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  • 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: 
    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 English
    Authors: 
    Amit Tirosh; Electron Kebebew;
    Publisher: Future Medicine Ltd

    Neuroendocrine tumors (NETs) are rare neoplasms that emerge mainly from the GI tract, pancreas and respiratory tract. The incidence of NETs has increased more than sixfold in the last decades. NETs typically express somatostatin receptors on their cell surface, which can be targeted by ‘cold’ somatostatin analogs for therapy or by ‘hot’ radiolabeled somatostatin analogs for tumor localization and treatment. 68-Gallium-DOTA peptides (DOTATATE, DOTATOC, DOTANOC) positron emission tomography/computed tomography is a highly accurate imaging modality for NETs that has been found to be more sensitive for NET detection than other imaging modalities. In the current review, we will discuss the clinical utility of 68-Gallium-DOTATATE positron emission tomography/computed tomography for the diagnosis and management of patients with NETs.

  • Open Access
    Authors: 
    Yasutada Akiba; M. Alfred; V. Andrieux; K. Aoki; N. Apadula; H. Asano; V. Babintsev; N. S. Bandara; K. N. Barish; S. Bathe; +190 more
    Publisher: American Physical Society (APS)

    We present the first measurements of long-range angular correlations and the transverse momentum dependence of elliptic flow $v_2$ in high-multiplicity $p$$+$Au collisions at $\sqrt{s_{_{NN}}}=200$ GeV. A comparison of these results with previous measurements in high-multiplicity $d$$+$Au and $^3{\rm He}$$+$Au collisions demonstrates a relation between $v_2$ and the initial collision eccentricity $\varepsilon_2$, suggesting that the observed momentum-space azimuthal anisotropies in these small systems have a collective origin and reflect the initial geometry. Good agreement is observed between the measured $v_2$ and hydrodynamic calculations for all systems, and an argument disfavoring theoretical explanations based on momentum-space domain correlations is presented. The set of measurements presented here allows us to leverage the distinct intrinsic geometry of each of these systems to distinguish between different theoretical descriptions of the long-range correlations observed in small collision systems.

  • Open Access
    Authors: 
    Juliana Smichenko; Efrat Gil; Anna Zisberg;
    Publisher: Oxford University Press (OUP)

    Abstract Background Sedative-hypnotic medications (SHMs) are frequently used in hospitalized older patients, despite undesirable effects on cognitive status. Although previous studies found a significant number of patients experience changes in SHM use during hospitalization, it is unclear which pattern of change leads to hospital-associated cognitive decline (HACD). This study tested the association between patterns of SHM change and HACD. Methods This secondary analysis study included 550 patients age 70+ who were cognitively intact at admission (Short Portable Mental Status Questionnaire [SPMSQ] ≥8). HACD was defined as at least 1-point decline in SPMSQ between admission and discharge. Changes in sedative burden (SB) before and during hospitalization (average SB of all hospitalization days) were coded using the Drug Burden Index sorting study participants into four groups: without SB (n = 254), without SB changes (n = 132), increased SB (n = 82), and decreased SB (n = 82). Results Incidence of HACD was 233/550 (42.4%). In multivariate logistic analysis controlling for demographic characteristics, length of stay, severity of acute illness, comorbidity, SB score at home, pain on admission and depression, the odds of HACD were 2.45 (95% CI: 1.16 to 5.13) among participants with increased SB, 2.10 (95% CI: 1.13 to 3.91) among participants without SB changes, compared with participants with decreased SB. Conclusion Older patients whose SB is increased or does not change are at higher risk for acquired cognitive decline than are those whose SB is reduced. Identifying patients with a potential increase in SB and intervening to reduce it may help to fight HACD.

  • Open Access
    Authors: 
    Zeb D. Jonker; Rick van der Vliet; Christopher M. Hauwert; Carolin Gaiser; Joke H.M. Tulen; Jos N. van der Geest; Opher Donchin; Gerard M. Ribbers; Maarten A. Frens; Ruud W. Selles;
    Publisher: Elsevier BV

    Abstract Background Changes in transcranial magnetic stimulation motor map parameters can be used to quantify plasticity in the human motor cortex. The golden standard uses a counting analysis of motor evoked potentials (MEPs) acquired with a predefined grid. Recently, digital reconstruction methods have been proposed, allowing MEPs to be acquired with a faster pseudorandom procedure. However, the reliability of these reconstruction methods has never been compared to the golden standard. Objective To compare the absolute reliability of the reconstruction methods with the golden standard. Methods In 21 healthy subjects, both grid and pseudorandom acquisition were performed twice on the first day and once on the second day. The standard error of measurement was calculated for the counting analysis and the digital reconstructions. Results The standard error of measurement was at least equal using digital reconstructions. Conclusion Pseudorandom acquisition and digital reconstruction can be used in intervention studies without sacrificing reliability.

  • Open Access
    Authors: 
    Johan Burisch; Jonas Halfvarson; Limas Kupčinskas; Vicent Hernandez; I. Kaimakliotis; D. Valpiani; Natalia Pedersen; Dana Duricova; Lisha Kievit; Jens Frederik Dahlerup; +18 more
    Publisher: Oxford University Press (OUP)

    Change in Crohn's disease behavior in a prospective European population-based inception cohort - the ECCO-EpiCom cohort

  • Open Access English
    Authors: 
    Irene Jiménez Guerrero; Francisco Pérez-Montaño; Gustavo Mateus da Silva; Naama Wagner; Dafna Shkedy; Mei Zhao; Lorena Pizarro; Maya Bar; Ron Walcott; Guido Sessa; +2 more
    Publisher: Cold Spring Harbor Laboratory

    AbstractMany Gram-negative plant and animal pathogenic bacteria employ a type III secretion system (T3SS) to secrete protein effectors into the cells of their hosts and promote disease. The plant pathogen Acidovorax citrulli requires a functional T3SS for pathogenicity. As with Xanthomonas and Ralstonia spp., an AraC-type transcriptional regulator, HrpX, regulates expression of genes encoding T3SS components and type III-secreted effectors (T3Es) in A. citrulli. A previous study reported eleven T3E genes in this pathogen, based on the annotation of a sequenced strain. We hypothesized that this was an underestimation. Guided by this hypothesis, we aimed at uncovering the T3E arsenal of the A. citrulli model strain, M6. We carried out a thorough sequence analysis searching for similarity to known T3Es from other bacteria. This analysis revealed 51 A. citrulli genes whose products are similar to known T3Es. Further, we combined machine learning and transcriptomics to identify novel T3Es. The machine learning approach ranked all A. citrulli M6 genes according to their propensity to encode T3Es. RNA-Seq revealed differential gene expression between wild-type M6 and a mutant defective in HrpX. Data combined from these approaches led to the identification of seven novel T3E candidates, that were further validated using a T3SS-dependent translocation assay. These T3E genes encode hypothetical proteins, do not show any similarity to known effectors from other bacteria, and seem to be restricted to plant pathogenic Acidovorax species. Transient expression in Nicotiana benthamiana revealed that two of these T3Es localize to the cell nucleus and one interacts with the endoplasmic reticulum. This study not only uncovered the arsenal of T3Es of an important pathogen, but it also places A. citrulli among the “richest” bacterial pathogens in terms of T3E cargo. It also revealed novel T3Es that appear to be involved in the pathoadaptive evolution of plant pathogenic Acidovorax species.Author summaryAcidovorax citrulli is a Gram-negative bacterium that causes bacterial fruit blotch (BFB) disease of cucurbits. This disease represents a serious threat to cucurbit crop production worldwide. Despite the agricultural importance of BFB, the knowledge about basic aspects of A. citrulli-plant interactions is rather limited. As many Gram-negative plant and animal pathogenic bacteria, A. citrulli employs a complex secretion system, named type III secretion system, to deliver protein virulence effectors into the host cells. In this work we aimed at uncovering the arsenal of type III-secreted effectors (T3Es) of this pathogen by combination of bioinformatics and experimental approaches. We found that this bacterium possesses at least 51 genes that are similar to T3E genes from other pathogenic bacteria. In addition, our study revealed seven novel T3Es that seem to occur only in A. citrulli strains and in other plant pathogenic Acidovorax species. We found that two of these T3Es localize to the plant cell nucleus while one partially interacts with the endoplasmic reticulum. Further characterization of the novel T3Es identified in this study may uncover new host targets of pathogen effectors and new mechanisms by which pathogenic bacteria manipulate their hosts.

  • Open Access
    Authors: 
    Michael Peer; Harald Prüss; Inbal Ben-Dayan; Friedemann Paul; Shahar Arzy; Carsten Finke;
    Publisher: Elsevier BV
  • Open Access English
    Authors: 
    Tonametl Sanchez; Andrey Polyakov; Emilia Fridman; Laurentiu Hetel;
    Publisher: HAL CCSD
    Country: France
    Project: ANR | DIGITSLID (ANR-18-CE40-0008)

    In this paper, we propose a state-dependent switching controller for multiple-input multiple-output (MIMO) bilinear systems with constant delays in both the state and the input. The control input is assumed to be restricted to take only a finite number of values. The stability analysis of the closed loop is based on a Lyapunov–Krasovskii functional, and the design is reduced to solve a system of linear matrix inequalities. The controller can be designed by considering (state) delay-dependent or delay-independent conditions.

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