New Method for Phase transitions in diblock copolymers: The Lamellar case

A new mean-field type theory is proposed to study order-disorder transitions (ODT) in block copolymers. The theory applies to both the weak segregation (WS) and the strong segregation (SS) regimes. A new energy functional is proposed without appealing to the random phase approximation (RPA). We find new terms unaccounted for within RPA. We work out in detail transitions to the lamellar state and compare the method to other existing theories of ODT and numerical simulations. We find good agreements with recent experimental results and predict that the intermediate segregation regime may have more than one scaling behavior.Comment: 23 pages, 8 figure

Inter-molecular structure factors of macromolecules in solution: integral equation results

The inter-molecular structure of semidilute polymer solutions is studied theoretically. The low density limit of a generalized Ornstein-Zernicke integral equation approach to polymeric liquids is considered. Scaling laws for the dilute-to-semidilute crossover of random phase (RPA) like structure are derived for the inter-molecular structure factor on large distances when inter-molecular excluded volume is incorporated at the microscopic level. This leads to a non-linear equation for the excluded volume interaction parameter. For macromolecular size-mass scaling exponents, $\nu$, above a spatial-dimension dependent value, $\nu_c=2/d$, mean field like density scaling is recovered, but for $\nu<\nu_c$ the density scaling becomes non-trivial in agreement with field theoretic results and justifying phenomenological extensions of RPA. The structure of the polymer mesh in semidilute solutions is discussed in detail and comparisons with large scale Monte Carlo simulations are added. Finally a new possibility to determine the correction to scaling exponent $\omega_{12}$ is suggested.Comment: 11 pages, 5 figures; to be published in Phys. Rev. E (1999

Increasing cassava root yield: additive-dominant genetic models for selection of parents and clones.

Genomic selection has been promising in situations where phenotypic assessments are expensive, laborious, and/or inefficient. This work evaluated the efficiency of genomic prediction methods combined with genetic models in clone and parent selection with the goal of increasing fresh root yield, dry root yield, as well as dry matter content in cassava roots. The bias and predictive ability of the combinations of prediction methods Genomic Best Linear Unbiased Prediction (G-BLUP), Bayes B, Bayes Cr, and Reproducing Kernel Hilbert Spaces with additive and additive-dominant genetic models were estimated. Fresh and dry root yield exhibited predominantly dominant heritability, while dry matter content exhibited predominantly additive heritability. The combination of prediction methods and genetic models did not show significant differences in the predictive ability for dry matter content. On the other hand, the prediction methods with additive-dominant genetic models had significantly higher predictive ability than the additive genetic models for fresh and dry root yield, allowing higher genetic gains in clone selection. However, higher predictive ability for genotypic values did not result in differences in breeding value predictions between additive and additive-dominant genetic models. G-BLUP with the classical additive-dominant genetic model had the best predictive ability and bias estimates for fresh and dry root yield. For dry matter content, the highest predictive ability was obtained by G-BLUP with the additive genetic model. Dry matter content exhibited the highest heritability, predictive ability, and bias estimates compared with other traits. The prediction methods showed similar selection gains with approximately 67% of the phenotypic selection gain. By shortening the breeding cycle time by 40%, genomic selection may overcome phenotypic selection by 10%, 13%, and 18% for fresh root yield, dry root yield, and dry matter content, respectively, with a selection proportion of 15%. The most suitable genetic model for each trait allows for genomic selection optimization in cassava with high selection gains, thereby accelerating the release of new varieties

Reproducibility of microvessel counts in breast cancer specimens

Assessment of tumour vascularity in core biopsy specimens may be a useful predictor of response to primary therapy. This study addresses practical methodological issues regarding accuracy of tumour vascularity assessments in different breast cancer specimens. Issues addressed in the study are variation caused by (i) inherent observer variation in the method, (ii) tumour heterogeneity and (iii) previous surgical manipulation of tumours. Microvessel counts were performed by two observers on separate occasions and by two different observers. Counts were performed on core biopsies and tumour sections taken simultaneously (n = 16) and with an intervening time interval (n = 21). In addition core biopsies were obtained from the same tumour on two separate occasions (n = 10). A highly significant correlation was found in counts performed by the same observers at different times and between two different observers. No significant correlation was found in counts of core biopsies and tumour sections taken either simultaneously or subsequently. No correlation was found between counts of sequential core biopsies. Study findings suggest that, although microvessel counts may be assessed reproducibly by the same and different observers, counts performed in core biopsies do not accurately reflect those of overall tumour, limiting their potential as predictive or prognostic markers. © 1999 Cancer Research Campaig

In silico genotyping of the maize nested association mapping population

Nested Association Mapping (NAM) has been proposed as a means to combine the power of linkage mapping with the resolution of association mapping. It is enabled through sequencing or array genotyping of parental inbred lines while using low-cost, low-density genotyping technologies for their segregating progenies. For purposes of data analyses of NAM populations, parental genotypes at a large number of Single Nucleotide Polymorphic (SNP) loci need to be projected to their segregating progeny. Herein we demonstrate how approximately 0.5 million SNPs that have been genotyped in 26 parental lines of the publicly available maize NAM population can be projected onto their segregating progeny using only 1,106 SNP loci that have been genotyped in both the parents and their 5,000 progeny. The challenge is to estimate both the genotype and genetic location of the parental SNP genotypes in segregating progeny. Both challenges were met by estimating their expected genotypic values conditional on observed flanking markers through the use of both physical and linkage maps. About 90%, of 500,000 genotyped SNPs from the maize HapMap project, were assigned linkage map positions using linear interpolation between the maize Accessioned Gold Path (AGP) and NAM linkage maps. Of these, almost 70% provided high probability estimates of genotypes in almost 5,000 recombinant inbred lines

Validation of a low-cost virtual reality system for training street-crossing. A comparative study in healthy, neglected and non-neglected stroke individuals

Unilateral spatial neglect is a common consequence of stroke that directly affects the performance of activities of daily living. This impairment is traditionally assessed with paper-and-pencil tests that can lack correspondence to real life and are easily compensated. Virtual reality can immerse patients in more ecological scenarios, thus providing therapists with new tools to assess and train the effects of this impairment in simulated real tasks. This paper presents the clinical validation and convergent validity of a low-cost virtual reality system for training street-crossing in stroke patients with and without neglect. The performance of neglect patients was significantly worse than the performance of non-neglect and healthy participants. In addition, several correlations between the scores in the system and in the traditional scales were detected.This study was funded in part by Ministerio de Educacion y Ciencia Spain, Projects Consolider-C (SEJ2006-14301/PSIC), "CIBER of Physiopathology of Obesity and Nutrition, an initiative of ISCIII" and the Excellence Research Program PROMETEO (Generalitat Valenciana. Conselleria de Educacion, 2008-157).Navarro, MD.; Llorens Rodríguez, R.; Noé, E.; Ferri, J.; Alcañiz Raya, ML. (2013). Validation of a low-cost virtual reality system for training street-crossing. A comparative study in healthy, neglected and non-neglected stroke individuals. Neuropsychological Rehabilitation. 23(4):597-618. https://doi.org/10.1080/09602011.2013.806269S597618234Allegri, R. F. (2000). Atención y negligencia: bases neurológicas, evaluación y trastornos. Revista de Neurología, 30(05), 491. doi:10.33588/rn.3005.99645Appelros, P., Karlsson, G. M., Seiger, &#x000C5;ke, & Nydevik, I. (2002). Neglect and Anosognosia After First-Ever Stroke: Incidence and Relationship to Disability. Journal of Rehabilitation Medicine, 34(5), 215-220. doi:10.1080/165019702760279206Baheux, K., Yoshizawa, M., & Yoshida, Y. (2007). Simulating hemispatial neglect with virtual reality. Journal of NeuroEngineering and Rehabilitation, 4(1). doi:10.1186/1743-0003-4-27Boian, R. F., Burdea, G. C., Deutsch, J. E. and Winter, S. H. Street crossing using a virtual environment mobility simulator.Paper presented at 3rd Annual International Workshop on Virtual Reality. Lausanne, Switzerland.Broeren, J., Samuelsson, H., Stibrant-Sunnerhagen, K., Blomstrand, C., & Rydmark, M. (2007). Neglect assessment as an application of virtual reality. Acta Neurologica Scandinavica, 116(3), 157-163. doi:10.1111/j.1600-0404.2007.00821.xBuxbaum, L. J., Ferraro, M. K., Veramonti, T., Farne, A., Whyte, J., Ladavas, E., … Coslett, H. B. (2004). Hemispatial neglect: Subtypes, neuroanatomy, and disability. Neurology, 62(5), 749-756. doi:10.1212/01.wnl.0000113730.73031.f4Buxbaum, L. J., Palermo, M. A., Mastrogiovanni, D., Read, M. S., Rosenberg-Pitonyak, E., Rizzo, A. A., & Coslett, H. B. (2008). Assessment of spatial attention and neglect with a virtual wheelchair navigation task. Journal of Clinical and Experimental Neuropsychology, 30(6), 650-660. doi:10.1080/13803390701625821Castiello, U., Lusher, D., Burton, C., Glover, S., & Disler, P. (2004). Improving left hemispatial neglect using virtual reality. Neurology, 62(11), 1958-1962. doi:10.1212/01.wnl.0000128183.63917.02Conners, C. K., Epstein, J. N., Angold, A., & Klaric, J. (2003). Journal of Abnormal Child Psychology, 31(5), 555-562. doi:10.1023/a:1025457300409Folstein, M. F., Folstein, S. E., & McHugh, P. R. (1975). «Mini-mental state». Journal of Psychiatric Research, 12(3), 189-198. doi:10.1016/0022-3956(75)90026-6Fordell, H., Bodin, K., Bucht, G., & Malm, J. (2011). A virtual reality test battery for assessment and screening of spatial neglect. Acta Neurologica Scandinavica, 123(3), 167-174. doi:10.1111/j.1600-0404.2010.01390.xGupta, V., Knott, B. A., Kodgi, S., & Lathan, C. E. (2000). Using the «VREye» System for the Assessment of Unilateral Visual Neglect: Two Case Reports. Presence: Teleoperators and Virtual Environments, 9(3), 268-286. doi:10.1162/105474600566790Hartman-Maeir, A., & Katz, N. (1995). Validity of the Behavioral Inattention Test (BIT): Relationships With Functional Tasks. American Journal of Occupational Therapy, 49(6), 507-516. doi:10.5014/ajot.49.6.507Jannink, M. J. A., Aznar, M., de Kort, A. C., van de Vis, W., Veltink, P., & van der Kooij, H. (2009). Assessment of visuospatial neglect in stroke patients using virtual reality: a pilot study. International Journal of Rehabilitation Research, 32(4), 280-286. doi:10.1097/mrr.0b013e3283013b1cJehkonen, M., Laihosalo, M., & Kettunen, J. (2006). Anosognosia after stroke: assessment, occurrence, subtypes and impact on functional outcome reviewed. Acta Neurologica Scandinavica, 114(5), 293-306. doi:10.1111/j.1600-0404.2006.00723.xKatz, N., Ring, H., Naveh, Y., Kizony, R., Feintuch, U., & Weiss, P. L. (2005). Interactive virtual environment training for safe street crossing of right hemisphere stroke patients with Unilateral Spatial Neglect. Disability and Rehabilitation, 27(20), 1235-1244. doi:10.1080/09638280500076079Kim, D. Y., Ku, J., Chang, W. H., Park, T. H., Lim, J. Y., Han, K., … Kim, S. I. (2010). Assessment of post-stroke extrapersonal neglect using a three-dimensional immersive virtual street crossing program. Acta Neurologica Scandinavica, 121(3), 171-177. doi:10.1111/j.1600-0404.2009.01194.xKim, J., Kim, K., Kim, D. Y., Chang, W. H., Park, C.-I., Ohn, S. H., … Kim, S. I. (2007). Virtual Environment Training System for Rehabilitation of Stroke Patients with Unilateral Neglect: Crossing the Virtual Street. CyberPsychology & Behavior, 10(1), 7-15. doi:10.1089/cpb.2006.9998Kim, K., Kim, J., Ku, J., Kim, D. Y., Chang, W. H., Shin, D. I., … Kim, S. I. (2004). A Virtual Reality Assessment and Training System for Unilateral Neglect. CyberPsychology & Behavior, 7(6), 742-749. doi:10.1089/cpb.2004.7.742Kim, Y. M., Chun, M. H., Yun, G. J., Song, Y. J., & Young, H. E. (2011). The Effect of Virtual Reality Training on Unilateral Spatial Neglect in Stroke Patients. Annals of Rehabilitation Medicine, 35(3), 309. doi:10.5535/arm.2011.35.3.309Krakauer, J. W. (2006). Motor learning: its relevance to stroke recovery and neurorehabilitation. Current Opinion in Neurology, 19(1), 84-90. doi:10.1097/01.wco.0000200544.29915.ccMcComas, J., MacKay, M., & Pivik, J. (2002). Effectiveness of Virtual Reality for Teaching Pedestrian Safety. CyberPsychology & Behavior, 5(3), 185-190. doi:10.1089/109493102760147150Myers, R. L., & Bierig, T. A. (2000). Virtual Reality and Left Hemineglect: A Technology for Assessment and Therapy. CyberPsychology & Behavior, 3(3), 465-468. doi:10.1089/10949310050078922Peskine, A., Rosso, C., Box, N., Galland, A., Caron, E., Rautureau, G., … Pradat-Diehl, P. (2010). Virtual reality assessment for visuospatial neglect: importance of a dynamic task. Journal of Neurology, Neurosurgery & Psychiatry, 82(12), 1407-1409. doi:10.1136/jnnp.2010.217513Romero, M., Sánchez, A., Marín, C., Navarro, M. D., Ferri, J., & Noé, E. (2012). Utilidad clínica de la versión en castellano del Mississippi Aphasia Screening Test (MASTsp): validación en pacientes con ictus. Neurología, 27(4), 216-224. doi:10.1016/j.nrl.2011.06.006Rose, F. D., Brooks, B. M., & Rizzo, A. A. (2005). Virtual Reality in Brain Damage Rehabilitation: Review. CyberPsychology & Behavior, 8(3), 241-262. doi:10.1089/cpb.2005.8.241Schwebel, D. C., & McClure, L. A. (2010). Using virtual reality to train children in safe street-crossing skills. Injury Prevention, 16(1), e1-e1. doi:10.1136/ip.2009.025288Simpson, G., Johnston, L., & Richardson, M. (2003). An investigation of road crossing in a virtual environment. Accident Analysis & Prevention, 35(5), 787-796. doi:10.1016/s0001-4575(02)00081-7Smith, J., Hebert, D., & Reid, D. (2007). Exploring the effects of virtual reality on unilateral neglect caused by stroke: Four case studies. Technology and Disability, 19(1), 29-40. doi:10.3233/tad-2007-19104Sugarman, H., Weisel-Eichler, A., Burstin, A. and Brown, R.Use of novel virtual reality system for the assessment and treatment of unilateral spatial neglect: A feasibility study. Paper presented at International Conference on Virtual Rehabilitation. Zürich.Tanaka, T., Sugihara, S., Nara, H., Ino, S., & Ifukube, T. (2005). Journal of NeuroEngineering and Rehabilitation, 2(1), 31. doi:10.1186/1743-0003-2-31Thomson, J. A., Tolmie, A. K., Foot, H. C., Whelan, K. M., Sarvary, P., & Morrison, S. (2005). Influence of Virtual Reality Training on the Roadside Crossing Judgments of Child Pedestrians. Journal of Experimental Psychology: Applied, 11(3), 175-186. doi:10.1037/1076-898x.11.3.175Weiss, P. L. (Tamar), Naveh, Y., & Katz, N. (2003). Design and testing of a virtual environment to train stroke patients with unilateral spatial neglect to cross a street safely. Occupational Therapy International, 10(1), 39-55. doi:10.1002/oti.176Witmer, B. G., & Singer, M. J. (1998). Measuring Presence in Virtual Environments: A Presence Questionnaire. Presence: Teleoperators and Virtual Environments, 7(3), 225-240. doi:10.1162/105474698565686Wu, H., Ashmead, D. H. and Bodenheimer, B.Using immersive virtual reality to evaluate pedestrian street crossing decisions at a roundabout. Paper presented at 6th Symposium on appied perception in Graphics and Visualization. Chania

New DArT markers for oat provide enhanced map coverage and global germplasm characterization

BACKGROUND: Genomic discovery in oat and its application to oat improvement have been hindered by a lack of genetic markers common to different genetic maps, and by the difficulty of conducting whole-genome analysis using high-throughput markers. This study was intended to develop, characterize, and apply a large set of oat genetic markers based on Diversity Array Technology (DArT). RESULTS: Approximately 19,000 genomic clones were isolated from complexity-reduced genomic representations of pooled DNA samples from 60 oat varieties of global origin. These were screened on three discovery arrays, with more than 2000 polymorphic markers being identified for use in this study, and approximately 2700 potentially polymorphic markers being identified for use in future studies. DNA sequence was obtained for 2573 clones and assembled into a non-redundant set of 1770 contigs and singletons. Of these, 705 showed highly significant (Expectation < 10E-10) BLAST similarity to gene sequences in public databases. Based on marker scores in 80 recombinant inbred lines, 1010 new DArT markers were used to saturate and improve the 'Kanota' × 'Ogle' genetic map. DArT markers provided map coverage approximately equivalent to existing markers. After binning markers from similar clones, as well as those with 99% scoring similarity, a set of 1295 non-redundant markers was used to analyze genetic diversity in 182 accessions of cultivated oat of worldwide origin. Results of this analysis confirmed that major clusters of oat diversity are related to spring vs. winter type, and to the presence of major breeding programs within geographical regions. Secondary clusters revealed groups that were often related to known pedigree structure. CONCLUSION: These markers will provide a solid basis for future efforts in genomic discovery, comparative mapping, and the generation of an oat consensus map. They will also provide new opportunities for directed breeding of superior oat varieties, and guidance in the maintenance of oat genetic diversity

Joint QTL Linkage Mapping for Multiple-Cross Mating Design Sharing One Common Parent

BACKGROUND: Nested association mapping (NAM) is a novel genetic mating design that combines the advantages of linkage analysis and association mapping. This design provides opportunities to study the inheritance of complex traits, but also requires more advanced statistical methods. In this paper, we present the detailed algorithm of a QTL linkage mapping method suitable for genetic populations derived from NAM designs. This method is called joint inclusive composite interval mapping (JICIM). Simulations were designed on the detected QTL in a maize NAM population and an Arabidopsis NAM population so as to evaluate the efficiency of the NAM design and the JICIM method. PRINCIPAL FINDINGS: Fifty-two QTL were identified in the maize population, explaining 89% of the phenotypic variance of days to silking, and nine QTL were identified in the Arabidopsis population, explaining 83% of the phenotypic variance of flowering time. Simulations indicated that the detection power of these identified QTL was consistently high, especially for large-effect QTL. For rare QTL having significant effects in only one family, the power of correct detection within the 5 cM support interval was around 80% for 1-day effect QTL in the maize population, and for 3-day effect QTL in the Arabidopsis population. For smaller-effect QTL, the power diminished, e.g., it was around 50% for maize QTL with an effect of 0.5 day. When QTL were linked at a distance of 5 cM, the likelihood of mapping them as two distinct QTL was about 70% in the maize population. When the linkage distance was 1 cM, they were more likely mapped as one single QTL at an intermediary position. CONCLUSIONS: Because it takes advantage of the large genetic variation among parental lines and the large population size, NAM is a powerful multiple-cross design for complex trait dissection. JICIM is an efficient and specialty method for the joint QTL linkage mapping of genetic populations derived from the NAM design

Extension of the bayesian alphabet for genomic selection

<p>Abstract</p> <p>Background</p> <p>Two Bayesian methods, BayesC<it>π </it>and BayesD<it>π</it>, were developed for genomic prediction to address the drawback of BayesA and BayesB regarding the impact of prior hyperparameters and treat the prior probability <it>π </it>that a SNP has zero effect as unknown. The methods were compared in terms of inference of the number of QTL and accuracy of genomic estimated breeding values (GEBVs), using simulated scenarios and real data from North American Holstein bulls.</p> <p>Results</p> <p>Estimates of <it>π </it>from BayesC<it>π</it>, in contrast to BayesD<it>π</it>, were sensitive to the number of simulated QTL and training data size, and provide information about genetic architecture. Milk yield and fat yield have QTL with larger effects than protein yield and somatic cell score. The drawback of BayesA and BayesB did not impair the accuracy of GEBVs. Accuracies of alternative Bayesian methods were similar. BayesA was a good choice for GEBV with the real data. Computing time was shorter for BayesC<it>π </it>than for BayesD<it>π</it>, and longest for our implementation of BayesA.</p> <p>Conclusions</p> <p>Collectively, accounting for computing effort, uncertainty as to the number of QTL (which affects the GEBV accuracy of alternative methods), and fundamental interest in the number of QTL underlying quantitative traits, we believe that BayesC<it>π </it>has merit for routine applications.</p