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Ghent University1, Forschungszentrum Jülich2, Aalto University3, Åbo Akademi University4, Vienna University of Technology5, Duke University6, University of Grenoble7, École Polytechnique Fédérale de Lausanne8, Durham University9, International School for Advanced Studies10, Max Planck Society11, Uppsala University12, Fritz Haber Institute of the Max Planck Society13, Humboldt University of Berlin14, Technical University of Denmark15, National Institute of Standards and Technology16, University of Udine17, Université catholique de Louvain18, University of Basel19, Harvard University20, University of California, Davis21, Rutgers University22, University of York23, Wake Forest University24, Science and Technology Facilities Council25, University of Oxford26, University of Vienna27, Leibniz Institute for Neurobiology28, Dresden University of Technology29, Radboud University Nijmegen30, University of Tokyo31, Centre national de la recherche scientifique32, University of Cambridge33, Royal Holloway, University of London34, University of California, Santa Barbara35, University of Luxembourg36, Los Alamos National Laboratory37, Harbin Institute of Technology38
TL;DR: A procedure to assess the precision of DFT methods was devised and used to demonstrate reproducibility among many of the most widely used DFT codes, demonstrating that the precisionof DFT implementations can be determined, even in the absence of one absolute reference code.
Abstract: The widespread popularity of density functional theory has given rise to an extensive range of dedicated codes for predicting molecular and crystalline properties. However, each code implements the formalism in a different way, raising questions about the reproducibility of such predictions. We report the results of a community-wide effort that compared 15 solid-state codes, using 40 different potentials or basis set types, to assess the quality of the Perdew-Burke-Ernzerhof equations of state for 71 elemental crystals. We conclude that predictions from recent codes and pseudopotentials agree very well, with pairwise differences that are comparable to those between different high-precision experiments. Older methods, however, have less precise agreement. Our benchmark provides a framework for users and developers to document the precision of new applications and methodological improvements.
1,141 citations
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TL;DR: This paper proposed several novel models that address critical problems in summarization that are not adequately modeled by the basic architecture, such as modeling key-words, capturing the hierarchy of sentence-to-word structure, and emitting words that are rare or unseen at training time.
Abstract: In this work, we model abstractive text summarization using Attentional Encoder-Decoder Recurrent Neural Networks, and show that they achieve state-of-the-art performance on two different corpora. We propose several novel models that address critical problems in summarization that are not adequately modeled by the basic architecture, such as modeling key-words, capturing the hierarchy of sentence-to-word structure, and emitting words that are rare or unseen at training time. Our work shows that many of our proposed models contribute to further improvement in performance. We also propose a new dataset consisting of multi-sentence summaries, and establish performance benchmarks for further research.
1,141 citations
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TL;DR: Oyente as discussed by the authors is a symbolic execution tool to find potential security bugs in the execution of smart contracts based on Ethereum in an open distributed network like those of Bitcoin and Ethereum.
Abstract: Cryptocurrencies record transactions in a decentralized data structure called a blockchain. Two of the most popular cryptocurrencies, Bitcoin and Ethereum, support the feature to encode rules or scripts for processing transactions. This feature has evolved to give practical shape to the ideas of smart contracts, or full-fledged programs that are run on blockchains. Recently, Ethereum's smart contract system has seen steady adoption, supporting tens of thousands of contracts, holding millions dollars worth of virtual coins. In this paper, we investigate the security of running smart contracts based on Ethereum in an open distributed network like those of cryptocurrencies. We introduce several new security problems in which an adversary can manipulate smart contract execution to gain profit. These bugs suggest subtle gaps in the understanding of the distributed semantics of the underlying platform. As a refinement, we propose ways to enhance the operational semantics of Ethereum to make contracts less vulnerable. For developers writing contracts for the existing Ethereum system, we build a symbolic execution tool called Oyente to find potential security bugs. Among 19, 336 existing Ethereum contracts, Oyente flags 8, 833 of them as vulnerable, including the TheDAO bug which led to a 60 million US dollar loss in June 2016. We also discuss the severity of other attacks for several case studies which have source code available and confirm the attacks (which target only our accounts) in the main Ethereum network.
1,141 citations
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TL;DR: An overview of exosome isolation techniques is provided, opening up new perspectives towards the development more innovative strategies and devices for more time saving, cost effective, and efficient isolations ofExosomes from a wide range of biological matrices.
Abstract: Exosomes are one type of membrane vesicles secreted into extracellular space by most types of cells. In addition to performing many biological functions particularly in cell-cell communication, cumulative evidence has suggested that several biological entities in exosomes like proteins and microRNAs are closely associated with the pathogenesis of most human malignancies and they may serve as invaluable biomarkers for disease diagnosis, prognosis, and therapy. This provides a commanding impetus and growing demands for simple, efficient, and affordable techniques to isolate exosomes. Capitalizing on the physicochemical and biochemical properties of exosomes, a number of techniques have been developed for the isolation of exosomes. This article summarizes the advances in exosome isolation techniques with an emphasis on their isolation mechanism, performance, challenges, and prospects. We hope that this article will provide an overview of exosome isolation techniques, opening up new perspectives towards the development more innovative strategies and devices for more time saving, cost effective, and efficient isolations of exosomes from a wide range of biological matrices.
1,140 citations
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TL;DR: Inspired by molecular modeling, the N,N-dimethylamino substituents in tetramethylrhodamine are replaced with four-membered azetidine rings, which doubles the quantum efficiency and improves the photon yield of the dye in applications ranging from in vitro single-molecule measurements to super-resolution imaging.
Abstract: Specific labeling of biomolecules with bright fluorophores is the keystone of fluorescence microscopy. Genetically encoded self-labeling tag proteins can be coupled to synthetic dyes inside living cells, resulting in brighter reporters than fluorescent proteins. Intracellular labeling using these techniques requires cell-permeable fluorescent ligands, however, limiting utility to a small number of classic fluorophores. Here we describe a simple structural modification that improves the brightness and photostability of dyes while preserving spectral properties and cell permeability. Inspired by molecular modeling, we replaced the N,N-dimethylamino substituents in tetramethylrhodamine with four-membered azetidine rings. This addition of two carbon atoms doubles the quantum efficiency and improves the photon yield of the dye in applications ranging from in vitro single-molecule measurements to super-resolution imaging. The novel substitution is generalizable, yielding a palette of chemical dyes with improved quantum efficiencies that spans the UV and visible range.
1,140 citations
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04 Nov 2016TL;DR: This work is the first to conduct an extensive study of the transferability over large models and a large scale dataset, and it is also theFirst to study the transferabilities of targeted adversarial examples with their target labels.
Abstract: An intriguing property of deep neural networks is the existence of adversarial examples, which can transfer among different architectures. These transferable adversarial examples may severely hinder deep neural network-based applications. Previous works mostly study the transferability using small scale datasets. In this work, we are the first to conduct an extensive study of the transferability over large models and a large scale dataset, and we are also the first to study the transferability of targeted adversarial examples with their target labels. We study both non-targeted and targeted adversarial examples, and show that while transferable non-targeted adversarial examples are easy to find, targeted adversarial examples generated using existing approaches almost never transfer with their target labels. Therefore, we propose novel ensemble-based approaches to generating transferable adversarial examples. Using such approaches, we observe a large proportion of targeted adversarial examples that are able to transfer with their target labels for the first time. We also present some geometric studies to help understanding the transferable adversarial examples. Finally, we show that the adversarial examples generated using ensemble-based approaches can successfully attack this http URL, which is a black-box image classification system.
1,140 citations
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TL;DR: This review aims at exploring the properties of polyphenols in anti-inflammation and oxidation and the mechanisms ofpolyphenols inhibiting molecular signaling pathways which are activated by oxidative stress, as well as the possible roles of poly phenols in inflammation-mediated chronic disorders.
Abstract: Oxidative stress is viewed as an imbalance between the production of reactive oxygen species (ROS) and their elimination by protective mechanisms, which can lead to chronic inflammation. Oxidative stress can activate a variety of transcription factors, which lead to the differential expression of some genes involved in inflammatory pathways. The inflammation triggered by oxidative stress is the cause of many chronic diseases. Polyphenols have been proposed to be useful as adjuvant therapy for their potential anti-inflammatory effect, associated with antioxidant activity, and inhibition of enzymes involved in the production of eicosanoids. This review aims at exploring the properties of polyphenols in anti-inflammation and oxidation and the mechanisms of polyphenols inhibiting molecular signaling pathways which are activated by oxidative stress, as well as the possible roles of polyphenols in inflammation-mediated chronic disorders. Such data can be helpful for the development of future antioxidant therapeutics and new anti-inflammatory drugs.
1,140 citations
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Newcastle upon Tyne Hospitals NHS Foundation Trust1, Newcastle University2, University of Exeter3, University of Cambridge4, Imperial College London5, Chelsea and Westminster Hospital NHS Foundation Trust6, Royal Liverpool and Broadgreen University Hospital NHS Trust7, University of Manchester8, Pennine Acute Hospitals NHS Trust9, King's College London10, Guy's and St Thomas' NHS Foundation Trust11, Barts Health NHS Trust12, Queen Mary University of London13, Leeds Teaching Hospitals NHS Trust14, University of Leeds15, Royal College of Surgeons in Ireland16, University of Edinburgh17, Western General Hospital18, University Hospitals Bristol NHS Foundation Trust19, University of Glasgow20, Glasgow Royal Infirmary21, University of Birmingham22, Queen Elizabeth Hospital Birmingham23, University College London Hospitals NHS Foundation Trust24, University College London25, Brighton and Sussex Medical School26, Brighton and Sussex University Hospitals NHS Trust27, University of Wolverhampton28, University Hospital of Wales29
TL;DR: Comprehensive up-to-date guidance is provided regarding indications for, initiation and monitoring of immunosuppressive therapies, nutrition interventions, pre-, peri- and postoperative management, as well as structure and function of the multidisciplinary team and integration between primary and secondary care.
Abstract: Ulcerative colitis and Crohn’s disease are the principal forms of inflammatory bowel disease. Both represent chronic inflammation of the gastrointestinal tract, which displays heterogeneity in inflammatory and symptomatic burden between patients and within individuals over time. Optimal management relies on understanding and tailoring evidence-based interventions by clinicians in partnership with patients. This guideline for management of inflammatory bowel disease in adults over 16 years of age was developed by Stakeholders representing UK physicians (British Society of Gastroenterology), surgeons (Association of Coloproctology of Great Britain and Ireland), specialist nurses (Royal College of Nursing), paediatricians (British Society of Paediatric Gastroenterology, Hepatology and Nutrition), dietitians (British Dietetic Association), radiologists (British Society of Gastrointestinal and Abdominal Radiology), general practitioners (Primary Care Society for Gastroenterology) and patients (Crohn’s and Colitis UK). A systematic review of 88 247 publications and a Delphi consensus process involving 81 multidisciplinary clinicians and patients was undertaken to develop 168 evidence- and expert opinion-based recommendations for pharmacological, non-pharmacological and surgical interventions, as well as optimal service delivery in the management of both ulcerative colitis and Crohn’s disease. Comprehensive up-to-date guidance is provided regarding indications for, initiation and monitoring of immunosuppressive therapies, nutrition interventions, pre-, peri- and postoperative management, as well as structure and function of the multidisciplinary team and integration between primary and secondary care. Twenty research priorities to inform future clinical management are presented, alongside objective measurement of priority importance, determined by 2379 electronic survey responses from individuals living with ulcerative colitis and Crohn’s disease, including patients, their families and friends.
1,140 citations
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TL;DR: This paper examined the impact of Chinese import competition on broad measures of technical change (patenting, IT, and TFP) using new panel data across twelve European countries from 1996 to 2007 and found that the absolute volume of innovation increases within the firms most affected by Chinese imports in their output markets.
Abstract: We examine the impact of Chinese import competition on broad measures of technical change—patenting, IT, and TFP—using new panel data across twelve European countries from 1996 to 2007. In particular, we establish that the absolute volume of innovation increases within the firms most affected by Chinese imports in their output markets. We correct for endogeneity using the removal of product-specific quotas following China's entry into the World Trade Organization in 2001. Chinese import competition led to increased technical change within firms and reallocated employment between firms towards more technologically advanced firms. These within and between effects were about equal in magnitude, and account for 14% of European technology upgrading over 2000–7 (and even more when we allow for offshoring to China). Rising Chinese import competition also led to falls in employment and the share of unskilled workers. In contrast to low-wage nations like China, developed countries had no significant effect on innovation.
1,139 citations
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TL;DR: This work proposes a new equilibrium enforcing method paired with a loss derived from the Wasserstein distance for training auto-encoder based Generative Adversarial Networks, which provides a new approximate convergence measure, fast and stable training and high visual quality.
Abstract: We propose a new equilibrium enforcing method paired with a loss derived from the Wasserstein distance for training auto-encoder based Generative Adversarial Networks. This method balances the generator and discriminator during training. Additionally, it provides a new approximate convergence measure, fast and stable training and high visual quality. We also derive a way of controlling the trade-off between image diversity and visual quality. We focus on the image generation task, setting a new milestone in visual quality, even at higher resolutions. This is achieved while using a relatively simple model architecture and a standard training procedure.
1,139 citations
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01 Jan 2016
TL;DR: This paper describes the SemEval 2016 shared task on Aspect Based Sentiment Analysis (ABSA), a continuation of the respective tasks of 2014 and 2015, which attracted 245 submissions from 29 teams and provided 19 training and 20 testing datasets.
Abstract: This paper describes the SemEval 2016 shared task on Aspect Based Sentiment Analysis (ABSA), a continuation of the respective tasks of 2014 and 2015. In its third year, the task provided 19 training and 20 testing datasets for 8 languages and 7 domains, as well as a common evaluation procedure. From these datasets, 25 were for sentence-level and 14 for text-level ABSA; the latter was introduced for the first time as a subtask in SemEval. The task attracted 245 submissions from 29 teams.
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TL;DR: It is shown that a TMPRSS2-expressing VeroE6 cell line is highly susceptible to Sars-CoV-2 infection, making it useful for isolating and propagating SARS-Cov-2.
Abstract: A novel betacoronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which caused a large respiratory outbreak in Wuhan, China in December 2019, is currently spreading across many countries globally. Here, we show that a TMPRSS2-expressing VeroE6 cell line is highly susceptible to SARS-CoV-2 infection, making it useful for isolating and propagating SARS-CoV-2. Our results reveal that, in common with SARS- and Middle East respiratory syndrome-CoV, SARS-CoV-2 infection is enhanced by TMPRSS2.
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TL;DR: RASPA as discussed by the authors is a software package for simulating adsorption and diffusion of molecules in flexible nanoporous materials, which implements the latest state-of-the-art algorithms for molecular dynamics and Monte Carlo (MC) in various ensembles including symplectic/measure-preserving integrators, Ewald summation, configurational-bias MC, continuous fractional component MC, reactive MC and Baker's minimisation.
Abstract: A new software package, RASPA, for simulating adsorption and diffusion of molecules in flexible nanoporous materials is presented. The code implements the latest state-of-the-art algorithms for molecular dynamics and Monte Carlo (MC) in various ensembles including symplectic/measure-preserving integrators, Ewald summation, configurational-bias MC, continuous fractional component MC, reactive MC and Baker's minimisation. We show example applications of RASPA in computing coexistence properties, adsorption isotherms for single and multiple components, self- and collective diffusivities, reaction systems and visualisation. The software is released under the GNU General Public License.
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TL;DR: This Review summarizes and draws connections between diverse streams of empirical research on privacy behavior: people’s uncertainty about the consequences of privacy-related behaviors and their own preferences over those consequences; the context-dependence of people's concern about privacy; and the degree to which privacy concerns are malleable—manipulable by commercial and governmental interests.
Abstract: This Review summarizes and draws connections between diverse streams of empirical research on privacy behavior. We use three themes to connect insights from social and behavioral sciences: people's uncertainty about the consequences of privacy-related behaviors and their own preferences over those consequences; the context-dependence of people's concern, or lack thereof, about privacy; and the degree to which privacy concerns are malleable—manipulable by commercial and governmental interests. Organizing our discussion by these themes, we offer observations concerning the role of public policy in the protection of privacy in the information age.
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University of Texas MD Anderson Cancer Center1, Princess Margaret Cancer Centre2, Memorial Sloan Kettering Cancer Center3, Hebron University4, European Institute of Oncology5, Ottawa Hospital Research Institute6, University of Manchester7, Catholic University of the Sacred Heart8, French Institute of Health and Medical Research9, Auckland City Hospital10, Royal Brisbane and Women's Hospital11, Ohio State University12, Johns Hopkins University13, University of Washington14, University of California, Los Angeles15, University of Glasgow16, Royal Melbourne Hospital17, Foundation Medicine18, University College London19, Ghent University Hospital20
TL;DR: This trial assessed rucaparib versus placebo after response to second-line or later platinum-based chemotherapy in patients with high-grade, recurrent, platinum-sensitive ovarian carcinoma harbouring a BRCA mutation or high percentage of genome-wide loss of heterozygosity.
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27 Nov 2017TL;DR: This paper develops an active learning framework for high dimensional data, a task which has been extremely challenging so far, with very sparse existing literature, and demonstrates its active learning techniques with image data, obtaining a significant improvement on existing active learning approaches.
Abstract: Even though active learning forms an important pillar of machine learning, deep learning tools are not prevalent within it. Deep learning poses several difficulties when used in an active learning setting. First, active learning (AL) methods generally rely on being able to learn and update models from small amounts of data. Recent advances in deep learning, on the other hand, are notorious for their dependence on large amounts of data. Second, many AL acquisition functions rely on model uncertainty, yet deep learning methods rarely represent such model uncertainty. In this paper we combine recent advances in Bayesian deep learning into the active learning framework in a practical way. We develop an active learning framework for high dimensional data, a task which has been extremely challenging so far, with very sparse existing literature. Taking advantage of specialised models such as Bayesian convolutional neural networks, we demonstrate our active learning techniques with image data, obtaining a significant improvement on existing active learning approaches. We demonstrate this on both the MNIST dataset, as well as for skin cancer diagnosis from lesion images (ISIC2016 task).
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TL;DR: This review focuses on recent developments in the understanding of the molecular actions of the core Hippo kinase cascade and discusses key open questions in the regulation and function of the Hippo pathway.
Abstract: The Hippo pathway was initially identified in Drosophila melanogaster screens for tissue growth two decades ago and has been a subject extensively studied in both Drosophila and mammals in the last several years. The core of the Hippo pathway consists of a kinase cascade, transcription coactivators, and DNA-binding partners. Recent studies have expanded the Hippo pathway as a complex signaling network with >30 components. This pathway is regulated by intrinsic cell machineries, such as cell-cell contact, cell polarity, and actin cytoskeleton, as well as a wide range of signals, including cellular energy status, mechanical cues, and hormonal signals that act through G-protein-coupled receptors. The major functions of the Hippo pathway have been defined to restrict tissue growth in adults and modulate cell proliferation, differentiation, and migration in developing organs. Furthermore, dysregulation of the Hippo pathway leads to aberrant cell growth and neoplasia. In this review, we focus on recent developments in our understanding of the molecular actions of the core Hippo kinase cascade and discuss key open questions in the regulation and function of the Hippo pathway.
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TL;DR: Based on hypotheses involving social exchange, attribution, and self-enhancement, this paper carried out a meta-analytic assessment of OST using results from 558 studies and found that OST was generally successful in its predictions concerning both the antecedents of POS (leadership, employee-organization context, human resource practices, and working conditions) and its consequences (employee orientation toward the organization and work, employee performance, and well-being).
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The Feinstein Institute for Medical Research1, Cold Spring Harbor Laboratory2, Cornell University3, Hofstra University4, McGill University5, University of Michigan6, University of California, San Francisco7, University of Texas MD Anderson Cancer Center8, McGill University Health Centre9, University of Utah10
TL;DR: Autopsy results and literature are presented supporting the hypothesis that neutrophil extracellular traps (NETs) may contribute to organ damage and mortality in COVID-19, and existing drugs that target NETs, although unspecific, may benefit CO VID-19 patients.
Abstract: Coronavirus disease 2019 (COVID-19) is a novel, viral-induced respiratory disease that in ∼10-15% of patients progresses to acute respiratory distress syndrome (ARDS) triggered by a cytokine storm. In this Perspective, autopsy results and literature are presented supporting the hypothesis that a little known yet powerful function of neutrophils-the ability to form neutrophil extracellular traps (NETs)-may contribute to organ damage and mortality in COVID-19. We show lung infiltration of neutrophils in an autopsy specimen from a patient who succumbed to COVID-19. We discuss prior reports linking aberrant NET formation to pulmonary diseases, thrombosis, mucous secretions in the airways, and cytokine production. If our hypothesis is correct, targeting NETs directly and/or indirectly with existing drugs may reduce the clinical severity of COVID-19.
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TL;DR: A Novel Coronavirus Emerging in China A novel coronavirus, designated as 2019-nCoV, emerged in Wuhan, China, at the end of 2019, although many details of the emergence of this virus remain unknown.
Abstract: A Novel Coronavirus Emerging in China A novel coronavirus, designated as 2019-nCoV, emerged in Wuhan, China, at the end of 2019. Although many details of the emergence of this virus remain unknown,...
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TL;DR: Although perovskite light-emitting devices are yet to become industrially relevant, in merely two years these devices have achieved the brightness and efficiencies that organic light-EMitting diodes accomplished in two decades.
Abstract: Organic-inorganic hybrid perovskites have cemented their position as an exceptional class of optoelectronic materials thanks to record photovoltaic efficiencies of 22.1%, as well as promising demonstrations of light-emitting diodes, lasers, and light-emitting transistors. Perovskite materials with photoluminescence quantum yields close to 100% and perovskite light-emitting diodes with external quantum efficiencies of 8% and current efficiencies of 43 cd A(-1) have been achieved. Although perovskite light-emitting devices are yet to become industrially relevant, in merely two years these devices have achieved the brightness and efficiencies that organic light-emitting diodes accomplished in two decades. Further advances will rely decisively on the multitude of compositional, structural variants that enable the formation of lower-dimensionality layered and three-dimensional perovskites, nanostructures, charge-transport materials, and device processing with architectural innovations. Here, the rapid advancements in perovskite light-emitting devices and lasers are reviewed. The key challenges in materials development, device fabrication, operational stability are addressed, and an outlook is presented that will address market viability of perovskite light-emitting devices.
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TL;DR: This work has developed a method called β-structure selection (BeStSel) for the secondary structure estimation that takes into account the twist of β-structures, and can predict the protein fold down to the topology level following the CATH classification from a single CD spectrum.
Abstract: Circular dichroism (CD) spectroscopy is a widely used technique for the study of protein structure. Numerous algorithms have been developed for the estimation of the secondary structure composition from the CD spectra. These methods often fail to provide acceptable results on α/β-mixed or β-structure–rich proteins. The problem arises from the spectral diversity of β-structures, which has hitherto been considered as an intrinsic limitation of the technique. The predictions are less reliable for proteins of unusual β-structures such as membrane proteins, protein aggregates, and amyloid fibrils. Here, we show that the parallel/antiparallel orientation and the twisting of the β-sheets account for the observed spectral diversity. We have developed a method called β-structure selection (BeStSel) for the secondary structure estimation that takes into account the twist of β-structures. This method can reliably distinguish parallel and antiparallel β-sheets and accurately estimates the secondary structure for a broad range of proteins. Moreover, the secondary structure components applied by the method are characteristic to the protein fold, and thus the fold can be predicted to the level of topology in the CATH classification from a single CD spectrum. By constructing a web server, we offer a general tool for a quick and reliable structure analysis using conventional CD or synchrotron radiation CD (SRCD) spectroscopy for the protein science research community. The method is especially useful when X-ray or NMR techniques fail. Using BeStSel on data collected by SRCD spectroscopy, we investigated the structure of amyloid fibrils of various disease-related proteins and peptides.
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TL;DR: The phase 1, dose-escalation, open-label trial of a messenger RNA vaccine, mRNA-1273, which encodes the stabilized prefusion SARS-CoV-2 spike protein in healthy adults found it induced higher binding- and neutralizing-antibody titers than the 25-μg dose, which supports the use of the 100- μg dose in a phase 3 vaccine trial.
Abstract: Background Testing of vaccine candidates to prevent infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in an older population is important, since increased inciden...
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12 Feb 2017TL;DR: ConceptNet as mentioned in this paper is a knowledge graph that connects words and phrases of natural language with labeled edges to represent the general knowledge involved in understanding language, improving natural language applications by allowing the application to better understand the meanings behind the words people use.
Abstract: Machine learning about language can be improved by supplying it with specific knowledge and sources of external information. We present here a new version of the linked open data resource ConceptNet that is particularly well suited to be used with modern NLP techniques such as word embeddings. ConceptNet is a knowledge graph that connects words and phrases of natural language with labeled edges. Its knowledge is collected from many sources that include expert-created resources, crowd-sourcing, and games with a purpose. It is designed to represent the general knowledge involved in understanding language, improving natural language applications by allowing the application to better understand the meanings behind the words people use. When ConceptNet is combined with word embeddings acquired from distributional semantics (such as word2vec), it provides applications with understanding that they would not acquire from distributional semantics alone, nor from narrower resources such as WordNet or DBPedia. We demonstrate this with state-of-the-art results on intrinsic evaluations of word relatedness that translate into improvements on applications of word vectors, including solving SAT-style analogies.
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TL;DR: This work proposes a method based on generative adversarial networks that learns to discover relations between different domains (DiscoGAN) and successfully transfers style from one domain to another while preserving key attributes such as orientation and face identity.
Abstract: While humans easily recognize relations between data from different domains without any supervision, learning to automatically discover them is in general very challenging and needs many ground-truth pairs that illustrate the relations. To avoid costly pairing, we address the task of discovering cross-domain relations given unpaired data. We propose a method based on generative adversarial networks that learns to discover relations between different domains (DiscoGAN). Using the discovered relations, our proposed network successfully transfers style from one domain to another while preserving key attributes such as orientation and face identity. Source code for official implementation is publicly available this https URL
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TL;DR: Among persons without dementia, the prevalence of cerebral amyloid pathology as determined by positron emission tomography or cerebrospinal fluid findings was associated with age, apolipoprotein E [APOE] genotype, sex, and education, and presence of cognitive impairment.
Abstract: Cerebral amyloid-β aggregation is an early pathological event in Alzheimer disease (AD), starting decades before dementia onset. Estimates of the prevalence of amyloid pathology in persons without dementia are needed to understand the development of AD and to design prevention studies.
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University of Oxford1, University of Michigan2, Wellcome Trust Sanger Institute3, Amgen4, University of Cambridge5, University of Copenhagen6, University of Liverpool7, University of Freiburg8, Boston University9, University of Tartu10, Erasmus University Medical Center11, Leiden University Medical Center12, Pasteur Institute13, Icahn School of Medicine at Mount Sinai14, UCLA Medical Center15, Vanderbilt University Medical Center16, Wake Forest University17, National University of Singapore18, London North West Healthcare NHS Trust19, Imperial College London20, Charité21, Innsbruck Medical University22, Washington University in St. Louis23, Queen Mary University of London24, University of Southern Denmark25, National and Kapodistrian University of Athens26, Robertson Centre for Biostatistics27, University of Exeter28, Uppsala University29, University of Düsseldorf30, Steno Diabetes Center31, Aalborg University32, University of Eastern Finland33, Broad Institute34, Frederiksberg Hospital35, University of Bergen36, Lund University37, Technische Universität München38, University of North Carolina at Chapel Hill39, University of Edinburgh40, Ninewells Hospital41, University of Minnesota42, University of Glasgow43, Ludwig Maximilian University of Munich44, University of Iceland45, Aarhus University46, Science for Life Laboratory47, Stanford University48, University of Helsinki49, National Institutes of Health50, University of Dundee51, Harvard University52
TL;DR: Combining 32 genome-wide association studies with high-density imputation provides a comprehensive view of the genetic contribution to type 2 diabetes in individuals of European ancestry with respect to locus discovery, causal-variant resolution, and mechanistic insight.
Abstract: We expanded GWAS discovery for type 2 diabetes (T2D) by combining data from 898,130 European-descent individuals (9% cases), after imputation to high-density reference panels. With these data, we (i) extend the inventory of T2D-risk variants (243 loci, 135 newly implicated in T2D predisposition, comprising 403 distinct association signals); (ii) enrich discovery of lower-frequency risk alleles (80 index variants with minor allele frequency 2); (iii) substantially improve fine-mapping of causal variants (at 51 signals, one variant accounted for >80% posterior probability of association (PPA)); (iv) extend fine-mapping through integration of tissue-specific epigenomic information (islet regulatory annotations extend the number of variants with PPA >80% to 73); (v) highlight validated therapeutic targets (18 genes with associations attributable to coding variants); and (vi) demonstrate enhanced potential for clinical translation (genome-wide chip heritability explains 18% of T2D risk; individuals in the extremes of a T2D polygenic risk score differ more than ninefold in prevalence).
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TL;DR: This paper presents an efficient solution that explores the visual patterns within individual cropped regions with minimal costs, and builds the framework upon a representative one-stage keypoint-based detector named CornerNet, which improves both precision and recall.
Abstract: In object detection, keypoint-based approaches often suffer a large number of incorrect object bounding boxes, arguably due to the lack of an additional look into the cropped regions. This paper presents an efficient solution which explores the visual patterns within each cropped region with minimal costs. We build our framework upon a representative one-stage keypoint-based detector named CornerNet. Our approach, named CenterNet, detects each object as a triplet, rather than a pair, of keypoints, which improves both precision and recall. Accordingly, we design two customized modules named cascade corner pooling and center pooling, which play the roles of enriching information collected by both top-left and bottom-right corners and providing more recognizable information at the central regions, respectively. On the MS-COCO dataset, CenterNet achieves an AP of 47.0%, which outperforms all existing one-stage detectors by at least 4.9%. Meanwhile, with a faster inference speed, CenterNet demonstrates quite comparable performance to the top-ranked two-stage detectors. Code is available at this https URL.
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TL;DR: A method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome, successfully inferred copy number at equivalent to 100-kilobase resolution genome-wide from a platform targeting as few as 293 genes.
Abstract: Germline copy number variants (CNVs) and somatic copy number alterations (SCNAs) are of significant importance in syndromic conditions and cancer. Massively parallel sequencing is increasingly used to infer copy number information from variations in the read depth in sequencing data. However, this approach has limitations in the case of targeted re-sequencing, which leaves gaps in coverage between the regions chosen for enrichment and introduces biases related to the efficiency of target capture and library preparation. We present a method for copy number detection, implemented in the software package CNVkit, that uses both the targeted reads and the nonspecifically captured off-target reads to infer copy number evenly across the genome. This combination achieves both exon-level resolution in targeted regions and sufficient resolution in the larger intronic and intergenic regions to identify copy number changes. In particular, we successfully inferred copy number at equivalent to 100-kilobase resolution genome-wide from a platform targeting as few as 293 genes. After normalizing read counts to a pooled reference, we evaluated and corrected for three sources of bias that explain most of the extraneous variability in the sequencing read depth: GC content, target footprint size and spacing, and repetitive sequences. We compared the performance of CNVkit to copy number changes identified by array comparative genomic hybridization. We packaged the components of CNVkit so that it is straightforward to use and provides visualizations, detailed reporting of significant features, and export options for integration into existing analysis pipelines. CNVkit is freely available from https://github.com/etal/cnvkit.
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TL;DR: A new approach to the development of plant disease recognition model, based on leaf image classification, by the use of deep convolutional networks, which is able to recognize 13 different types of plant diseases out of healthy leaves.
Abstract: The latest generation of convolutional neural networks (CNNs) has achieved impressive results in the field of image classification. This paper is concerned with a new approach to the development of plant disease recognition model, based on leaf image classification, by the use of deep convolutional networks. Novel way of training and the methodology used facilitate a quick and easy system implementation in practice. The developed model is able to recognize 13 different types of plant diseases out of healthy leaves, with the ability to distinguish plant leaves from their surroundings. According to our knowledge, this method for plant disease recognition has been proposed for the first time. All essential steps required for implementing this disease recognition model are fully described throughout the paper, starting from gathering images in order to create a database, assessed by agricultural experts. Caffe, a deep learning framework developed by Berkley Vision and Learning Centre, was used to perform the deep CNN training. The experimental results on the developed model achieved precision between 91% and 98%, for separate class tests, on average 96.3%.