Showing papers by "New York University published in 2011"
Journal Article•
TL;DR: A unified neural network architecture and learning algorithm that can be applied to various natural language processing tasks including part-of-speech tagging, chunking, named entity recognition, and semantic role labeling is proposed.
Abstract: We propose a unified neural network architecture and learning algorithm that can be applied to various natural language processing tasks including part-of-speech tagging, chunking, named entity recognition, and semantic role labeling. This versatility is achieved by trying to avoid task-specific engineering and therefore disregarding a lot of prior knowledge. Instead of exploiting man-made input features carefully optimized for each task, our system learns internal representations on the basis of vast amounts of mostly unlabeled training data. This work is then used as a basis for building a freely available tagging system with good performance and minimal computational requirements.
6,734 citations
Book•
31 Aug 2011TL;DR: The programming of a proof procedure is discussed in connection with trial runs and possible improvements.
Abstract: The programming of a proof procedure is discussed in connection with trial runs and possible improvements.
3,296 citations
Book•
11 Aug 2011TL;DR: The authors describe an algorithm that reconstructs a close approximation of 1-D and 2-D signals from their multiscale edges and shows that the evolution of wavelet local maxima across scales characterize the local shape of irregular structures.
Abstract: A multiscale Canny edge detection is equivalent to finding the local maxima of a wavelet transform. The authors study the properties of multiscale edges through the wavelet theory. For pattern recognition, one often needs to discriminate different types of edges. They show that the evolution of wavelet local maxima across scales characterize the local shape of irregular structures. Numerical descriptors of edge types are derived. The completeness of a multiscale edge representation is also studied. The authors describe an algorithm that reconstructs a close approximation of 1-D and 2-D signals from their multiscale edges. For images, the reconstruction errors are below visual sensitivity. As an application, a compact image coding algorithm that selects important edges and compresses the image data by factors over 30 has been implemented. >
3,187 citations
TL;DR: This article investigates how content producers navigate ‘imagined audiences’ on Twitter, talking with participants who have different types of followings to understand their techniques, including targeting different audiences, concealing subjects, and maintaining authenticity.
Abstract: Social media technologies collapse multiple audiences into single contexts, making it difficult for people to use the same techniques online that they do to handle multiplicity in face-to-face conversation. This article investigates how content producers navigate ‘imagined audiences’ on Twitter. We talked with participants who have different types of followings to understand their techniques, including targeting different audiences, concealing subjects, and maintaining authenticity. Some techniques of audience management resemble the practices of ‘micro-celebrity’ and personal branding, both strategic self-commodification. Our model of the networked audience assumes a many-to-many communication through which individuals conceptualize an imagined audience evoked through their tweets.
3,062 citations
TL;DR: This work has uncovered a role for non-coding RNA in the recruitment of PRC2 to target genes, and expanded the perspectives on its function and regulation.
Abstract: Polycomb group proteins maintain the gene-expression pattern of different cells that is set during early development by regulating chromatin structure. In mammals, two main Polycomb group complexes exist — Polycomb repressive complex 1 (PRC1) and 2 (PRC2). PRC1 compacts chromatin and catalyses the monoubiquitylation of histone H2A. PRC2 also contributes to chromatin compaction, and catalyses the methylation of histone H3 at lysine 27. PRC2 is involved in various biological processes, including differentiation, maintaining cell identity and proliferation, and stem-cell plasticity. Recent studies of PRC2 have expanded our perspectives on its function and regulation, and uncovered a role for non-coding RNA in the recruitment of PRC2 to target genes.
2,783 citations
TL;DR: In this paper, the authors describe likelihood-based statistical tests for use in high energy physics for the discovery of new phenomena and for construction of confidence intervals on model parameters, focusing on the properties of the test procedures that allow one to account for systematic uncertainties.
Abstract: We describe likelihood-based statistical tests for use in high energy physics for the discovery of new phenomena and for construction of confidence intervals on model parameters. We focus on the properties of the test procedures that allow one to account for systematic uncertainties. Explicit formulae for the asymptotic distributions of test statistics are derived using results of Wilks and Wald. We motivate and justify the use of a representative data set, called the “Asimov data set”, which provides a simple method to obtain the median experimental sensitivity of a search or measurement as well as fluctuations about this expectation.
2,418 citations
Daniel J. Eisenstein1, Daniel J. Eisenstein2, David H. Weinberg3, Eric Agol4 +260 more•Institutions (62)
TL;DR: SDSS-III as mentioned in this paper is a program of four spectroscopic surveys on three scientific themes: dark energy and cosmological parameters, the history and structure of the Milky Way, and the population of giant planets around other stars.
Abstract: Building on the legacy of the Sloan Digital Sky Survey (SDSS-I and II), SDSS-III is a program of four spectroscopic surveys on three scientific themes: dark energy and cosmological parameters, the history and structure of the Milky Way, and the population of giant planets around other stars. In keeping with SDSS tradition, SDSS-III will provide regular public releases of all its data, beginning with SDSS DR8 (which occurred in Jan 2011). This paper presents an overview of the four SDSS-III surveys. BOSS will measure redshifts of 1.5 million massive galaxies and Lya forest spectra of 150,000 quasars, using the BAO feature of large scale structure to obtain percent-level determinations of the distance scale and Hubble expansion rate at z 100 per resolution element), H-band (1.51-1.70 micron) spectra of 10^5 evolved, late-type stars, measuring separate abundances for ~15 elements per star and creating the first high-precision spectroscopic survey of all Galactic stellar populations (bulge, bar, disks, halo) with a uniform set of stellar tracers and spectral diagnostics. MARVELS will monitor radial velocities of more than 8000 FGK stars with the sensitivity and cadence (10-40 m/s, ~24 visits per star) needed to detect giant planets with periods up to two years, providing an unprecedented data set for understanding the formation and dynamical evolution of giant planet systems. (Abridged)
2,265 citations
TL;DR: The authors developed a quantitative monetary DSGE model with financial intermediaries that face endogenously determined balance sheet constraints and used the model to evaluate the effects of the central bank using unconventional monetary policy to combat a simulated financial crisis.
2,158 citations
TL;DR: In this paper, a series of programs run by a company called OPOWER to send Home Energy Report letters to residential utility customers comparing their electricity use to that of their neighbors is evaluated.
2,142 citations
TL;DR: The central roles of macrophages in each of the stages of disease pathogenesis are discussed, including atherosclerosis, stroke, and sudden cardiac death.
1,986 citations
TL;DR: Four-dimensional covariant nonlinear theories of massive gravity are constructed which are ghost-free in the decoupling limit to all orders, and the Hamiltonian constraint is maintained at least up to and including quartic order in nonlinearities, hence excluding the possibility of the Boulware-Deser ghost up to this order.
Abstract: We construct four-dimensional covariant nonlinear theories of massive gravity which are ghost-free in the decoupling limit to all orders. These theories resum explicitly all the nonlinear terms of an effective field theory of massive gravity. We show that away from the decoupling limit the Hamiltonian constraint is maintained at least up to and including quartic order in nonlinearities, hence excluding the possibility of the Boulware-Deser ghost up to this order. We also show that the same remains true to all orders in a similar toy model.
TL;DR: The emphasis of this review is on psychophysical studies, but relevant electrophysiological and neuroimaging studies and models regarding how and where neuronal responses are modulated are also discussed.
TL;DR: The Alzheimer Disease Genetics Consortium performed a genome-wide association study of late-onset Alzheimer disease using a three-stage design consisting of a discovery stage (stage 1), two replication stages (stages 2 and 3), and both joint analysis and meta-analysis approaches were used.
Abstract: The Alzheimer Disease Genetics Consortium (ADGC) performed a genome-wide association study of late-onset Alzheimer disease using a three-stage design consisting of a discovery stage (stage 1) and two replication stages (stages 2 and 3). Both joint analysis and meta-analysis approaches were used. We obtained genome-wide significant results at MS4A4A (rs4938933; stages 1 and 2, meta-analysis P (P(M)) = 1.7 × 10(-9), joint analysis P (P(J)) = 1.7 × 10(-9); stages 1, 2 and 3, P(M) = 8.2 × 10(-12)), CD2AP (rs9349407; stages 1, 2 and 3, P(M) = 8.6 × 10(-9)), EPHA1 (rs11767557; stages 1, 2 and 3, P(M) = 6.0 × 10(-10)) and CD33 (rs3865444; stages 1, 2 and 3, P(M) = 1.6 × 10(-9)). We also replicated previous associations at CR1 (rs6701713; P(M) = 4.6 × 10(-10), P(J) = 5.2 × 10(-11)), CLU (rs1532278; P(M) = 8.3 × 10(-8), P(J) = 1.9 × 10(-8)), BIN1 (rs7561528; P(M) = 4.0 × 10(-14), P(J) = 5.2 × 10(-14)) and PICALM (rs561655; P(M) = 7.0 × 10(-11), P(J) = 1.0 × 10(-10)), but not at EXOC3L2, to late-onset Alzheimer's disease susceptibility.
TL;DR: If the Brazilian health system is to overcome the challenges with which it is presently faced, strengthened political support is needed so that financing can be restructured and the roles of both the public and private sector can be redefined.
University of North Carolina at Chapel Hill1, University of Washington2, Vanderbilt University3, New York University4, University of California, San Francisco5, Carnegie Mellon University6, Johns Hopkins University7, Washington University in St. Louis8, University of Kansas9, Stanford University10, Fred Hutchinson Cancer Research Center11
TL;DR: This chapter describes the requirements for the ROSETTA molecular modeling program's new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform.
Abstract: We have recently completed a full re-architecturing of the ROSETTA molecular modeling program, generalizing and expanding its existing functionality. The new architecture enables the rapid prototyping of novel protocols by providing easy-to-use interfaces to powerful tools for molecular modeling. The source code of this rearchitecturing has been released as ROSETTA3 and is freely available for academic use. At the time of its release, it contained 470,000 lines of code. Counting currently unpublished protocols at the time of this writing, the source includes 1,285,000 lines. Its rapid growth is a testament to its ease of use. This chapter describes the requirements for our new architecture, justifies the design decisions, sketches out central classes, and highlights a few of the common tasks that the new software can perform.
TL;DR: Using genetic engineering in mice, approximately 20 Cre and inducible CreER knockin driver lines that reliably target major classes and lineages of GABAergic neurons are generated, thereby enabling a systematic and comprehensive analysis from cell fate specification, migration, and connectivity, to their functions in network dynamics and behavior.
Proceedings Article•
01 Jan 2011TL;DR: Torch7 is a versatile numeric computing framework and machine learning library that extends Lua that can easily be interfaced to third-party software thanks to Lua’s light interface.
Abstract: Torch7 is a versatile numeric computing framework and machine learning library that extends Lua. Its goal is to provide a flexible environment to design and train learning machines. Flexibility is obtained via Lua, an extremely lightweight scripting language. High performance is obtained via efficient OpenMP/SSE and CUDA implementations of low-level numeric routines. Torch7 can easily be interfaced to third-party software thanks to Lua’s light interface.
Hiroaki Aihara1, Carlos Allende Prieto2, Carlos Allende Prieto3, Deokkeun An4 +191 more•Institutions (58)
TL;DR: The first data release of SDSS-III is described in this article, which includes five-band imaging of roughly 5200 deg2 in the southern Galactic cap, bringing the total footprint of the Sloan Digital Sky Survey imaging to 14,555 deg2, or over a third of the Celestial Sphere.
Abstract: The Sloan Digital Sky Survey (SDSS) started a new phase in 2008 August, with new instrumentation and new surveys focused on Galactic structure and chemical evolution, measurements of the baryon oscillation feature in the clustering of galaxies and the quasar Lyα forest, and a radial velocity search for planets around ~8000 stars. This paper describes the first data release of SDSS-III (and the eighth counting from the beginning of the SDSS). The release includes five-band imaging of roughly 5200 deg2 in the southern Galactic cap, bringing the total footprint of the SDSS imaging to 14,555 deg2, or over a third of the Celestial Sphere. All the imaging data have been reprocessed with an improved sky-subtraction algorithm and a final, self-consistent photometric recalibration and flat-field determination. This release also includes all data from the second phase of the Sloan Extension for Galactic Understanding and Exploration (SEGUE-2), consisting of spectroscopy of approximately 118,000 stars at both high and low Galactic latitudes. All the more than half a million stellar spectra obtained with the SDSS spectrograph have been reprocessed through an improved stellar parameter pipeline, which has better determination of metallicity for high-metallicity stars.
TL;DR: This Review describes how RAS oncogenes exploit their extensive signalling reach to affect multiple cellular processes that drive tumorigenesis.
Abstract: RAS proteins are essential components of signalling pathways that emanate from cell surface receptors. Oncogenic activation of these proteins owing to missense mutations is frequently detected in several types of cancer. A wealth of biochemical and genetic studies indicates that RAS proteins control a complex molecular circuitry that consists of a wide array of interconnecting pathways. In this Review, we describe how RAS oncogenes exploit their extensive signalling reach to affect multiple cellular processes that drive tumorigenesis.
TL;DR: A new web site with improved tools for pathway browsing and data analysis is developed, and orthology-based inferences of pathways in non-human species are made, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species.
Abstract: Reactome (http://www.reactome.org) is a collaboration among groups at the Ontario Institute for Cancer Research, Cold Spring Harbor Laboratory, New York University School of Medicine and The European Bioinformatics Institute, to develop an open source curated bioinformatics database of human pathways and reactions. Recently, we developed a new web site with improved tools for pathway browsing and data analysis. The Pathway Browser is an Systems Biology Graphical Notation (SBGN)-based visualization system that supports zooming, scrolling and event highlighting. It exploits PSIQUIC web services to overlay our curated pathways with molecular interaction data from the Reactome Functional Interaction Network and external interaction databases such as IntAct, BioGRID, ChEMBL, iRefIndex, MINT and STRING. Our Pathway and Expression Analysis tools enable ID mapping, pathway assignment and overrepresentation analysis of user-supplied data sets. To support pathway annotation and analysis in other species, we continue to make orthology-based inferences of pathways in non-human species, applying Ensembl Compara to identify orthologs of curated human proteins in each of 20 other species. The resulting inferred pathway sets can be browsed and analyzed with our Species Comparison tool. Collaborations are also underway to create manually curated data sets on the Reactome framework for chicken, Drosophila and rice.
TL;DR: An overview of the multifaceted notion of context is provided, several approaches for incorporating contextual information in recommendation process are discussed, and the usage of such approaches in several application areas where different types of contexts are exploited are illustrated.
Abstract: Context-aware recommender systems (CARS) generate more relevant recommendations by adapting them to the specific contextual situation of the user. This article explores how contextual information can be used to create more intelligent and useful recommender systems. It provides an overview of the multifaceted notion of context, discusses several approaches for incorporating contextual information in recommendation process, and illustrates the usage of such approaches in several application areas where different types of contexts are exploited. The article concludes by discussing the challenges and future research directions for context-aware recommender systems.
TL;DR: Examination of rates and sociodemographic correlates of lifetime mental health service use by severity, type, and number of DSM-IV disorders in the National Comorbidity Survey-Adolescent Supplement foundmarked racial disparities in lifetime rates of mental health treatment highlight the urgent need to identify and combat barriers to the recognition and treatment of these conditions.
Abstract: Objective Mental health policy for youth has been constrained by a paucity of nationally representative data concerning patterns and correlates of mental health service utilization in this segment of the population. The objectives of this investigation were to examine the rates and sociodemographic correlates of lifetime mental health service use by severity, type, and number of DSM-IV disorders in the National Comorbidity Survey–Adolescent Supplement. Method Face-to-face survey of mental disorders from 2002 to 2004 using a modified version of the fully structured World Health Organization Composite International Diagnostic Interview in a nationally representative sample of 6,483 adolescents 13 to 18 years old for whom information on service use was available from an adolescent and a parent report. Total and sector-specific mental health service use was also assessed. Results Approximately one third of adolescents with mental disorders received services for their illness (36.2%). Although disorder severity was significantly associated with an increased likelihood of receiving treatment, half of adolescents with severely impairing mental disorders had never received mental health treatment for their symptoms. Service rates were highest in those with attention-deficit/hyperactivity disorder (59.8%) and behavior disorders (45.4%), but fewer than one in five affected adolescents received services for anxiety, eating, or substance use disorders. Comorbidity and severe impairment were strongly associated with service utilization, particularly in youth with behavior disorders. Hispanic and non-Hispanic Black adolescents were less likely than their White counterparts to receive services for mood and anxiety disorders, even when such disorders were associated with severe impairment. Conclusions Despite advances in public awareness of mental disorders in youth, a substantial proportion of young people with severe mental disorders have never received specialty mental health care. Marked racial disparities in lifetime rates of mental health treatment highlight the urgent need to identify and combat barriers to the recognition and treatment of these conditions.
TL;DR: This article examined the long-term impacts of Africa's slave trade and found that individuals whose ancestors were heavily raided during the slave trade are less trusting today, which may persist to this day.
Abstract: In a recent study, Nunn (2008) examines the long-term impacts of Africa’s slave trade. He finds that the slave trade, which occurred over a period of more than 400 years, had a significant negative effect on long-term economic development. Although the article arguably identifies a negative causal relationship between the slave trade and income today, the analysis is unable to establish the exact causal mechanisms underlying this reduced-form relationship. In this article, we examine one of the channels through which the slave trade may affect economic development today. Combining contemporary individual-level survey data with historical data on slave shipments by ethnic group, we ask whether the slave trade caused a culture of mistrust to develop within Africa. Initially, slaves were captured primarily through state organized raids and warfare, but as the trade progressed, the environment of ubiquitous insecurity caused individuals to turn on others—including friends and family members—and to kidnap, trick, and sell each other into slavery (Sigismund Wilhelm Koelle 1854; P. E. H. Hair 1965; Charles Piot 1996). We hypothesize that in this environment, a culture of mistrust may have evolved, which may persist to this day. We show that current differences in trust levels within Africa can be traced back to the transatlantic and Indian Ocean slave trades. Combining contemporary individual-level survey data with historical data on slave shipments by ethnic group, we find that individuals whose ancestors were heavily raided during the slave trade are less trusting today. Evidence from a variety of identification strategies suggests that the relationship is causal. Examining causal mechanisms, we show that most of the impact of the slave trade is through factors that are internal to the individual, such as cultural norms, beliefs, and values. (JEL J15, N57, Z13)
Boston University1, University of Manchester2, Medical University of Vienna3, University of Ottawa4, VU University Amsterdam5, Leiden University6, Columbia University7, Johns Hopkins University8, University of Pisa9, University of Melbourne10, University of York11, University of Florence12, University of Paris13, University of Leeds14, University of California, Los Angeles15, University of Santiago de Compostela16, University of Toronto17, University of Bristol18, Maastricht University19, University of Nebraska Medical Center20, Autonomous University of Madrid21, New York University22, Food and Drug Administration23, Genentech24, Stanford University25, University of Basel26, MedImmune27, University of Kansas28
TL;DR: It is proposed that a patient's RA can be defined as being in remission based on one of two definitions: (1) when scores on the tender joint count, swollen joint counts, CRP level, and patient global assessment are all ≤1, or (2) when the score on the Simplified Disease Activity Index is ≤3.
Abstract: Objective Remission in rheumatoid arthritis (RA) is an increasingly attainable goal, but there is no widely used defi nition of remission that is stringent but achievable and could be applied uniformly as an outcome measure in clinical trials. This work was undertaken to develop such a defi nition. Methods A committee consisting of members of the American College of Rheumatology, the European League Against Rheumatism, and the Outcome Measures in Rheumatology Initiative met to guide the process and review prespecifi ed analyses from RA clinical trials. The committee requested a stringent defi nition (little, if any, active disease) and decided to use core set measures including, as a minimum, joint counts and levels of an acute-phase reactant to defi ne remission. Members were surveyed to select the level of each core set measure that would be consistent with remission. Candidate defi nitions of remission were tested, including those that constituted a number of individual measures of remission (Boolean approach) as well as defi nitions using disease activity indexes. To select a defi nition of remission, trial data were analysed to examine the added contribution of patient-reported outcomes and the ability of candidate measures to predict later good radiographic and functional outcomes. Results Survey results for the defi nition of remission suggested indexes at published thresholds and a count of core set measures, with each measure scored as 1 or less (eg, tender and swollen joint counts, C reactive protein (CRP) level, and global assessments on a 0–10 scale). Analyses suggested the need to include a patientreported measure. Examination of 2-year follow-up data suggested that many candidate defi nitions performed comparably in terms of predicting later good radiographic and functional outcomes, although 28-joint Disease Activity Score–based measures of remission did not
06 Nov 2011
TL;DR: A hierarchical model that learns image decompositions via alternating layers of convolutional sparse coding and max pooling, relying on a novel inference scheme that ensures each layer reconstructs the input, rather than just the output of the layer directly beneath, as is common with existing hierarchical approaches.
Abstract: We present a hierarchical model that learns image decompositions via alternating layers of convolutional sparse coding and max pooling. When trained on natural images, the layers of our model capture image information in a variety of forms: low-level edges, mid-level edge junctions, high-level object parts and complete objects. To build our model we rely on a novel inference scheme that ensures each layer reconstructs the input, rather than just the output of the layer directly beneath, as is common with existing hierarchical approaches. This makes it possible to learn multiple layers of representation and we show models with 4 layers, trained on images from the Caltech-101 and 256 datasets. When combined with a standard classifier, features extracted from these models outperform SIFT, as well as representations from other feature learning methods.
Mayo Clinic1, New York University2, University of Hamburg3, Children's National Medical Center4, University of Girona5, Johns Hopkins University6, St George's, University of London7, Harvard University8, University of Ottawa9, University of Toronto10, University of Miami11, University of Paris12, University College London13, University of Münster14, University of Sydney15, Cincinnati Children's Hospital Medical Center16, University of Oxford17, University of Amsterdam18, Indiana University19
TL;DR: This dissertation aims to provide a history of modern medicine and some of the techniques and practices used in modern medicine, as well as some new approaches, that were introduced in the field of medicine more than 40 years ago.
TL;DR: This evidence-based guideline was developed using the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) system to describe both the strength of recommendations and the quality of evidence for diagnosis and treatment of hyperprolactinemia.
Abstract: Objective: The aim was to formulate practice guidelines for the diagnosis and treatment of hyperprolactinemia. Participants: The Task Force consisted of Endocrine Society-appointed experts, a methodologist, and a medical writer. Evidence: This evidence-based guideline was developed using the Grading of Recommendations, Assessment, Development, and Evaluation (GRADE) system to describe both the strength of recommendations and the quality of evidence. Consensus Process: One group meeting, several conference calls, and e-mail communications enabled consensus. Committees and members of The Endocrine Society, The European Society of Endocrinology, and The Pituitary Society reviewed and commented on preliminary drafts of these guidelines. Conclusions: Practice guidelines are presented for diagnosis and treatment of patients with elevated prolactin levels. These include evidence-based approaches to assessing the cause of hyperprolactinemia, treating drug-induced hyperprolactinemia, and managing prolactinomas in nonpregnant and pregnant subjects. Indications and side effects of therapeutic agents for treating prolactinomas are also presented. (J Clin Endocrinol Metab 96: 273–288, 2011)
TL;DR: The universal modulation of these neurons by serotonin and acetylcholine via ionotropic receptors suggests that they might be involved in shaping cortical circuits during specific brain states andbehavioral contexts.
Abstract: An understanding of the diversity of cortical GABAergic interneurons is critical to understand the function of the cerebral cortex. Recent data suggest that neurons expressing three markers, the Ca2+-binding protein parvalbumin (PV), the neuropeptide somatostatin (SST), and the ionotropic serotonin receptor 5HT3a (5HT3aR) account for nearly 100% of neocortical interneurons. Interneurons expressing each of these markers have a different embryological origin. Each group includes several types of interneurons that differ in morphological and electrophysiological properties and likely have different functions in the cortical circuit. The PV group accounts for ∼40% of GABAergic neurons and includes fast spiking basket cells and chandelier cells. The SST group, which represents ∼30% of GABAergic neurons, includes the Martinotti cells and a set of neurons that specifically target layerIV. The 5HT3aR group, which also accounts for ∼30% of the total interneuronal population, is heterogeneous and includes all of the neurons that express the neuropeptide VIP, as well as an equally numerous subgroup of neurons that do not express VIP and includes neurogliaform cells. The universal modulation of these neurons by serotonin and acetylcholine via ionotropic receptors suggests that they might be involved in shaping cortical circuits during specific brain states and behavioral contexts.
Indiana University1, University of Notre Dame2, Utah State University3, University of New Hampshire4, University of California, Santa Barbara5, University of Tokyo6, United States Department of Energy7, Ludwig Maximilian University of Munich8, National Institutes of Health9, J. Craig Venter Institute10, University of Illinois at Urbana–Champaign11, Hebrew University of Jerusalem12, University of North Texas13, Harvard University14, University of Geneva15, Research Institute of Molecular Pathology16, Oregon State University17, Utrecht University18, University of California, Davis19, University of Iowa20, Hoffmann-La Roche21, University of Strasbourg22, University of Washington23, University of Texas at Arlington24, University of California, Santa Cruz25, Life Technologies26, New York University27, University of Guelph28, Imperial College London29, University of California, Berkeley30
TL;DR: The Daphnia genome reveals a multitude of genes and shows adaptation through gene family expansions, and the coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random.
Abstract: We describe the draft genome of the microcrustacean Daphnia pulex, which is only 200 megabases and contains at least 30,907 genes. The high gene count is a consequence of an elevated rate of gene duplication resulting in tandem gene clusters. More than a third of Daphnia's genes have no detectable homologs in any other available proteome, and the most amplified gene families are specific to the Daphnia lineage. The coexpansion of gene families interacting within metabolic pathways suggests that the maintenance of duplicated genes is not random, and the analysis of gene expression under different environmental conditions reveals that numerous paralogs acquire divergent expression patterns soon after duplication. Daphnia-specific genes, including many additional loci within sequenced regions that are otherwise devoid of annotations, are the most responsive genes to ecological challenges.
TL;DR: More IDUs have anti-HCV than HIV infection, and viral hepatitis poses a key challenge to public health, which will inform efforts to prevent and treat HCV and HBV in IDUs.