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Why R&D Should Be Allocated To Subpart F And Gilti, Stephen E. Shay, Reuven S. Avi-Yonah, Patrick Driessen, J. Clifton Fleming Jr., Robert J. Peroni Jun 2020

Why R&D Should Be Allocated To Subpart F And Gilti, Stephen E. Shay, Reuven S. Avi-Yonah, Patrick Driessen, J. Clifton Fleming Jr., Robert J. Peroni

Articles

This article responds to the notice of proposed rulemaking under sections 861 and 904 (REG105495-19) published in the Federal Register December 17, 2019 (the proposed regulations). The proposed regulations would not allocate U.S. shareholder deductions for research and development or experimentation (R&D or R&E) expenditures under section 174 (R&D deductions) to a gross income inclusion under section 951 (subpart F inclusion) or section 951A (global intangible low-taxed income)1 from a controlled foreign corporation for foreign tax credit limitation purposes.


Increasing The Trust In Refactoring Through Visualization, Alex Bogart, Eman Abdullah Alomar, Mohamed Wiem Mkaouer, Ali Ouni Jun 2020

Increasing The Trust In Refactoring Through Visualization, Alex Bogart, Eman Abdullah Alomar, Mohamed Wiem Mkaouer, Ali Ouni

Articles

In software development, maintaining good design is essential. The process of refactoring enables developers to improve this design during development without altering the program’s existing behavior. However, this process can be time-consuming, introduce semantic errors, and be difficult for developers inexperienced with refactoring or unfamiliar with a given code base. Automated refactoring tools can help not only by applying these changes, but by identifying opportunities for refactoring. Yet, developers have not been quick to adopt these tools due to a lack of trust between the developer and the tool. We propose an approach in the form of a visualization to …


Medical Marijuana, Taxation, And Internal Revenue Code Section 280e, Douglas A. Kahn, Howard J. Bromberg Jun 2020

Medical Marijuana, Taxation, And Internal Revenue Code Section 280e, Douglas A. Kahn, Howard J. Bromberg

Articles

Congress enacted § 280E of the Internal Revenue Code in 1982 to punish businesses engaged in illegal drug trafficking, including marijuana. Section 280E denies all credits and deductions, including ordinary business expenses, from gross income of businesses illegally trafficking in a Schedule I or II controlled substance. This provision violates the principle that the tax code should foster a consistent treatment of income, regardless of source; and that the income tax is ill-used for punitive measures. Now that marijuana has been legalized in some form in at least 46 states for therapeutic purposes, this federal tax penalty transgresses principles of …


Asynchronous Assistance: A Social Network Analysis Of Influencing Peer Interactions In Peerwise, Tomas Shields, Geraldine Gray, Barry J. Ryan Jun 2020

Asynchronous Assistance: A Social Network Analysis Of Influencing Peer Interactions In Peerwise, Tomas Shields, Geraldine Gray, Barry J. Ryan

Articles

This mixed methods, investigative case study explored student patterns of use within the online PeerWise platform to identify the most influencing activities and to build a model capable of predicting performance based on these influencing activities. Peerwise is designed to facilitate student peer-to-peer engagement through creating, answering and ranking multiple choice questions; this study sought to understand the relationship between student engagement in Peerwise and learning performance. To address the research question, various usage metrics were explored, visualized and modelled, using social network analysis with Gephi, Tableau and Python. These findings were subsequently analyzed in light of the qualitative survey …


On The Relationship Between Developer Experience And Refactoring: An Exploratory Study And Preliminary Results, Eman Abdullah Alomar, Anthony Peruma, Christian D. Newman, Mohamed Wiem Mkaouer, Ali Ouni Jun 2020

On The Relationship Between Developer Experience And Refactoring: An Exploratory Study And Preliminary Results, Eman Abdullah Alomar, Anthony Peruma, Christian D. Newman, Mohamed Wiem Mkaouer, Ali Ouni

Articles

Refactoring is one of the means of managing technical debt and maintaining a healthy software structure through enforcing best design practices, or coping with design defects. Previous refactoring surveys have shown that these code restructurings are mainly executed by developers who have sufficient knowledge of the system’s design, and disposing of leadership roles in their development teams. However, these surveys were mainly limited to specific projects and companies. In this paper, we explore the generalizability of the previous results though analyzing 800 open-source projects. We mine their refactoring activities, and we identify their corresponding contributors. Then, we associate an expertise …


A Proposal Digital Marketing Strategy For Marcheluzzo Srl: Training And Evaluating A Prediction Model For The Number Of Adv. Impressions, Charles Alves De Castro Jun 2020

A Proposal Digital Marketing Strategy For Marcheluzzo Srl: Training And Evaluating A Prediction Model For The Number Of Adv. Impressions, Charles Alves De Castro

Articles

This research aims to describe a digital marketing strategy elaborated to be deployed in the MarcheluzzoSrl Company located in Italy. In addition, it intends to give a wide range of information to the company about its customers, target, competitors, market, digital marketing strategy, and potential recommendations. It is also important to highlight that this strategy is focused on the Brazilian market. Most of the information collected for the situational analysis and many other components for this research were gathered through the author`s perception during his internship in the company. The methodology includes secondary data collected through field observation in the …


Rapid Restoration Techniques For Software-Defined Networks, Ali Malik, Ruairí De Fréin, Benjamin Aziz May 2020

Rapid Restoration Techniques For Software-Defined Networks, Ali Malik, Ruairí De Fréin, Benjamin Aziz

Articles

There is increasing demand in modern day business applications for communication networks to be robust and reliable due to the complexity and critical nature of such applications. As such, data delivery is expected to be reliable and secure even in the harshest of environments. Software-Defined Networking (SDN) is gaining traction as a promising approach for designing network architectures which are robust and flexible. One reason for this is that separating the data plane from the control plane, increases the controller’s ability to configure the network rapidly. When network failure events occur, the network manager may trade-off the optimality of the …


Assessing The Market Niche Of Eurasian Rail Freight In The Belt And Road Era., Xu Zhang, Hans-Joachim Schramm May 2020

Assessing The Market Niche Of Eurasian Rail Freight In The Belt And Road Era., Xu Zhang, Hans-Joachim Schramm

Articles

This paper presents an overview of the recent development of Eurasian rail freight in the Belt and Road era and further evaluates its service quality in terms of transit times and transport costs compared to other transport modes in containerised supply chains between Europe and China.

A trade-off model of transit time and transport costs based on quantitative data from primary and secondary sources is developed to demonstrate the market niche for Eurasian rail freight vis-a-vis the more established modes of transport of sea, air, and sea/air. In a scenario analysis, further cargo attributes influencing modal choice are employed to …


A Generalisable Bottom-Up Methodology For Deriving A Residential Stock Model From Large Empirical Databases., Ciara Ahern, Brian Norton May 2020

A Generalisable Bottom-Up Methodology For Deriving A Residential Stock Model From Large Empirical Databases., Ciara Ahern, Brian Norton

Articles

Average reference dwellings representing a predominant housing typology are defined in this work. Specifying such reference buildings is a prerequisite for (i) calculating cost-optimal energy performance requirements for buildings and building elements and (ii) ensuring valid calculations of national building energy consumption. In the EU, an Energy Performance Certificate (EPC) rating is an assessment of the energy consumption of a dwelling. The use of inappropriate default-values for the building envelope thermal transmittance coefficients (U-values) and standardised thermal bridging transmittance coefficients (Y-values) in the production of EPCs leads to an over-estimation of potential energy savings from interventions in the existing dwelling …


Undergraduate Textbook Representations Of Meiosis Neglect Essential Elements, Leslie Kate Wright, Grace Elizabeth C. Dy, Dina L. Newman May 2020

Undergraduate Textbook Representations Of Meiosis Neglect Essential Elements, Leslie Kate Wright, Grace Elizabeth C. Dy, Dina L. Newman

Articles

The process of meiosis is an essential topic that secondary and postsecondary students struggle with. The important meiosis-related concepts of homology, ploidy, and segregation can be described using the DNA Triangle framework, which connects them to the multidimensional nature of DNA (chromosomal, molecular, and informational levels). We have previously established that undergraduate biology students typically fail to describe and/or link appropriate levels to their explanations of meiosis. We hypothesize that students' understanding mirrors the resources they are given – in other words, textbook figures often lack many of the important connections that experts include when talking about meiosis. Prior work …


Toward The Automatic Classification Of Self-Affirmed Refactoring, Mohamed Wiem Mkaouer, Eman Abdullah Alomar, Ali Ouni May 2020

Toward The Automatic Classification Of Self-Affirmed Refactoring, Mohamed Wiem Mkaouer, Eman Abdullah Alomar, Ali Ouni

Articles

The concept of Self-Affirmed Refactoring (SAR) was introduced to explore how developers document their refactoring activities in commit messages, i.e., developers explicit documentation of refactoring operations intentionally introduced during a code change. In our previous study, we have manually identified refactoring patterns and defined three main common quality improvement categories including internal quality attributes, external quality attributes, and code smells, by only considering refactoring-related commits. However, this approach heavily depends on the manual inspection of commit messages. In this paper, we propose a two-step approach to first identify whether a commit describes developer-related refactoring events, then to classify it according …


Theory Of The Nudnik: The Future Of Consumer Activism And What We Can Do To Stop It, Yonathan A. Arbel, Roy Shapira May 2020

Theory Of The Nudnik: The Future Of Consumer Activism And What We Can Do To Stop It, Yonathan A. Arbel, Roy Shapira

Articles

How do consumers hold sellers accountable and enforce market norms? This Article contributes to our understanding of consumer markets in three ways. First, the Article identifies the role of a small subset of consumers-the titular "nudniks"-as engines of market discipline. Nudniks are those who call to complain, speak with managers, post online reviews, and file lawsuits. Typified by an idiosyncratic utility function and certain unique personality traits, nudniks pursue action where most consumers remain passive. Although derided in courtrooms and the court of public opinion, we show that nudniks can solve consumer collective action problems, leading to broad market improvements. …


Pollution Prevention Via Recovery Of Cerium (Iv) Oxide In Optics Company, Eugene Park, William Gallagher, Sydor Optics, Flint Creek Resources May 2020

Pollution Prevention Via Recovery Of Cerium (Iv) Oxide In Optics Company, Eugene Park, William Gallagher, Sydor Optics, Flint Creek Resources

Articles

Pollution prevention methods were applied at an optics manufacturer in an effort to improve recovery of a valuable polishing component, cerium oxide (ceria), 77% of which was lost to dragout and sewer discharge. Centrifugation and microfiltratiion were evaluated to develop a process that would increase recovery of used ceria, which would then be sent back to the ceria supplier for reclamation and reuse. Full-scale implementation included a high-speed centrifuge that operates continuously with a microfiltration system through recirculation in a single process tank. Sydor Optics has improved ceria recovery from 23% to 48%, saving thousands of dollars annually.


How Do Developers Refactor Code To Improve Code Reusability?, Eman Abdullah Alomar, Philip T. Rodriguez, Jordan Bowman, Tianjia Wang, Benjamin Adepoju, Kevin Lopez, Christian D. Newman, Ali Ouni, Mohamed Wiem Mkaouer May 2020

How Do Developers Refactor Code To Improve Code Reusability?, Eman Abdullah Alomar, Philip T. Rodriguez, Jordan Bowman, Tianjia Wang, Benjamin Adepoju, Kevin Lopez, Christian D. Newman, Ali Ouni, Mohamed Wiem Mkaouer

Articles

. Refactoring is the de-facto practice to optimize software health. While there has been several studies proposing refactoring strategies to optimize software design through applying design patterns and removing design defects, little is known about how developers actually refactor their code to improve its reuse. Therefore, we extract, from 1,828 open source projects, a set of refactorings which were intended to improve the software reusability. We analyze the impact of reusability refactorings on state-of-the-art reusability metrics, and we compare the distribution of reusability refactoring types, with the distribution of the remaining mainstream refactorings. Overall, we found that the distribution of …


An Exploratory Study On How Software Reuse Is Discussed In Stack Overflow, Mohamed Wiem Mkaouer, Eman Abdullah Alomar, Jiaqian Liu, Ali Ouni, Christian D. Newman, Diego Barinas May 2020

An Exploratory Study On How Software Reuse Is Discussed In Stack Overflow, Mohamed Wiem Mkaouer, Eman Abdullah Alomar, Jiaqian Liu, Ali Ouni, Christian D. Newman, Diego Barinas

Articles

Software reuse is an important and crucial quality attribute in modern software engineering, where almost all software projects, open source or commercial, no matter small or ultra-large, source code reuse in one way or another. Although software reuse has experienced an increased adoption throughout the years with the exponentially growing number of available third-party libraries, frameworks and APIs, little knowledge exists to investigate what aspects of code reuse developers discuss. In this study, we look into bridging this gap by examining Stack Overflow to understand the challenges developers encounter when trying to reuse code. Using the Stack Overflow tags “code-reuse” …


How We Refactor And How We Document It? On The Use Of Supervised Machine Learning Algorithms To Classify Refactoring Documentation, Eman Abdullah Alomar, Anthony Peruma, Mohamed Wiem Mkaouer, Christian D. Newman, Marouane Kessentini, Ali Ouni May 2020

How We Refactor And How We Document It? On The Use Of Supervised Machine Learning Algorithms To Classify Refactoring Documentation, Eman Abdullah Alomar, Anthony Peruma, Mohamed Wiem Mkaouer, Christian D. Newman, Marouane Kessentini, Ali Ouni

Articles

Refactoring is the art of improving the structural design of a software system without altering its external behavior. Today, refactoring has become a well-established and disciplined software engineering practice that has attracted a significant amount of research presuming that refactoring is primarily motivated by the need to improve system structures. However, recent studies have shown that developers may incorporate refactoring strategies in other development-related activities that go beyond improving the design especially with the emerging challenges in contemporary software engineering. Unfortunately, these studies are limited to developer interviews and a reduced set of projects. To cope with the above-mentioned limitations, …


Nonlinear Photon Pair Generation In A Highly Dispersive Medium, David J. Starling, Jacob Poirier, Michael Fanto, Jeffrey A. Steidle, Christopher C. Tison, Gregory A. Howland, Stefan F. Preble Apr 2020

Nonlinear Photon Pair Generation In A Highly Dispersive Medium, David J. Starling, Jacob Poirier, Michael Fanto, Jeffrey A. Steidle, Christopher C. Tison, Gregory A. Howland, Stefan F. Preble

Articles

Photon pair generation in silicon photonic integrated circuits relies on four wave mixing via the third order nonlinearity. Due to phase matching requirements and group velocity dispersion, this method has typically required TE polarized light. Here, we demonstrate TM polarized photon pair production in linearly uncoupled silicon resonators with more than an order of magnitude more dispersion than previous work. We achieve measured rates above 2.8 kHz and a heralded second order correlation of . This method enables phase matching in dispersive media and paves the way for novel entanglement generation in silicon photonic devices


3d Mammalian Cell Culture Models In Toxicology Testing, Janith Wanigasekara, Brijesh K. Tiwari, James Curtin Apr 2020

3d Mammalian Cell Culture Models In Toxicology Testing, Janith Wanigasekara, Brijesh K. Tiwari, James Curtin

Articles

3D cell culture can be successfully used as an alternative to laboratory animals, and as a cost effective and time-saving tissue culture technique, which also reduces the trial period for drug testing.


Simulating Cement Hydration Using Hydcem, Niall Holmes, Denis Kelliher, Mark Tyrer Apr 2020

Simulating Cement Hydration Using Hydcem, Niall Holmes, Denis Kelliher, Mark Tyrer

Articles

HYDCEM is a new cement hydration model to simulate volumetric changes and predict phase assemblage, degree of hydration, heat release, compressive strength and chemical shrinkage over time for PC and limestone binders undergoing hydration for any w/c ratio and curing temperatures between 5 and 45 °C. While models should never completely remove experimental analysis, they are an aid to better understand cement hydration and microstructure development by allowing users analyse different binders in a relatively short time. HYDCEM, written in MATLAB®, is aimed at complementing more sophisticated thermodynamic models giving users a reasonable prediction of hydration behaviour over time, using …


The Application Of Evolutionary Algorithms In Multi-Objective Design And Optimization Of Air Cooled Heatsinks, Younis Osama Abdelsalam, Sajad Alimohammadi, Tim Persoons Apr 2020

The Application Of Evolutionary Algorithms In Multi-Objective Design And Optimization Of Air Cooled Heatsinks, Younis Osama Abdelsalam, Sajad Alimohammadi, Tim Persoons

Articles

Genetic algorithms (GAs) are considered to be one of the main types of evolutionary algorithms (EAs) and are being increasingly used in various engineering design applications. To a large extent, plate-fin heatsinks are used in the thermal management of compact electronic equipment and data centers. The shape optimization of the heatsinks is not rigorously investigated during the design process of high power electronics. Any improvements in the effectiveness of the heatsinks impact the energy consumed by large-scale information communication technology (ICT) facilities including data centers and telecommunication systems and promote a more sustainable use of raw materials. This paper investigates …


Smart Cities At Play: Technology And Emerging Forms Of Playfulness, Konstantinos Papangelis, Michael Saker, Catherine Jones Apr 2020

Smart Cities At Play: Technology And Emerging Forms Of Playfulness, Konstantinos Papangelis, Michael Saker, Catherine Jones

Articles

Editorial. No abstract is available.


Study Of The Effect Of Methyldiethanolamine Initiator On The Recording Properties Of Acrylamide Based Photopolymer, Brian Rogers, Izabela Naydenova, Suzanne Martin Mar 2020

Study Of The Effect Of Methyldiethanolamine Initiator On The Recording Properties Of Acrylamide Based Photopolymer, Brian Rogers, Izabela Naydenova, Suzanne Martin

Articles

The use of Holographic Optical Elements (HOEs) in applications, such as in light shaping and redirection, requires certain characteristics such as a high Diffraction Efficiency, low angular selectivity and stability against UV damage. In order to maximize the performance of the HOEs, photosensitive materials are needed that have been optimised for the characteristics that are of particular importance in that application. At the core of the performance of these devices is the refractive index modulation created during holographic recording. Typically, a higher refractive index modulation will enable greater light Diffraction Efficiency and also operation with thinner devices, which in turn …


Capturing The City’S Heritage On-The-Go: Design Requirements For Mobile Crowdsourced Cultural Heritage, Bas Hannewijk, Federica Lucia Vinella, Vassilis-Javed Khan, Ioanna Lykourentzou, Konstantinos Papangelis, Judith Masthoff Mar 2020

Capturing The City’S Heritage On-The-Go: Design Requirements For Mobile Crowdsourced Cultural Heritage, Bas Hannewijk, Federica Lucia Vinella, Vassilis-Javed Khan, Ioanna Lykourentzou, Konstantinos Papangelis, Judith Masthoff

Articles

Intangible Cultural Heritage is at a continuous risk of extinction. Where historical artefacts engine the machinery of intercontinental mass-tourism, socio-technical changes are reshaping the anthropomorphic landscapes everywhere on the globe, at an unprecedented rate. There is an increasing urge to tap into the hidden semantics and the anecdotes surrounding people, memories and places. The vast cultural knowledge made of testimony, oral history and traditions constitutes a rich cultural ontology tying together human beings, times, and situations. Altogether, these complex, multidimensional features make the task of data-mapping of intangible cultural heritage a problem of sustainability and preservation. This paper addresses a …


Corporate Law And The Myth Of Efficient Market Control, William Wilson Bratton, Simone M. Sepe Mar 2020

Corporate Law And The Myth Of Efficient Market Control, William Wilson Bratton, Simone M. Sepe

Articles

In recent times, there has been an unprecedented shift in power from managers to shareholders, a shift that realizes the long-held theoretical aspiration of market control of the corporation. This Article subjects the market control paradigm to comprehensive economic examination and finds it wanting.

The market control paradigm relies on a narrow economic model that focuses on one problem only: management agency costs. With the rise of shareholder power, we need a wider lens that also takes in market prices, investor incentives, and information asymmetries. General equilibrium (GE) theory provides that lens. Several lessons follow from reference to this higher-order …


Three-Phase Hydrodynamic Simulation And Experimental Validation Of An Upflow Anaerobic Sludge Blanket Reactor, Camila D' Bastiani, Jéferson Luis Alba, Gabriel Tomazzoni Mazzarotto, Severino Rodrigues De Farias Neto, Anthony Reynolds, David Kennedy, Lademir Luiz Beal Mar 2020

Three-Phase Hydrodynamic Simulation And Experimental Validation Of An Upflow Anaerobic Sludge Blanket Reactor, Camila D' Bastiani, Jéferson Luis Alba, Gabriel Tomazzoni Mazzarotto, Severino Rodrigues De Farias Neto, Anthony Reynolds, David Kennedy, Lademir Luiz Beal

Articles

This research focuses on performing multiphase solid/liquid/gas CFD simulations of a UASB reactor in order to obtain a validated model that provides a clearer understanding of the hydrodynamic behaviour of the three phases in UASB reactors. Eulerian–Eulerian, laminar, three-dimensional, multiphase simulations are carried out using Fluent 16.2. The liquid phase velocity and flow profile are validated through PIV experiments. A liquid mean velocity difference of 8.45% is found between the experimental and numerical results, thus validating the CFD model. Shadowgraphy is applied successfully to validate the biogas phase velocity and bubble size. Based on the hydrodynamic analysis results, the reactor …


Sport Diplomacy And Uk Soft Power: The Case Of Mount Everest, Richard Woodward Mar 2020

Sport Diplomacy And Uk Soft Power: The Case Of Mount Everest, Richard Woodward

Articles

Sport is widely acknowledged as an important contributor to the United Kingdom’s soft power resources. This article aims to broaden and deepen our understanding of sport and soft power in the United Kingdom through a case study of British expeditions to, and the eventual conquest of, Mount Everest. Based on original archival research, the article demonstrates that British state institutions intervened systematically and strategically to expedite, and massage the story of, the ascent of Everest to burnish British prestige and present a favourable image to the world. In doing so, the article provides evidence that sport has been intrinsic to …


The Influence Of Road Geometry On Vehicle Rollover And Skidding, Yanna Yin, Huiying Wen, Lu Sun, Wei Hou Mar 2020

The Influence Of Road Geometry On Vehicle Rollover And Skidding, Yanna Yin, Huiying Wen, Lu Sun, Wei Hou

Articles

This paper analyzes the influence of single and combined unfavorable road geometry on rollover and skidding risks of D-class mid-sized sport utility vehicles (SUVs) with front-wheel drive for roads with design speeds at 80 km/h. A closed-loop simulation model of human-vehicle-road interactions is established to examine the systematic influence of road geometry on vehicle rollover and skidding. The effects of different road geometry on rollover and skidding on SUVs are studied for pavement surface with good and poor friction when vehicles are in the action of steady state cornering. The rollover and skidding risks of the most unfavorable road segments …


A Novel Self-Healing System: Towards A Sustainable Porous Asphalt, Shi Xu, Xueyan Liu, Amir Tabakovic, Erik Schlangen Mar 2020

A Novel Self-Healing System: Towards A Sustainable Porous Asphalt, Shi Xu, Xueyan Liu, Amir Tabakovic, Erik Schlangen

Articles

Self-healing asphalt, aimed to produce a sustainable asphalt pavement using green technology, has been studied in the past two decades. Technologies including encapsulated rejuvenator and induction heating have been proposed, demonstrated in the laboratory, and gradually evaluated in field application. This paper looks into the synergy effect of the above two technologies, where induction heating serves as the asphalt damage repair mechanism, requiring just 2 min heating time and encapsulated rejuvenator will replenish (rejuvenate) aged asphalt binder and reinstate bitumen’s healing ability. Moreover, the increased temperature from induction heating could in turn accelerate the diffusion process of rejuvenator into aged …


The Dynamism Of Health Law: Expanded Insurance Coverage As The Engine Of Regulatory Reform, Gabriel Scheffler Mar 2020

The Dynamism Of Health Law: Expanded Insurance Coverage As The Engine Of Regulatory Reform, Gabriel Scheffler

Articles

Can law improve the delivery of health care? The predominant view is that law serves as a barrier to reforming the health care delivery system. Health law scholars of all stripes blame regulations for impeding innovation, limiting competition, and exacerbating fragmentation in health care.

I argue that this view neglects an important-but overlooked-feature of health law: the dynamic relationship between laws that expand health insurance coverage and laws that regulate the delivery of health care. By expanding health insurance coverage and increasing the demand for health care, laws such as Medicare, Medicaid and the Affordable Care Act catalyze policymakers to …


Rapid Inference Of Antibiotic Resistance And Susceptibility By Genomic Neighbour Typing, Karel Břinda, Alanna Callendrello, Kevin C. Ma, Derek R. Macfadden, Themoula Charalampous, Robyn S. Lee, Lauren Cowley, Crista B. Wadsworth, Yonatan H. Grad, Gregory Kucherov, Justin O'Grady, Michael Baym, William P. Hanage Feb 2020

Rapid Inference Of Antibiotic Resistance And Susceptibility By Genomic Neighbour Typing, Karel Břinda, Alanna Callendrello, Kevin C. Ma, Derek R. Macfadden, Themoula Charalampous, Robyn S. Lee, Lauren Cowley, Crista B. Wadsworth, Yonatan H. Grad, Gregory Kucherov, Justin O'Grady, Michael Baym, William P. Hanage

Articles

Surveillance of drug-resistant bacteria is essential for healthcare providers to deliver effective empirical antibiotic therapy. However, traditional molecular epidemiology does not typically occur on a timescale that could affect patient treatment and outcomes. Here, we present a method called ‘genomic neighbour typing’ for inferring the phenotype of a bacterial sample by identifying its closest relatives in a database of genomes with metadata. We show that this technique can infer antibiotic susceptibility and resistance for both Streptococcus pneumoniae and Neisseria gonorrhoeae. We implemented this with rapid k-mer matching, which, when used on Oxford Nanopore MinION data, can run in real time. …