bluuebunny/crossref_metadata_2025 huggingface dataset:
Transfer of orthogonal stimulus–response mappings to an orthogonal Simon task
Authors: Bae Gi Yeul , Cho Yang Seok , Proctor Robert W.
Published: September 2008

When up–down stimulus locations are mapped to left–right keypresses, an overall advantage for the up–right/down–left mapping is often obtained that varies as a function of response eccentricity. This orthogonal stimulus–response compatibility (SRC) effect also occurs when stimulus location is irrelevant, a phenomenon called the orthogonal Simon effect, and has been attributed to correspondence of stimulus and response code polarities. The Simon effect for horizontal stimulus–response (S–R) arrangements has been shown to be affected by short-term S–R associations established through the mapping used for a prior SRC task in which stimulus location was relevant. We examined whether such associations also transfer between orthogonal SRC and Simon tasks and whether correspondence of code polarities continues to contribute to performance in the Simon task. In Experiment 1, the orthogonal Simon effect was larger after practising with an up–right/down–left mapping of visual stimuli to responses than with the alternative mapping, for which the orthogonal Simon effect tended to reverse. Experiment 2 showed similar results when practice was with high (up) and low (down) pitch tones, though the influence of practice mapping was not as large as that in Experiment 1, implying that the short-term S–R associations acquired in practice are at least in part not modality specific. In Experiment 3, response eccentricity and practice mapping were shown to have separate influences on the orthogonal Simon effect, as expected if both code polarity and acquired S–R associations contribute to performance.
Pseudoneglect for the Bisection of Mental Number Lines
Authors: Loftus Andrea M. , Nicholls Michael E. R. , Mattingley Jason B. , Chapman Heidi L. , Bradshaw John L.
Published: September 2008

Patients with unilateral neglect of the left side bisect physical lines to the right whereas individuals with an intact brain bisect lines slightly to the left (pseudoneglect). Similarly, for mental number lines, which are arranged in a left-to-right ascending sequence, neglect patients bisect to the right. This study determined whether individuals with an intact brain show pseudoneglect for mental number lines. In Experiment 1, participants were presented with visual number triplets (e.g., 16, 36, 55) and determined whether the numerical distance was greater on the left or right side of the inner number. Despite changing the spatial configuration of the stimuli, or their temporal order, the numerical length on the left was consistently overestimated. The fact that the bias was unaffected by physical stimulus changes demonstrates that the bias is based on a mental representation. The leftward bias was also observed for sets of negative numbers (Experiment 2)—demonstrating not only that the number line extends into negative space but also that the bias is not the result of an arithmetic distortion caused by logarithmic scaling. The leftward bias could be caused by a rounding-down effect. Using numbers that were prone to large or small rounding-down errors, Experiment 3 showed no effect of rounding down. The task demands were changed in Experiment 4 so that participants determined whether the inner number was the true arithmetic centre or not. Participants mistook inner numbers shifted to the left to be the true numerical centre—reflecting leftward overestimation. The task was applied to 3 patients with right parietal damage with severe, moderate, or no spatial neglect (Experiment 5). A rightward bias was observed, which depended on the severity of neglect symptoms. Together, the data demonstrate a reliable and robust leftward bias for mental number line bisection, which reverses in clinical neglect. The bias mirrors pseudoneglect for physical lines and most likely reflects an expansion of the space occupied by lower numbers on the left side of the line and a contraction of space for higher numbers located on the right.
Short Article: Individual differences in self-initiated processing at encoding and retrieval: A latent variable analysis
Authors: Unsworth Nash
Published: September 2008

The current study examined individual differences in self-initiated processing (SIP) in memory tasks. Participants performed four memory tasks that varied the amount of SIP required at encoding, retrieval, or both as well as cognitive ability measures. It was found that the correlation between recall performance and cognitive abilities changed as a function of the amount of SIP required. Additionally, it was found that although both free and cued recall measures accounted for variance in cognitive abilities, only the free recall accounted for unique variance in cognitive abilities. It is suggested that the predictive power of a task is determined in part based on the amount of SIP required.
GM-CSF mediates autoimmunity by enhancing IL-6–dependent Th17 cell development and survival
Authors: Sonderegger Ivo , Iezzi Giandomenica , Maier Reinhard , Schmitz Nicole , Kurrer Michael , Kopf Manfred
Published: September 2008

Granulocyte macrophage–colony stimulating factor (GM-CSF) is critically involved in development of organ-related autoimmune inflammatory diseases including experimental allergic encephalitis and collagen-induced arthritis. Roles of GM-CSF in the initiation and in the effector phase of the autoimmune response have been proposed. Our study was designed to investigate the mechanisms of GM-CSF in autoimmunity using a model of autoimmune heart inflammatory disease (myocarditis). The pathological sequel after immunization with heart myosin has been shown previously to depend on IL-1, IL-6, IL-23, and IL-17. We found that innate GM-CSF was critical for IL-6 and IL-23 responses by dendritic cells and generation of pathological Th17 cells in vivo. Moreover, GM-CSF promoted autoimmunity by enhancing IL-6–dependent survival of antigen specific CD4+ T cells. These results suggest a novel role for GM-CSF in promoting generation and maintenance of Th17 cells by regulation of IL-6 and IL-23 in vivo.
CD45 regulates retention, motility, and numbers of hematopoietic progenitors, and affects osteoclast remodeling of metaphyseal trabecules
Authors: Shivtiel Shoham , Kollet Orit , Lapid Kfir , Schajnovitz Amir , Goichberg Polina , Kalinkovich Alexander , Shezen Elias , Tesio Melania , Netzer Neta , Petit Isabelle , Sharir Amnon , Lapidot Tsvee
Published: September 2008

The CD45 phosphatase is uniquely expressed by all leukocytes, but its role in regulating hematopoietic progenitors is poorly understood. We show that enhanced CD45 expression on bone marrow (BM) leukocytes correlates with increased cell motility in response to stress signals. Moreover, immature CD45 knockout (KO) cells showed defective motility, including reduced homing (both steady state and in response to stromal-derived factor 1) and reduced granulocyte colony-stimulating factor mobilization. These defects were associated with increased cell adhesion mediated by reduced matrix metalloproteinase 9 secretion and imbalanced Src kinase activity. Poor mobilization of CD45KO progenitors by the receptor activator of nuclear factor κB ligand, and impaired modulation of the endosteal components osteopontin and stem cell factor, suggested defective osteoclast function. Indeed, CD45KO osteoclasts exhibited impaired bone remodeling and abnormal morphology, which we attributed to defective cell fusion and Src function. This led to irregular distribution of metaphyseal bone trabecules, a region enriched with stem cell niches. Consequently, CD45KO mice had less primitive cells in the BM and increased numbers of these cells in the spleen, yet with reduced homing and repopulation potential. Uncoupling environmental and intrinsic defects in chimeric mice, we demonstrated that CD45 regulates progenitor movement and retention by influencing both the hematopoietic and nonhematopoietic compartments.
Early growth response gene 2 (Egr-2) controls the self-tolerance of T cells and prevents the development of lupuslike autoimmune disease
Authors: Zhu Bo , Symonds Alistair L.J. , Martin Joanne E. , Kioussis Dimitris , Wraith David C. , Li Suling , Wang Ping
Published: September 2008

Maintaining tolerance of T cells to self-antigens is essential to avoid autoimmune disease. How self-reactive T cells are kept functionally inactive is, however, unknown. In this study, we show that early growth response gene 2 (Egr-2), a zinc-finger transcription factor, is expressed in CD44high T cells and controls their proliferation and activation. In the absence of Egr-2, CD44high, but not CD44low T cells, are hyperreactive and hyperproliferative in vivo. The accumulation of activated CD4+CD44high T cells leads to the development of a late onset lupuslike autoimmune disease characterized by the accumulation of interferon (IFN)-γ and interleukin (IL)-17–producing CD4+ T cells, loss of tolerance to nuclear antigens, massive infiltration of T cells into multiple organs and glomerulonephritis. We found that the expression of cyclin-dependent kinase inhibitor p21cip1 was impaired in Egr-2–deficient T cells, whereas the expression of IFN-γ and IL-17 in response to T cell receptor ligation was significantly increased, suggesting that Egr-2 activates the expression of genes involved in the negative regulation of T cell proliferation and inflammation. These results demonstrate that Egr-2 is an intrinsic regulator of effector T cells and controls the expansion of self-reactive T cells and development of autoimmune disease.
Delayed protection by ESAT-6–specific effector CD4+ T cells after airborne M. tuberculosis infection
Authors: Gallegos Alena M. , Pamer Eric G. , Glickman Michael S.
Published: September 2008

Mycobacterium tuberculosis infection induces complex CD4 T cell responses that include T helper type 1 (Th1) cells and regulatory T cells. Although Th1 cells control infection, they are unable to fully eliminate M. tuberculosis, suggesting that Th1-mediated immunity is restrained from its full sterilizing potential. Investigation into T cell–mediated defense is hindered by difficulties in expanding M. tuberculosis–specific T cells. To circumvent this problem, we cloned CD4+ T cells from M. tuberculosis–infected B6 mice and generated transgenic mice expressing a T cell receptor specific for the immunodominant antigen early secreted antigenic target 6 (ESAT-6). Adoptively transferred naive ESAT-6–specific CD4+ T cells are activated in pulmonary lymph nodes between 7 and 10 d after aerosol infection and undergo robust expansion before trafficking to the lung. Adoptive transfer of activated ESAT-6–specific Th1 cells into naive recipients before aerosol M. tuberculosis infection dramatically enhances resistance, resulting in 100-fold fewer bacteria in infected lungs. However, despite large numbers of Th1 cells in the lungs of mice at the time of M. tuberculosis challenge, protection was not manifested until after 7 d following infection. Our results demonstrate that pathogen-specific Th1 cells can provide protection against inhaled M. tuberculosis, but only after the first week of infection.
OmicsViz: Cytoscape plug-in for visualizing omics data across species
Authors: Xia Tian , Dickerson Julie A.
Published: September 2008

Motivation: OmicsViz is a Cytoscape plug-in for mapping and visualizing large-scale omics datasets across species, including those with many-to-many mappings between homologs. This allows users to map their data onto pathways of related model organisms. Mapping schemas across species or different experimental protocols allow users to comparatively analyze the omics data. The data can also be visualized in parallel-coordinate plots.

Availability: The latest version of OmicsViz with documentation, tutorial and jar files can be downloaded from http://metnet.vrac.iastate.edu/MetNet_fcmodeler.htm

Contact:  julied@iastate.edu
Predicting gene targets of perturbations via network-based filtering of mRNA expression compendia
Authors: Cosgrove Elissa J. , Zhou Yingchun , Gardner Timothy S. , Kolaczyk Eric D.
Published: September 2008

Motivation: DNA microarrays are routinely applied to study diseased or drug-treated cell populations. A critical challenge is distinguishing the genes directly affected by these perturbations from the hundreds of genes that are indirectly affected. Here, we developed a sparse simultaneous equation model (SSEM) of mRNA expression data and applied Lasso regression to estimate the model parameters, thus constructing a network model of gene interaction effects. This inferred network model was then used to filter data from a given experimental condition of interest and predict the genes directly targeted by that perturbation.

Results: Our proposed SSEM–Lasso method demonstrated substantial improvement in sensitivity compared with other tested methods for predicting the targets of perturbations in both simulated datasets and microarray compendia. In simulated data, for two different network types, and over a wide range of signal-to-noise ratios, our algorithm demonstrated a 167% increase in sensitivity on average for the top 100 ranked genes, compared with the next best method. Our method also performed well in identifying targets of genetic perturbations in microarray compendia, with up to a 24% improvement in sensitivity on average for the top 100 ranked genes. The overall performance of our network-filtering method shows promise for identifying the direct targets of genetic dysregulation in cancer and disease from expression profiles.

Availability: Microarray data are available at the Many Microbe Microarrays Database (M3D, http://m3d.bu.edu). Algorithm scripts are available at the Gardner Lab website (http://gardnerlab.bu.edu/SSEMLasso).

Contact:  kolaczyk@math.bu.edu

Supplementary information:  Supplementary Data are available at Bioinformatics on line.
The role of closed areas in rebuilding monkfish populations in the Gulf of Maine
Authors: Smith Melissa D. , Grabowski Jonathan H. , Yund Philip O.
Published: September 2008

Smith, M. D., Grabowski, J. H., and Yund, P. O. 2008. The role of closed areas in rebuilding monkfish populations in the Gulf of Maine. – ICES Journal of Marine Science, 65: 1326–1333. The use of fish closures as a management tool to protect juvenile fish habitat and adult spawning grounds has become increasingly popular, although knowledge of the direct effects of marine closures on juvenile fish populations is limited. Given that monkfish landings account for a considerable percentage of the monetary value derived from the groundfish fishery in new England, investigating the factors that influence monkfish population dynamics will assist managers in sustaining this important natural resource. We conducted bottom-trawl surveys to determine the effects of closure status [inside vs. outside the Western Gulf of Maine Closure Area (WGMCA)] and habitat type (mud bottom in isolation from gravel or cobble bottom vs. mud that is next to these more complex habitats) on the distribution, abundance, and diet composition of monkfish (Lophius americanus) in the Gulf of Maine. Surprisingly, the abundance of adult monkfish did not differ in vs. out of the closure, and juvenile monkfish were more abundant outside of the WGMCA, where they also exhibited higher feeding intensity and consumed more prey biomass. Monkfish diet and condition results implied that the boulder and ledge bottom is essential monkfish habitat and that these effects were independent of the WGMCA.
Descriptors from Posidonia oceanica (L.) Delile meadows in coastal waters of Valencia, Spain, in the context of the EU Water Framework Directive
Authors: Fernández-Torquemada Yolanda , Díaz-Valdés Marta , Colilla Francisco , Luna Beatriz , Sánchez-Lizaso José Luis , Ramos-Esplá Alfonso A.
Published: September 2008

Fernández-Torquemada, Y., Díaz-Valdés, M., Colilla, F., Luna, B., Sánchez-Lizaso, J. L., and Ramos-Esplá, A. A. 2008. Descriptors from Posidonia oceanica (L.) Delile meadows in coastal waters of Valencia, Spain, in the context of the EU Water Framework Directive. – ICES Journal of Marine Science, 65: 1492–1497. Evaluations are provided of 21 descriptors of Posidonia oceanica meadows along the coast of Valencia, Spain, with a view to using these in implementing the European Water Framework Directive (WFD). The descriptors selected are known to respond to a variety of anthropogenic disturbances. Data were collected at 17 locations during three consecutive years. A principal components analysis was used to classify the ecological status of each locality according to five classes as prescribed by the WFD. To identify the descriptors that contributed most to similarity among localities within each class and to dissimilarity between adjacent classes, a similarity percentage analysis was performed. We also correlated the descriptors with an independent set of indicators for various types of anthropogenic pressures on the water bodies associated with the different localities. The descriptors providing the most consistent information on status as well as demonstrating a significant relationship with estimated pressures were: shoot density, shoot foliar surface, dead-matte cover, meadow cover, herbivore pressure, rhizome baring/burial, foliar necrosis, percentage of plagiotropic rhizomes, and leaf-epiphyte biomass.
Transmission ofGrapevine leafroll-associated virus3 by the Vine Mealybug (Planococcus ficus)
Authors: Tsai C.-W. , Chau J. , Fernandez L. , Bosco D. , Daane K. M. , Almeida R. P. P.
Published: September 2008

Grapevine leafroll disease is caused by grapevine leafroll-associated viruses (GLRaVs). Within this virus complex, GLRaV-3 is the predominant species in the world. Several GLRaVs have been shown to be transmitted from vine to vine by mealybugs although a detailed characterization of transmission biology is lacking. The introduction of the vine mealybug (Planococcus ficus) in California and other regions of the world may result in increasing disease incidence of established GLRaVs. We studied the characteristics of GLRaV-3 transmission by the vine mealybug. Our results indicate that the vine mealybug transmits GLRaV-3 in a semipersistent manner. First instars were more efficient vectors than adult mealybugs. GLRaV-3 transmission lacked a latent period in the vector. Virus transmission occurred with a 1-h acquisition access period (AAP) and peaked with a 24-h AAP. Mealybugs inoculated GLRaV-3 with a 1-h inoculation access period (IAP), and transmission efficiency increased with longer plant access period up to 24 h, after which transmission rate remained constant. After an AAP of 24 h, mealybugs lost GLRaV-3 and infectivity 4 days after virus acquisition. In addition, GLRaV-3 was not transovarially transmitted from infected females to their progeny as detected by reverse transcription polymerase chain reaction. In summary, we systematically analyzed transmission parameters of GLRaV-3 by the vine mealybug and showed that transmission of this virus occurs in a semipersistent manner. This research fills in important gaps in knowledge of leafroll virus transmission, which is critical for development of leafroll disease management practices.
Analysis of Expressed Sequence Tags fromUromyces appendiculatusHyphae and Haustoria and Their Comparison to Sequences from Other Rust Fungi
Authors: Puthoff D. P. , Neelam A. , Ehrenfried M. L. , Scheffler B. E. , Ballard L. , Song Q. , Campbell K. B. , Cooper B. , Tucker M. L.
Published: September 2008

Hyphae, 2 to 8 days postinoculation (dpi), and haustoria, 5 dpi, were isolated from Uromyces appendiculatus infected bean leaves (Phaseolus vulgaris cv. Pinto 111) and a separate cDNA library prepared for each fungal preparation. Approximately 10,000 hyphae and 2,700 haustoria clones were sequenced from both the 5′ and 3′ ends. Assembly of all of the fungal sequences yielded 3,359 contigs and 927 singletons. The U. appendiculatus sequences were compared with sequence data for other rust fungi, Phakopsora pachyrhizi, Uromyces fabae, and Puccinia graminis. The U. appendiculatus haustoria library included a large number of genes with unknown cellular function; however, summation of sequences of known cellular function suggested that haustoria at 5 dpi had fewer transcripts linked to protein synthesis in favor of energy metabolism and nutrient uptake. In addition, open reading frames in the U. appendiculatus data set with an N-terminal signal peptide were identified and compared with other proteins putatively secreted from rust fungi. In this regard, a small family of putatively secreted RTP1-like proteins was identified in U. appendiculatus and P. graminis.
Effects of Soil Temperature, Moisture, and Burial Depths on Carpogenic Germination ofSclerotinia sclerotiorumandS. minor
Authors: Wu B. M. , Subbarao K. V.
Published: September 2008

Extensive studies have been conducted on the carpogenic germination of Sclerotinia sclerotiorum, but carpogenic germination in S. minor has not been studied adequately. It remains unclear why apothecia of this pathogen have seldom been observed in nature. In this study, a new method was developed to produce apothecia in the absence of soil or sand, and carpogenic germination without preconditioning was recorded for 95 of the 96 S. sclerotiorum isolates tested. Carpogenic germination of the two species was compared under a variety of temperature, soil moisture, burial depths, and short periods of high temperature and low soil moisture. The optimal temperatures for rapid germination and for maximum germination rates were both lower for S. minor than for S. sclerotiorum. The temperature range for carpogenic germination was also narrower for S. minor than for S. sclerotiorum. A 5-day period at 30°C, either starting on the 10th or 20th day of incubation, did not significantly affect carpogenic germination of S. sclerotiorum. For both S. minor and S. sclerotiorum, the percentage of carpogenically germinated sclerotia increased as soil water potential increased from –0.3 to –0.01 MPa. In the greenhouse, a 10- or 20-day dry period completely arrested carpogenic germination of S. sclerotiorum, and new apothecia appeared after an interval of 35 days following rewetting, similar to the initial carpogenic germination regardless of when the dry period was imposed. In naturally infested fields, the number of sclerotia in 100 cc of soil decreased as depth increased from 0 to 10 cm before tillage, but became uniform between 0 and 10 cm after conventional tillage for both species. Most apothecia of S. minor were, however, produced from sclerotia located at a depth shallower than 0.5 cm while some apothecia of S. sclerotiorum were produced from sclerotia located as deep as 4 to 5 cm. These results provide the much needed information to assess the epidemiological roles of inoculum from sexual reproduction in diseases caused by the two Sclerotinia species in different geographical regions. However, more studies on effects of shorter and incompletely dry periods are still needed to predict production of apothecia of S. sclerotiorum in commercial fields under fluctuating soil temperature and moisture.
Extreme sequential polyandry insures against nest failure in a frog
Authors: Byrne Phillip G , Keogh J. Scott
Published: September 2008

Sequential polyandry may evolve as an insurance mechanism to reduce the risk of choosing a mate that is infertile, closely related, genetically inferior or incompatible, but polyandry also might insure against nest failure in unpredictable environments. Most animals are oviparous, and in species where males provide nest sites whose quality varies substantially and unpredictably, polyandrous females might insure offspring success by distributing their eggs across multiple nests. Here, we test this hypothesis in a wild population of an Australian terrestrial toadlet, a polyandrous species, where males construct nests and remain with broods. We found that females partitioned their eggs across the nests of two to eight males and that more polyandrous females gained a significant increase in mean offspring survivorship. Our results provide evidence for the most extreme case of sequential polyandry yet discovered in a vertebrate and also suggest that insurance against nest failure might favour the evolution of polyandry. We propose that insurance against nest failure might be widespread among oviparous taxa and provide an important explanation for the prevalence of sequential polyandry in nature.
Autumn leaves seen through herbivore eyes
Authors: Döring Thomas F , Archetti Marco , Hardie Jim
Published: September 2008

Why leaves of some trees turn red in autumn has puzzled biologists for decades, as just before leaf fall the pigments causing red coloration are newly synthesized. One idea to explain this apparently untimely investment is that red colour signals the tree's quality to herbivorous insects, particularly aphids. However, it is unclear whether red leaves are indeed less attractive to aphids than green leaves. Because aphids lack a red photoreceptor, it was conjectured that red leaves could even be indiscernable from green ones for these insects. Here we show, however, that the colour of autumnal tree leaves that appear red to humans are on average much less attractive to aphids than green leaves, whereas yellow leaves are much more attractive. We conclude that, while active avoidance of red leaves by aphids is unlikely, red coloration in autumn could still be a signal of the tree's quality, or alternatively serve to mask the over-attractive yellow that is unveiled when the green chlorophyll is recovered from senescing leaves. Our study shows that in sensory ecology, receiver physiology alone is not sufficient to reveal the whole picture. Instead, the combined analysis of behaviour and a large set of natural stimuli unexpectedly shows that animals lacking a red photoreceptor may be able to differentiate between red and green leaves.
Aphid aerial density profiles are consistent with turbulent advection amplifying flight behaviours: abandoning the epithet ‘passive’
Authors: Reynolds Andy M , Reynolds Don R
Published: September 2008

Seminal field studies led by C. G. Johnson in the 1940s and 1950s showed that aphid aerial density diminishes with height above the ground such that the linear regression coefficient,b, of log density on log height provides a single-parameter characterization of the vertical density profile. This coefficient decreases with increasing atmospheric stability, ranging from −0.27 for a fully convective boundary layer to −2.01 for a stable boundary layer. We combined a well-established Lagrangian stochastic model of atmospheric dispersal with simple models of aphid behaviour in order to account for the range of aerial density profiles. We show that these density distributions are consistent with the aphids producing just enough lift to become neutrally buoyant when they are in updraughts and ceasing to produce lift when they are in downdraughts. This active flight behaviour in a weak flier is thus distinctly different from the aerial dispersal of seeds and wingless arthropods, which is passive once these organisms have launched into the air. The novel findings from the model indicate that the epithet ‘passive’ often applied to the windborne migration of small winged insects is misleading and should be abandoned. The implications for the distances traversed by migrating aphids under various boundary-layer conditions are outlined.
Experimental evidence for paternal effects on offspring growth rate in Arctic charr (
Salvelinus alpinus
)
Authors: Eilertsen Eirik Mack , Bårdsen Bård-Jørgen , Liljedal Ståle , Rudolfsen Geir , Folstad Ivar
Published: September 2008

Sexual selection theory predicts that females should choose males that signal viability and quality. However, few studies have found fitness benefits among females mating with highly ornamented males. Here, we use Arctic charr (
Salvelinus alpinus
), a teleost fish with no parental care, to investigate whether females could gain fitness benefits by mating with highly ornamented and large-sized males. Carotenoid-based coloration signalled by males during spawning is believed to be an indicator of good genes for this species. Paternal effects on offspring size (body length and dry body mass) were examined experimentally by crossing eggs and sperm
in vitro
from 12 females and 24 males in a split-brood design and raising larvae to 30 days past hatching. We clearly demonstrated that there was a relationship between offspring size and paternal coloration. However, a negative interaction between paternal length and coloration was evident for offspring length, indicating that positive effects of paternal coloration were only present for smaller males. Thus, the red spawning coloration of the male Arctic charr seems to be an indicator of good genes, but the effect of paternal coloration on offspring length, an indicator of ‘offspring quality’, is size dependent.
The evolution of superstitious and superstition-like behaviour
Authors: Foster Kevin R , Kokko Hanna
Published: September 2008

Superstitious behaviours, which arise through the incorrect assignment of cause and effect, receive considerable attention in psychology and popular culture. Perhaps owing to their seeming irrationality, however, they receive little attention in evolutionary biology. Here we develop a simple model to define the condition under which natural selection will favour assigning causality between two events. This leads to an intuitive inequality—akin to an amalgam of Hamilton's rule and Pascal's wager—-that shows that natural selection can favour strategies that lead to frequent errors in assessment as long as the occasional correct response carries a large fitness benefit. It follows that incorrect responses are the most common when the probability that two events are really associated is low to moderate: very strong associations are rarely incorrect, while natural selection will rarely favour making very weak associations. Extending the model to include multiple events identifies conditions under which natural selection can favour associating events that are never causally related. Specifically, limitations on assigning causal probabilities to pairs of events can favour strategies that lump non-causal associations with causal ones. We conclude that behaviours which are, or appear, superstitious are an inevitable feature of adaptive behaviour in all organisms, including ourselves.
Human-related processes drive the richness of exotic birds in Europe
Authors: Chiron François , Shirley Susan , Kark Salit
Published: September 2008

Both human-related and natural factors can affect the establishment and distribution of exotic species. Understanding the relative role of the different factors has important scientific and applied implications. Here, we examined the relative effect of human-related and natural factors in determining the richness of exotic bird species established across Europe. Using hierarchical partitioning, which controls for covariation among factors, we show that the most important factor is the human-related community-level propagule pressure (the number of exotic species introduced), which is often not included in invasion studies due to the lack of information for this early stage in the invasion process. Another, though less important, factor was the human footprint (an index that includes human population size, land use and infrastructure). Biotic and abiotic factors of the environment were of minor importance in shaping the number of established birds when tested at a European extent using 50×50 km2grid squares. We provide, to our knowledge, the first map of the distribution of exotic bird richness in Europe. The richest hotspot of established exotic birds is located in southeastern England, followed by areas in Belgium and The Netherlands. Community-level propagule pressure remains the major factor shaping the distribution of exotic birds also when tested for the UK separately. Thus, studies examining the patterns of establishment should aim at collecting the crucial and hard-to-find information on community-level propagule pressure or develop reliable surrogates for estimating this factor. Allowing future introductions of exotic birds into Europe should be reconsidered carefully, as the number of introduced species is basically the main factor that determines the number established.
The porcine fat mass and obesity associated (FTO) gene is associated with fat deposition in Italian Duroc pigs
Authors: Fontanesi L. , Scotti E. , Buttazzoni L. , Davoli R. , Russo V.
Published: September 2008

In humans, common variants in the fat mass and obesity associated (FTO) gene are associated with body mass index and obesity. Here we sequenced exon 4, parts of introns 3 and 4 and two portions of the 3′‐untranslated region of the porcine FTO gene in a panel of nine pigs of different breeds and identified three SNPs. Allele frequencies of the g.276T>G (AM931150) mutation were studied in seven pig breeds. This mutation was used to linkage‐map FTO to SSC6. Association analyses between the g.276T>G polymorphism and several traits [pH of semimembranosus muscle and estimated breeding values (EBV) for average daily gain, back fat thickness, lean cuts, ham weight and feed:gain ratio] were carried out in 257 sib‐tested Italian Large White pigs. Only feed:gain ratio showed P < 0.05. A selective genotyping approach was applied, analysing two extreme and divergent groups of Italian Large White pigs selected on the basis of back fat thickness EBV (50 with most positive and 50 with most negative values). Fisher’s exact test (two‐tailed) was not significant when comparing the allele frequencies of these two groups. The same approach was used in the Italian Duroc breed for which two extreme and divergent groups of animals were selected according to visible intermuscular fat EBV. Differences of allele frequencies between these two groups were highly significant (P < 0.00001, P < 0.001 and P < 0.0001, considering all animals or only two‐ or three‐generation unrelated animals respectively), indicating association between the analysed FTO marker and intermuscular fat deposition.
Silence of ClC‐3 chloride channel inhibits cell proliferation and the cell cycle via G1/S phase arrest in rat basilar arterial smooth muscle cells
Authors: Tang Y.‐B. , Liu Y.‐J. , Zhou J.‐G. , Wang G.‐L. , Qiu Q.‐Y. , Guan Y.‐Y.
Published: September 2008

Abstract.  Objectives: Previously, we have found that the ClC‐3 chloride channel is involved in endothelin‐1 (ET‐1)‐induced rat aortic smooth muscle cell proliferation. The present study was to investigate the role of ClC‐3 in cell cycle progression/distribution and the underlying mechanisms of proliferation. Materials and methods: Small interference RNA (siRNA) is used to silence ClC‐3 expression. Cell proliferation, cell cycle distribution and protein expression were measured or detected with cell counting, bromodeoxyuridine (BrdU) incorporation, Western blot and flow cytometric assays respectively. Results: ET‐1‐induced rat basilar vascular smooth muscle cell (BASMC) proliferation was parallel to a significant increase in endogenous expression of ClC‐3 protein. Silence of ClC‐3 by siRNA inhibited expression of ClC‐3 protein, prevented an increase in BrdU incorporation and cell number induced by ET‐1. Silence of ClC‐3 also caused cell cycle arrest in G0/G1 phase and prevented the cells’ progression from G1 to S phase. Knockdown of ClC‐3 potently inhibited cyclin D1 and cyclin E expression and increased cyclin‐dependent kinase inhibitors (CDKIs) p27KIP and p21CIP expression. Furthermore, ClC‐3 knockdown significantly attenuated phosphorylation of Akt and glycogen synthase kinase‐3β (GSK‐3β) induced by ET‐1. Conclusion: Silence of ClC‐3 protein effectively suppressed phosphorylation of the Akt/GSK‐3β signal pathway, resulting in down‐regulation of cyclin D1 and cyclin E, and up‐regulation of p27KIP and p21CIP. In these BASMCs, integrated effects lead to cell cycle G1/S arrest and inhibition of cell proliferation.
Human amnion‐derived mesenchymal stem cells are a potential source for uterine stem cell therapy
Authors: Han K. , Lee J. E. , Kwon S. J. , Park S. Y. , Shim S. H. , Kim H. , Moon J. H. , Suh C. S. , Lim H. J.
Published: September 2008

Abstract.  Objectives: Human amnion is an easy‐to‐obtain novel source of human mesenchymal stem cells, which poses little or no ethical dilemmas. We have previously shown that human amnion‐derived mesenchymal (HAM) cells exhibit certain mesenchymal stem cell‐like characteristics with respect to expression of stem cell markers and differentiation potentials. Materials and methods: In this study, we further characterized HAM cells’ potential for in vivo therapeutic application. Results: Flow cytometric analyses of HAM cells show that they express several stem cell‐related cell surface markers, including CD90, CD105, CD59, CD49d, CD44 and HLA‐ABC, but not CD45, CD34, CD31, CD106 or HLA‐DR. HAM cells at the 10th passage showed normal karyotype. More interestingly, the AbdB‐like HOXA genes HOXA9, HOXA10 and HOXA11 that are expressed in the mesenchyme of the developing female reproductive tract and pregnant uteri are also expressed in HAM cells, suggesting similarities between these two mesenchymal cell types. Progesterone receptor is also highly expressed in HAM cells and expression of genes or proteins in HAM cells could be manipulated with the aid of lentivirus technology or cell‐permeable peptides. To test potentials of HAM cells for in vivo application, we introduced enhanced green fluorescence protein (EGFP)‐expressing HAM cells to mice by intrauterine infusion (into uteri) or by intravenous injection (into the circulation). Presence of EGFP‐expressing cells within the uterine mesenchyme after intrauterine infusion or in lungs after intravenous injection was noted within 1–4 weeks. Conclusions: Collectively, these results suggest that HAM cells are a potential source of mesenchymal stem cells with therapeutic potential.
Street‐level bureaucracy and family group decision making in the USA
Authors: Vesneski William
Published: September 2008

Since its official recognition in New Zealand law in 1989, family group decision making (FGDM) has been utilized by a growing number of child welfare workers throughout the world. In the USA, social workers in 35 states utilize FGDM. The seeming popularity of the practice, however, belies its complex position in American child welfare policy. This brief analytic essay examines this position by focusing on the relationship between street‐level bureaucracy and FGDM. Specifically, it describes the role of street‐level bureaucracy in FGDM's diffusion throughout the USA during a time of considerable policy skepticism towards family support, and it explains the dilution of the FGDM model through use of street‐level bureaucracy theory. The essay concludes by raising important policy questions concerning the use and replication of FGDM in the USA.
Measurement of solid phase permittivity for volcanic soils by time domain reflectometry
Authors: Kameyama K. , Miyamoto T.
Published: September 2008

Dielectric properties of soils are widely used to estimate their water content. Andisols are unique soils in terms of aggregate structure and show dielectric properties different from other mineral soils. To understand the relationship between the dielectric properties and soil physical properties, multi‐phase dielectric mixing models are often used. However, solid phase permittivity (ɛs) for Andisols, which is required for calculating the model output, has not been directly measured yet. Therefore, the objectives for this study were to measure ɛs for Andisols in Japan. In addition, the measured ɛs values were compared with those calculated from the traditional method, which applies two‐phase mixing models to estimate ɛs values based on effective permittivities of repacked soil samples. The applicability of the traditional method to estimate such values for Andisols is also discussed. The effects of bound water and aggregate structure on measured ɛs values were evaluated prior to their measurements. We found that the aggregate structural effects were negligible. However, the amount of bound water caused overestimates of ɛs. Four Andisols from the A and B horizons of soils in Memuro Hokkaido (northern part of Japan), from the A horizon of a soil in Tsukuba Ibaraki (central part of Japan), and from the A horizon of a soil in Koshi Kumamoto (southern part of Japan) were used in this study. The ɛs values obtained fall between 5.6 and 6.1, and deviated from the estimated ɛs values derived from the traditional method. Therefore, the traditional method is probably unsuitable to estimate ɛs values for Andisols.
UK National Clinical Guidelines in Paediatric Dentistry: stainless steel preformed crowns for primary molars
Authors: KINDELAN S. A. , DAY P. , NICHOL R. , WILLMOTT N. , FAYLE S. A.
Published: September 2008

This revised Clinical Guideline in Paediatric Dentistry replaces the previously published sixth guideline (Fayle SA. Int J Paediatr Dent 1999; 9: 311–314). The process of guideline production began in 1994, resulting in first publication in 1997. Each guideline has been circulated widely for consultation to all UK consultants in paediatric dentistry, council members of the British Society of Paediatric Dentistry (BSPD), and to people of related specialities recognized to have expertise in the subject. The final version of this guideline is produced from a combination of this input and thorough review of the published literature. The intention is to encourage improvement in clinical practice and to stimulate research and clinical audit in areas where scientific evidence is inadequate. Evidence underlying recommendations is scored according to the SIGN classification and guidelines should be read in this context. Further details regarding the process of paediatric dentistry guideline production in the UK is described in the Int J Paediatr Dent 1997; 7: 267–268.
New strategies for the control of arthropod vectors of disease in dogs and cats
Authors: OTRANTO D. , WALL R.
Published: September 2008

AbstractArthropod‐borne diseases (ABDs) in cats and dogs have a major impact on animal health and welfare and, in many cases, also on human health. Many ABDs are expected to increase in prevalence as a result of changing social habits, habitat modifications, introductions of exotic vectors and climate change. Control has, historically, focused on the use of insecticides and chemotherapy. We review alternative, emerging approaches to ABDs that currently offer promise, particularly modelling and molecular techniques and the development of novel vaccines that target molecules produced by arthropods during the bloodmeal. We argue that there is an urgent need to establish effective surveillance systems for most ABDs across various countries in order to facilitate a detailed risk analysis, which should include evaluation of potential spread to new areas and the possible introduction of new exotic species or disease agents. This will require clear and exhaustive knowledge on the distribution of ABDs in different areas, understanding of the diagnostic limitations pertaining to ABDs and standardization of techniques among reference laboratories in different countries. Continuous monitoring of insecticide resistance and the development of management strategies to minimize its onset are also essential. Ultimately, it is probable that approaches which attempt to reduce vector abundance or treat hosts with chemotherapy alone are unlikely to be effective in the long term. More suitable approaches may include greater use of a range of mutually compatible options in integrated management programmes.
σ54‐RNA polymerase controls σ70‐dependent transcription from a non‐overlapping divergent promoter
Authors: Johansson Linda U. M. , Solera Dafne , Bernardo Lisandro M. D. , Moscoso Joana A. , Shingler Victoria
Published: September 2008

Divergent transcription of a regulatory gene and a cognate promoter under its control is a common theme in bacterial regulatory circuits. This genetic organization is found for the dmpR gene that encodes the substrate‐responsive specific regulator of the σ54‐dependent Po promoter, which controls (methyl)phenol catabolism. Here we identify the Pr promoter of dmpR as a σ70‐dependent promoter that is regulated by a novel mechanism in which σ54‐RNA polymerase occupancy of the non‐overlapping σ54‐Po promoter stimulates σ70‐Pr output. In addition, we show that DmpR stimulates its own production through Po activity both in vivo and in vitro. Hence, the demonstrated regulatory circuit reveals a novel role for σ54‐RNA polymerase, namely regulation of a σ70‐dependent promoter, and a new mechanism that places a single promoter under dual control of two alternative forms of RNA polymerase. We present a model in which guanosine tetra‐phosphate plays a major role in the interplay between σ54‐ and σ70‐dependent transcription to ensure metabolic integration to couple σ70‐Pr output to both low‐energy conditions and the presence of substrate.
Compensatory thio–redox interactions between DsbA, CcdA and CcmG unveil the apocytochrome c holdase role of CcmG during cytochrome c maturation
Authors: Turkarslan Serdar , Sanders Carsten , Ekici Seda , Daldal Fevzi
Published: September 2008

During cytochrome c maturation (Ccm), the DsbA‐dependent thio‐oxidative protein‐folding pathway is thought to introduce a disulphide bond into the haem‐binding motif of apocytochromes c. This disulphide bond is believed to be reduced through a thio‐reductive pathway involving the Ccm components CcdA (DsbD), CcmG and CcmH. Here, we show in Rhodobacter capsulatus that in the absence of DsbA cytochrome c levels were decreased and CcdA or CcmG or the putative glutathione transporter CydDC was not needed for Ccm. This decrease was not due to overproduction of the periplasmic protease DegP as a secondary effect of DsbA absence. In contrast, CcmH was absolutely necessary regardless of DsbA, indicating that compensatory thio–redox interactions excluded it. Remarkably, the double (DsbA–CcmG) and triple (DsbA–CcmG–CcdA) mutants produced cytochromes c at lower levels than the DsbA‐null mutants, unless they contained a CcmG derivative (CcmG*) lacking its thio‐reductive activity. Purified CcmG* can bind apocytochrome c in vitro, revealing for the first time a thiol‐independent, direct interaction between apocytochrome c and CcmG. Furthermore, elimination of the thio–redox components does not abolish cytochrome c production, restricting the number of Ccm components essential for haem–apocyt c ligation per se during Ccm.
Antibodies elicited by the secretions from schistosome cercariae and eggs are predominantly against glycan epitopes
Authors: KARIUKI T. M. , FARAH I. O. , WILSON R. A. , COULSON P. S.
Published: September 2008

The glycoproteins secreted by Schistosoma mansoni cercariae and eggs play a key role in parasite transmission to and from the mammalian host. We used secreted preparations from these two life cycle stages to characterize the reactivity of sera from baboons exposed to normal and/or attenuated cercariae, in comparison with somatic antigen preparations and defined glycan epitopes. Periodate treatment of native antigens revealed that responses to the two secreted preparations were overwhelmingly directed against glycans rather than peptides. Considerable immunological cross‐reactivity between glycans in the two preparations was inferred from a comparison of sera from infected‐only and vaccinated‐only animals, predominantly exposed to egg and cercarial secretions, respectively. In contrast, when somatic antigen preparations derived from adult worms or eggs were used to probe sera, a stronger antipeptide response was seen that accounted for up to 66% of maximum reactivity. Probing of sera with defined glycan structures confirmed the time course of responses and the presence of cross‐reactive epitopes. In spite of the intense antiglycan response elicited in mice by administration of live eggs, no protection against a cercarial challenge was observed. Our data further support the hypothesis that antiglycan responses are a smokescreen with negligible protective potential.