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Whole-Genome Sequencing of SARS-CoV-2 from Quarantine Hotel Outbreak.

Lex E X Leong, Julien Soubrier, Mark Turra, Emma Denehy, Luke Walters, Karin Kassahn, Geoff Higgins, Tom Dodd, Robert Hall, Katina D'Onise, Nicola Spurrier, Ivan Bastian, Chuan K Lim,

Hotel quarantine for international travelers has been used to prevent coronavirus disease spread into Australia. A quarantine hotel-associated community outbreak was detected in South Australia. Real-time genomic sequencing enabled rapid confirmation tracking the outbreak to a recently returned traveler and linked 2 cases of infection in travelers at the same ... Read more >>

Emerg Infect Dis (Emerging infectious diseases)
[2021, 27(8):2219-2221]

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Impacts of detritivore diversity loss on instream decomposition are greatest in the tropics.

Luz Boyero, Naiara López-Rojo, Alan M Tonin, Javier Pérez, Francisco Correa-Araneda, Richard G Pearson, Jaime Bosch, Ricardo J Albariño, Sankarappan Anbalagan, Leon A Barmuta, Ana Basaguren, Francis J Burdon, Adriano Caliman, Marcos Callisto, Adolfo R Calor, Ian C Campbell, Bradley J Cardinale, J Jesús Casas, Ana M Chará-Serna, Eric Chauvet, Szymon Ciapała, Checo Colón-Gaud, Aydeé Cornejo, Aaron M Davis, Monika Degebrodt, Emerson S Dias, María E Díaz, Michael M Douglas, Andrea C Encalada, Ricardo Figueroa, Alexander S Flecker, Tadeusz Fleituch, Erica A García, Gabriela García, Pavel E García, Mark O Gessner, Jesús E Gómez, Sergio Gómez, Jose F Gonçalves, Manuel A S Graça, Daniel C Gwinn, Robert O Hall, Neusa Hamada, Cang Hui, Daichi Imazawa, Tomoya Iwata, Samuel K Kariuki, Andrea Landeira-Dabarca, Kelsey Laymon, María Leal, Richard Marchant, Renato T Martins, Frank O Masese, Megan Maul, Brendan G McKie, Adriana O Medeiros, Charles M M' Erimba, Jen A Middleton, Silvia Monroy, Timo Muotka, Junjiro N Negishi, Alonso Ramírez, John S Richardson, José Rincón, Juan Rubio-Ríos, Gisele M Dos Santos, Romain Sarremejane, Fran Sheldon, Augustine Sitati, Nathalie S D Tenkiano, Scott D Tiegs, Janine R Tolod, Michael Venarsky, Anne Watson, Catherine M Yule,

The relationship between detritivore diversity and decomposition can provide information on how biogeochemical cycles are affected by ongoing rates of extinction, but such evidence has come mostly from local studies and microcosm experiments. We conducted a globally distributed experiment (38 streams across 23 countries in 6 continents) using standardised methods ... Read more >>

Nat Commun (Nature communications)
[2021, 12(1):3700]

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Mass spectrometry-based metabolomics: a guide for annotation, quantification and best reporting practices.

Saleh Alseekh, Asaph Aharoni, Yariv Brotman, Kévin Contrepois, John D'Auria, Jan Ewald, Jennifer C Ewald, Paul D Fraser, Patrick Giavalisco, Robert D Hall, Matthias Heinemann, Hannes Link, Jie Luo, Steffen Neumann, Jens Nielsen, Leonardo Perez de Souza, Kazuki Saito, Uwe Sauer, Frank C Schroeder, Stefan Schuster, Gary Siuzdak, Aleksandra Skirycz, Lloyd W Sumner, Michael P Snyder, Huiru Tang, Takayuki Tohge, Yulan Wang, Weiwei Wen, Si Wu, Guowang Xu, Nicola Zamboni, Alisdair R Fernie,

Mass spectrometry-based metabolomics approaches can enable detection and quantification of many thousands of metabolite features simultaneously. However, compound identification and reliable quantification are greatly complicated owing to the chemical complexity and dynamic range of the metabolome. Simultaneous quantification of many metabolites within complex mixtures can additionally be complicated by ion ... Read more >>

Nat Methods (Nature methods)
[2021, 18(7):747-756]

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Functional genomics of GPR126 in airway smooth muscle and bronchial epithelial cells.

Robert J Hall, Jonathan O'Loughlin, Charlotte K Billington, Dhruma Thakker, Ian P Hall, Ian Sayers,

GPR126 is an adhesion G protein-coupled receptor which lies on chromosome 6q24. Genetic variants in this region are reproducibly associated with lung function and COPD in genome wide association studies (GWAS). The aims of this study were to define the role of GPR126 in the human lung and in pulmonary ... Read more >>

FASEB J (FASEB journal : official publication of the Federation of American Societies for Experimental Biology)
[2021, 35(7):e21300]

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Stir bar sorptive extraction of aroma compounds in soy sauce: Revealing the chemical diversity

Carmen Diez-Simon, Charlotte Eichelsheim, Doris M Jacobs, Roland Mumm, Robert D Hall,

Fermented soy sauce is used worldwide to enhance the flavour of many dishes. Many types of soy sauce are on the market, and their differences are mostly related to the country of origin, the production process applied and the ratio of ingredients used. Consequently, several aromas, tastes, colours, and textures ... Read more >>

Food Res Int (Food research international (Ottawa, Ont.))
[2021, 144:Not Available]

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Repatriation operation in South Australia during the COVID-19 pandemic: initial planning and preparedness.

Sonali Meena, Joel Chan, Tuong-Vi Phan, Samantha Butenko, Jenny Hurley, Paul McGowen, Emily Kirkpatrick, Lisa Upton, Razlyn Abdul Rahim, Matthew McConnell, Robert Hall,

<h4>Abstract</h4>With COVID-19 affecting millions of people around the globe, quarantine of international arrivals is a critical public health measure to prevent further disease transmission in local populations. This measure has also been applied in the repatriation of citizens, undertaken by several countries as an ethical obligation and legal responsibility. This ... Read more >>

Commun Dis Intell (2018) (Communicable diseases intelligence (2018))
[2021, 45:]

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Maltodextrin improves physical properties and volatile compound retention of spray-dried asparagus concentrate

Joanne W Siccama, Eirini Pegiou, Lu Zhang, Roland Mumm, Robert D Hall, Remko M Boom, Maarten A I Schutyser,

Traditional hot air drying of asparagus is known to lead to a powder with a poor aroma profile. We here concentrated asparagus juice into asparagus concentrate (21.7% w/w) and spray-dried it with maltodextrin DE12 as carrier agent to improve the volatile profiles of asparagus powder and to valorise fresh asparagus ... Read more >>

Lebensm Wiss Technol (Lebensmittel-Wissenschaft + [i.e. und] Technologie.)
[2021, 142:Not Available]

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Latitude dictates plant diversity effects on instream decomposition.

Luz Boyero, Javier Pérez, Naiara López-Rojo, Alan M Tonin, Francisco Correa-Araneda, Richard G Pearson, Jaime Bosch, Ricardo J Albariño, Sankarappan Anbalagan, Leon A Barmuta, Leah Beesley, Francis J Burdon, Adriano Caliman, Marcos Callisto, Ian C Campbell, Bradley J Cardinale, J Jesús Casas, Ana M Chará-Serna, Szymon Ciapała, Eric Chauvet, Checo Colón-Gaud, Aydeé Cornejo, Aaron M Davis, Monika Degebrodt, Emerson S Dias, María E Díaz, Michael M Douglas, Arturo Elosegi, Andrea C Encalada, Elvira de Eyto, Ricardo Figueroa, Alexander S Flecker, Tadeusz Fleituch, André Frainer, Juliana S França, Erica A García, Gabriela García, Pavel García, Mark O Gessner, Paul S Giller, Jesús E Gómez, Sergio Gómez, Jose F Gonçalves, Manuel A S Graça, Robert O Hall, Neusa Hamada, Luiz U Hepp, Cang Hui, Daichi Imazawa, Tomoya Iwata, Edson S A Junior, Samuel Kariuki, Andrea Landeira-Dabarca, María Leal, Kaisa Lehosmaa, Charles M'Erimba, Richard Marchant, Renato T Martins, Frank O Masese, Megan Camden, Brendan G McKie, Adriana O Medeiros, Jen A Middleton, Timo Muotka, Junjiro N Negishi, Jesús Pozo, Alonso Ramírez, Renan S Rezende, John S Richardson, José Rincón, Juan Rubio-Ríos, Claudia Serrano, Angela R Shaffer, Fran Sheldon, Christopher M Swan, Nathalie S D Tenkiano, Scott D Tiegs, Janine R Tolod, Michael Vernasky, Anne Watson, Mourine J Yegon, Catherine M Yule,

Running waters contribute substantially to global carbon fluxes through decomposition of terrestrial plant litter by aquatic microorganisms and detritivores. Diversity of this litter may influence instream decomposition globally in ways that are not yet understood. We investigated latitudinal differences in decomposition of litter mixtures of low and high functional diversity ... Read more >>

Sci Adv (Science advances)
[2021, 7(13):]

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Stir bar sorptive extraction of aroma compounds in soy sauce: Revealing the chemical diversity.

Carmen Diez-Simon, Charlotte Eichelsheim, Doris M Jacobs, Roland Mumm, Robert D Hall,

Fermented soy sauce is used worldwide to enhance the flavour of many dishes. Many types of soy sauce are on the market, and their differences are mostly related to the country of origin, the production process applied and the ratio of ingredients used. Consequently, several aromas, tastes, colours, and textures ... Read more >>

Food Res Int (Food research international (Ottawa, Ont.))
[2021, 144:110348]

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Water column contributions to the metabolism and nutrient dynamics of mid-sized rivers

Alexander J Reisinger, Jennifer L Tank, Robert O Hall, Emma J Rosi, Michelle A Baker, Laurel Genzoli,

Lotic and lentic ecosystems are traditionally viewed as dominated by either benthic or water column processes. However, mid-sized rivers represent a transition zone where both benthic and water column processes may both contribute substantially to ecosystem dynamics. Ecosystem processes such as gross primary production (GPP), ecosystem respiration (ER), or nutrient ... Read more >>

(Biogeochemistry.)
[2021, 153(1):67-84]

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Clinical Outcomes of Low-Cost, Anchorless Repair of the Triceps Tendon Using a Proximal Knot Technique.

Robert R Hall, Alison K Sarokhan, Nicky L Leung,

<h4>Purpose</h4>To use validated outcome measures to evaluate the clinical results of surgical repair of distal triceps tendon ruptures using transosseous tunnels and high-strength sutures with proximally based knots.<h4>Methods</h4>A consecutive series of traumatic distal triceps tendon ruptures at a single institution was studied. All cases were surgically repaired by 1 surgeon ... Read more >>

Arthrosc Sports Med Rehabil (Arthroscopy, sports medicine, and rehabilitation)
[2021, 3(2):e535-e541]

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Corrigendum to: An Application to Support COVID-19 Occupational Health and Patient Tracking at a Veterans Affairs Medical Center.

Nathanael R Fillmore, Danne C Elbers, Jennifer La, Theodore C Feldman, Feng-Chi Sung, Robert B Hall, Vinh Nguyen, Nicholas Link, Robert Zwolinski, Svitlana Dipietro, Stephen J Miller, Anahit Aleksanyan, Sergey D Goryachev, Paul Corcoran, Steven J Bergstrom, Michael A Parenteau, Robert S Sprague, David J Thornton, Jane A Driver, Judith M Strymish, Stewart Evans, Benjamin Colonna, Mary T Brophy, Nhan V Do,

J Am Med Inform Assoc (Journal of the American Medical Informatics Association : JAMIA)
[2021, 28(3):673]

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Ecological outcomes of hybridization vary extensively in Catostomus fishes

Elizabeth Mandeville, Robert Hall, Alex Buerkle,

Hybridization has been studied extensively to learn about speciation and mechanisms of reproductive isolation, but increasingly we recognize that hybridization outcomes vary geo-graphically and can depend on the environment. At the same time, hybridization can reshape biotic interactions in an ecosystem, leading to ecological shifts where hybridization occurs. Identifying how ... Read more >>

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An application to support COVID-19 occupational health and patient tracking at a Veterans Affairs medical center.

Nathanael R Fillmore, Danne C Elbers, Jennifer La, Theodore C Feldman, Feng-Chi Sung, Robert B Hall, Vinh Nguyen, Nicholas Link, Robert Zwolinski, Svitlana Dipietro, Steven J Miller, Anahit Aleksanyan, Sergey D Goryachev, Paul Corcoran, Steven J Bergstrom, Michael A Parenteau, Robert S Sprague, David J Thornton, Jane A Driver, Judith M Strymish, Stewart Evans, Benjamin Colonna, Mary T Brophy, Nhan V Do,

<h4>Objective</h4>Reducing risk of coronavirus disease 2019 (COVID-19) infection among healthcare personnel requires a robust occupational health response involving multiple disciplines. We describe a flexible informatics solution to enable such coordination, and we make it available as open-source software.<h4>Materials and methods</h4>We developed a stand-alone application that integrates data from several sources, ... Read more >>

J Am Med Inform Assoc (Journal of the American Medical Informatics Association : JAMIA)
[2020, 27(11):1716-1720]

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Towards superior plant-based foods using metabolomics.

Doris M Jacobs, Marco A van den Berg, Robert D Hall,

Metabolomics is proving a useful approach for many of the main future goals in agronomy and food production such as sustainability/crop resilience, food quality, safety, storage, and nutrition. Targeted and/or untargeted small-molecule analysis, coupled to chemometric analysis, has already unveiled a great deal of the complexity of plant-based foods, but ... Read more >>

Curr Opin Biotechnol (Current opinion in biotechnology)
[2020, 70:23-28]

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LNX1 Modulates Notch1 Signaling to Promote Expansion of the Glioma Stem Cell Population During Temozolomide Therapy in Glioblastoma

Shivani Baisiwala, Robert Hall, Miranda Saathoff, Jack Shireman, Cheol Park, Louisa Warnke, Clare Hardiman, Jenny Wang, Chirag Goel, Shreya Budhiraja, Kathleen McCortney, Craig Horbinski, Atique Ahmed,

<h4>ABSTRACT</h4> Glioblastoma (GBM) is the most common primary brain malignancy in adults, with a 100% recurrence rate and a 21-month median survival. Our lab and others have shown that GBM contains a subpopulation of glioma stem cells (GSCs) that expand with chemotherapy, and that may contribute to therapeutic resistance and ... Read more >>

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Chemical and Sensory Characteristics of Soy Sauce: A Review.

Carmen Diez-Simon, Charlotte Eichelsheim, Roland Mumm, Robert D Hall,

Soy sauce is a fermented product, and its flavor is a complex mixture of individual senses which, in combination, create a strong palatable condiment for many Eastern and Western dishes. This Review focuses on our existing knowledge of the chemical compounds present in soy sauce and their potential relevance to ... Read more >>

J Agric Food Chem (Journal of agricultural and food chemistry)
[2020, 68(42):11612-11630]

Cited: 2 times

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The Veterans Affairs Precision Oncology Data Repository, a Clinical, Genomic, and Imaging Research Database.

Danne C Elbers, Nathanael R Fillmore, Feng-Chi Sung, Spyridon S Ganas, Andrew Prokhorenkov, Christopher Meyer, Robert B Hall, Samuel J Ajjarapu, Daniel C Chen, Frank Meng, Robert L Grossman, Mary T Brophy, Nhan V Do,

The Veterans Affairs Precision Oncology Data Repository (VA-PODR) is a large, nationwide repository of de-identified data on patients diagnosed with cancer at the Department of Veterans Affairs (VA). Data include longitudinal clinical data from the VA's nationwide electronic health record system and the VA Central Cancer Registry, targeted tumor sequencing ... Read more >>

Patterns (N Y) (Patterns (New York, N.Y.))
[2020, 1(6):100083]

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Amicus cum Laude: Ethnodramatic Inquiry Regarding Sharing Mental Health in College.

Robert D Hall,

In this manuscript, I utilize an ethnodramatic methodology in reanalyzing two data sets about college friends disclosing and receiving mental health-related information. After describing ethnodrama and how this methodology applies to mental health-related inquiry, I detail my process of creating an ethnodrama from two extant data sets. The result is ... Read more >>

Qual Health Res (Qualitative health research)
[2020, 30(14):2173-2191]

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Comparison of volatile trapping techniques for the comprehensive analysis of food flavourings by Gas Chromatography-Mass Spectrometry.

Carmen Diez-Simon, Brenda Ammerlaan, Marco van den Berg, John van Duynhoven, Doris Jacobs, Roland Mumm, Robert D Hall,

Trapping volatiles is a convenient way to study aroma compounds but it is important to determine which volatile trapping method is most comprehensive in extracting the most relevant aroma components when investigating complex food products. Awareness of their limitations is also crucial. (Un)targeted metabolomic approaches were used to determine the ... Read more >>

J Chromatogr A (Journal of chromatography. A)
[2020, 1624:461191]

Cited: 1 time

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Primary prevention of venous thromboembolism with apixaban for multiple myeloma patients receiving immunomodulatory agents.

Robert F Cornell, Samuel Z Goldhaber, Brian G Engelhardt, Javid Moslehi, Madan Jagasia, Shelton Harrell, Samuel M Rubinstein, Robert Hall, Houston Wyatt, Gregory Piazza,

Immunomodulatory drugs (IMiDs) have improved survival of patients with multiple myeloma (MM) and comprise the therapeutic backbone at all phases of therapy. Although well-tolerated, IMiDs increase rates of venous thromboembolism (VTE). In this phase IV, single-arm pilot study, fifty patients with MM on IMiDs received apixaban 2·5 mg orally twice daily ... Read more >>

Br J Haematol (British journal of haematology)
[2020, 190(4):555-561]

Cited: 1 time

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Emergence of Attenuated Measles Illness Among IgG-positive/IgM-negative Measles Cases: Victoria, Australia, 2008-2017.

Katherine B Gibney, Lucy O Attwood, Suellen Nicholson, Thomas Tran, Julian Druce, Julia Healy, Janet Strachan, Lucinda Franklin, Robert Hall, Gail B Cross,

<h4>Background</h4>Waning measles immunity among vaccinated individuals may result in an attenuated illness. This study compares the epidemiological, clinical, and laboratory profile of measles cases with waning immunity with other measles cases.<h4>Methods</h4>Polymerase chain reaction-positive (+) measles cases notified to Victoria's Department of Health and Human Services from 2008 to 2017 with ... Read more >>

Clin Infect Dis (Clinical infectious diseases : an official publication of the Infectious Diseases Society of America)
[2020, 70(6):1060-1067]

Cited: 5 times

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Variation in secondary metabolites in a unique set of tomato accessions collected in Turkey.

Sena Bakir, Esra Capanoglu, Robert D Hall, Ric C H de Vos,

In this study, 50 tomato landraces grown in Turkey were investigated in terms of their secondary metabolite profiles. Each accession was planted in 2016 and 2017 in 3 replicates in an open field. In this study, color, pH and brix of the fruit samples were measured and an unbiased LCMS-based ... Read more >>

Food Chem (Food chemistry)
[2020, 317:126406]

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Metabolomics should be deployed in the identification and characterization of gene-edited crops.

Paul D Fraser, Asaph Aharoni, Robert D Hall, Sanwen Huang, James J Giovannoni, Uwe Sonnewald, Alisdair R Fernie,

Gene-editing techniques are currently revolutionizing biology, allowing far greater precision than previous mutagenic and transgenic approaches. They are becoming applicable to a wide range of plant species and biological processes. Gene editing can rapidly improve a range of crop traits, including disease resistance, abiotic stress tolerance, yield, nutritional quality and ... Read more >>

Plant J (The Plant journal : for cell and molecular biology)
[2020, 102(5):897-902]

Cited: 5 times

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Correction Terms for Calculating Binding Free Energy Using Rates from Nonequilibrium Simulations

Robert Hall, Tom Dixon, Alex Dickson,

<div>The free energy of a process is the fundamental quantity that determines its spontaneity or propensity at a given temperature. Binding free energy of a drug candidate to its biomolecular target is used as an objective quantity in drug design. Binding kinetics -- rates of association (k<sub>on</sub>) and dissociation (k<sub>off</sub>) ... Read more >>

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