bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simultaneous and Successive Contrast Effects in the Perception of Depth from Motion-Parallax and Stereoscopic Information
Authors: Graham Maureen , Rogers Brian 
Published: January 2007

Prolonged inspection of a three-dimensional corrugated surface resulted in a successive contrast effect, or aftereffect, of depth, whereby a subsequently-viewed physically-flat test surface appeared to be corrugated in depth with the opposite phase to the adapting surface. The aftereffect occurred both when the depth was specified by motion parallax, in the absence of all other sources of depth information, and when it was specified solely by stereoscopic information. The depth aftereffect was measured by ‘nulling’ the apparent depth in the test surface with physical relative motion or binocular disparity until the test surface appeared flat. Up to 70% of the depth in the adapting surface was necessary to null the aftereffect. Simultaneous contrast effects in the perception of three-dimensional surfaces were used to investigate the spatial interactions that exist in the processing of motion-parallax and stereoscopic information. A physically vertical surface appeared to slope in depth in the opposite direction to the slope of a surrounding surface. In this case up to 50% of the slope of the inducing surface was necessary to null the contrast effect. Similar results were again obtained for motion-parallax and stereoscopic depth.
Flicker Haloes Observed with Subjective Borders
Authors: Remole Arnulf , Ng Albert S Y , Bathe Linda L , Padfield Paul D , Spafford Marlee M , Szymkiw Mary A 
Published: January 2007

Subjective borders are known to behave quite similarly to real borders when the stimulus presents fragments of visually meaningful forms. There is less information on whether this also applies to unfamiliar stimulus elements. Thus, if a dark/bright stimulus border is presented intermittently at certain frequencies below flicker fusion, the bright border enhancement band increases greatly in width and takes on a textured appearance, resembling a halo streaming from the border. The percept is spontaneous and unlike anything experienced in real life. Preliminary observations showed that the effect occurs also at subjective borders. The extent of the halo from the border was measured for various flicker frequencies and compared with similar measurements obtained with real borders. It was found that the extent varies with frequency in an identical manner for real and virtual borders. Also, the halo was judged equal in qualitative appearance for both kinds of border. The striking similarity between virtual and real effects in this respect is best explained in terms of physiological border perception processes, possibly instigated by a cognitive mechanism.
The Interaction of Oculomotor Cues and Stimulus Size in Stereoscopic Depth Constancy
Authors: Collett Thomas S , Schwarz Urs , Sobel Erik C 
Published: January 2007

In the natural world, observers perceive an object to have a relatively fixed size and depth over a wide range of distances. Retinal image size and binocular disparity are to some extent scaled with distance to give observers a measure of size constancy. The angle of convergence of the two eyes and their accommodative states are one source of scaling information, but even at close range this must be supplemented by other cues. We have investigated how angular size and oculomotor state interact in the perception of size and depth at different distances. Computer-generated images of planar and stereoscopically simulated 3-D surfaces covered with an irregular blobby texture were viewed on a computer monitor. The monitor rested on a movable sled running on rails within a darkened tunnel. An observer looking into the tunnel could see nothing but the simulated surface so that oculomotor signals provided the major potential cues to the distance of the image. Observers estimated the height of the surface, their distance from it, or the stereoscopically simulated depth within it over viewing distances which ranged from 45 cm to 130 cm. The angular width of the images lay between 2 deg and 10 deg. Estimates of the magnitude of a constant simulated depth dropped with increasing viewing distance when surfaces were of constant angular size. But with surfaces of constant physical size, estimates were more nearly independent of viewing distance. At any one distance, depths appeared to be greater, the smaller the angular size of the image. With most observers, the influence of angular size on perceived depth grew with increasing viewing distance. These findings suggest that there are two components to scaling. One is independent of angular size and related to viewing distance. The second component is related to angular size, and the weighting accorded to it grows with viewing distance. Control experiments indicate that in the tunnel, oculomotor state provides the principal cue to viewing distance. Thus, the contribution of oculomotor signals to depth scaling is gradually supplanted by other cues as viewing distance grows. Binocular estimates of the heights and distances of planar surfaces of different sizes revealed that angular size and viewing distance interact in a similar way to determine perceived size and perceived distance.
Convergent and Divergent Perspective
Authors: Deręgowski Jan B , Parker Denis M 
Published: January 2007

Use of divergent (or inverse) perspective in pictures is often regarded as arbitrary or even as erroneous in spite of the fact that entire schools of art exist in which this kind of perspective is regularly used. An experiment is reported which shows that a significant trend towards divergent perspective is experienced by subjects viewing laterally displaced three-dimensional arrays. Centrally viewed arrays show the expected perceptual convergence. It is therefore argued that divergent perspective, under appropriate conditions, is as perceptually legitimate an experience as convergent perspective.
The Neural Representation of Stereoscopic Depth Contrast
Authors: Mitchison Graeme 
Published: January 2007

Stereoscopic vision provides examples of contrast phenomena broadly analogous to those seen with brightness. Several authors have suggested that lateral inhibition between disparity-tuned neurons might underlie these phenomena. This type of lateral inhibition would differ from the more familiar kind which occurs with retinal ganglion cells, where an inhibitory surround has essentially a linear subtractive effect. Lateral inhibition by disparity-tuned units would introduce the nonlinearity of the tuning curve. I argue here that the evidence nonetheless suggests that a linear subtractive mechanism operates in the stereo realm—in fact, that there is a stereo equivalent of the classical centre-surround. This seems at first sight implausible, partly because of the occurrence of the nonlinearity mentioned above, but also because disparity is only provided at certain locations in the retinal field, namely those where appropriate features are matched. I show that both objections can be easily overcome, the first because Laplacian-like centre–surrounds can be constructed from disparity-tuned cells, the second because interpolation can fill in between features, and can provide precisely the quantitative dependence upon disparities of neighbouring features which matches the experimental data.
I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition
Authors: Orlowski Jerzy , Boniecki Michal , Bujnicki Janusz M. 
Published: January 2007

AbstractMotivation: Restriction endonucleases (REases) and homing endonucleases (HEases) are biotechnologically important enzymes. Nearly all structurally characterized REases belong to the PD-(D/E)XK superfamily of nucleases, while most HEases belong to an unrelated LAGLIDADG superfamily. These two protein folds are typically associated with very different modes of protein-DNA recognition, consistent with the different mechanisms of action required to achieve high specificity. REases recognize short DNA sequences using multiple contacts per base pair, while HEases recognize very long sites using a few contacts per base pair, thereby allowing for partial degeneracy of the target sequence. Thus far, neither REases with the LAGLIDADG fold, nor HEases with the PD-(D/E)XK fold, have been found.Results: Using protein fold recognition, we have identified the first member of the PD-(D/E)XK superfamily among homing endonucleases, a cyanobacterial enzyme I-Ssp6803I. We present a model of the I-Ssp6803I-DNA complex based on the structure of Type II restriction endonuclease R.BglI and predict the active site and residues involved in specific DNA sequence recognition by I-Ssp6803I. Our finding reveals a new unexpected evolutionary link between HEases and REases and suggests how PD-(D/E)XK nucleases may develop a ‘HEase-like’ way of interacting with the extended DNA sequence. This in turn may be exploited to study the evolution of DNA sequence specificity and to engineer nucleases with new substrate specificities.Contact: iamb@genesilico.pl
The crystal structure of leucyl/phenylalanyl‐tRNA‐protein transferase from Escherichia coli
Authors: Dong Xuesong , Kato‐Murayama Miyuki , Muramatsu Tomonari , Mori Hirotada , Shirouzu Mikako , Bessho Yoshitaka , Yokoyama Shigeyuki 
Published: January 2007

AbstractLeucyl/phenylalanyl‐tRNA‐protein transferase (L/F‐transferase) is an N‐end rule pathway enzyme, which catalyzes the transfer of Leu and Phe from aminoacyl‐tRNAs to exposed N‐terminal Arg or Lys residues of acceptor proteins. Here, we report the 1.6 Å resolution crystal structure of L/F‐transferase (JW0868) from Escherichia coli, the first three‐dimensional structure of an L/F‐transferase. The L/F‐transferase adopts a monomeric structure consisting of two domains that form a bilobate molecule. The N‐terminal domain forms a small lobe with a novel fold. The large C‐terminal domain has a highly conserved fold, which is observed in the GCN5‐related N‐acetyltransferase (GNAT) family. Most of the conserved residues of L/F‐transferase reside in the central cavity, which exists at the interface between the N‐terminal and C‐terminal domains. A comparison of the structures of L/F‐transferase and the bacterial peptidoglycan synthase FemX, indicated a structural homology in the C‐terminal domain, and a similar domain interface region. Although the peptidyltransferase function is shared between the two proteins, the enzymatic mechanism would differ. The conserved residues in the central cavity of L/F‐transferase suggest that this region is important for the enzyme catalysis.
Population structure at the S‐locus of Sorbus aucuparia L. (Rosaceae: Maloideae)
Authors: RASPÉ OLIVIER , KOHN JOSHUA R. 
Published: January 2007

AbstractLow sequence divergence within functional alleles is predicted for the self‐incompatibility locus because of strong negative frequency‐dependent selection. Nevertheless, sequence variation within functional alleles is essential for current models of the evolution of new mating types. We genotyped the stylar self‐incompatibility RNase of 20 Sorbus aucuparia from a population in the Pyrenees mountains of France in order to compare alleles found there to those previously sampled in a Belgian population. Both populations returned 20 different alleles from samples of 20 individuals, providing maximum‐likelihood estimates of 24.4 (95% CI 20–34) alleles in each. Ten alleles occurred in both samples. The maximum likelihood (ML) estimate of the overlap in the alleles present in both populations was 16, meaning that an estimated eight alleles are private to each population, and a total of 32 alleles occur across the two populations examined. We used Fisher's (1961) missing plot method to estimate that 40 alleles occur in the species. In accord with population genetics theory, we observed at most one synonymous sequence difference between copies of alleles sampled from the different populations and no variation within populations. Phylogenetic analysis shows that nearly every allele in S. aucuparia arose prior to divergence of this species from members of three different genera of the Rosaceae subfamily, Maloideae. Lack of observable sequence variation within alleles, coupled with the slow pace of allelic relative to taxonomic diversification, implies that finding intermediate stages in the process of new allele creation will be difficult in this group.
Effects of human apolipoprotein E isoforms on the amyloid β‐protein concentration and lipid composition in brain low‐density membrane domains
Authors: Morishima‐Kawashima Maho , Han Xianlin , Tanimura Yu , Hamanaka Hiroki , Kobayashi Mariko , Sakurai Takashi , Yokoyama Minesuke , Wada Koji , Nukina Nobuyuki , Fujita Shinobu C. , Ihara Yasuo 
Published: January 2007

AbstractApolipoprotein E4 (apoE4) encoded by ε4 allele is a strong genetic risk factor for Alzheimer’s disease (AD). ApoE4 carriers have accelerated amyloid β‐protein (Aβ) deposition in their brains, which may account for their unusual susceptibility to AD. We hypothesized that the accelerated Aβ deposition in the brain of apoE4 carriers is mediated through cholesterol‐enriched low‐density membrane (LDM) domains. Thus, the concentrations of Aβ and various lipids in LDM domains were quantified in the brains of homozygous apoE3 and apoE4 knock‐in (KI) mice, and in the brains of those mice bred with β‐amyloid precursor protein (APP) transgenic mice (Tg2576). The Aβ40 and Aβ42 concentrations and the Aβ42 proportions in LDM domains did not differ between apoE3 and apoE4 KI mice up to 18 months of age. The Aβ40 concentration in the LDM domains was slightly, but significantly higher in apoE3/APP mice than in apoE4/APP mice. The lipid composition of LDM domains was modulated in an apoE isoform‐specific manner, but its significance for Aβ deposition remains unknown. These data show that the apoE isoform‐specific effects on the Aβ concentration in LDM domains do not occur in KI mouse models.
Amyotrophic lateral sclerosis: all roads lead to Rome
Authors: Aguilar Jose‐Luis Gonzalez de , Echaniz‐Laguna Andoni , Fergani Anissa , René Frédérique , Meininger Vincent , Loeffler Jean‐Philippe , Dupuis Luc 
Published: January 2007

AbstractAmyotrophic lateral sclerosis (ALS) is the most frequent adult‐onset motor neuron disease characterized by degeneration of upper and lower motor neurons, generalized weakness and muscle atrophy. Most cases of ALS appear sporadically but some forms of the disease result from mutations in the gene encoding the antioxidant enzyme Cu/Zn superoxide dismutase (SOD1). Several other mutated genes have also been found to predispose to ALS including, among others, one that encodes the regulator of axonal retrograde transport dynactin. As all roads lead to the proverbial Rome, we discuss here how distinct molecular pathways may converge to the same final result that is motor neuron death. We critically review the basic research on SOD1‐linked ALS to propose a pioneering model of a ‘systemic’ form of the disease, causally involving multiple cell types, either neuronal or non‐neuronal. Contrasting this, we also postulate that other neuron‐specific defects, as those triggered by dynactin dysfunction, may account for a primary motor neuron disease that would represent ‘pure’ neuronal forms of ALS. Identifying different disease subtypes is an unavoidable step toward the understanding of the physiopathology of ALS and will hopefully help to design specific treatments for each subset of patients.
A pooling approach to detect signatures of selective sweeps in genome scans using microsatellites
Authors: THOMAS MEIKE , MÖLLER FRIEDRICH , WIEHE THOMAS , TAUTZ DIETHARD 
Published: January 2007

AbstractWe have evaluated a pooling approach that can reduce the number of polymerase chain reactions in a screen for selective sweeps by more than an order of magnitude. We show that the complex peak pattern that results from pooling of all samples from a given population is a faithful reflection of the composite pattern of the individual alleles, although with an under‐representation of the larger alleles. Candidate loci for selective sweeps can be identified by visual inspection of the pool patterns. We have also implemented a software tool, which can find suitable microsatellite loci in the vicinity of annotated genes.
Morphometric analysis of murine skin wound healing: Standardization of experimental procedures and impact of an advanced multitissue array technique
Authors: Gerharz Michael , Baranowsky Ankev , Siebolts Udo , Eming Sabine , Nischt Roswitha , Krieg Thomas , Wickenhauser Claudia 
Published: January 2007

ABSTRACTMorphometric data based on skin wounding offer important information for the characterization of the phenotype of transgenic mouse models. The goal of this study was the comparison of technical procedures concerning wounding, processing, and evaluation of samples in different mouse strains. The multitissue array technique was used to estimate its adaptability for standardized analysis in wound healing. Skin wounds between days 1 and 14 after wounding were analyzed. The influence of mouse strain (C57BI/6 vs. FVB/N mice), sex, size of the punch biopsies, and preparation of the tissue sections was investigated on 94 mice. The parameters distance between the migration tongues (δMT) and surface not covered by epithelium were evaluated to describe the reepithelialization, and the distance between the adnexa was chosen to measure wound contraction. In addition, the techniques to measure the area of granulation tissue (GT) were evaluated. The data illustrate the requirement of standardized conditions for skin wound‐healing experiments and demonstrate that histological preparation in serial sections is mandatory to detect slight differences in wound contraction. For the analysis of cellular composition in GT, multitissue arrays are useful tools in wound‐healing studies.
Erythropoietin after a century of research: younger than ever
Authors: Jelkmann Wolfgang 
Published: January 2007

AbstractIn the light of the enthusiasm regarding the use of recombinant human erythropoietin (Epo) and its analogues for treatment of the anaemias of chronic renal failure and malignancies it is worth remembering that today's success has been based on a century of laborious research. The concept of the humoral regulation of haematopoiesis was first formulated in 1906. The term ‘erythropoietin’ for the erythropoiesis‐stimulating hormone was introduced in 1948. Native human Epo was isolated in 1977 and its gene cloned in 1985. During the last 15 yr, major progress has been made in identifying the molecules controlling Epo gene expression, primarily the hypoxia‐inducible transcription factors (HIF) that are regulated by specific O2 and oxoglutarate requiring Fe2+‐containing dioxygenases. With respect to the action of Epo, its dimeric receptor (Epo‐R) has been characterised and shown to signal through protein kinases, anti‐apoptotic proteins and transcription factors. The demonstration of Epo‐R in non‐haematopoietic tissues indicates that Epo is a pleiotropic viability and growth factor. The neuroprotective and cardioprotective potentials of Epo are reviewed with a focus on clinical research. In addition, studies utilising the Epo derivatives with prolonged half‐life, peptidic and non‐peptidic Epo mimetics, orally active drugs stimulating endogenous Epo production and Epo gene transfer are reviewed.
EFFECT OF PSYCHROPHILIC BACTERIA TO ESTIMATE FISH QUALITY
Authors: MOL SUHENDAN , ERKAN NURAY , ÜÇOK DIDEM , TOSUN Ş. YASEMIN 
Published: January 2007

ABSTRACT Growth of psychrophilic microorganisms in chilled seafoods is important but they have limited use in shelf‐life studies because there is not an acceptability limit. In this study, pH, total volatile bases nitrogen (TVB‐N), trimethylamine nitrogen (TMA‐N), total mesophilic and psychrophilic aerobic bacteria analyses were used to estimate the shelf life of cold stored (+4 ± 1C) fish. Shelf life of horse mackerel was determined as 1 day, while cod and anchovy spoiled on the second day, and rainbow trout spoiled on the third day of storage. Total mesophilic aerobic bacteria counts did not indicate the spoilage remaining lower than the acceptability limit; but psychrophilic aerobic bacteria counts were around 6 log cfu/g, when the samples spoiled. It was determined that, estimation of the psychrophilic microorganisms gives better results to the shelf‐life estimation of chilled fish than mesophilic bacteria and 6 log cfu/g could be accepted as the acceptability limit.PRACTICAL APPLICATIONSSeafood is mostly stored and transported under chilled conditions. However, there is not a limit of acceptability for the psychrophilic microorganisms which are important to estimate spoilage of chilled foods. Thanks to this study, a limit of acceptability (6 log cfu/g) was determined for these microorganisms in cold storage conditions. This limit will be helpful in further studies to estimate the shelf life of chilled seafoods definitively.
Murine Innate Immune Response to Virulent Toxigenic and NontoxigenicBacillus anthracisStrains
Authors: Drysdale Melissa , Olson Gwyneth , Koehler Theresa M. , Lipscomb Mary F. , Lyons C. Rick 
Published: January 2007

ABSTRACTEffective treatment of anthrax is hampered by our limited understanding of the pathophysiology ofBacillus anthracisinfection. We used a genetically complete (pXO1+pXO2+) virulentB. anthracisstrain and four isogenic toxin-null mutants to determine the effects of the anthrax edema toxin (ET; edema factor [EF] plus protective antigen [PA]) and lethal toxin (LT; lethal factor [LF] plus PA) on the host innate response during systemic infection. Using the spleen as an indicator for host response, we found that intravenous inoculation of LT-deficient mutants into C57BL/6 mice significantly increased production of several cytokines over that observed after infection with the parent strain or an EF-deficient mutant. Bacteria producing one or both of the toxins were capable of inducing significant apoptosis of cells present in spleens, whereas apoptosis was greatly reduced in mice infected with nontoxigenic mutants. Mice infected with toxin-producing strains also showed increased splenic neutrophil recruitment compared to mice infected with nontoxigenic strains and neutrophil depletion prior to infection with toxin-producing strains, leading to decreased levels of apoptosis. Together, these studies indicate that anthrax LT suppresses cytokine secretion during infection, but both EF and LF play roles in inducing neutrophil recruitment and enhancing apoptosis. Interestingly, in the absence of LF the effect of EF-induced cell recruitment is further enhanced, perhaps because LF so effectively suppresses the secretion of chemokines.
Concurrent transcriptional deregulation of AML1/RUNX1 and GATA factors by the AML1-TRPS1 chimeric gene in t(8;21)(q24;q22) acute myeloid leukemia
Authors: Asou Norio , Yanagida Masatoshi , Huang Liqun , Yamamoto Masayuki , Shigesada Katsuya , Mitsuya Hiroaki , Ito Yoshiaki , Osato Motomi 
Published: January 2007

Abstract
The Runt domain transcription factor AML1/RUNX1 is essential for the generation of hematopoietic stem cells and is the most frequent target of chromosomal translocations associated with leukemia. Here, we present a new AML1 translocation found in a patient with acute myeloid leukemia M4 with t(8;21)(q24;q22) at the time of relapse. This translocation generated an in-frame chimeric gene consisting of the N-terminal portion of AML1, retaining the Runt domain, fused to the entire length of TRPS1 on the C-terminus. TRPS1 encodes a putative multitype zinc finger (ZF) protein containing 9 C2H2 type ZFs and 1 GATA type ZF. AML1-TRPS1 stimulated proliferation of hematopoietic colony-forming cells and repressed the transcriptional activity of AML1 and GATA-1 by 2 different mechanisms: competition at their cognate DNA-binding sites and physical sequestrations of AML1 and GATA-1, suggesting that simultaneous deregulation of AML1 and GATA factors constitutes a basis for leukemogenesis.