo Anne
Published: June 2011

Over the past 10 years, rust diseases have become increasingly prevalent on certain cultivars of Kentucky bluegrass. This pattern suggests that new races or new species of rust fungi may have emerged. To test this hypothesis, 66 samples of turfgrass rust fungi collected from across the United States were evaluated based on sequences of the internal transcribed spacer (ITS)-5.8S rDNA region. Phylogenetic analysis revealed three species: Puccinia coronata, P. graminis, and P. striiformis, comprising 67, 28, and 5% of the samples, respectively. P. coronata was frequently found in association with Kentucky bluegrass, a host–pathogen relationship that has not been previously reported. Comparison of molecular analyses with the use of standard field identification techniques—host association and pustule pigmentation—showed that 58% of the Kentucky bluegrass samples would have been incorrectly diagnosed using nonmolecular criteria. To avoid such misidentifications, a real-time polymerase chain reaction diagnostic protocol was developed for turfgrass-associated P. graminis, P. coronata, and P. striiformis using ITS sequences. Accurate, reproducible, species-specific identifications were made using as few as 50 to 150 urediniospores, even in mixed infections. This study represents the first DNA-based evaluation of turfgrass rust fungi and provides a quick and reliable sequence-based protocol as an alternative to less reliable field-based identification techniques.
First Report of Alfalfa mosaic virus Infection in Viburnum tinus in Chile
Authors: Peña E. , Olate E. , Chorbadjian R. A. , Rosales I. M.
Published: June 2011

Viburnum tinus L., commonly known as laurustinus, is an ornamental shrub that is widely used as a garden plant and flower crop. V. tinus is popular because of its desirable characteristics such as evergreen foliage, tolerance to pruning, winter blooms, and its adaptation to cold temperate zones. It is also relatively easy to grow and is commonly used as a windbreak. Infection of this ornamental species by Alfalfa mosaic virus (AMV) has been associated with yellow mottling or variegated leaf coloring, including light green and white, and has been referred to as the “Viburnum Calico” (1,4). In April 2011, at the onset of winter in the Southern Hemisphere, intense yellow spotting and mottling was observed on V. tinus leaves in the San Joaquin Campus at Pontificia Universidad Catolica de Chile. Presence of Aphis spiraecola Patch was observed on the shrubs, however, in the area it is also common to find other aphid species such as Toxoptera aurantii (Boyer de Fonscolombe) and A. fabae Scopoli. Leaf tissue samples from 10 asymptomatic and 10 symptomatic plants were examined for the presence of AMV by tissue-blot immunoassay with a commercially available polyclonal antibody (Agdia Inc., Elkhart, IN) along with the Goat affinity purified anti-rabbit IgG conjugated (Whole Molecule) (Molecular Probes, Invitrogen Corp., Carlsbad, CA). First-strand cDNA synthesis and PCR were performed with specific primers CP-AMV1 and CP-AMV2 (3). AMV was detected in all symptomatic leaves and also in two of the asymptomatic tissue analyzed by tissue blot assay. Reverse transcription (RT)-PCR produced 753-bp amplicons in all samples that were positive to AMV by tissue printing. No amplification product was observed when water control or seronegative samples were used as templates in the RT-PCR assays. Two amplicons were directly sequenced in both directions to confirm the identification of AMV in the leaf samples. The sequences obtained were homologous and BLASTN analysis of the submitted sequence (GenBank Accession No. JN040542) showed 99% nucleotide sequence identity to an AMV isolate described from Nicotiana tabacum L. (GenBank Accession No. FJ527749). These results demonstrate the presence of AMV in V. tinus in Chile. This pathogen has also been described to be affecting V. tinus in France (1) and V. lucidum Mill. in Spain (2). In Chile, V. tinum is increasingly grown as an ornamental plant. Therefore, care should be taken to ensure that the propagative materials of V. tinum are devoid of AMV infection to prevent further spread of this virus.

References: (1) L. Cardin et al. Plant Dis. 90:1115, 2006. (2) M. Cebrián et al. Plant Dis. 92:1132, 2008. (3) M. Finetti-Sialer et al. J. Plant Pathol. 79:115, 1997. (4) H. E. Williams et al. Phytopathology 61:1305, 1971.
The Absence of Adrenal Gland Enlargement during Septic Shock Predicts Mortality
Authors: Jung Boris , Nougaret Stephanie , Chanques Gérald , Mercier Gregoire , Cisse Moussa , Aufort Sophie , Gallix Benoit , Annane Djillali , Jaber Samir
Published: June 2011

Background

: Assessment and management of septic shock associated adrenal function remain controversial. The aim of this study was to explore the prognostic value of adrenal gland volume in adults with septic shock.

Methods

: A short cosyntropin test and determination of adrenal volume by computed tomography were performed within 48 h of shock in patients with septic shock (n = 184) and in 2 control groups: 40 ambulatory patients and 15 nonseptic critically ill patients. The primary endpoint was intensive care unit mortality.

Results

: At intensive care unit discharge, 59 patients with septic shock died. Adrenal volume was 12.5 cm [95% CI, 11.3-13.3] and 8 cm [95% CI, 6.8-10.1] in the nonseptic group (P < 0.05 with both septic cohorts) and 7.2 cm [95%CI, 6.3-8.5] in the ambulatory patient group (P < 0.05 in patients with septic shock). In patients with septic shock, adrenal volume less than 10 cm was associated with higher 28-day mortality rates with an area under the receiver operating curve of 0.84 [95% CI, 0.78-0.89]. Adrenal volume above 10 cm was an independent predictor of intensive care unit survival (hazard ratio = 0.014; 95% CI [0.004-0.335]).

Conclusion

: A total adrenal gland volume less than 10 cm during septic shock was associated in univariate and multivariate analysis with mortality at day 28 in patients with septic shock. Whether adrenal gland volume can be a surrogate of adrenal gland function and used to guide hydrocortisone therapy in septic shock patients needs to be further investigated.
Comparison of the Accuracy of Noninvasive Hemoglobin Monitoring by Spectrophotometry (SpHb) and HemoCue® with Automated Laboratory Hemoglobin Measurement
Authors: Lamhaut Lionel , Apriotesei Roxana , Combes Xavier , Lejay Marc , Carli Pierre , Vivien Benoît
Published: June 2011

Background

The reference method for hemoglobin concentration measurement remains automated analysis in the laboratory. Although point-of-care devices such as the HemoCue® 201+ (HemoCue, Ängelholm, Sweden) provide immediate hemoglobin values, a noninvasive, spectrophotometry-based technology (Radical-7®; Masimo Corp., Irvine, CA) that provides continuous online hemoglobin (SpHb) measurements has been introduced. This clinical study aimed to test the hypothesis that SpHb monitoring was equivalent to that of HemoCue® (the automated hemoglobin measurement in the laboratory taken as a reference method) during acute surgical hemorrhage.

Methods

Blood for laboratory analysis was sampled after induction of anesthesia, during surgery according to the requirements of the anesthesiologist, and finally after the transfer of the patient to the recovery room. When each blood sample was taken, capillary samples were obtained for analysis with HemoCue®. SpHb monitoring was performed continuously during surgery. Using the automated hemoglobin measurement in the laboratory as a reference method, the authors tested the hypothesis that SpHb monitoring is equivalent to that of HemoCue®. The agreement between two methods was evaluated by linear regression and Bland and Altman analysis.

Results

Eighty-five simultaneous measurements from SpHb, HemoCue®, and the laboratory were obtained from 44 patients. Bland and Altman comparison of SpHb and HemoCue® with the laboratory measurement showed, respectively, bias of -0.02 ± 1.39 g · dl(-1) and -0.17 ± 1.05 g · dl(-1), and a precision of 1.11 ± 0.83 g · dl(-1) and 0.67 ± 0.83 g · dl(-1). Considering an acceptable difference of ± 1.0 g · dl(-1) with the laboratory measurement, the percentage of outliers was significantly higher for SpHb than for HemoCue® (46% vs. 16%, P < 0.05).

Conclusions

Taking automated laboratory hemoglobin measurement as a reference, the study shows that SpHb monitoring with Radical-7® gives lower readings than does the HemoCue® for assessment of hemoglobin concentration during hemorrhagic surgery.
Porphyromonas gingivalis enzymes enhance infection with human metapneumovirus in vitro
Authors: Pyrc Krzysztof , Strzyz Paulina , Milewska Aleksandra , Golda Anna , Schildgen Oliver , Potempa Jan
Published: June 2011

Relatively recently discovered, human metapneumovirus (HMPV) is a human pathogen with worldwide prevalence, accounting for a substantial percentage of respiratory tract diseases. Concurrent viral and bacterial infections enable intricate mechanisms of cooperation between pathogens, which complicate the symptoms and outcome of the disease. Such bilateral interactions are based on the modulation of bacterial growth on epithelium pathologically altered during viral illness and the modulation of immune responses, as well as the enhancement of virus replication by bacterial virulence factors. This study showed that proteases produced byPorphyromonas gingivalis, a Gram-negative bacterium implicated in the development of periodontitis, named gingipains, facilitated HMPV replication in LLC-MK2 cells and may contribute to HMPV pathogenicity in patients with periodontitis. Gingipains at low nanomolar concentrations enabled HMPV replication and allowed virus propagationin vitro. In contrast to previously published data for influenza virus, however,Staphylococcus aureusproteases and human neutrophil elastase did not affect virus replication.
Assembly of homogeneous norovirus-like particles accomplished by amino acid substitution
Authors: Someya Yuichi , Shirato Haruko , Hasegawa Kazuya , Kumasaka Takashi , Takeda Naokazu
Published: June 2011

Infection of insect cells with recombinant baculoviruses carrying the VP1 gene from Chiba strain norovirus resulted in the production of 57 and 50 kDa proteins, and the assembly of a smaller, 23 nm form of the virus-like particles (VLPs), together with the normal, 38 nm form of the VLPs. The N-terminal residues of the 57 and 50 kDa proteins were Ala4 and Thr45, respectively. When the tripeptide Leu43-Ala44-Thr45 was changed to Ala-Pro-Val, only 38 nm VLPs were assembled. The 38 nm VLPs showed essentially the same pattern of carbohydrate binding as the 23 nm VLPs, despite the significant difference in the degree of Lewis b antigen binding.
The relative ratio of condensin I to II determines chromosome shapes
Authors: Shintomi Keishi , Hirano Tatsuya
Published: June 2011

To understand how chromosome shapes are determined by actions of condensins and cohesin, we devised a series of protocols in which their levels are precisely changed in Xenopus egg extracts. When the relative ratio of condensin I to II is forced to be smaller, embryonic chromosomes become shorter and thicker, being reminiscent of somatic chromosomes. Further depletion of condensin II unveils its contribution to axial shortening of chromosomes. Cohesin helps juxtapose sister chromatid arms by collaborating with condensin I and counteracting condensin II. Thus, chromosome shaping is achieved by an exquisite balance among condensin I and II and cohesin.
Investigating the Contribution of the Phosphate Transport Pathway to Arsenic Accumulation in Rice
Authors: Wu Zhongchang , Ren Hongyan , McGrath Steve P. , Wu Ping , Zhao Fang-Jie
Published: June 2011

Arsenic (As) accumulation in rice (Oryza sativa) may pose a significant health risk to consumers. Plants take up different As species using various pathways. Here, we investigated the contribution of the phosphate (Pi) transport pathway to As accumulation in rice grown hydroponically or under flooded soil conditions. In hydroponic experiments, a rice mutant defective in OsPHF1 (for phosphate transporter traffic facilitator1) lost much of the ability to take up Pi and arsenate and to transport them from roots to shoots, whereas transgenic rice overexpressing either the Pi transporter OsPht1;8 (OsPT8) or the transcription factor OsPHR2 (for phosphate starvation response2) had enhanced abilities of Pi and arsenate uptake and translocation. OsPT8 was found to have a high affinity for both Pi and arsenate, and its overexpression increased the maximum influx by 3- to 5-fold. In arsenate-treated plants, both arsenate and arsenite were detected in the xylem sap, with the proportion of the latter increasing with the exposure time. Under the flooded soil conditions, the phf1 mutant took up less Pi whereas the overexpression lines took up more Pi. But there were no similar effects on As accumulation and distribution. Rice grain contained predominantly dimethylarsinic acid and arsenite, with arsenate being a minor species. These results suggest that the Pi transport pathway contributed little to As uptake and transport to grain in rice plants grown in flooded soil. Transgenic approaches to enhance Pi acquisition from paddy soil through the overexpression of Pi transporters may not increase As accumulation in rice grain.
Response of subtype‐specific human breast cancer‐derived cells to poly(ADP‐ribose) polymerase and checkpoint kinase 1 inhibition
Authors: Shibata Hidetaka , Miuma Satoshi , Saldivar Joshua C. , Huebner Kay
Published: June 2011

When DNA damage is detected, checkpoint signal networks are activated to stop the cell cycle, and DNA repair processes begin. Inhibitory compounds targeting components of DNA damage response pathways have been identified and are being used in clinical trials, in combination with chemotherapeutic agents, to enhance cancer therapy. Inhibitors of checkpoint kinases, Chk1 and Chk2, have been shown to sensitize tumor cells to DNA damaging agents, and treatment of BRCA1/2‐deficient tumor cells, as well as triple negative breast cancers, with poly(ADP‐ribose) polymerase (PARP) inhibitors has shown promise. But systematic studies to determine which tumor subtypes are likely to respond to these specific inhibitors have not been reported. The current study was designed to test sensitivity of specific breast cancer subtype‐derived cells to two classes of these new inhibitory drugs, PARP and Chk1 inhibitors. Luminal, HER2 overexpressing, and triple negative breast cancer‐derived cells were tested for sensitivity to killing by PARP inhibitors, ABT‐888 and BSI‐201, and Chk1 inhibitor, PF‐00477736, alone or in combination with gemcitabine or carboplatin. Each of the triple negative breast cancer cell lines showed strong sensitivity to the Chk1 inhibitor, but only the BRCA1‐deficient breast cancer cell lines showed sensitivity to the PARP inhibitors, suggesting that in vitro testing of cancer cell lines of specific subtypes, with panels of the different PARP and Chk1 inhibitors, will contribute to stratification of patients for clinical trials using these classes of inhibitors. (Cancer Sci 2011; 102: 1882–1888)
Overexpression of estrogen receptor‐α in human papillary thyroid carcinomas studied by laser‐capture microdissection and molecular biology
Authors: Di Vito Maura , De Santis Elena , Perrone Giulietta Anna , Mari Emanuela , Giordano Maria Chiara , De Antoni Enrico , Coppola Luigi , Fadda Guido , Tafani Marco , Carpi Angelo , Russo Matteo A.
Published: June 2011

The expression pattern of estrogen receptor (ER) isoforms in normal and tumor thyroid tissues is still controversial and poor defined, therefore, a more detailed study of the distribution of these molecules is needed. Most discrepancies might be due to the methods utilized. We studied the expression of ER isoforms in human papillary thyroid carcinoma (PTC), in fine‐needle aspiration biopsy‐derived specimens, and in cells, using more accurate techniques, such as laser‐capture microdissection, real‐time quantitative PCR, and Western blot. Laser‐capture microdissection allowed us to isolate homogeneous cell populations from human PTC surgical samples. Tumor, peritumor, or normal host tissue of the same sample were separately dissected and analyzed by RT‐PCR and Western blot. Estrogen receptor‐α mRNA was more expressed in cancer‐microdissected cells from human PTC, as compared with microdissected cells obtained from surrounding normal host tissue (450 vs 12, P = 0.001). A similar pattern was observed with Western blot for the ER‐α protein. By contrast, ER‐β mRNA expression was not detected among the microdissected tissue fractions. Fine‐needle aspiration biopsy‐derived specimens showed a similar expression pattern to ER. Moreover, human PTC cell line BCPAP and cancer stem cells from PTC, analyzed under hypoxic conditions, showed a hypoxia‐driven increase in ER‐α expression. In conclusion, ER‐α might have an important role in human PTC, and its overexpression can be studied in routine needle aspirate as a possible marker of malignancy. (Cancer Sci 2011; 102: 1921–1927)