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  • 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: 
    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: 
    Krishna Kumar Singh; Dhruv Mahajan; Kristen Grauman; Yong Jae Lee; Matt Feiszli; Deepti Ghadiyaram;
    Publisher: IEEE

    Existing models often leverage co-occurrences between objects and their context to improve recognition accuracy. However, strongly relying on context risks a model's generalizability, especially when typical co-occurrence patterns are absent. This work focuses on addressing such contextual biases to improve the robustness of the learnt feature representations. Our goal is to accurately recognize a category in the absence of its context, without compromising on performance when it co-occurs with context. Our key idea is to decorrelate feature representations of a category from its co-occurring context. We achieve this by learning a feature subspace that explicitly represents categories occurring in the absence of context along side a joint feature subspace that represents both categories and context. Our very simple yet effective method is extensible to two multi-label tasks -- object and attribute classification. On 4 challenging datasets, we demonstrate the effectiveness of our method in reducing contextual bias.

  • 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.

  • Publication . Article . Preprint . 2014
    Open Access English
    Authors: 
    Kerner, Dmitry;
    Project: EC | DURFEE (334347)

    Consider rectangular matrices over a local ring R. In the previous work we have obtained criteria for block-diagonalization of such matrices, i.e. U A V=A_1\oplus A_2, where U,V are invertible matrices over R. In this short note we extend the criteria to the decomposability of quiver representations over R. Preliminary brief announcement

  • Open Access English
    Authors: 
    Biskup, Marek; Louidor, Oren;
    Project: EC | MOTTPROXIMITY (276923), NSF | Large Scale Phenomena in ... (1407558)

    We study the extremal process associated with the Discrete Gaussian Free Field on the square lattice and elucidate how the conformal symmetries manifest themselves in the scaling limit. Specifically, we prove that the joint process of spatial positions ($x$) and centered values ($h$) of the extreme local maxima in lattice versions of a bounded domain $D\subset\mathbb C$ converges, as the lattice spacing tends to zero, to a Poisson point process with intensity measure $Z^D(dx)\otimes e^{-\alpha h}d h$, where $\alpha$ is a constant and $Z^D$ is a random a.s.-finite measure on $D$. The random measures $\{Z^D\}$ are naturally interrelated; restrictions to subdomains are governed by a Gibbs-Markov property and images under analytic bijections $f$ by the transformation rule $(Z^{f(D)}\circ f)(d x)\overset{\text{law}}=|f'(x)|^4\, Z^D(d x)$. Conditions are given that determine the laws of these measures uniquely. These identify $Z^D$ with the critical Liouville Quantum Gravity associated with the Continuum Gaussian Free Field. Comment: 58 pages, 4 figs, version to appear in Commun. Math. Phys

  • 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: 
    Spencer Bastani; Tomer Blumkin; Luca Micheletto;

    In this paper we highlight a novel role played by the non-linear income tax in the presence of adverse selection in the labor market due to asymmetric information between workers and firms. Relying on the Rothschild and Stiglitz equilibrium concept, we show that an appropriate choice of the tax schedule enables the government to affect the wage distribution by controlling the transmission of information in the labor market. This represents an additional channel through which the government can foster the pursuit of its redistributive goals.

  • 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.

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