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Showing papers by "University of Adelaide published in 2021"


Journal ArticleDOI
Arang Rhie1, Shane A. McCarthy2, Shane A. McCarthy3, Olivier Fedrigo4, Joana Damas5, Giulio Formenti4, Sergey Koren1, Marcela Uliano-Silva6, William Chow2, Arkarachai Fungtammasan, J. H. Kim7, Chul Hee Lee7, Byung June Ko7, Mark Chaisson8, Gregory Gedman4, Lindsey J. Cantin4, Françoise Thibaud-Nissen1, Leanne Haggerty9, Iliana Bista3, Iliana Bista2, Michelle Smith2, Bettina Haase4, Jacquelyn Mountcastle4, Sylke Winkler10, Sylke Winkler11, Sadye Paez4, Jason T. Howard, Sonja C. Vernes12, Sonja C. Vernes11, Sonja C. Vernes13, Tanya M. Lama14, Frank Grützner15, Wesley C. Warren16, Christopher N. Balakrishnan17, Dave W Burt18, Jimin George19, Matthew T. Biegler4, David Iorns, Andrew Digby, Daryl Eason, Bruce C. Robertson20, Taylor Edwards21, Mark Wilkinson22, George F. Turner23, Axel Meyer24, Andreas F. Kautt24, Andreas F. Kautt25, Paolo Franchini24, H. William Detrich26, Hannes Svardal27, Hannes Svardal28, Maximilian Wagner29, Gavin J. P. Naylor30, Martin Pippel11, Milan Malinsky2, Milan Malinsky31, Mark Mooney, Maria Simbirsky, Brett T. Hannigan, Trevor Pesout32, Marlys L. Houck33, Ann C Misuraca33, Sarah B. Kingan34, Richard Hall34, Zev N. Kronenberg34, Ivan Sović34, Christopher Dunn34, Zemin Ning2, Alex Hastie, Joyce V. Lee, Siddarth Selvaraj, Richard E. Green32, Nicholas H. Putnam, Ivo Gut35, Jay Ghurye36, Erik Garrison32, Ying Sims2, Joanna Collins2, Sarah Pelan2, James Torrance2, Alan Tracey2, Jonathan Wood2, Robel E. Dagnew8, Dengfeng Guan3, Dengfeng Guan37, Sarah E. London38, David F. Clayton19, Claudio V. Mello39, Samantha R. Friedrich39, Peter V. Lovell39, Ekaterina Osipova11, Farooq O. Al-Ajli40, Farooq O. Al-Ajli41, Simona Secomandi42, Heebal Kim7, Constantina Theofanopoulou4, Michael Hiller43, Yang Zhou, Robert S. Harris44, Kateryna D. Makova44, Paul Medvedev44, Jinna Hoffman1, Patrick Masterson1, Karen Clark1, Fergal J. Martin9, Kevin L. Howe9, Paul Flicek9, Brian P. Walenz1, Woori Kwak, Hiram Clawson32, Mark Diekhans32, Luis R Nassar32, Benedict Paten32, Robert H. S. Kraus11, Robert H. S. Kraus24, Andrew J. Crawford45, M. Thomas P. Gilbert46, M. Thomas P. Gilbert47, Guojie Zhang, Byrappa Venkatesh48, Robert W. Murphy49, Klaus-Peter Koepfli50, Beth Shapiro51, Beth Shapiro32, Warren E. Johnson52, Warren E. Johnson50, Federica Di Palma53, Tomas Marques-Bonet, Emma C. Teeling54, Tandy Warnow55, Jennifer A. Marshall Graves56, Oliver A. Ryder33, Oliver A. Ryder57, David Haussler32, Stephen J. O'Brien58, Jonas Korlach34, Harris A. Lewin5, Kerstin Howe2, Eugene W. Myers11, Eugene W. Myers10, Richard Durbin2, Richard Durbin3, Adam M. Phillippy1, Erich D. Jarvis51, Erich D. Jarvis4 
National Institutes of Health1, Wellcome Trust Sanger Institute2, University of Cambridge3, Rockefeller University4, University of California, Davis5, Leibniz Association6, Seoul National University7, University of Southern California8, European Bioinformatics Institute9, Dresden University of Technology10, Max Planck Society11, University of St Andrews12, Radboud University Nijmegen13, University of Massachusetts Amherst14, University of Adelaide15, University of Missouri16, East Carolina University17, University of Queensland18, Clemson University19, University of Otago20, University of Arizona21, Natural History Museum22, Bangor University23, University of Konstanz24, Harvard University25, Northeastern University26, University of Antwerp27, National Museum of Natural History28, University of Graz29, University of Florida30, University of Basel31, University of California, Santa Cruz32, Zoological Society of San Diego33, Pacific Biosciences34, Pompeu Fabra University35, University of Maryland, College Park36, Harbin Institute of Technology37, University of Chicago38, Oregon Health & Science University39, Qatar Airways40, Monash University Malaysia Campus41, University of Milan42, Goethe University Frankfurt43, Pennsylvania State University44, University of Los Andes45, Norwegian University of Science and Technology46, University of Copenhagen47, Agency for Science, Technology and Research48, Royal Ontario Museum49, Smithsonian Institution50, Howard Hughes Medical Institute51, Walter Reed Army Institute of Research52, University of East Anglia53, University College Dublin54, University of Illinois at Urbana–Champaign55, La Trobe University56, University of California, San Diego57, Nova Southeastern University58
28 Apr 2021-Nature
TL;DR: The Vertebrate Genomes Project (VGP) as mentioned in this paper is an international effort to generate high quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.
Abstract: High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

647 citations


Journal ArticleDOI
TL;DR: The regulation of gene expression by coding and non-coding RNA is introduced and both established and emerging roles for RNAs in cancer are discussed, highlighting the potential mechanisms by which these RNA subtypes contribute to cancer.
Abstract: While the processing of mRNA is essential for gene expression, recent findings have highlighted that RNA processing is systematically altered in cancer. Mutations in RNA splicing factor genes and the shortening of 3' untranslated regions are widely observed. Moreover, evidence is accumulating that other types of RNAs, including circular RNAs, can contribute to tumorigenesis. In this Review, we highlight how altered processing or activity of coding and non-coding RNAs contributes to cancer. We introduce the regulation of gene expression by coding and non-coding RNA and discuss both established roles (microRNAs and long non-coding RNAs) and emerging roles (selective mRNA processing and circular RNAs) for RNAs, highlighting the potential mechanisms by which these RNA subtypes contribute to cancer. The widespread alteration of coding and non-coding RNA demonstrates that altered RNA biogenesis contributes to multiple hallmarks of cancer.

582 citations


Journal ArticleDOI
TL;DR: Sotorasib showed anticancer activity in patients with KRAS p.G12C-mutated advanced solid tumors in a phase 1 study as discussed by the authors, and particularly promising anti-cancer activity was observed i...
Abstract: Background Sotorasib showed anticancer activity in patients with KRAS p.G12C–mutated advanced solid tumors in a phase 1 study, and particularly promising anticancer activity was observed i...

571 citations


Posted Content
TL;DR: Nearly 50% COVID-19 patients could not reach obvious clinical and radiological remission within 10 days after hospitalization, and the patients with male sex, anorexia and no fever on admission predicted poor efficacy.
Abstract: South Australia is presently in the throes of major changes to its regulatory system governing land use, development of land and the development of planning policy against which development assessment decisions are to be made. Eventually the planning and development control system established under the Development Act 1993 (SA) will be replaced by a new system implemented by the Planning, Development and Infrastructure Act 2016 (SA) (the new Act).

568 citations


Journal ArticleDOI
TL;DR: A comprehensive survey of deep anomaly detection with a comprehensive taxonomy is presented in this paper, covering advancements in 3 high-level categories and 11 fine-grained categories of the methods.
Abstract: Anomaly detection, a.k.a. outlier detection or novelty detection, has been a lasting yet active research area in various research communities for several decades. There are still some unique problem complexities and challenges that require advanced approaches. In recent years, deep learning enabled anomaly detection, i.e., deep anomaly detection, has emerged as a critical direction. This article surveys the research of deep anomaly detection with a comprehensive taxonomy, covering advancements in 3 high-level categories and 11 fine-grained categories of the methods. We review their key intuitions, objective functions, underlying assumptions, advantages, and disadvantages and discuss how they address the aforementioned challenges. We further discuss a set of possible future opportunities and new perspectives on addressing the challenges.

560 citations


Journal ArticleDOI
Richard J. Abbott1, T. D. Abbott2, Sheelu Abraham3, Fausto Acernese4  +1428 moreInstitutions (155)
TL;DR: In this article, the population of 47 compact binary mergers detected with a false-alarm rate of 0.614 were dynamically assembled, and the authors found that the BBH rate likely increases with redshift, but not faster than the star formation rate.
Abstract: We report on the population of 47 compact binary mergers detected with a false-alarm rate of 0.01 are dynamically assembled. Third, we estimate merger rates, finding RBBH = 23.9-+8.614.3 Gpc-3 yr-1 for BBHs and RBNS = 320-+240490 Gpc-3 yr-1 for binary neutron stars. We find that the BBH rate likely increases with redshift (85% credibility) but not faster than the star formation rate (86% credibility). Additionally, we examine recent exceptional events in the context of our population models, finding that the asymmetric masses of GW190412 and the high component masses of GW190521 are consistent with our models, but the low secondary mass of GW190814 makes it an outlier.

468 citations


Journal ArticleDOI
TL;DR: In this paper, the authors highlight the synthetic strategies, characterisation, and computation of carbon-based SACs, and for the first time, showcase their innovative applications in advanced oxidation processes.
Abstract: Emerging single atom catalysts (SACs), especially carbon-based SACs are appealing materials in environmental catalysis because of their ultrahigh performances, environmental friendliness, structural/chemical robustness, and the maximum utilization of active metal sites. The metal centres, carbon matrixes, and coordination characteristics collectively determine the electronic features of carbon-based SACs, and their behaviours in catalysing peroxide activation and efficiencies in advanced oxidation processes (AOPs). However, there is lack of a comprehensive and critical review reporting the successful marriage of carbon-based SACs in AOP-based remediation technologies. It is particularly necessary to systematically compare and reveal the catalytic sites and the associated mechanisms of carbon-based SACs in diverse AOP systems. In this review, we highlight the synthetic strategies, characterisation, and computation of carbon-based SACs, and for the first time, showcase their innovative applications in AOP technologies. We unveil the origins of versatile catalytic oxidation pathways in different AOP systems and the mechanisms of micropollutant degradation over carbon-based SACs, distinguished from the upsized counterparts (metals/oxides and carbon substrates). We also provide directions to the rational design of on-demand SACs for green chemistry and environmental sustainability. Also, we suggest a designated and integrated experimental/theoretical protocol for revealing the structure-catalysis relations of SACs in AOP applications, and propose the prospects for future opportunities and challenges.

395 citations


Journal ArticleDOI
Richard J. Abbott1, T. D. Abbott2, Sheelu Abraham3, Fausto Acernese4  +1692 moreInstitutions (195)
TL;DR: In this article, the authors reported the observation of gravitational waves from two compact binary coalescences in LIGO's and Virgo's third observing run with properties consistent with neutron star-black hole (NSBH) binaries.
Abstract: We report the observation of gravitational waves from two compact binary coalescences in LIGO’s and Virgo’s third observing run with properties consistent with neutron star–black hole (NSBH) binaries. The two events are named GW200105_162426 and GW200115_042309, abbreviated as GW200105 and GW200115; the first was observed by LIGO Livingston and Virgo and the second by all three LIGO–Virgo detectors. The source of GW200105 has component masses 8.9−1.5+1.2 and 1.9−0.2+0.3M⊙ , whereas the source of GW200115 has component masses 5.7−2.1+1.8 and 1.5−0.3+0.7M⊙ (all measurements quoted at the 90% credible level). The probability that the secondary’s mass is below the maximal mass of a neutron star is 89%–96% and 87%–98%, respectively, for GW200105 and GW200115, with the ranges arising from different astrophysical assumptions. The source luminosity distances are 280−110+110 and 300−100+150Mpc , respectively. The magnitude of the primary spin of GW200105 is less than 0.23 at the 90% credible level, and its orientation is unconstrained. For GW200115, the primary spin has a negative spin projection onto the orbital angular momentum at 88% probability. We are unable to constrain the spin or tidal deformation of the secondary component for either event. We infer an NSBH merger rate density of 45−33+75Gpc−3yr−1 when assuming that GW200105 and GW200115 are representative of the NSBH population or 130−69+112Gpc−3yr−1 under the assumption of a broader distribution of component masses.

374 citations


Journal ArticleDOI
University of Michigan1, Cornell University2, University of Pennsylvania3, University of Massachusetts Medical School4, University of Naples Federico II5, Baylor College of Medicine6, Spanish National Research Council7, Complutense University of Madrid8, New York University9, Boston Children's Hospital10, University of Rome Tor Vergata11, NewYork–Presbyterian Hospital12, University of Pittsburgh13, University of Paris14, French Institute of Health and Medical Research15, National University of Cuyo16, Albert Einstein College of Medicine17, University of New Mexico18, Goethe University Frankfurt19, Weizmann Institute of Science20, University of Turku21, Sapienza University of Rome22, Virginia Commonwealth University23, St. Jude Children's Research Hospital24, Discovery Institute25, University of Copenhagen26, University of Tromsø27, Eötvös Loránd University28, Merck & Co.29, University of Freiburg30, Babraham Institute31, University of South Australia32, University of Adelaide33, University of Oviedo34, University of Chicago35, University of Graz36, National Institutes of Health37, Queens College38, City University of New York39, University of Tokyo40, University of Zurich41, Austrian Academy of Sciences42, University of British Columbia43, University of California, San Francisco44, Russian Academy of Sciences45, University Medical Center Groningen46, University of Cambridge47, University of Glasgow48, Rutgers University49, University of Padua50, Kazan Federal University51, University of Bern52, University of Oxford53, University of Oslo54, Oslo University Hospital55, Foundation for Research & Technology – Hellas56, University of Crete57, Francis Crick Institute58, Osaka University59, Chinese Academy of Sciences60, Harvard University61, Icahn School of Medicine at Mount Sinai62, Shanghai Jiao Tong University63, Karolinska Institutet64
TL;DR: In this paper, preclinical data linking autophagy dysfunction to the pathogenesis of major human disorders including cancer as well as cardiovascular, neurodegenerative, metabolic, pulmonary, renal, infectious, musculoskeletal, and ocular disorders.
Abstract: Autophagy is a core molecular pathway for the preservation of cellular and organismal homeostasis. Pharmacological and genetic interventions impairing autophagy responses promote or aggravate disease in a plethora of experimental models. Consistently, mutations in autophagy-related processes cause severe human pathologies. Here, we review and discuss preclinical data linking autophagy dysfunction to the pathogenesis of major human disorders including cancer as well as cardiovascular, neurodegenerative, metabolic, pulmonary, renal, infectious, musculoskeletal, and ocular disorders.

365 citations


Journal ArticleDOI
TL;DR: In this paper, a similar antisolvent strategy was proposed to boost Zn reversibility via regulation of the electrolyte on a molecular level. But this strategy is not applicable to other solvents, indicating its practical universality.
Abstract: Antisolvent addition has been widely studied in crystallization in the pharmaceutical industries by breaking the solvation balance of the original solution. Here we report a similar antisolvent strategy to boost Zn reversibility via regulation of the electrolyte on a molecular level. By adding for example methanol into ZnSO4 electrolyte, the free water and coordinated water in Zn2+ solvation sheath gradually interact with the antisolvent, which minimizes water activity and weakens Zn2+ solvation. Concomitantly, dendrite-free Zn deposition occurs via change in the deposition orientation, as evidenced by in situ optical microscopy. Zn reversibility is significantly boosted in antisolvent electrolyte of 50 % methanol by volume (Anti-M-50 %) even under harsh environments of -20 °C and 60 °C. Additionally, the suppressed side reactions and dendrite-free Zn plating/stripping in Anti-M-50 % electrolyte significantly enhance performance of Zn/polyaniline coin and pouch cells. We demonstrate this low-cost strategy can be readily generalized to other solvents, indicating its practical universality. Results will be of immediate interest and benefit to a range of researchers in electrochemistry and energy storage.

343 citations


Journal ArticleDOI
TL;DR: In this paper, an overview of the current scenario of arsenic contamination of groundwater in various countries across the globe with an emphasis on the Indian Peninsula is presented and the corrective measures available include removing arsenic from groundwater using filters, exploring deeper or alternative aquifers, treatment of the aquifer itself, dilution method by artificial recharge to groundwater, conjunctive use and installation of nano-filter, among other procedures.
Abstract: More than 2.5 billion people on the globe rely on groundwater for drinking and providing high-quality drinking water has become one of the major challenges of human society. Although groundwater is considered as safe, high concentrations of heavy metals like arsenic (As) can pose potential human health concerns and hazards. In this paper, we present an overview of the current scenario of arsenic contamination of groundwater in various countries across the globe with an emphasis on the Indian Peninsula. With several newly affected regions reported during the last decade, a significant increase has been observed in the global scenario of arsenic contamination. It is estimated that nearly 108 countries are affected by arsenic contamination in groundwater (with concentration beyond maximum permissible limit of 10 ppb recommended by the World Health Organization. The highest among these are from Asia (32) and Europe (31), followed by regions like Africa (20), North America (11), South America (9) and Australia (4). More than 230 million people worldwide, which include 180 million from Asia, are at risk of arsenic poisoning. Southeast Asian countries, Bangladesh, India, Pakistan, China, Nepal, Vietnam, Burma, Thailand and Cambodia, are the most affected. In India, 20 states and 4 Union Territories have so far been affected by arsenic contamination in groundwater. An attempt to evaluate the correlation between arsenic poisoning and aquifer type shows that the groundwater extracted from unconsolidated sedimentary aquifers, particularly those which are located within the younger orogenic belts of the world, are the worst affected. More than 90% of arsenic pollution is inferred to be geogenic. We infer that alluvial sediments are the major source for arsenic contamination in groundwater and we postulate a strong relation with plate tectonic processes, mountain building, erosion and sedimentation. Prolonged consumption of arsenic-contaminated groundwater results in severe health issues like skin, lung, kidney and bladder cancer; coronary heart disease; bronchiectasis; hyperkeratosis and arsenicosis. Since the major source of arsenic in groundwater is of geogenic origin, the extend of pollution is complexly linked with aquifer geometry and aquifer properties of a region. Therefore, remedial measures are to be designed based on the source mineral, climatological and hydrogeological scenario of the affected region. The corrective measures available include removing arsenic from groundwater using filters, exploring deeper or alternative aquifers, treatment of the aquifer itself, dilution method by artificial recharge to groundwater, conjunctive use, and installation of nano-filter, among other procedures. The vast majority of people affected by arsenic contamination in the Asian countries are the poor who live in rural areas and are not aware of the arsenic poisoning and treatment protocols. Therefore, creating awareness and providing proper medical care to these people remain as a great challenge. Very few policy actions have been taken at international level over the past decade to reduce arsenic contamination in drinking water, with the goal of preventing toxic impacts on human health. We recommend that that United Nations Environment Programme (UNEP) and WHO should take stock of the global arsenic poisoning situation and launch a global drive to create awareness among people/medical professionals/health workers/administrators on this global concern.

Journal ArticleDOI
TL;DR: Children and adolescents are more likely to experience high rates of depression and anxiety during and after a pandemic, and it is critical that future researchers explore effective mental health strategies that are tailored to the needs of children and adolescents.
Abstract: Background: The COVID‑19 pandemic and associated public health measures have disrupted the lives of people around the world. It is already evident that the direct and indirect psychological and social effects of the COVID‑19 pandemic are insidious and affect the mental health of young children and adolescents now and will in the future. The aim and objectives of this knowledge-synthesis study were to identify the impact of the pandemic on children's and adolescent's mental health and to evaluate the effectiveness of different interventions employed during previous and the current pandemic to promote children's and adolescents' mental health. Methodology: We conducted the systematic review according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines and included experimental randomized and nonrandomized controlled trials, observational studies, and qualitative studies. Results: Of the 5828 articles that we retrieved, 18 articles met the inclusion criteria. We thematically analyzed them and put the major findings under the thematic areas of impact of the pandemic on children's and adolescents' mental health. These studies reported that pandemics cause stress, worry, helplessness, and social and risky behavioral problems among children and adolescents (e.g., substance abuse, suicide, relationship problems, academic issues, and absenteeism from work). Interventions such as art-based programs, support services, and clinician-led mental health and psychosocial services effectively decrease mental health issues among children and adolescents. Conclusion: Children and adolescents are more likely to experience high rates of depression and anxiety during and after a pandemic. It is critical that future researchers explore effective mental health strategies that are tailored to the needs of children and adolescents. Explorations of effective channels regarding the development and delivery of evidenced-based, age-appropriate services are vital to lessen the effects and improve long-term capacities for mental health services for children and adolescents. Key Practitioner Message: The COVID-19 pandemic's physical restrictions and social distancing measures have affected each and every domain of life. Although the number of children and adolescents affected by the disease is small, the disease and the containment measures such as social distancing, school closure, and isolation have negatively impacted the mental health and well-being of children and adolescents. The impact of COVID-19 on the mental health of children and adolescents is of great concern. Anxiety, depression, disturbances in sleep and appetite, as well as impairment in social interactions are the most common presentations. It has been indicated that compared to adults, this pandemic may continue to have increased long term adverse consequences on children's and adolescents' mental health. As the pandemic continues, it is important to monitor the impact on children's and adolescents' mental health status and how to help them to improve their mental health outcomes in the time of the current or future pandemics.

Journal ArticleDOI
Richard J. Abbott1, T. D. Abbott2, Sheelu Abraham3, Fausto Acernese4  +1335 moreInstitutions (144)
TL;DR: The data recorded by these instruments during their first and second observing runs are described, including the gravitational-wave strain arrays, released as time series sampled at 16384 Hz.

Journal ArticleDOI
TL;DR: In this article, the authors used single-atom catalysts (SACs) in acidic oxygen reduction reaction (ORR) and reported the structure-property relationship of catalysts and showed for the first time that molecular level local structure, including first and second coordination spheres (CSs), rather than individual active atoms, synergistically determines the electrocatalytic response.
Abstract: Product selectivity in multielectron electrocatalytic reactions is crucial to energy conversion efficiency and chemical production. However, a present practical drawback is the limited understanding of actual catalytic active sites. Here, using as a prototype single-atom catalysts (SACs) in acidic oxygen reduction reaction (ORR), we report the structure-property relationship of catalysts and show for the first time that molecular-level local structure, including first and second coordination spheres (CSs), rather than individual active atoms, synergistically determines the electrocatalytic response. ORR selectivity on Co-SACs can be tailored from a four-electron to a two-electron pathway by modifying first (N or/and O coordination) and second (C-O-C groups) CSs. Using combined theoretical predictions and experiments, including X-ray absorption fine structure analyses and in situ infrared spectroscopy, we confirm that the unique selectivity change originates from the structure-dependent shift of active sites from the center Co atom to the O-adjacent C atom. We show this optimizes the electronic structure and *OOH adsorption behavior on active sites to give the present "best" activity and selectivity of >95% for acidic H2O2 electrosynthesis.

Journal ArticleDOI
Richard R. Orlandi1, Todd T. Kingdom2, Timothy L. Smith3, Benjamin S. Bleier4, Adam S. DeConde5, Amber U Luong6, David M. Poetker7, Zachary M. Soler8, Kevin C. Welch9, Sarah K. Wise10, Nithin D. Adappa11, Jeremiah A. Alt1, Wilma Terezinha Anselmo-Lima12, Claus Bachert13, Claus Bachert14, Claus Bachert15, Fuad M. Baroody16, Pete S. Batra17, Manuel Bernal-Sprekelsen18, Daniel M. Beswick19, Neil Bhattacharyya4, Rakesh K. Chandra20, Eugene H. Chang21, Alexander G. Chiu22, Naweed I. Chowdhury20, Martin J. Citardi6, Noam A. Cohen11, David B. Conley9, John M. DelGaudio10, Martin Desrosiers23, Richard G. Douglas24, Jean Anderson Eloy25, Wytske Fokkens26, Stacey T. Gray4, David A. Gudis27, Daniel L. Hamilos4, Joseph K. Han28, Richard J. Harvey29, Peter Hellings30, Eric H. Holbrook4, Claire Hopkins31, Peter H. Hwang32, Amin R. Javer33, Rong San Jiang, David N. Kennedy11, Robert C. Kern9, Tanya M. Laidlaw4, Devyani Lal34, Andrew P. Lane35, Heung Man Lee36, Jivianne T. Lee19, Joshua M. Levy10, Sandra Y. Lin35, Valerie J. Lund, Kevin C. McMains37, Ralph Metson4, Joaquim Mullol18, Robert M. Naclerio35, Gretchen M. Oakley1, Nobuyoshi Otori38, James N. Palmer11, Sanjay R. Parikh39, Desiderio Passali40, Zara M. Patel32, Anju T. Peters9, Carl Philpott41, Alkis J. Psaltis42, Vijay R. Ramakrishnan2, Murugappan Ramanathan35, Hwan Jung Roh43, Luke Rudmik44, Raymond Sacks29, Rodney J. Schlosser8, Ahmad R. Sedaghat45, Brent A. Senior46, Raj Sindwani47, Kristine A. Smith48, Kornkiat Snidvongs49, Michael G. Stewart50, Jeffrey D. Suh19, Bruce K. Tan9, Justin H. Turner20, Cornelis M. van Drunen26, Richard Louis Voegels12, De Yun Wang51, Bradford A. Woodworth52, Peter-John Wormald42, Erin D. Wright53, Carol H. Yan5, Luo Zhang54, Bing Zhou54 
University of Utah1, University of Colorado Denver2, Oregon Health & Science University3, Harvard University4, University of California, San Diego5, University of Texas Health Science Center at Houston6, Medical College of Wisconsin7, Medical University of South Carolina8, Northwestern University9, Emory University10, University of Pennsylvania11, University of São Paulo12, Karolinska Institutet13, Ghent University14, Sun Yat-sen University15, University of Chicago16, Rush University Medical Center17, University of Barcelona18, University of California, Los Angeles19, Vanderbilt University20, University of Arizona21, University of Kansas22, Université de Montréal23, University of Auckland24, Rutgers University25, University of Amsterdam26, Columbia University27, Eastern Virginia Medical School28, University of New South Wales29, Katholieke Universiteit Leuven30, Guy's Hospital31, Stanford University32, University of British Columbia33, Mayo Clinic34, Johns Hopkins University35, Korea University36, Uniformed Services University of the Health Sciences37, Jikei University School of Medicine38, University of Washington39, University of Siena40, University of East Anglia41, University of Adelaide42, Pusan National University43, University of Calgary44, University of Cincinnati45, University of North Carolina at Chapel Hill46, Cleveland Clinic47, University of Winnipeg48, Chulalongkorn University49, Cornell University50, National University of Singapore51, University of Alabama at Birmingham52, University of Alberta53, Capital Medical University54
TL;DR: The 5 years since the publication of the first International Consensus Statement on Allergy and Rhinology: Rhinosinusitis (ICAR‐RS) has witnessed foundational progress in the understanding and treatment of rhinologic disease.
Abstract: I. Executive summary BACKGROUND: The 5 years since the publication of the first International Consensus Statement on Allergy and Rhinology: Rhinosinusitis (ICAR-RS) has witnessed foundational progress in our understanding and treatment of rhinologic disease. These advances are reflected within the more than 40 new topics covered within the ICAR-RS-2021 as well as updates to the original 140 topics. This executive summary consolidates the evidence-based findings of the document. Methods ICAR-RS presents over 180 topics in the forms of evidence-based reviews with recommendations (EBRRs), evidence-based reviews, and literature reviews. The highest grade structured recommendations of the EBRR sections are summarized in this executive summary. Results ICAR-RS-2021 covers 22 topics regarding the medical management of RS, which are grade A/B and are presented in the executive summary. Additionally, 4 topics regarding the surgical management of RS are grade A/B and are presented in the executive summary. Finally, a comprehensive evidence-based management algorithm is provided. Conclusion This ICAR-RS-2021 executive summary provides a compilation of the evidence-based recommendations for medical and surgical treatment of the most common forms of RS.

Journal ArticleDOI
TL;DR: BiSeNet V2 as mentioned in this paper proposes to treat these spatial details and categorical semantics separately to achieve high accuracy and high efficiency for real-time semantic segmentation, which achieves 72.6% Mean IoU on the Cityscapes test set with a speed of 156 FPS on one NVIDIA GeForce GTX 1080 Ti card, which is significantly faster than existing methods, yet they achieve better segmentation accuracy.
Abstract: Low-level details and high-level semantics are both essential to the semantic segmentation task. However, to speed up the model inference, current approaches almost always sacrifice the low-level details, leading to a considerable decrease in accuracy. We propose to treat these spatial details and categorical semantics separately to achieve high accuracy and high efficiency for real-time semantic segmentation. For this purpose, we propose an efficient and effective architecture with a good trade-off between speed and accuracy, termed Bilateral Segmentation Network (BiSeNet V2). This architecture involves the following: (i) A detail branch, with wide channels and shallow layers to capture low-level details and generate high-resolution feature representation; (ii) A semantics branch, with narrow channels and deep layers to obtain high-level semantic context. The detail branch has wide channel dimensions and shallow layers, while the semantics branch has narrow channel dimensions and deep layers. Due to the reduction in the channel capacity and the use of a fast-downsampling strategy, the semantics branch is lightweight and can be implemented by any efficient model. We design a guided aggregation layer to enhance mutual connections and fuse both types of feature representation. Moreover, a booster training strategy is designed to improve the segmentation performance without any extra inference cost. Extensive quantitative and qualitative evaluations demonstrate that the proposed architecture shows favorable performance compared to several state-of-the-art real-time semantic segmentation approaches. Specifically, for a $$2048\times 1024$$ input, we achieve 72.6% Mean IoU on the Cityscapes test set with a speed of 156 FPS on one NVIDIA GeForce GTX 1080 Ti card, which is significantly faster than existing methods, yet we achieve better segmentation accuracy. The code and trained models are available online at https://git.io/BiSeNet .

Journal ArticleDOI
01 Mar 2021
TL;DR: The JBI Scoping Review Methodology Group developed guidance for conducting a JBI scoping review, with a focus on new updates to the approach and development of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (the PRISMA-ScR) as mentioned in this paper.
Abstract: OBJECTIVE The objective of this paper is to describe the updated methodological guidance for conducting a JBI scoping review, with a focus on new updates to the approach and development of the Preferred Reporting Items for Systematic Reviews and Meta-Analyses extension for Scoping Reviews (the PRISMA-ScR) INTRODUCTION Scoping reviews are an increasingly common approach to informing decision-making and research based on the identification and examination of the literature on a given topic or issue Scoping reviews draw on evidence from any research methodology and may also include evidence from non-research sources, such as policy In this manner, scoping reviews provide a comprehensive overview to address broader review questions than traditionally more specific systematic reviews of effectiveness or qualitative evidence The increasing popularity of scoping reviews has been accompanied by the development of a reporting guideline: the PRISMA-ScR In 2014, the JBI Scoping Review Methodology Group developed guidance for scoping reviews that received minor updates in 2017 and was most recently updated in 2020 The updates reflect ongoing and substantial developments in approaches to scoping review conduct and reporting As such, the JBI Scoping Review Methodology Group recognized the need to revise the guidance to align with the current state of knowledge and reporting standards in evidence synthesis METHODS Between 2015 and 2020, the JBI Scoping Review Methodology Group expanded its membership; extensively reviewed the literature; engaged via annual face-to-face meetings, regular teleconferences, and email correspondence; sought advice from methodological experts; facilitated workshops; and presented at scientific conferences This process led to updated guidance for scoping reviews published in the JBI Manual for Evidence Synthesis The updated chapter was endorsed by JBI's International Scientific Committee in 2020 RESULTS The updated JBI guidance for scoping reviews includes additional guidance on several methodological issues, such as when a scoping review is (or is not) appropriate, and how to extract, analyze, and present results, and provides clarification for implications for practice and research Furthermore, it is aligned with the PRISMA-ScR to ensure consistent reporting CONCLUSIONS The latest JBI guidance for scoping reviews provides up-to-date guidance that can be used by authors when conducting a scoping review Furthermore, it aligns with the PRISMA-ScR, which can be used to report the conduct of a scoping review A series of ongoing and future methodological projects identified by the JBI Scoping Review Methodology Group to further refine the methodology are planned

Journal ArticleDOI
TL;DR: An AI system that automatically analyzes CT images and provides the probability of infection to rapidly detect COVID-19 pneumonia and is able to overcome a series of challenges in this particular situation and deploy the system in four weeks.

Journal ArticleDOI
TL;DR: The worldwide prevalence of gaming disorder appears to be comparable to obsessive-compulsive disorder and some substance-related addictions, but lower than compulsive buying and higher than problem gambling.
Abstract: Background:Gaming disorder was included in the latest revision of the International Classification of Diseases (11th ed.). Worldwide, prevalence estimates of gaming disorder are considerably hetero...

Journal ArticleDOI
TL;DR: A review of the characterization methodologies used for enzyme/MOF-immobilized enzymes can be found in this article, where the authors discuss enzyme protection via encapsulation, pore infiltration and surface adsorption and summarizes strategies to form multicomponent composites.
Abstract: Because of their efficiency, selectivity, and environmental sustainability, there are significant opportunities for enzymes in chemical synthesis and biotechnology. However, as the three-dimensional active structure of enzymes is predominantly maintained by weaker noncovalent interactions, thermal, pH, and chemical stressors can modify or eliminate activity. Metal-organic frameworks (MOFs), which are extended porous network materials assembled by a bottom-up building block approach from metal-based nodes and organic linkers, can be used to afford protection to enzymes. The self-assembled structures of MOFs can be used to encase an enzyme in a process called encapsulation when the MOF is synthesized in the presence of the biomolecule. Alternatively, enzymes can be infiltrated into mesoporous MOF structures or surface bound via covalent or noncovalent processes. Integration of MOF materials and enzymes in this way affords protection and allows the enzyme to maintain activity in challenge conditions (e.g., denaturing agents, elevated temperature, non-native pH, and organic solvents). In addition to forming simple enzyme/MOF biocomposites, other materials can be introduced to the composites to improve recovery or facilitate advanced applications in sensing and fuel cell technology. This review canvasses enzyme protection via encapsulation, pore infiltration, and surface adsorption and summarizes strategies to form multicomponent composites. Also, given that enzyme/MOF biocomposites straddle materials chemistry and enzymology, this review provides an assessment of the characterization methodologies used for MOF-immobilized enzymes and identifies some key parameters to facilitate development of the field.

Journal ArticleDOI
01 Nov 2021
TL;DR: In this article, the authors argue that explainability is a false hope for explainable AI and that current explainability methods are unlikely to achieve these goals for patient-level decision support, and advocate for rigorous internal and external validation of AI models as a more direct means of achieving the goals often associated with explainability.
Abstract: Summary The black-box nature of current artificial intelligence (AI) has caused some to question whether AI must be explainable to be used in high-stakes scenarios such as medicine. It has been argued that explainable AI will engender trust with the health-care workforce, provide transparency into the AI decision making process, and potentially mitigate various kinds of bias. In this Viewpoint, we argue that this argument represents a false hope for explainable AI and that current explainability methods are unlikely to achieve these goals for patient-level decision support. We provide an overview of current explainability techniques and highlight how various failure cases can cause problems for decision making for individual patients. In the absence of suitable explainability methods, we advocate for rigorous internal and external validation of AI models as a more direct means of achieving the goals often associated with explainability, and we caution against having explainability be a requirement for clinically deployed models.

Journal ArticleDOI
TL;DR: In this paper, the evolution of bio-Fe in Enteromorpha during thermal pyrolysis and the role of the derived Fe-N-C in peroxymonosulfate (PMS) activation and organic degradation was revealed.
Abstract: Enteromorpha as a seawater pollutant was innovatively converted into a functional carbocatalyst to driven Fenton-like reactions.After direct pyrolysis of Enteromorpha at 900 °C without additional chemicals, a large number of Fe clusters and single Fe sites are anchored onto N-doped carbon matrixes (Enteromorpha-derived Fe-N-C) with a high Fe loading of 0.84 wt.%. The Enteromorpha-derived Fe-N-C exhibits a high activity in the heterogeneous activation of peroxymonosulfate (PMS) for organic pollutant degradation. Radical quenching experiments and electrochemical analysis tests verify the nonradical oxidation by high-valence iron-oxo species and an electron-transfer pathway. The single Fe atoms, which only accounted for the minority of the Fe species in Fe-N-C, acted as the dominated reactive sites for the formation of highly oxidizing FeIV=O and FeV=O sites. This work unveils the evolution of bio-Fe in Enteromorpha during thermal pyrolysis and the role of the derived Fe-N-C in PMS activation and organic degradation.

Book ChapterDOI
27 Sep 2021
TL;DR: Xie et al. as mentioned in this paper proposed a deformable self-attention mechanism for 3D medical image segmentation, which pays attention only to a small set of key positions.
Abstract: Convolutional neural networks (CNNs) have been the de facto standard for nowadays 3D medical image segmentation. The convolutional operations used in these networks, however, inevitably have limitations in modeling the long-range dependency due to their inductive bias of locality and weight sharing. Although Transformer was born to address this issue, it suffers from extreme computational and spatial complexities in processing high-resolution 3D feature maps. In this paper, we propose a novel framework that efficiently bridges a Convolutional neural network and a Transformer (CoTr) for accurate 3D medical image segmentation. Under this framework, the CNN is constructed to extract feature representations and an efficient deformable Transformer (DeTrans) is built to model the long-range dependency on the extracted feature maps. Different from the vanilla Transformer which treats all image positions equally, our DeTrans pays attention only to a small set of key positions by introducing the deformable self-attention mechanism. Thus, the computational and spatial complexities of DeTrans have been greatly reduced, making it possible to process the multi-scale and high-resolution feature maps, which are usually of paramount importance for image segmentation. We conduct an extensive evaluation on the Multi-Atlas Labeling Beyond the Cranial Vault (BCV) dataset that covers 11 major human organs. The results indicate that our CoTr leads to a substantial performance improvement over other CNN-based, transformer-based, and hybrid methods on the 3D multi-organ segmentation task. Code is available at: https://github.com/YtongXie/CoTr.

Posted ContentDOI
TL;DR: In this paper, an ultrathin, fluorinated two-dimensional porous covalent organic framework (FCOF) film was developed as a protective layer on the Zn surface.
Abstract: Rechargeable aqueous zinc-ion batteries (RZIBs) provide a promising complementarity to the existing lithium-ion batteries due to their low cost, non-toxicity and intrinsic safety. However, Zn anodes suffer from zinc dendrite growth and electrolyte corrosion, resulting in poor reversibility. Here, we develop an ultrathin, fluorinated two-dimensional porous covalent organic framework (FCOF) film as a protective layer on the Zn surface. The strong interaction between fluorine (F) in FCOF and Zn reduces the surface energy of the Zn (002) crystal plane, enabling the preferred growth of (002) planes during the electrodeposition process. As a result, Zn deposits show horizontally arranged platelet morphology with (002) orientations preferred. Furthermore, F-containing nanochannels facilitate ion transport and prevent electrolyte penetration for improving corrosion resistance. The FCOF@Zn symmetric cells achieve stability for over 750 h at an ultrahigh current density of 40 mA cm−2. The high-areal-capacity full cells demonstrate hundreds of cycles under high Zn utilization conditions. Rechargeable aqueous zinc-ion batteries are promising but the zinc anode suffers from dendrite growth and electrolyte corrosion. Here, the authors develop a fluorinated covalent organic framework film as a protective layer for aqueous zinc anode battery.

Journal ArticleDOI
TL;DR: In this paper, the authors present fundamentals of heterogeneous electrocatalysis and some primary reactions, and then implement these to establish the framework of e-refinery by coupling in situ generated intermediates (integrated reactions) or products (tandem reactions).
Abstract: Compared to modern fossil-fuel-based refineries, the emerging electrocatalytic refinery (e-refinery) is a more sustainable and environmentally benign strategy to convert renewable feedstocks and energy sources into transportable fuels and value-added chemicals. A crucial step in conducting e-refinery processes is the development of appropriate reactions and optimal electrocatalysts for efficient cleavage and formation of chemical bonds. However, compared to well-studied primary reactions (e.g., O2 reduction, water splitting), the mechanistic aspects and materials design for emerging complex reactions are yet to be settled. To address this challenge, herein, we first present fundamentals of heterogeneous electrocatalysis and some primary reactions, and then implement these to establish the framework of e-refinery by coupling in situ generated intermediates (integrated reactions) or products (tandem reactions). We also present a set of materials design principles and strategies to efficiently manipulate the reaction intermediates and pathways.

Journal ArticleDOI
TL;DR: A multidisciplinary group of researchers and practitioners revisit the current status of Sensitivity analysis, and outline research challenges in regard to both theoretical frameworks and their applications to solve real-world problems.
Abstract: Sensitivity analysis (SA) is en route to becoming an integral part of mathematical modeling. The tremendous potential benefits of SA are, however, yet to be fully realized, both for advancing mechanistic and data-driven modeling of human and natural systems, and in support of decision making. In this perspective paper, a multidisciplinary group of researchers and practitioners revisit the current status of SA, and outline research challenges in regard to both theoretical frameworks and their applications to solve real-world problems. Six areas are discussed that warrant further attention, including (1) structuring and standardizing SA as a discipline, (2) realizing the untapped potential of SA for systems modeling, (3) addressing the computational burden of SA, (4) progressing SA in the context of machine learning, (5) clarifying the relationship and role of SA to uncertainty quantification, and (6) evolving the use of SA in support of decision making. An outlook for the future of SA is provided that underlines how SA must underpin a wide variety of activities to better serve science and society.

Journal ArticleDOI
TL;DR: The proposed CAAD model outperforms binary classification models on the clinical X-VIRAL dataset that contains 5,977 viral pneumonia (no COVID-19) cases, 37,393 non-viral pneumonia or healthy cases and achieves an AUC of 83.61% and sensitivity of 71.70%, which is comparable to the performance of radiologists reported in the literature.
Abstract: Clusters of viral pneumonia occurrences over a short period may be a harbinger of an outbreak or pandemic. Rapid and accurate detection of viral pneumonia using chest X-rays can be of significant value for large-scale screening and epidemic prevention, particularly when other more sophisticated imaging modalities are not readily accessible. However, the emergence of novel mutated viruses causes a substantial dataset shift, which can greatly limit the performance of classification-based approaches. In this paper, we formulate the task of differentiating viral pneumonia from non-viral pneumonia and healthy controls into a one-class classification-based anomaly detection problem. We therefore propose the confidence-aware anomaly detection (CAAD) model, which consists of a shared feature extractor, an anomaly detection module, and a confidence prediction module. If the anomaly score produced by the anomaly detection module is large enough, or the confidence score estimated by the confidence prediction module is small enough, the input will be accepted as an anomaly case ( i.e. , viral pneumonia). The major advantage of our approach over binary classification is that we avoid modeling individual viral pneumonia classes explicitly and treat all known viral pneumonia cases as anomalies to improve the one-class model. The proposed model outperforms binary classification models on the clinical X-VIRAL dataset that contains 5,977 viral pneumonia (no COVID-19) cases, 37,393 non-viral pneumonia or healthy cases. Moreover, when directly testing on the X-COVID dataset that contains 106 COVID-19 cases and 107 normal controls without any fine-tuning, our model achieves an AUC of 83.61% and sensitivity of 71.70%, which is comparable to the performance of radiologists reported in the literature.

Journal ArticleDOI
TL;DR: Y.H.Z. as mentioned in this paper used services offered from the National Computational Infrastructure (NCI) and Phoenix High Performance Computing, which are supported by the Australian Government and the University of Adelaide.
Abstract: This work was financially supported by the Australian Research Council (FL170100154, DP160104866, and DP190103472). Y.H.Z. acknowledges financial support from Zhejiang Provincial Natural Science Foundation of China (LR18B030003), National Natural Science Foundation of China (51701181, 21771161), and the Thousand Talents Program for Distinguished Young Scholars. J.S. was supported by the Chinese CSC Scholarship Program. DFT computations were performed by using services offered from the National Computational Infrastructure (NCI) and Phoenix High Performance Computing, which are supported by the Australian Government and the University of Adelaide. XAS measurements were conducted at the Beijing Synchrotron Radiation Facility (1W1B, BSRF)

Journal ArticleDOI
David V. Conti1, Burcu F. Darst1, Lilit C. Moss1, Edward J. Saunders2  +251 moreInstitutions (100)
TL;DR: This paper conducted a meta-analysis of prostate cancer genome-wide association studies (107,247 cases and 127,006 controls) and identified 86 new genetic risk variants independently associated with prostate cancer risk, bringing the total to 269 known risk variants.
Abstract: Prostate cancer is a highly heritable disease with large disparities in incidence rates across ancestry populations. We conducted a multiancestry meta-analysis of prostate cancer genome-wide association studies (107,247 cases and 127,006 controls) and identified 86 new genetic risk variants independently associated with prostate cancer risk, bringing the total to 269 known risk variants. The top genetic risk score (GRS) decile was associated with odds ratios that ranged from 5.06 (95% confidence interval (CI), 4.84–5.29) for men of European ancestry to 3.74 (95% CI, 3.36–4.17) for men of African ancestry. Men of African ancestry were estimated to have a mean GRS that was 2.18-times higher (95% CI, 2.14–2.22), and men of East Asian ancestry 0.73-times lower (95% CI, 0.71–0.76), than men of European ancestry. These findings support the role of germline variation contributing to population differences in prostate cancer risk, with the GRS offering an approach for personalized risk prediction.

Journal ArticleDOI
TL;DR: An overview of PPOH system is provided and the future research direction of the system in practical treatment of antibiotic wastewater is outlined and the performance of antibiotic degradation and internal mechanism in the coupled oxidation system are analyzed comprehensively.