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  • Publication . Other literature type . Article . 2005
    Open Access
    Authors: 
    Rikkert L. Snoeckx; Patrick L. M. Huygen; Delphine Feldmann; Sandrine Marlin; Françoise Denoyelle; Jaroslaw Waligora; Małgorzata Mueller-Malesińska; Agneszka Pollak; Rafał Płoski; Alessandra Murgia; +54 more
    Countries: Belgium, Netherlands
    Project: NIH | Non-Syndromic Hearing Los... (5R01DC002842-21)

    Hearing impairment (HI) affects 1 in 650 newborns, which makes it the most common congenital sensory impairment. Despite extraordinary genetic heterogeneity, mutations in one gene, GJB2, which encodes the connexin 26 protein and is involved in inner ear homeostasis, are found in up to 50% of patients with autosomal recessive nonsyndromic hearing loss. Because of the high frequency of GJB2 mutations, mutation analysis of this gene is widely available as a diagnostic test. In this study, we assessed the association between genotype and degree of hearing loss in persons with HI and biallelic GJB2 mutations. We performed cross-sectional analyses of GJB2 genotype and audiometric data from 1,531 persons, from 16 different countries, with autosomal recessive, mild-to-profound nonsyndromic HI. The median age of all participants was 8 years; 90% of persons were within the age range of 0-26 years. Of the 83 different mutations identified, 47 were classified as nontruncating, and 36 as truncating. A total of 153 different genotypes were found, of which 56 were homozygous truncating (T/T), 30 were homozygous nontruncating (NT/NT), and 67 were compound heterozygous truncating/nontruncating (T/NT). The degree of HI associated with biallelic truncating mutations was significantly more severe than the HI associated with biallelic nontruncating mutations (P<.0001). The HI of 48 different genotypes was less severe than that of 35delG homozygotes. Several common mutations (M34T, V37I, and L90P) were associated with mild-to-moderate HI (median 25-40 dB). Two genotypes--35delG/R143W (median 105 dB) and 35delG/dela(GJB6-D13S1830) (median 108 dB)--had significantly more-severe HI than that of 35delG homozygotes.

  • Publication . Article . Other literature type . Preprint . 2016
    Open Access English
    Authors: 
    Eyal Elyashiv; Shmuel Sattath; Tina T. Hu; Alon Strutsovsky; Graham McVicker; Peter Andolfatto; Graham Coop; Guy Sella;
    Publisher: Public Library of Science (PLoS)
    Country: United States
    Project: NSF | Collaborative Research: A... (1262645)

    © 2016 Elyashiv et al. Natural selection at one site shapes patterns of genetic variation at linked sites. Quantifying the effects of “linked selection” on levels of genetic diversity is key to making reliable inference about demography, building a null model in scans for targets of adaptation, and learning about the dynamics of natural selection. Here, we introduce the first method that jointly infers parameters of distinct modes of linked selection, notably background selection and selective sweeps, from genome-wide diversity data, functional annotations and genetic maps. The central idea is to calculate the probability that a neutral site is polymorphic given local annotations, substitution patterns, and recombination rates. Information is then combined across sites and samples using composite likelihood in order to estimate genome-wide parameters of distinct modes of selection. In addition to parameter estimation, this approach yields a map of the expected neutral diversity levels along the genome. To illustrate the utility of our approach, we apply it to genome-wide resequencing data from 125 lines in Drosophila melanogaster and reliably predict diversity levels at the 1Mb scale. Our results corroborate estimates of a high fraction of beneficial substitutions in proteins and untranslated regions (UTR). They allow us to distinguish between the contribution of sweeps and other modes of selection around amino acid substitutions and to uncover evidence for pervasive sweeps in untranslated regions (UTRs). Our inference further suggests a substantial effect of other modes of linked selection and of adaptation in particular. More generally, we demonstrate that linked selection has had a larger effect in reducing diversity levels and increasing their variance in D. melanogaster than previously appreciated.

  • Publication . Conference object . Article . Preprint . 2019 . Embargo End Date: 01 Jan 2019
    Open Access
    Authors: 
    Fedor Vladimirovich Borisyuk; Albert Gordo; Viswanath Sivakumar;
    Publisher: arXiv

    In this paper we present a deployed, scalable optical character recognition (OCR) system, which we call Rosetta, designed to process images uploaded daily at Facebook scale. Sharing of image content has become one of the primary ways to communicate information among internet users within social networks such as Facebook and Instagram, and the understanding of such media, including its textual information, is of paramount importance to facilitate search and recommendation applications. We present modeling techniques for efficient detection and recognition of text in images and describe Rosetta's system architecture. We perform extensive evaluation of presented technologies, explain useful practical approaches to build an OCR system at scale, and provide insightful intuitions as to why and how certain components work based on the lessons learnt during the development and deployment of the system. Comment: Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery & Data Mining (KDD) 2018, London, United Kingdom

  • Open Access
    Authors: 
    Harvey Babkoff; Yehuda Ben-Uriah;
    Publisher: Elsevier BV

    Two experiments were performed to study lexical decision time to word and non-word Hebrew trigrams as a function of stimulus probability, visual hemifield and responding hand. The results indicate that lexical decision time to words is shorter than to non-words. In addition, although decision time to words is significantly shorter with right hemifield stimulation than with left hemifield stimulation, decision time to non-words is the same whether they are presented to the right or left hemifield. Decision time to non-words decreases almost linearly as stimulus probability increases from 0.25 to 0.75, whereas decision time to words decreases in a concave manner apparently approaching an asymptote at a stimulus probability of 0.75. Responding hand is not significant as a main effect or in any interaction with any other variable. The data are discussed in terms of several models of hemispheric linguistic superiority.

  • Open Access
    Authors: 
    Roni Ostreiher;
    Publisher: Oxford University Press (OUP)
  • Open Access
    Authors: 
    Moshe Goldsmith; Barad S; Knafo M; Alon Savidor; Shifra Ben-Dor; Alexander Brandis; Tevie Mehlman; Yoav Peleg; Shira Albeck; Orly Dym; +2 more
    Publisher: Cold Spring Harbor Laboratory

    AbstractGrass pea (Lathyrus sativus L.) is a grain legume commonly grown in parts of Asia and Africa for food and forage. While being a highly nutritious and robust crop, able to survive both drought and floods, it produces a neurotoxic compound, β-N-oxalyl-L-α,β-diaminopropionic acid (β-ODAP), which can cause a severe neurological disorder if consumed as a main diet component. So far, the enzyme that catalyzes the formation of β-ODAP has not been identified. By combining protein purification and enzymatic assays with transcriptomic and proteomic analyses, we were able to identify the enzyme β-ODAP synthetase (BOS) from grass pea. We show that BOS is an HXXXD-type acyltransferase of the BAHD superfamily and that its crystal structure is highly similar to that of plant hydroxycinnamoyl transferases. The identification of BOS, more than 50 years after it was proposed, paves the way towards the generation of non-toxic grass pea cultivars safe for human and animal consumption.

  • Open Access
    Authors: 
    Ilan Hirshberg; Eberhard Kirchberg; Stuart White;
    Publisher: Elsevier BV

    Abstract We show that nuclear C ∗ -algebras have a refined version of the completely positive approximation property, in which the maps that approximately factorize through finite dimensional algebras are convex combinations of order zero maps. We use this to show that a separable nuclear C ∗ -algebra A which is closely contained in a C ∗ -algebra B embeds into B .

  • Open Access
    Authors: 
    Yuval Porat; Yoni Pertzov; Ehud Zohary;
    Publisher: Association for Research in Vision and Ophthalmology (ARVO)

    Viewed object-oriented actions elicit widespread fMRI activation in the dorsal and ventral visual pathways. This activation is typically stronger in the hemisphere contralateral to the visual field in which action is seen. However, since in previous studies participants kept fixation at the same screen position throughout the scan, it was impossible to infer if the viewed actions are represented in retina-based coordinates or in a more elaborated coordinate system. Here, participants changed their gaze between experimental conditions, such that some conditions shared the same retinotopic coordinates (but differed in their screen position), while other pairs of conditions shared the opposite trait. The degree of similarity between the patterns of activation elicited by the various conditions was assessed using multivoxel pattern analysis methods. Regions of interest, showing robust overall activation, included the intraparietal sulcus (IPS) and the occipitotemporal cortex. In these areas, the correlation between activation patterns for conditions sharing the same retinotopic coordinates was significantly higher than that of those having different retinotopic coordinates. In contrast, the correlations between activation patterns for conditions with the same spatiotopic coordinates were not significantly greater than for non-spatiotopic conditions. These results suggest that viewed object-oriented actions are likely to be maintained in retinotopic-framed coordinates.

  • Open Access
    Authors: 
    Esther Zoref-Shani; Asher Shainberg; Gania Kesler-Icekson; Lina Wasserman; Oded Sperling;
    Publisher: Springer Science and Business Media LLC

    PURINE NUCLEOTIDE METABOLISM IN CULTURED RAT SKELETAL AND HEART MUSCLE: A COMPERATIVE STUDY OF THE MECHANISMS OF ATP CONSERVATION: 238

  • Open Access English
    Authors: 
    M. Adinolfi; A. Aloisio; F. Ambrosino; A. Andryakov; A. Antonelli; M. Antonelli; F. Anulli; C. Bacci; A. Bankamp; G. Barbiellini; +132 more
    Country: Italy

    Abstract The main aim of the KLOE experiment at DAΦNE, the Frascati φ-factory, is to study CP violation in the K0– K 0 system. Requirements on shower detection are very stringent. An hermetic, lead-scintillating fiber sampling calorimeter has been chosen and built. A review of the methods used to calibrate and reconstruct energy and timing is reported in this paper. Emphasis is given to the calibration procedures developed using the 2.4 pb−1 collected in 1999. An energy resolution of 5.7%/ E/ GeV is achieved together with a linearity in energy response better than 1% above 50 MeV. A time resolution of ∼54 ps / E/ GeV is also measured on samples of radiative Bhabha and Φ decays.

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