bluuebunny/crossref_metadata_2025 huggingface dataset:
Analyses of the Extent of Shared Synteny and Conserved Gene Orders between the Genome of Fugu rubripes and Human 20q
Authors: Smith Sarah F. , Snell Philip , Gruetzner Frank , Bench Anthony J. , Haaf Thomas , Metcalfe Judith A. , Green Anthony R. , Elgar Greg
Published: July 2008

Cosmid and BAC contig maps have been constructed across twoFugu genomic regions containing the orthologs of human genes mapping to human chromosome 20q. Contig gene contents have been assessed by sample sequencing and comparative database analyses. Contigs are centered around two Fugu topoisomerase1 (top1) genes that were initially identified by sequence similarity to humanTOP1 (20q12). Two other genes (SNAI1 andKRML) mapping to human chromosome 20 are also duplicated inFugu. The two contigs have been mapped to separateFugu chromosomes. Our data indicate that these linkage groups result from the duplication of an ancestral chromosome segment containing at least 40 genes that now map to the long arm of human chromosome 20. Although there is considerable conservation of synteny, gene orders are not well conserved between Fugu and human, with only very short sections of two to three adjacent genes being maintained in both organisms. Comparative analyses have allowed this duplication event to be dated before the separation of Fuguand zebrafish. Our data (which are best explained by regional duplication, followed by substantial gene loss) support the hypothesis that there have been a large number of gene and regional duplications (and corresponding gene loss) in the fish lineage, possibly resulting from a single whole genome duplication event.

[Reagents, samples, and unpublished information freely provided by D. Barnes and I.D. Hickson.]
Single Nucleotide Polymorphism Mapping Using Genome-Wide Unique Sequences
Authors: Chen Leslie Y.Y. , Lu Szu-Hsien , Shih Edward S.C. , Hwang Ming-Jing
Published: July 2008

As more and more genomic DNAs are sequenced to characterize human genetic variations, the demand for a very fast and accurate method to genomically position these DNA sequences is high. We have developed a new mapping method that does not require sequence alignment. In this method, we first identified DNA fragments of 15 bp in length that are unique in the human genome and then used them to position single nucleotide polymorphism (SNP) sequences. By use of four desktop personal computers with AMD K7 (1 GHz) processors, our new method mapped more than 1.6 million SNP sequences in 20 hr and achieved a very good agreement with mapping results from alignment-based methods.
rVistafor Comparative Sequence-Based Discovery of Functional Transcription Factor Binding Sites
Authors: Loots Gabriela G. , Ovcharenko Ivan , Pachter Lior , Dubchak Inna , Rubin Edward M.
Published: July 2008

Identifying transcriptional regulatory elements represents a significant challenge in annotating the genomes of higher vertebrates. We have developed a computational tool,rVISTA, for high-throughput discovery ofcis-regulatory elements that combines clustering of predicted transcription factor binding sites (TFBSs) and the analysis of interspecies sequence conservation to maximize the identification of functional sites. To assess the ability ofrVISTAto discover true positive TFBSs while minimizing the prediction of false positives, we analyzed the distribution of several TFBSs across 1 Mb of the well-annotated cytokine gene cluster (Hs5q31; Mm11). Because a large number of AP-1, NFAT, and GATA-3 sites have been experimentally identified in this interval, we focused our analysis on the distribution of all binding sites specific for these transcription factors. The exploitation of the orthologous human–mouse dataset resulted in the elimination of >95% of the ∼58,000 binding sites predicted on analysis of the human sequence alone, whereas it identified 88% of the experimentally verified binding sites in this region.
Pattern of Organization of Human Mitochondrial Pseudogenes in the Nuclear Genome
Authors: Woischnik Markus , Moraes Carlos T.
Published: July 2008

Mitochondrial pseudogenes in the human nuclear genome have been previously described, mostly as a source of artifacts during the analysis of the mitochondrial genome. With the availability of the complete human genome sequence, we performed a comprehensive analysis of mtDNA insertions into the nucleus. We found 612 independent integrations that are evenly distributed among all chromosomes as well as within each individual chromosome. The identified pseudogenes account for a content of at least 0.016% of the human nuclear DNA. Up to 30% of a chromosome's mtDNA pseudogene content is composed of fragments that encompass two or more adjacent mitochondrial genes, and we found no correlation between the abundance of mitochondrial transcripts and the multiplicity of integrations. These observations indicate that the migrations of mitochondrial DNA sequences to the nucleus were predominantly DNA mediated. Phylogenetic analysis of the mtDNA pseudogenes and mtDNA sequences of primates indicate a continuous transfer into the nucleus. Because of the limited window of opportunity for mtDNA transfer to the germline, sperm mtDNA, which is released from degenerating mitochondria after fertilization, could be an important source of nuclear mtDNA pseudogenes.

[Online supplemental material available athttp://www.genome.org]
Multiplex Three-Dimensional Brain Gene Expression Mapping in a Mouse Model of Parkinson's Disease
Authors: Brown Vanessa M. , Ossadtchi Alex , Khan Arshad H. , Yee Simon , Lacan Goran , Melega William P. , Cherry Simon R. , Leahy Richard M. , Smith Desmond J.
Published: July 2008

To facilitate high-throughput 3D imaging of brain gene expression, a new method called voxelation has been developed. Spatially registered voxels (cubes) are analyzed, resulting in multiple volumetric maps of gene expression analogous to the images reconstructed in biomedical imaging systems. Using microarrays, 40 voxel images for 9000 genes were acquired from brains of both normal mice and mice in which a pharmacological model of Parkinson's disease (PD) had been induced by methamphetamine. Quality-control analyses established the reproducibility of the voxelation procedure. The investigation revealed a common network of coregulated genes shared between the normal and PD brain, and allowed identification of putative control regions responsible for these networks. In addition, genes involved in cell/cell interactions were found to be prominently regulated in the PD brains. Finally, singular value decomposition (SVD), a mathematical method used to provide parsimonious explanations of complex data sets, identified gene vectors and their corresponding images that distinguished between normal and PD brain structures, most pertinently the striatum.

[All study results and supplementary data are available on the web athttp://www.pharmacology.ucla.edu/smithlab/genome_multiplex and athttp://www.genome.org. Microarray data are also available at GEO,http://www.ncbi.nlm.nih.gov/geo, under the series accession no. GSE30.]
The Human Genome Browser at UCSC
Authors: Kent W. James , Sugnet Charles W. , Furey Terrence S. , Roskin Krishna M. , Pringle Tom H. , Zahler Alan M. , Haussler and David
Published: July 2008

As vertebrate genome sequences near completion and research refocuses to their analysis, the issue of effective genome annotation display becomes critical. A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided athttp://genome.ucsc.edu. This browser displays assembly contigs and gaps, mRNA and expressed sequence tag alignments, multiple gene predictions, cross-species homologies, single nucleotide polymorphisms, sequence-tagged sites, radiation hybrid data, transposon repeats, and more as a stack of coregistered tracks. Text and sequence-based searches provide quick and precise access to any region of specific interest. Secondary links from individual features lead to sequence details and supplementary off-site databases. One-half of the annotation tracks are computed at the University of California, Santa Cruz from publicly available sequence data; collaborators worldwide provide the rest. Users can stably add their own custom tracks to the browser for educational or research purposes. The conceptual and technical framework of the browser, its underlying MYSQL database, and overall use are described. The web site currently serves over 50,000 pages per day to over 3000 different users.
BLAT—The BLAST-Like Alignment Tool
Authors: Kent W. James
Published: July 2008

Analyzing vertebrate genomes requires rapid mRNA/DNA and cross-species protein alignments. A new tool, BLAT, is more accurate and 500 times faster than popular existing tools for mRNA/DNA alignments and 50 times faster for protein alignments at sensitivity settings typically used when comparing vertebrate sequences. BLAT's speed stems from an index of all nonoverlapping K-mers in the genome. This index fits inside the RAM of inexpensive computers, and need only be computed once for each genome assembly. BLAT has several major stages. It uses the index to find regions in the genome likely to be homologous to the query sequence. It performs an alignment between homologous regions. It stitches together these aligned regions (often exons) into larger alignments (typically genes). Finally, BLAT revisits small internal exons possibly missed at the first stage and adjusts large gap boundaries that have canonical splice sites where feasible. This paper describes how BLAT was optimized. Effects on speed and sensitivity are explored for various K-mer sizes, mismatch schemes, and number of required index matches. BLAT is compared with other alignment programs on various test sets and then used in several genome-wide applications. http://genome.ucsc.edu hosts a web-basedBLAT server for the human genome.
Long-Range Heterogeneity at the 3′ Ends of Human mRNAs
Authors: Iseli Christian , Stevenson Brian J. , de Souza Sandro J. , Samaia Helena B. , Camargo Anamaria A. , Buetow Kenneth H. , Strausberg Robert L. , Simpson Andrew J.G. , Bucher Philipp , Jongeneel C. Victor
Published: July 2008

The publication of a draft of the human genome and of large collections of transcribed sequences has made it possible to study the complex relationship between the transcriptome and the genome. In the work presented here, we have focused on mapping mRNA 3′ ends onto the genome by use of the raw data generated by the expressed sequence tag (EST) sequencing projects. We find that at least half of the human genes encode multiple transcripts whose polyadenylation is driven by multiple signals. The corresponding transcript 3′ ends are spread over distances in the kilobase range. This finding has profound implications for our understanding of gene expression regulation and of the diversity of human transcripts, for the design of cDNA microarray probes, and for the interpretation of gene expression profiling experiments.

[The following individuals kindly provided reagents, samples or unpublished information as indicated in the paper: G. Riggins, C. Ruegg, J.-B. Demoulin, P. Olsson, F. Funari, P. Schneider, L.F. Reis, and J.-C. Renauld]
A Computer-Based Method of Selecting Clones for a Full-Length cDNA Project: Simultaneous Collection of Negligibly Redundant and Variant cDNAs
Authors: Osato Naoki , Itoh Masayoshi , Konno Hideaki , Kondo Shinji , Shibata Kazuhiro , Carninci Piero , Shiraki Toshiyuki , Shinagawa Akira , Arakawa Takahiro , Kikuchi Shoshi , Sato Kouji , Kawai Jun , Hayashizaki Yoshihide
Published: July 2008

We describe a computer-based method that selects representative clones for full-length sequencing in a full-length cDNA project. Our method classifies end sequences using two kinds of criteria, grouping, and clustering. Grouping places together variant cDNAs, family genes, and cDNAs with sequencing errors. Clustering separates those cDNA clones into distinct clusters. The full-length sequences of the clones selected by grouping are determined preferentially, and then the sequences selected by clustering are determined. Grouping reduced the number of rice cDNA clones for full-length sequencing to 21% and mouse cDNA clones to 25%. Rice full-length sequences selected by grouping showed a 1.07-fold redundancy. Mouse full-length sequences showed a 1.04-fold redundancy, which can be reduced by ∼30% from the selection using our previous method. To estimate the coverage of unique genes, we used FANTOM (Functional Annotation of RIKEN Mouse cDNA Clones) clusters (the RIKEN Genome Exploration Research Group 2001). Grouping covered almost all unique genes (93% of FANTOM clusters), and clustering covered all genes. Therefore, our method is useful for the selection of appropriate representative clones for full-length sequencing, thereby greatly reducing the cost, labor, and time necessary for this process.

[The programs used in this paper are available online at http://genome.gsc.riken.go.jp/software/2C.]
Essential Genes Are More Evolutionarily Conserved Than Are Nonessential Genes in Bacteria
Authors: Jordan I. King , Rogozin Igor B. , Wolf Yuri I. , Koonin Eugene V.
Published: July 2008

The “knockout-rate” prediction holds that essential genes should be more evolutionarily conserved than are nonessential genes. This is because negative (purifying) selection acting on essential genes is expected to be more stringent than that for nonessential genes, which are more functionally dispensable and/or redundant. However, a recent survey of evolutionary distances between Saccharomyces cerevisiae and Caenorhabditis elegans proteins did not reveal any difference between the rates of evolution for essential and nonessential genes. An analysis of mouse and rat orthologous genes also found that essential and nonessential genes evolved at similar rates when genes thought to evolve under directional selection were excluded from the analysis. In the present study, we combine genomic sequence data with experimental knockout data to compare the rates of evolution and the levels of selection for essential versus nonessential bacterial genes. In contrast to the results obtained for eukaryotic genes, essential bacterial genes appear to be more conserved than are nonessential genes over both relatively short (microevolutionary) and longer (macroevolutionary) time scales.
Functional Analysis of Arabidopsis Postprenylation CaaX Processing Enzymes and Their Function in Subcellular Protein Targeting
Authors: Bracha-Drori Keren , Shichrur Keren , Lubetzky Tsofnat Cohen , Yalovsky Shaul
Published: July 2008

Prenylation is a posttranslational protein modification essential for developmental processes and response to abscisic acid. Following prenylation, the three C-terminal residues are proteoliticaly removed and in turn the free carboxyl group of the isoprenyl cysteine is methylated. The proteolysis and methylation, collectively referred to as CaaX processing, are catalyzed by Ste24 endoprotease or Rce1 endoprotease and by an isoprenyl cysteine methyltransferase (ICMT). Arabidopsis (Arabidopsis thaliana) contains single STE24 and RCE1 and two ICMT homologs. Here we show that in yeast (Saccharomyces cerevisiae) AtRCE1 promoted a-mating factor secretion and membrane localization of a ROP GTPase. Furthermore, green fluorescent protein fusion proteins of AtSTE24, AtRCE1, AtICMTA, and AtICMTB are colocalized in the endoplasmic reticulum, indicating that prenylated proteins reach this compartment and that CaaX processing is likely required for subcellular targeting. AtICMTB can process yeast a-factor more efficiently than AtICMTA. Sequence and mutational analyses revealed that the higher activity AtICMTB is conferred by five residues, which are conserved between yeast Ste14p, human ICMT, and AtICMTB but not in AtICMTA. Quantitative real-time reverse transcription-polymerase chain reaction and microarray data show that AtICMTA expression is significantly lower compared to AtICMTB. AtICMTA null mutants have a wild-type phenotype, indicating that its function is redundant. However, AtICMT RNAi lines had fasciated inflorescence stems, altered phylotaxis, and developed multiple buds without stem elongation. The phenotype of the ICMT RNAi lines is similar to farnesyltransferase β-subunit mutant enhanced response to abscisic acid2 but is more subtle. Collectively, the data suggest that AtICMTB is likely the major ICMT and that methylation modulates activity of prenylated proteins.
Monogalactosyldiacylglycerol Deficiency in Arabidopsis Affects Pigment Composition in the Prolamellar Body and Impairs Thylakoid Membrane Energization and Photoprotection in Leaves
Authors: Aronsson Henrik , Schöttler Mark A. , Kelly Amélie A. , Sundqvist Christer , Dörmann Peter , Karim Sazzad , Jarvis Paul
Published: July 2008

Monogalactosyldiacylglycerol (MGDG) is the major lipid constituent of chloroplast membranes and has been proposed to act directly in several important plastidic processes, particularly during photosynthesis. In this study, the effect of MGDG deficiency, as observed in the monogalactosyldiacylglycerol synthase1-1 (mgd1-1) mutant, on chloroplast protein targeting, phototransformation of pigments, and photosynthetic light reactions was analyzed. The targeting of plastid proteins into or across the envelope, or into the thylakoid membrane, was not different from wild-type in the mgd1 mutant, suggesting that the residual amount of MGDG in mgd1 was sufficient to maintain functional targeting mechanisms. In dark-grown plants, the ratio of bound protochlorophyllide (Pchlide, F656) to free Pchlide (F631) was increased in mgd1 compared to the wild type. Increased levels of the photoconvertible pigment-protein complex (F656), which is photoprotective and suppresses photooxidative damage caused by an excess of free Pchlide, may be an adaptive response to the mgd1 mutation. Leaves of mgd1 suffered from a massively impaired capacity for thermal dissipation of excess light due to an inefficient operation of the xanthophyll cycle; the mutant contained less zeaxanthin and more violaxanthin than wild type after 60 min of high-light exposure and suffered from increased photosystem II photoinhibition. This is attributable to an increased conductivity of the thylakoid membrane at high light intensities, so that the proton motive force is reduced and the thylakoid lumen is less acidic than in wild type. Thus, the pH-dependent activation of the violaxanthin de-epoxidase and of the PsbS protein is impaired.
Induced Plant Defenses in the Natural Environment:Nicotiana attenuataWRKY3 and WRKY6 Coordinate Responses to Herbivory
Authors: Skibbe Melanie , Qu Nan , Galis Ivan , Baldwin Ian T.
Published: July 2008

A plant-specific family of WRKY transcription factors regulates plant responses to pathogens and abiotic stresses. Here, we identify two insect-responsive WRKY genes in the native tobacco Nicotiana attenuata: WRKY3, whose transcripts accumulate in response to wounding, and WRKY6, whose wound responses are significantly amplified when fatty acid–amino acid conjugates (FACs) in larval oral secretions are introduced into wounds during feeding. WRKY3 is required for WRKY6 elicitation, yet neither is elicited by treatment with the phytohormone wound signal jasmonic acid. Silencing either WRKY3 or WRKY6, or both, by stable transformation makes plants highly vulnerable to herbivores under glasshouse conditions and in their native habitat in the Great Basin Desert, Utah, as shown in three field seasons. This susceptibility is associated with impaired jasmonate (JA) accumulation and impairment of the direct (trypsin proteinase inhibitors) and indirect (volatiles) defenses that JA signaling mediates. The response to wounding and herbivore-specific signals (FACs) demonstrates that these WRKYs help plants to differentiate mechanical wounding from herbivore attack, mediating a plant's herbivore-specific defenses. Differences in responses to single and multiple elicitations indicate an important role of WRKY3 and WRKY6 in potentiating and/or sustaining active JA levels during continuous insect attack.
SCREAM/ICE1andSCREAM2Specify Three Cell-State Transitional Steps Leading toArabidopsisStomatal Differentiation
Authors: Kanaoka Masahiro M. , Pillitteri Lynn Jo , Fujii Hiroaki , Yoshida Yuki , Bogenschutz Naomi L. , Takabayashi Junji , Zhu Jian-Kang , Torii Keiko U.
Published: July 2008

Differentiation of specialized cell types in multicellular organisms requires orchestrated actions of cell fate determinants. Stomata, valves on the plant epidermis, are formed through a series of differentiation events mediated by three closely related basic-helix-loop-helix proteins: SPEECHLESS (SPCH), MUTE, and FAMA. However, it is not known what mechanism coordinates their actions. Here, we identify two paralogous proteins, SCREAM (SCRM) and SCRM2, which directly interact with and specify the sequential actions of SPCH, MUTE, and FAMA. The gain-of-function mutation in SCRM exhibited constitutive stomatal differentiation in the epidermis. Conversely, successive loss of SCRM and SCRM2 recapitulated the phenotypes of fama, mute, and spch, indicating that SCRM and SCRM2 together determined successive initiation, proliferation, and terminal differentiation of stomatal cell lineages. Our findings identify the core regulatory units of stomatal differentiation and suggest a model strikingly similar to cell-type differentiation in animals. Surprisingly, map-based cloning revealed that SCRM is INDUCER OF CBF EXPRESSION1, a master regulator of freezing tolerance, thus implicating a potential link between the transcriptional regulation of environmental adaptation and development in plants.
Population structure of the parasitic nematodeAnguillicola crassus, an invader of declining North Atlantic eel stocks
Authors: WIELGOSS SÉBASTIEN , TARASCHEWSKI HORST , MEYER AXEL , WIRTH THIERRY
Published: July 2008

Probably half of all animal species exhibit a parasitic lifestyle and numerous parasites have recently expanded their distribution and host ranges due to anthropogenic activities. Here, we report on the population genetic structure of the invasive nematodeAnguillicola crassus,a parasite in freshwater eels, which recently spread from Asia to Europe and North America. Samples were collected from the newly colonized naïve host speciesAnguilla anguilla(Europe) andAnguilla rostrata(North America), and from indigenousAnguilla japonicain Taiwan and Japan. Using seven microsatellite loci and one mitochondrial marker, we show that the parasite's population structure in Europe mirrors the zoogeographic Boreal–Lusitanian break along the English Channel. Both the north‐to‐south decline of nuclear allelic diversity and the loss of private alleles in the same direction are consistent with a significant isolation‐by‐distance pattern based on ρSTvalues. In combination with the specific topology of the distance tree among nematode populations, our data suggest that Europe was invaded only once from Taiwan, and that subsequently, genetic diversity was lost due to random drift. On the contrary, the North American sample shares distinct nuclear and mitochondrial signatures with Japanese specimens. We propose that the genetic structure in Europe was shaped by long‐range anthropogenic eel host transfers in the north and a single dispersal event into the southwest. The genetically distinct Brittany sample at the edge of the Boreal–Lusitanian boundary is indicative of natural dispersal of fish hosts since recruitment occurs naturally there and invertebrate host dissemination is interrupted due to oceanic currents.
The continental record of Ediacaran volcano‐sedimentary successions in southern Brazil and their global implications
Authors: Janikian Liliane , De Almeida Renato Paes , Da Trindade Ricardo Ivan Ferreira , Fragoso‐Cesar Antonio Romalino Santos , D′Agrella‐Filho Manoel Souza , Dantas Elton Luis , Tohver Eric
Published: July 2008

The Ediacaran is one of the most important periods on Earth evolution, including the first appearance of soft‐bodied macrofossils, major climatic changes and a supposed rise in free oxygen. In southernmost Brazil, this period is represented by Camaquã Supergroup, including the Bom Jardim Group and the Acampamento Velho Formation, both of which record continental palaeoenvironmental changes in a more than 5000 m thick stratigraphic succession. Age constraints are given by seven Ar‐Ar and U‐Pb determinations on volcanic rocks, which bracket these units between c. 605 and 574 Ma, revealing the best dated and most continuous documented Ediacaran continental succession to date. Depositional systems evolution supports a Phanerozoic‐type glacial context during the last Neoproterozoic glacial event and presents the Picada das Graças Formation (580 ± 3.6 Ma) as the first dated non‐glacial unit coeval to the Gaskiers Formation.
probeCheck – a central resource for evaluating oligonucleotide probe coverage and specificity
Authors: Loy Alexander , Arnold Roland , Tischler Patrick , Rattei Thomas , Wagner Michael , Horn Matthias
Published: July 2008

The web server probeCheck, freely accessible at http://www.microbial‐ecology.net/probecheck, provides a pivotal forum for rapid specificity and coverage evaluations of probes and primers against selected databases of phylogenetic and functional marker genes. Currently, 24 widely used sequence collections including the Ribosomal Database Project (RDP) II, Greengenes, SILVA and the Functional Gene Pipeline/Repository can be queried. For this purpose, probeCheck integrates a new online version of the popular ARB probe match tool with free energy (ΔG) calculations for each perfectly matched and mismatched probe‐target hybrid, allowing assessment of the theoretical binding stabilities of oligo‐target and non‐target hybrids. For each output sequence, the accession number, the GenBank taxonomy and a link to the respective entry at GenBank, EMBL and, if applicable, the query database are displayed. Filtering options allow customizing results on the output page. In addition, probeCheck is linked with probe match tools of RDP II and Greengenes, NCBI blast, the Oligonucleotide Properties Calculator, the two‐state folding tool of the DINAMelt server and the rRNA‐targeted probe database probeBase. Taken together, these features provide a multifunctional platform with maximal flexibility for the user in the choice of databases and options for the evaluation of published and newly developed probes and primers.
‘I WILL NOT CUT . . . ’: THE OATH THAT DEFINED UROLOGY
Authors: Herr Harry W.
Published: July 2008

OBJECTIVE

To explore different interpretations of the clause embedded in the Hippocratic Oath, prohibiting surgery for stones, and its relevance for urology.

METHODS

Various translations of the Oath, from the original Greek edition to historical revisions, were reviewed.

RESULTS

Controversy surrounds different translations and interpretations of the Oath about the practice of lithotomy among ancient healers. The reasons Hippocratic physicians were prohibited from performing lithotomy are several, but the consensus is that untrained physicians pledged not to undertake such a complicated procedure, but to refer their patients to other healers who specialized in that practice.

CONCLUSION

The Hippocratic Oath actually defined, identified and legitimized urology as the first medical speciality.
Recalibrating Color Categories Using World Knowledge
Authors: Mitterer Holger , de Ruiter Jan Peter
Published: July 2008

When the perceptual system uses color to facilitate object recognition, it must solve the color-constancy problem: The light an object reflects to an observer's eyes confounds properties of the source of the illumination with the surface reflectance of the object. Information from the visual scene (bottom-up information) is insufficient to solve this problem. We show that observers use world knowledge about objects and their prototypical colors as a source of top-down information to improve color constancy. Specifically, observers use world knowledge to recalibrate their color categories. Our results also suggest that similar effects previously observed in language perception are the consequence of a general perceptual process.
Vision Merges With Touch in a Purely Tactile Discrimination
Authors: Arabzadeh Ehsan , Clifford Colin W.G. , Harris Justin A.
Published: July 2008

To construct a coherent percept of the world, the brain continuously combines information across multiple sensory modalities. Simple stimuli from different modalities are usually assumed to be processed in distinct brain areas. However, there is growing evidence that simultaneous stimulation of multiple modalities can influence the activity in unimodal sensory areas and improve or impair performance in unimodal tasks. Do these effects reflect a genuine cross-modal integration of sensory signals, or are they due to changes in the perceiver's ability to locate the stimulus in time and space? We used a behavioral measure to differentiate between these explanations. Our results demonstrate that, under certain circumstances, a noninformative flash of light can have facilitative or detrimental effects on a simple tactile discrimination. The effect of the visual flash mimics that produced by a constant tactile pedestal stimulus. These findings reveal that sensory signals from different modalities can be integrated, even for perceptual judgments within a single modality.
“Perceptual Scotomas”
Authors: New Joshua J. , Scholl Brian J.
Published: July 2008

In motion-induced blindness (MIB), salient objects in full view can repeatedly fluctuate into and out of conscious awareness when superimposed onto certain global moving patterns. Here we suggest a new account of this striking phenomenon: Rather than being a failure of visual processing, MIB may be a functional product of the visual system's attempt to separate distal stimuli from artifacts of damage to the visual system itself. When a small object is invariant despite changes that are occurring to a global region of the surrounding visual field, the visual system may discount that stimulus as akin to a scotoma, and may thus expunge it from awareness. We describe three experiments demonstrating new phenomena predicted by this account and discuss how it can also explain several previous results.
Figure-Ground Segmentation Can Occur Without Attention
Authors: Kimchi Ruth , Peterson Mary A.
Published: July 2008

The question of whether or not figure-ground segmentation can occur without attention is unresolved. Early theorists assumed it can, but the evidence is scant and open to alternative interpretations. Recent research indicating that attention can influence figure-ground segmentation raises the question anew. We examined this issue by asking participants to perform a demanding change-detection task on a small matrix presented on a task-irrelevant scene of alternating regions organized into figures and grounds by convexity. Independently of any change in the matrix, the figure-ground organization of the scene changed or remained the same. Changes in scene organization produced congruency effects on target-change judgments, even though, when probed with surprise questions, participants could report neither the figure-ground status of the region on which the matrix appeared nor any change in that status. When attending to the scene, participants reported figure-ground status and changes to it highly accurately. These results clearly demonstrate that figure-ground segmentation can occur without focal attention.
If I'm Not Hot, Are You Hot or Not?
Authors: Lee Leonard , Loewenstein George , Ariely Dan , Hong James , Young Jim
Published: July 2008

Prior research has established that people's own physical attractiveness affects their selection of romantic partners. This article provides further support for this effect and also examines a different, yet related, question: When less attractive people accept less attractive dates, do they persuade themselves that the people they choose to date are more physically attractive than others perceive them to be? Our analysis of data from the popular Web site HOTorNOT.com suggests that this is not the case: Less attractive people do not delude themselves into thinking that their dates are more physically attractive than others perceive them to be. Furthermore, the results also show that males, compared with females, are less affected by their own attractiveness when choosing whom to date.
Statistical Learning Using Real-World Scenes
Authors: Brady Timothy F. , Oliva Aude
Published: July 2008

Recent work has shown that observers can parse streams of syllables, tones, or visual shapes and learn statistical regularities in them without conscious intent (e.g., learn that A is always followed by B). Here, we demonstrate that these statistical-learning mechanisms can operate at an abstract, conceptual level. In Experiments 1 and 2, observers incidentally learned which semantic categories of natural scenes covaried (e.g., kitchen scenes were always followed by forest scenes). In Experiments 3 and 4, category learning with images of scenes transferred to words that represented the categories. In each experiment, the category of the scenes was irrelevant to the task. Together, these results suggest that statistical-learning mechanisms can operate at a categorical level, enabling generalization of learned regularities using existing conceptual knowledge. Such mechanisms may guide learning in domains as disparate as the acquisition of causal knowledge and the development of cognitive maps from environmental exploration.
Objects on a Collision Path With the Observer Demand Attention
Authors: Lin Jeffrey Y. , Franconeri Steven , Enns James T.
Published: July 2008

How observers distribute limited processing resources to regions of a scene is based on a dynamic balance between current goals and reflexive tendencies. Past research showed that these reflexive tendencies include orienting toward objects that expand as if they were looming toward the observer, presumably because this signal indicates an impending collision. Here we report that during visual search, items that loom abruptly capture attention more strongly when they approach from the periphery rather than from near the center of gaze (Experiment 1), and target objects are more likely to be attended when they are on a collision path with the observer rather than on a near-miss path (Experiment 2). Both effects are exaggerated when search is performed in a large projection dome (Experiment 3). These findings suggest that the human visual system prioritizes events that are likely to require a behaviorally urgent response.
Induced Perceptual Grouping
Authors: Vickery Timothy J.
Published: July 2008

The term perceptual grouping is associated with classical principles such as similarity and proximity. This article reports induced perceptual grouping, a phenomenon that occurs when placement of a uniform set of items near a structured set induces grouping within the otherwise uniform set. For example, when items grouped pair-wise by similarity are placed near another set of unstructured items, an analogous pair-wise grouping links elements of the second set. Induced grouping affected reaction times in two different visual search tasks, with reaction times depending on whether the target properties were contained within a group or crossed group boundaries as defined by induced grouping due to similarity, proximity, or common fate. Induced grouping was reduced when grouping between the structured and unstructured sets was weakened by means of a common-region cue or decreased similarity. Induced grouping appears to reflect the computation of hierarchical structure in visual images.
Sweet Silent Thought
Authors: Lea R. Brooke , Rapp David N. , Elfenbein Andrew , Mitchel Aaron D. , Romine Russell Swinburne
Published: July 2008

Poetic devices like alliteration can heighten readers' aesthetic experiences and enhance poets' recall of their epic pieces. The effects of such devices on memory for and appreciation of poetry are well known; however, the mechanisms underlying these effects are not yet understood. We used current theories of language comprehension as a framework for understanding how alliteration affects comprehension processes. Across three experiments, alliterative cues reactivated readers' memories for previous information when it was phonologically similar to the cue. These effects were obtained when participants read aloud and when they read silently, and with poetry and prose. The results support everyday intuitions about the effects of poetry and aesthetics, and explain the nature of such effects. These findings extend the scope of general memory models by indicating their capacity to explain the influence of nonsemantic discourse features.
Angry, Disgusted, or Afraid?
Authors: Aviezer Hillel , Hassin Ran R. , Ryan Jennifer , Grady Cheryl , Susskind Josh , Anderson Adam , Moscovitch Morris , Bentin Shlomo
Published: July 2008

Current theories of emotion perception posit that basic facial expressions signal categorically discrete emotions or affective dimensions of valence and arousal. In both cases, the information is thought to be directly “read out” from the face in a way that is largely immune to context. In contrast, the three studies reported here demonstrated that identical facial configurations convey strikingly different emotions and dimensional values depending on the affective context in which they are embedded. This effect is modulated by the similarity between the target facial expression and the facial expression typically associated with the context. Moreover, by monitoring eye movements, we demonstrated that characteristic fixation patterns previously thought to be determined solely by the facial expression are systematically modulated by emotional context already at very early stages of visual processing, even by the first time the face is fixated. Our results indicate that the perception of basic facial expressions is not context invariant and can be categorically altered by context at early perceptual levels.
Effects of Salience Are Short-Lived
Authors: Donk Mieke , van Zoest Wieske
Published: July 2008

A salient event in the visual field tends to attract attention and the eyes. To account for the effects of salience on visual selection, models generally assume that the human visual system continuously holds information concerning the relative salience of objects in the visual field. Here we show that salience in fact drives vision only during the short time interval immediately following the onset of a visual scene. In a saccadic target-selection task, human performance in making an eye movement to the most salient element in a display was accurate when response latencies were short, but was at chance when response latencies were long. In a manual discrimination task, performance in making a judgment of salience was more accurate with brief than with long display durations. These results suggest that salience is represented in the visual system only briefly after a visual image enters the brain.
Why Does Writing About Important Values Reduce Defensiveness?
Authors: Crocker Jennifer , Niiya Yu , Mischkowski Dominik
Published: July 2008

Previous research has repeatedly shown that writing about an important value, compared with writing about an unimportant value, reduces defensiveness in response to self-threatening information, but has not identified why. Study 1 showed that participants who wrote about an important value reported more positive other-directed feelings, such as love and connection, than participants who wrote about an unimportant value. Study 2 replicated this effect, and showed that loving and connected feelings, but not positive or negative self-directed feelings, completely accounted for the effect of a values-affirmation manipulation on smokers' acceptance of information indicating that smoking harms health. These studies, in concert with previous research, suggest that values affirmation reduces defensiveness via self-transcendence, rather than self-integrity (i.e., self-worth or self-images).
Exchange Rate Stability, Inflation, and Growth in (South) Eastern and Central Europe
Authors: De Grauwe Paul , Schnabl Gunther
Published: July 2008

The authors analyze the impact of the exchange rate regime on inflation and output in (South) Eastern and Central Europe. For the whole observation period the estimations reveal a significant impact of exchange rate stability on low inflation as well as a highly significant positive impact of exchange stability on real growth. When subdividing the period into a “high‐inflation” period (1994–97) and a “low‐inflation period” (1998–2004), and when removing outliers from the sample, the evidence in favor of a positive association between exchange rate stability and inflation disappears. The association of exchange rate stability with higher real growth remains robust. These findings suggest that membership of the (South) Eastern and Central European countries in the European Monetary Union would have a positive impact on these countries' growth rates.
The Enlargement of the European Union and the Behavior of Real Exchange Rates
Authors: Kutan Ali M. , Zhou Su
Published: July 2008

The authors further investigate the conditional variance and the persistence of real exchange rate (RER) shocks between Germany and some core European Union (EU) members from January, 1973 through 2004. Using data for all EU15 countries, they test whether the enlargement of the Union has reduced the variability and the persistence of RER shocks between Germany and the rest of the members during the 1990s. They also examine the impact of the introduction of the euro on the variance and persistence of real exchange rate shocks. Finally, the authors extend the analysis to the new members who joined in May, 2004. The results have implications for the economic cost of joining the Union, as well as assessing the timing of the newest members to enter the eurozone.
EU Enlargement and Trade Integration: Lessons from a Gravity Model
Authors: Bussière Matthieu , Fidrmuc Jarko , Schnatz Bernd
Published: July 2008

The authors estimate gravity models using a large panel of bilateral trade flows across 61 countries between 1980 and 2003, which are applied as a benchmark for the integration of Central and South Eastern European countries with the euro area. They show that a careful examination of the fixed effects of the model is crucial for the proper interpretation of the results. The results suggest that trade integration between most new EU member states and the euro area is already relatively advanced, while the remaining Central and Eastern European countries have significant scope to strengthen trade links with the euro area.
Exchange Rate Regimes, Foreign Exchange Volatility, and Export Performance in Central and Eastern Europe: Just another Blur Project?
Authors: Égert Balázs , Morales‐Zumaquero Amalia
Published: July 2008

The authors attempt to analyze the direct impact of exchange rate volatility on the export performance of ten Central and Eastern European transition economies, as well as its indirect impact via changes in exchange rate regimes. Not only aggregate but also bilateral and sectoral export flows are studied. To this end, the authors first analyze shifts in exchange rate volatility linked to changes in the exchange rate regimes and, second, they use these changes to construct the dummy variables that they include in their export function. The results suggest that the size and the direction of the impact of forex volatility and of regime changes on exports vary considerably across sectors and countries and that they may be related to specific periods.
Equilibrium Exchange Rates in New EU Members: External Imbalances versus Real Convergence
Authors: Alberola Enrique , Navia Daniel
Published: July 2008

In new EU members, the accumulation of net foreign liabilities has gone hand‐in‐hand with real exchange rate appreciations, contrary to intuition. This may be due to the induced effect that capital inflows on productivity and competitiveness (Balassa‐Samuelson effect). An extended empirical model comprising relative productivity and net foreign assets is well‐suited to capture this indirect, opposite effect of liabilities accumulation on the equilibrium exchange rates for the three largest economies: Poland, Hungary and Czech Republic. The model makes it possible to estimate equilibrium exchange rates and misalignments. Going forward, sustaining high productivity growth will be essential to ensure a smooth transition towards euro membership.
Rigidities and Inflationary Bias in a Monetary Union: The Consequences of EU Enlargement
Authors: Campoy Juan Cristóbal , Negrete Juan Carlos
Published: July 2008

The authors analyze how the design of the central bank interacts with the implementation of structural reforms in a monetary union. They show that the first‐best is achieved when the common central bank is collectively designed, irrespective of whether or not reforms are cooperatively implemented. On the other hand, in the case where the central bank has been designed, an enlargement of the union worsens the incumbent members' welfare unless the inflation target of the monetary authorities diminishes or the accession countries implement a sufficient level of reforms prior to joining in.
The New Member States and the Process towards EMU
Authors: García‐Solanes José , María‐Dolores Ramón
Published: July 2008

The authors apply two complementary empirical criteria to eight new member states (NMSs) of the European Union to assess how ready they are to adopt the euro. As a first step, they recover demand and supply shocks and calculate the social losses implied by the two relevant exchange rate regimes: flexible rates and currency board. As a second step, the authors calculate the real exchange rates variability that these countries are currently experiencing and compare it to that of three Mediterranean countries during a similar period before they joined the EMU. The combination of the results of both tests shows that Estonia and Slovenia are the only countries that seem ready to adopt the euro within the shortest period of time foreseen by the Maastricht criteria; that is, after the two mandatory years in the ERM2. The rest of the countries will probably still need some exchange rate flexibility to absorb external shocks in the coming years.
TAR Panel Unit Root Tests and Real Convergence
Authors: Beyaert Arielle , Camacho Maximo
Published: July 2008

The authors propose a new panel data methodology to test real convergence in a non‐linear framework. This extends the existing methods by combining three approaches: the threshold model, the panel data unit root tests, and the computation of critical values by bootstrap simulation. The authors apply their methodology to the per capita outputs of a total of 15 European countries, including some of the East European countries that have recently joined the EU.
Risk Sharing and Efficiency Implications of Progressive Pension Arrangements*
Authors: Fehr Hans , Habermann Christian
Published: July 2008

This paper aims to quantify the welfare effects of progressive pension arrangements in Germany. Starting from a purely contribution‐related benefit system, we introduce basic allowances for contributions and a flat benefit fraction. Since our overlapping‐generations model takes into account variable labor supply, borrowing constraints as well as stochastic income risk, we can compare the labor supply, the liquidity and the insurance effects of the policy reform. Our simulations indicate that it would be optimal to introduce a flat benefit share of 50 percent and a basic allowance that amounts to 30 percent of average income. Such a reform would yield an aggregate efficiency gain of 3.3 percent of resources.