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author:("Yu, depue")
1.  Sensory factors limiting horizontal and vertical visual span for letter recognition 
Journal of Vision  2014;14(9):23.
Reading speed for English text is slower for text oriented vertically than horizontally. Yu, Park, Gerold, and Legge (2010) showed that slower reading of vertical text is associated with a smaller visual span (the number of letters recognized with high accuracy without moving the eyes). Three possible sensory determinants of the size of the visual span are: resolution (decreasing acuity at letter positions farther from the midline), mislocations (uncertainty about the relative position of letters in strings), and crowding (interference from flanking letters in recognizing the target letter). In the present study, we asked which of these factors is most important in determining the size of the visual span, and likely in turn in determining the horizontal/vertical difference in reading when letter size is above the critical print size for reading. We used a decomposition analysis to represent constraints due to resolution, mislocations, and crowding as losses in information transmitted (in bits) about letter recognition. Across vertical and horizontal conditions, crowding accounted for 75% of the loss in information, mislocations accounted for 19% of the loss, and declining acuity away from fixation accounted for only 6%. We conclude that crowding is the major factor limiting the size of the visual span, and that the horizontal/vertical difference in the size of the visual span is associated with stronger crowding along the vertical midline.
doi:10.1167/14.9.23
PMCID: PMC4144171
visual span; crowding; reading; vertical text; acuity; mislocation
2.  Evolutionary study of the isoflavonoid pathway based on multiple copies analysis in soybean 
BMC Genetics  2014;15:76.
Background
Previous studies suggest that the metabolic pathway structure influences the selection and evolution rates of involved genes. However, most of these studies have exclusively considered a single gene copy encoding each enzyme in the metabolic pathway. Considering multiple-copy encoding enzymes could provide direct evidence of gene evolution and duplication patterns in metabolic pathways. We conducted a detailed analysis of the phylogeny, synteny, evolutionary rate and selection pressure of the genes in the isoflavonoid metabolic pathway of soybeans.
Results
The results revealed that 1) only the phenylalanine ammonia-lyase (PAL) gene family most upstream from the pathway preserved all of the ancient and recent segmental duplications and maintained a strongly conserved synteny among these duplicated segments; gene families encoding branch-point enzymes with higher pleiotropy tended to retain more types of duplication; and genes encoding chalcone reductase (CHR) and isoflavone synthase (IFS) specific for legumes retained only recent segmental duplications; 2) downstream genes evolved faster than upstream genes and were subject to positive selection or relaxed selection constraints; 3) gene members encoding enzymes with high pleiotropy at the branching points were more likely to have undergone evolutionary differentiation, which may correspond to their functional divergences.
Conclusions
We reconciled our results with existing controversies and proposed that gene copies at branch points with higher connectivity might be under stronger selective constraints and that the gene copies controlling metabolic flux allocation underwent positive selection. Our analyses demonstrated that the structure and function of a metabolic pathway shapes gene duplication and the evolutionary constraints of constituent enzymes.
doi:10.1186/1471-2156-15-76
PMCID: PMC4076065  PMID: 24962214
Isoflavonoid phytoalexin pathway; Duplication pattern; Evolution divergence; Multiple copies; Soybean
3.  RNA-Seq analysis reveals that multiple phytohormone biosynthesis and signal transduction pathways are reprogrammed in curled-cotyledons mutant of soybean [Glycine max (L.) Merr.] 
BMC Genomics  2014;15(1):510.
Background
Soybean is one of the most economically important crops in the world. The cotyledon is the nutrient storage area in seeds, and it is critical for seed quality and yield. Cotyledon mutants are important for the genetic dissection of embryo patterning and seed development. However, the molecular mechanisms underlying soybean cotyledon development are largely unexplored.
Results
In this study, we characterised a soybean curled-cotyledon (cco) mutant. Compared with wild-type (WT), anatomical analysis revealed that the cco cotyledons at the torpedo stage became more slender and grew outward. The entire embryos of cco mutant resembled the “tail of swallow”. In addition, cco seeds displayed reduced germination rate and gibberellic acid (GA3) level, whereas the abscisic acid (ABA) and auxin (IAA) levels were increased. RNA-seq identified 1,093 differentially expressed genes (DEGs) between WT and the cco mutant. The KEGG pathway analysis showed many DEGs were mapped to the hormone biosynthesis and signal transduction pathways. Consistent with assays of hormones in seeds, the results of RNA-seq indicated auxin and ABA biosynthesis and signal transduction in cco were more active than in WT, while an early step in GA biosynthesis was blocked, as well as conversion rate of inactive GAs to bioactive GAs in GA signaling. Furthermore, genes participated in other hormone biosynthesis and signalling pathways such as cytokinin (CK), ethylene (ET), brassinosteroid (BR), and jasmonate acid (JA) were also affected in the cco mutant.
Conclusions
Our data suggest that multiple phytohormone biosynthesis and signal transduction pathways are reprogrammed in cco, and changes in these pathways may partially contribute to the cco mutant phenotype, suggesting the involvement of multiple hormones in the coordination of soybean cotyledon development.
Electronic supplementary material
The online version of this article (doi:10.1186/1471-2164-15-510) contains supplementary material, which is available to authorized users.
doi:10.1186/1471-2164-15-510
PMCID: PMC4078243  PMID: 24952381
Soybean; RNA-seq; Plant hormone; Curled-cotyledon; Mutant
4.  A soybean MADS-box protein modulates floral organ numbers, petal identity and sterility 
BMC Plant Biology  2014;14:89.
Background
The MADS-box transcription factors play fundamental roles in reproductive developmental control. Although the roles of many plant MADS-box proteins have been extensively studied, there are almost no functional studies of them in soybean, an important protein and oil crop in the world. In addition, the MADS-box protein orthologs may have species-specific functions. Controlling male fertility is an important goal in plant hybrid breeding but is difficult in some crops like soybean. The morphological structure of soybean flowers prevents the cross-pollination. Understanding the molecular mechanisms for floral development will aid in engineering new sterile materials that could be applied in hybrid breeding programs in soybean.
Result
Through microarray analysis, a flower-enriched gene in soybean was selected and designated as GmMADS28. GmMADS28 belongs to AGL9/SEP subfamily of MADS-box proteins, localized in nucleus and showed specific expression patterns in floral meristems as well as stamen and petal primordia. Expression of GmMADS28 in the stamens and petals of a soybean mutant NJS-10Hfs whose stamens are converted into petals was higher than in those of wild-type plants. Constitutive expression of GmMADS28 in tobacco promoted early flowering and converted stamens and sepals to petals. Interestingly, transgenic plants increased the numbers of sepal, petal and stamen from five to six and exhibited male sterility due to the shortened and curly filaments and the failure of pollen release from the anthers. The ectopic expression of GmMADS28 was found to be sufficient to activate expression of tobacco homologs of SOC1, LEAFY, AGL8/FUL, and DEF. In addition, we observed the interactions of GmMADS28 with soybean homologs of SOC1, AP1, and AGL8/FUL proteins.
Conclusion
In this study, we observed the roles of GmMADS28 in the regulation of floral organ number and petal identity. Compared to other plant AGL9/SEP proteins, GmMADS28 specifically regulates floral organ number, filament length and pollen release. The sterility caused by the ectopic expression of GmMADS28 offers a promising way to genetically produce new sterile material that could potentially be applied in the hybrid breeding of crops like soybean.
doi:10.1186/1471-2229-14-89
PMCID: PMC4021551  PMID: 24693922
Fertility; Floral organ number; Petal identity; Glycine max; MADS-box transcription factors
5.  Association mapping of yield-related traits and SSR markers in wild soybean (Glycine soja Sieb. and Zucc.) 
Breeding Science  2014;63(5):441-449.
Wild soybean, the progenitor of cultivated soybean, is an important gene pool for ongoing soybean breeding efforts. To identify yield-enhancing quantitative trait locus (QTL) or gene from wild soybean, 113 wild soybeans accessions were phenotyped for five yield-related traits and genotyped with 85 simple sequence repeat (SSR) markers to conduct association mapping. A total of 892 alleles were detected for the 85 SSR markers, with an average 10.49 alleles; the corresponding PIC values ranged from 0.07 to 0.92, with an average 0.73. The genetic diversity of each SSR marker ranged from 0.07 to 0.93, with an average 0.75. A total of 18 SSR markers were identified for the five traits. Two SSR markers, sct_010 and satt316, which are associated with the yield per plant were stably expressed over two years at two experimental locations. Our results suggested that association mapping can be an effective approach for identifying QTL from wild soybean.
doi:10.1270/jsbbs.63.441
PMCID: PMC3949580  PMID: 24757383
wild soybean; genetic diversity; population structure; association mapping; yield-related traits
6.  The Acid Phosphatase-Encoding Gene GmACP1 Contributes to Soybean Tolerance to Low-Phosphorus Stress 
PLoS Genetics  2014;10(1):e1004061.
Phosphorus (P) is essential for all living cells and organisms, and low-P stress is a major factor constraining plant growth and yield worldwide. In plants, P efficiency is a complex quantitative trait involving multiple genes, and the mechanisms underlying P efficiency are largely unknown. Combining linkage analysis, genome-wide and candidate-gene association analyses, and plant transformation, we identified a soybean gene related to P efficiency, determined its favorable haplotypes and developed valuable functional markers. First, six major genomic regions associated with P efficiency were detected by performing genome-wide associations (GWAs) in various environments. A highly significant region located on chromosome 8, qPE8, was identified by both GWAs and linkage mapping and explained 41% of the phenotypic variation. Then, a regional mapping study was performed with 40 surrounding markers in 192 diverse soybean accessions. A strongly associated haplotype (P = 10−7) consisting of the markers Sat_233 and BARC-039899-07603 was identified, and qPE8 was located in a region of approximately 250 kb, which contained a candidate gene GmACP1 that encoded an acid phosphatase. GmACP1 overexpression in soybean hairy roots increased P efficiency by 11–20% relative to the control. A candidate-gene association analysis indicated that six natural GmACP1 polymorphisms explained 33% of the phenotypic variation. The favorable alleles and haplotypes of GmACP1 associated with increased transcript expression correlated with higher enzyme activity. The discovery of the optimal haplotype of GmACP1 will now enable the accurate selection of soybeans with higher P efficiencies and improve our understanding of the molecular mechanisms underlying P efficiency in plants.
Author Summary
In soybean plants, low-phosphorus (P) stress is more detrimental than other nutrient deficiencies, toxicities or diseases; however, it is difficult to select soybean varieties with high P efficiencies based on phenotypes. Although QTL map-based cloning is a powerful method, it is time-consuming, and the QTLs underlying P efficiency in soybeans have not been identified. Combining linkage and association analyses, we identified a highly significant region on chromosome 8, qPE8, which is associated with soybean P efficiency. Gene expression and plant transformation experiments indicated that the gene GmACP1 within qPE8 affects P efficiency. A haplotype survey of GmACP1 identified 10 haplotypes that explained 33% of the variation in P efficiency. The discovery of the optimal haplotype of GmACP1 will improve the accuracy of selecting soybeans with higher P efficiencies and increase our understanding of the molecular mechanisms underlying P efficiency in plants.
doi:10.1371/journal.pgen.1004061
PMCID: PMC3879153  PMID: 24391523
7.  Variation in Rubisco activase (RCAβ) gene promoters and expression in soybean [Glycine max (L.) Merr.] 
Journal of Experimental Botany  2013;65(1):47-59.
Variation in Rubisco activase gene promoters (RCAβ) could affect diversity of expression level, which provided a new approach for enhancing soybean productivity by altering the expression level of RCAβ
Understanding the genetic basis of Rubisco activase (RCA) gene regulation and altering its expression levels to optimize Rubisco activation may provide an approach to enhance plant productivity. However, the genetic mechanisms and the effect of RCA expression on phenotype are still unknown in soybean. This work analysed the expression of RCA genes and demonstrated that two RCA isoforms presented different expression patterns. Compared with GmRCAα, GmRCAβ was expressed at higher mRNA and protein levels. In addition, GmRCAα and GmRCAβ were positively correlated with chlorophyll fluorescence parameters and seed yield, suggesting that changes in expression of RCA has a potential applicability in breeding for enhanced soybean productivity. To identify the genetic factors that cause expression level variation of GmRCAβ, expression quantitative trait loci (eQTL) mapping was combined with allele mining in a natural population including 219 landraces. The eQTL mapping showed that a combination of both cis- and trans-acting eQTLs might control GmRCAβ expression. As promoters can affect both cis- and trans-acting eQTLs by altering cis-acting regulatory elements or transcription factor binding sites, this work subsequently focused on the promoter region of GmRCAβ. Single-nucleotide polymorphisms in the GmRCAβ promoter were identified and shown to correlate with expression level diversity. These SNPs were classified into two groups, A and B. Further transient expression showed that GUS expression driven by the group A promoter was stronger than that by the group B promoter, suggesting that promoter sequence types could influence gene expression levels. These results would improve understanding how variation within promoters affects gene expression and, ultimately, phenotypic diversity in natural populations.
doi:10.1093/jxb/ert346
PMCID: PMC3883283  PMID: 24170743
Allele mining; eQTL; photosynthesis; promoter; Rubisco activase; seed yield; soybean [Glycine max (L.) Merr.]
8.  Identification and Characterization of a Novel Monoterpene Synthase from Soybean Restricted to Neryl Diphosphate Precursor 
PLoS ONE  2013;8(10):e75972.
Terpenes are important defensive compounds against herbivores and pathogens. Here, we report the identification of a new monoterpene synthase gene, GmNES, from soybean. The transcription of GmNES was up-regulated in soybean plants that were infested with cotton leafworm (Prodenia litura), mechanically wounded or treated with salicylic acid (SA). Gas chromatography-mass spectrometry (GC-MS) analysis revealed that recombinant GmNES enzyme exclusively produced nerol, generated from a newly identified substrate for monoterpene synthase: neryl diphosphate (NPP). This finding indicates that GmNES is a nerol synthase gene in soybean. Subcellular localization using GFP fusions showed that GmNES localized to the chloroplasts. Transgenic tobacco overexpressing GmNES was generated. In dual-choice assays, the GmNES-expressing tobacco lines significantly repelled cotton leafworm. In feeding tests with transgenic plants, the growth and development of cotton leafworm were significantly retarded. This study confirms the ecological role of terpenoids and provides new insights into their metabolic engineering in transgenic plants.
doi:10.1371/journal.pone.0075972
PMCID: PMC3790869  PMID: 24124526
9.  GmNAC5, a NAC Transcription Factor, Is a Transient Response Regulator Induced by Abiotic Stress in Soybean 
The Scientific World Journal  2013;2013:768972.
GmNAC5 is a member of NAM subfamily belonging to NAC transcription factors in soybean (Glycine max (L.) Merr.). Studies on NAC transcription factors have shown that this family functioned in the regulation of shoot apical meristem (SAM), hormone signalling, and stress responses. In this study, we examined the expression levels of GmNAC5. GmNAC5 was highly expressed in the roots and immature seeds, especially strongly in immature seeds of 40 days after flowering. In addition, we found that GmNAC5 was induced by mechanical wounding, high salinity, and cold treatments but was not induced by abscisic acid (ABA). The subcellular localization assay suggested that GmNAC5 was targeted at nucleus. Together, it was suggested that GmNAC5 might be involved in seed development and abiotic stress responses in soybean.
doi:10.1155/2013/768972
PMCID: PMC3745988  PMID: 23983646
10.  Sensory and cognitive influences on the training-related improvement of reading speed in peripheral vision 
Journal of Vision  2013;13(7):14.
Reading speed in normal peripheral vision is slow but can be increased through training on a letter-recognition task. The aim of the present study is to investigate the sensory and cognitive factors responsible for this improvement. The visual span is hypothesized to be a sensory bottleneck limiting reading speed. Three sensory factors—letter acuity, crowding, and mislocations (errors in the spatial order of letters)—may limit the size of the visual span. Reading speed is also influenced by cognitive factors including the utilization of information from sentence context. We conducted a perceptual training experiment to investigate the roles of these factors. Training consisted of four daily sessions of trigram letter-recognition trials at 10° in the lower visual field. Subjects' visual-span profiles and reading speeds were measured in pre- and posttests. Effects of the three sensory factors were isolated through a decomposition analysis of the visual span profiles. The impact of sentence context was indexed by context gain, the ratio of reading speeds for ordered and unordered text. Following training, visual spans increased in size by 5.4 bits of information transmitted, and reading speeds increased by 45%. Training induced a substantial reduction in the magnitude of crowding (4.8 bits) and a smaller reduction for mislocations (0.7 bits), but no change in letter acuity or context gain. These results indicate that the basis of the training-related improvement in reading speed is a large reduction in the interfering effect of crowding and a small reduction of mislocation errors.
doi:10.1167/13.7.14
PMCID: PMC3692378  PMID: 23798030
reading; peripheral vision; visual span; crowding; context gain
11.  Identification and Detection of Simple 3D Objects with Severely Blurred Vision 
Purpose.
Detecting and recognizing three-dimensional (3D) objects is an important component of the visual accessibility of public spaces for people with impaired vision. The present study investigated the impact of environmental factors and object properties on the recognition of objects by subjects who viewed physical objects with severely reduced acuity.
Methods.
The experiment was conducted in an indoor testing space. We examined detection and identification of simple convex objects by normally sighted subjects wearing diffusing goggles that reduced effective acuity to 20/900. We used psychophysical methods to examine the effect on performance of important environmental variables: viewing distance (from 10–24 feet, or 3.05–7.32 m) and illumination (overhead fluorescent and artificial window), and object variables: shape (boxes and cylinders), size (heights from 2–6 feet, or 0.61–1.83 m), and color (gray and white).
Results.
Object identification was significantly affected by distance, color, height, and shape, as well as interactions between illumination, color, and shape. A stepwise regression analysis showed that 64% of the variability in identification could be explained by object contrast values (58%) and object visual angle (6%).
Conclusions.
When acuity is severely limited, illumination, distance, color, height, and shape influence the identification and detection of simple 3D objects. These effects can be explained in large part by the impact of these variables on object contrast and visual angle. Basic design principles for improving object visibility are discussed.
This research examines the effects of illumination, viewing distance, color, height, and shape on the visibility of simple convex objects in low-resolution viewing conditions. Basic design principles for improving object visibility are discussed.
doi:10.1167/iovs.12-10013
PMCID: PMC4113330  PMID: 23111613
12.  Diversifying Selection on Flavanone 3-Hydroxylase and Isoflavone Synthase Genes in Cultivated Soybean and Its Wild Progenitors 
PLoS ONE  2013;8(1):e54154.
Soybean isoflavone synthase (IFS) and flavanone 3-hydroxylase (F3H) are two key enzymes catalyzing the biosynthesis of isoflavonoids and flavonoids, both of which play diverse roles in stress responses. However, little is known about the evolutionary pattern of these genes in cultivated soybean and its wild progenitors. Herein, we investigated the nucleotide polymorphisms in Isoflavone synthase (IFS1, IFS2) and Flavanone 3-hydroxylase (F3H2) genes from 33 soybean accessions, including 17 cultivars (Glycine max) and 16 their wild progenitors (Glycine soja). Our data showed that the target genes shared the levels of nucleotide polymorphism with three reference genes involved in plant-microbe interactions, but possessed a much higher nucleotide polymorphism than other reference genes. Moreover, no significant genetic differentiation was found between cultivated soybean and its wild relatives in three target genes, despite of considering bottleneck and founder effect during domestication. These results indicate that IFS and F3H genes could have experienced gene introgressions or diversifying selection events during domestication process. Especially, F3H2 gene appears to evolve under positive selection and enjoy a faster evolutionary rate than IFS1 and IFS2 genes.
doi:10.1371/journal.pone.0054154
PMCID: PMC3546919  PMID: 23342093
13.  The Mechanism of Word Crowding 
Vision research  2011;52(1):61-69.
Word reading speed in peripheral vision is slower when words are in close proximity of other words (Chung, 2004). This word crowding effect could arise as a consequence of interaction of low-level letter features between words, or the interaction between high-level holistic representations of words. We evaluated these two hypotheses by examining how word crowding changes for five configurations of flanking words: the control condition — flanking words were oriented upright; scrambled — letters in each flanking word were scrambled in order; horizontal-flip — each flanking word was the left-right mirror-image of the original; letter-flip — each letter of the flanking word was the left-right mirror-image of the original; and vertical-flip — each flanking word was the up-down mirror-image of the original. The low-level letter feature interaction hypothesis predicts similar word crowding effect for all the different flanker configurations, while the high-level holistic representation hypothesis predicts less word crowding effect for all the alternative flanker conditions, compared with the control condition. We found that oral reading speed for words flanked above and below by other words, measured at 10° eccentricity in the nasal field, showed the same dependence on the vertical separation between the target and its flanking words, for the various flanker configurations. The result was also similar when we rotated the flanking words by 90° to disrupt the periodic vertical pattern, which presumably is the main structure in words. The remarkably similar word crowding effect irrespective of the flanker configurations suggests that word crowding arises as a consequence of interactions of low-level letter features.
doi:10.1016/j.visres.2011.10.015
PMCID: PMC3246086  PMID: 22079315
crowding; word recognition; peripheral vision; features; holistic representation
14.  Mapping QTLs for Tissue Culture Response in Soybean (Glycine max (L.) Merr.) 
Molecules and Cells  2011;32(4):337-342.
Quantitative trait loci (QTLs) that control the tissue culture response in soybean were detected by using 184 recombinant inbred lines (RILs) derived from two varieties: Kefeng No.1 and Nannong 1138-2. The molecular map consisting of 834 molecular markers using this population covered space 2307.83 cM of the genome throughout 24 linkage groups. The performance of tissue culture in soybean was evaluated by two indices: callus induction frequency (CIF) and somatic embryos initiation frequency (SEIF). They were expressed as the number of explants producing callus/ the number of total explants and the number of explants producing somatic embryos/ the number of total explants, respectively. The RIL lines showed continuous segregation for both indices. With the composite interval mapping (CIM) described in Windows QTL Cartographer Version 2.5, three quantitative trait loci (QTLs) were identified for the frequency of callus induction, on chromosomes B2 and D2, accounting for phenotypic variation from 5.84% to 16.60%; four QTLs on chromosome G were detected for the frequency of somatic embryos initiation and explained the phenotypic variation from 7.79% to 14.16%. The information of new QTLs identified in the present study will contribute to genetic improvement of regeneration traits with marker-assisted selection (MAS) in soybean.
doi:10.1007/s10059-011-0063-1
PMCID: PMC3887643  PMID: 21952936
quantitative trait loci; recombinant inbred line population; somatic embryogenesis; soybean (Glycine max (L.) Merr.); tissue culture response
15.  Proteome Analysis of the Wild and YX-1 Male Sterile Mutant Anthers of Wolfberry (Lycium barbarum L.) 
PLoS ONE  2012;7(7):e41861.
Pollen development is disturbed in the early tetrad stage of the YX-1 male sterile mutant of wolfberry (Lycium barbarum L.). The present study aimed to identify differentially expressed anther proteins and to reveal their possible roles in pollen development and male sterility. To address this question, the proteomes of the wild-type (WT) and YX-1 mutant were compared. Approximately 1760 protein spots on two-dimensional differential gel electrophoresis (2D-DIGE) gels were detected. A number of proteins whose accumulation levels were altered in YX-1 compared with WT were identified by mass spectrometry and the NCBInr and Viridiplantae EST databases. Proteins down-regulated in YX-1 anthers include ascorbate peroxidase (APX), putative glutamine synthetase (GS), ATP synthase subunits, chalcone synthase (CHS), CHS-like, putative callose synthase catalytic subunit, cysteine protease, 5B protein, enoyl-ACP reductase, 14-3-3 protein and basic transcription factor 3 (BTF3). Meanwhile, activities of APX and GS, RNA expression levels of apx and atp synthase beta subunit were low in YX-1 anthers which correlated with the expression of male sterility. In addition, several carbohydrate metabolism-related and photosynthesis-related enzymes were also present at lower levels in the mutant anthers. In contrast, 26S proteasome regulatory subunits, cysteine protease inhibitor, putative S-phase Kinase association Protein 1(SKP1), and aspartic protease, were expressed at higher levels in YX-1 anthers relative to WT anthers. Regulation of wolfberry pollen development involves a complex network of differentially expressed genes. The present study lays the foundation for future investigations of gene function linked with wolfberry pollen development and male sterility.
doi:10.1371/journal.pone.0041861
PMCID: PMC3408462  PMID: 22860020
16.  Critical Orientation for Face Identification in Central Vision Loss 
Purpose
Difficulty identifying faces is a common complaint of people with central vision loss. Dakin and Watt (2009) reported that the horizontal components of face images are most informative for face identification in normal vision. In this study, we examined whether people with central vision loss similarly rely primarily on the horizontal components of face images for face identification.
Methods
Seven observers with central vision loss (mean age = 69 ± 9 [SD]) and five age-matched observers with normal vision (mean age = 65 ± 6) participated in the study. We measured observers’ accuracy for reporting the identity of face images spatially filtered using an orientation filter with center orientation ranging from 0° (horizontal) to 150° in steps of 30°, with a bandwidth of 23°. Face images without filtering were also tested.
Results
For all observers, accuracy for identifying filtered face images was highest around the horizontal orientation, dropping systematically as the filter orientation deviated systematically from horizontal, and was the lowest at the vertical orientation. Compared with control observers, observers with central vision loss showed (1) a larger difference in accuracy between identifying filtered (at peak performance) and unfiltered face images; (2) a reduced accuracy at peak performance and (3) a smaller difference in performance for identifying filtered images between the horizontal and the vertical filter orientation.
Conclusions
Spatial information around the horizontal orientation in face images is the most important for face identification, for people with normal vision and central vision loss alike. While the horizontal information alone can support reasonably good performance for identifying faces in people in normal vision, people with central vision loss seem to also rely on information along other orientations.
doi:10.1097/OPX.0b013e318213933c
PMCID: PMC3100384  PMID: 21399554
low vision; spatial vision; psychophysics; face identification; central vision loss
17.  Proteomic analysis of soybean defense response induced by cotton worm (prodenia litura, fabricius) feeding 
Proteome Science  2012;10:16.
Background
Cotton worm is one of the main insects of soybean in southern China. Plants may acquire defense mechanisms that confer protection from predation by herbivores. Induced responses can lead to increased resistance against herbivores in many species. This study focuses on searching changed proteins in soybean defense response induced by cotton worm feeding.
Results
Ten protein spots that are changed in abundance in response to cotton worm feeding were identified by Two-dimensional gel electrophoresis (2-DE). A total of 11 unique proteins from these spots were identified by MALDI-TOF MS. The mRNA and protein relative expression levels of most changed proteins were up-regulated. These proteins were mainly involved in physiological processes, including active oxygen removal, defense signal transduction, and metabolism regulation.
Conclusion
This is the first proteomic analysis of the soybean defense response induced by cotton worm. The differentially expressed proteins could work together to play a major role in the induced defense response. PAL and SAMS were up-regulated at both the protein and mRNA levels. These genes can be strongest candidates for further functional research.
doi:10.1186/1477-5956-10-16
PMCID: PMC3325874  PMID: 22397523
Soybean; Induced resistance; 2-DE; qRT-PCR
18.  Reading Speed in the peripheral visual field of older adults: Does it benefit from perceptual learning? 
Vision research  2010;50(9):860-869.
Enhancing reading ability in peripheral vision is important for the rehabilitation of people with central-visual-field loss from age-related macular degeneration (AMD). Previous research has shown that perceptual learning, based on a trigram letter-recognition task, improved peripheral reading speed among normally-sighted young adults (Chung, Legge & Cheung, 2004). Here we ask whether the same happens in older adults in an age range more typical of the onset of AMD. Eighteen normally-sighted subjects, aged 55 to 76 years, were randomly assigned to training or control groups. Visual-span profiles (plots of letter-recognition accuracy as a function of horizontal letter position) and RSVP reading speeds were measured at 10° above and below fixation during pre- and post-tests for all subjects. Training consisted of repeated measurements of visual-span profiles at 10° below fixation, in 4 daily sessions. The control subjects did not receive any training. Perceptual learning enlarged the visual spans in both trained (lower) and untrained (upper) visual fields. Reading speed improved in the trained field by 60% when the trained print size was used. The training benefits for these older subjects were weaker than the training benefits for young adults found by Chung et al. Despite the weaker training benefits, perceptual learning remains a potential option for low-vision reading rehabilitation among older adults.
doi:10.1016/j.visres.2010.02.006
PMCID: PMC2858588  PMID: 20156473
19.  Development of a training protocol to improve reading performance in peripheral vision 
Vision research  2010;50(1):36-45.
People with central-field loss must use peripheral vision for reading. Previous studies have shown that reading performance in peripheral vision can improve with extensive practice on a trigram letter-recognition task. The present study compared training on this task with training on two other character-based tasks (lexical decision and RSVP (Rapid Serial Visual Presentation) reading) which might plausibly produce more improvement in peripheral reading speed. Twenty-eight normally sighted young adults were trained at 10° in the lower visual field in a pre/post design. All three training methods produced significant improvements in reading speed, with average gains of 39% for lexical-decision, 54% for trigram letter-recognition, and 72% for RSVP training. Although the RSVP training was most effective, the lexical-decision task has the advantage of easy self administration making it more practical for home-based training.
doi:10.1016/j.visres.2009.10.005
PMCID: PMC2794940  PMID: 19819251
visual span; reading speed; perceptual learning; peripheral vision; visual training
20.  VISUAL ACCESSIBILITY OF RAMPS AND STEPS 
Journal of vision  2010;10(11):8.
The visual accessibility of a space refers to the effectiveness with which vision can be used to travel safely through the space. For people with low vision, the detection of steps and ramps is an important component of visual accessibility. We used ramps and steps as visual targets to examine the interacting effects of lighting, object geometry, contrast, viewing distance and spatial resolution. Wooden staging was used to construct a sidewalk with transitions to ramps or steps. 48 normally sighted subjects viewed the sidewalk monocularly through acuity-reducing goggles, and made recognition judgments about the presence of the ramps or steps. The effects of variation in lighting were milder than expected. Performance declined for the largest viewing distance, but exhibited a surprising reversal for nearer viewing. Of relevance to pedestrian safety, the step up was more visible than the step down. We developed a probabilistic cue model to explain the pattern of target confusions. Cues determined by discontinuities in the edge contours of the sidewalk at the transition to the targets were vulnerable to changes in viewing conditions. Cues associated with the height in the picture plane of the targets were more robust.
doi:10.1167/10.11.8
PMCID: PMC2951310  PMID: 20884503
visual accessibility; low vision; mobility; visual acuity; visual contrast; visual recognition; steps; ramps
21.  Comparing Reading Speed for Horizontal and Vertical English Text 
Journal of vision  2010;10(2):21.1-2117.
There are three formats for arranging English text for vertical reading—upright letters arranged vertically (marquee), and horizontal text rotated 90° clockwise or counterclockwise. Previous research has shown that reading is slower for all three vertical formats than for horizontal text, with marquee being slowest. It has been proposed that the size of the visual span—the number of letters recognized with high accuracy without moving the eyes—is a visual factor limiting reading speed. We predicted that reduced visual-span size would be correlated with the slower reading for the three vertical formats. We tested this prediction with uppercase and lowercase letters. Reading performance was measured using two presentation methods: RSVP (Rapid Serial Visual Presentation) and flashcard (a block of text on four lines). On average, reading speed for horizontal text was 139% faster than marquee text and 81% faster than the rotated texts. Size of the visual span was highly correlated with changes in reading speed for both lowercase and uppercase letters and for both RSVP and flashcard reading. Our results are consistent with the view that slower reading of vertical text is due to a decrease in the size of the visual span for vertical reading.
doi:10.1167/10.2.21
PMCID: PMC2921212  PMID: 20462322
Visual span; Letter recognition; Reading speed; Vertical reading
22.  Effect of letter spacing on visual span and reading speed 
Journal of vision  2007;7(2):2.1-210.
S. T. L. Chung (2002) has shown that rapid serial visual presentation (RSVP) reading speed varies with letter spacing, peaking near the standard letter spacing for text and decreasing for both smaller and larger spacings. In this study, we tested the hypothesis that the dependence of reading speed on letter spacing is mediated by the size of the visual span—the number of letters recognized with high accuracy without moving the eyes. If so, the size of the visual span and reading speed should show a similar dependence on letter spacing. We tested this prediction for RSVP reading and asked whether it generalizes to the reading of blocks of text requiring eye movements. We measured visual-span profiles and reading speeds as a function of letter spacing. Visual-span profiles, measured with trigrams (strings of three random letters), are plots of letter-recognition accuracy as a function of letter position left or right of fixation. Size of the visual span was quantified by a measure of the area under the visual-span profile. Reading performance was measured using two presentation methods: RSVP and flashcard (a short block of text on four lines). We found that the size of the visual span and the reading speeds measured by the two presentation methods showed a qualitatively similar dependence on letter spacing and that they were highly correlated. These results are consistent with the view that the size of the visual span is a primary visual factor that limits reading speed.
doi:10.1167/7.2.2
PMCID: PMC2729067  PMID: 18217817
visual span; reading speed; letter spacing; visual crowding
23.  The case for the visual span as a sensory bottleneck in reading 
Journal of vision  2007;7(2):9.1-915.
The visual span for reading is the number of letters, arranged horizontally as in text, that can be recognized reliably without moving the eyes. The visual-span hypothesis states that the size of the visual span is an important factor that limits reading speed. From this hypothesis, we predict that changes in reading speed as a function of character size or contrast are determined by corresponding changes in the size of the visual span. We tested this prediction in two experiments in which we measured the size of the visual span and reading speed on groups of five subjects as a function of either character size or character contrast. We used a “trigram method” for characterizing the visual span as a profile of letter-recognition accuracy as a function of distance left and right of the midline (G. E. Legge, J. S. Mansfield, & S. T. L. Chung, 2001). The area under this profile was taken as an operational measure of the size of the visual span. Reading speed was measured with the Rapid Serial Visual Presentation (RSVP) method. We found that the size of the visual span and reading speed showed the same qualitative dependence on character size and contrast, reached maximum values at the same critical points, and exhibited high correlations at the level of individual subjects. Additional analysis of data from four studies provides evidence for an invariant relationship between the size of the visual span and RSVP reading speed; an increase in the visual span by one letter is associated with a 39% increase in reading speed. Our results confirm the visual-span hypothesis and provide a theoretical framework for understanding the impact of stimulus attributes, such as contrast and character size, on reading speed. Evidence for the visual span as a determinant of reading speed implies the existence of a bottom–up, sensory limitation on reading, distinct from attentional, motor, or linguistic influences.
doi:10.1167/7.2.9
PMCID: PMC2729064  PMID: 18217824
vision; contrast; character size; visual span; low vision; reading; reading speed

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