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Article ; Online: Digital exposure notification tools: A global landscape analysis.

Nebeker, Camille / Kareem, Daniah / Yong, Aidan / Kunowski, Rachel / Malekinejad, Mohsen / Aronoff-Spencer, Eliah

PLOS digital health

2023 Volume 2, Issue 9, Page(s) e0000287

Abstract: Background: As the COVID-19 pandemic continues, digital exposure notification systems are increasingly used to support traditional contact tracing and other preventive strategies. Likewise, a plethora of COVID-19 mobile applications have emerged. ... ...

Abstract	Background: As the COVID-19 pandemic continues, digital exposure notification systems are increasingly used to support traditional contact tracing and other preventive strategies. Likewise, a plethora of COVID-19 mobile applications have emerged. Objective: To characterize the global landscape of pandemic related mobile applications, including digital exposure notification and contact tracing tools. Data sources and methods: The following queries were entered into the Google search engine: "(country name COVID app) OR (COVID app country name) OR (COVID app country name+) OR (country name+ COVID app)". The App Store, Google Play, and official government websites were then accessed to collect descriptive data for each application. Descriptive data were qualified and quantified using standard methods. COVID-19 Exposure Notification Systems (ENS) and non-Exposure Notification products were categorized and summarized to provide a global landscape review. Results: Our search resulted in a global count of 224 COVID-19 mobile applications, in 127 countries. Of these 224 apps, 128 supported exposure notification, with 75 employing the Google Apple Exposure Notification (GAEN) application programming interface (API). Of the 75 apps using the GAEN API, 15 apps were developed using Exposure Notification Express, a GAEN turnkey solution. COVID-19 applications that did not include exposure notifications (n = 96) focused on COVID-19 Self-Assessment (35·4%), COVID-19 Statistics and Information (32·3%), and COVID-19 Health Advice (29·2%). Conclusions: The digital response to COVID-19 generated diverse and novel solutions to support non-pharmacologic public health interventions. More research is needed to evaluate the extent to which these services and strategies were useful in reducing viral transmission.
Language	English
Publishing date	2023-09-01
Publishing country	United States
Document type	Journal Article
ISSN	2767-3170
ISSN (online)	2767-3170
DOI	10.1371/journal.pdig.0000287
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Corona Detective: a simple, scalable, and robust SARS-CoV-2 detection method based on reverse transcription loop-mediated isothermal amplification.

Aidelberg, Guy / Aronoff, Rachel / Eliseeva, Tatiana / Quero, Francisco Javier / Vielfaure, Hortense / Codyre, Martin / Hadasch, Kathrin / Lindner, Ariel B

Journal of biomolecular techniques : JBT

2022 Volume 32, Issue 3, Page(s) 89–97

Abstract: Surveillance screening at scale to identify people infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) prior to extensive transmission is key to bringing an end to the coronavirus disease 2019 (COVID-19) pandemic, even though ... ...

Abstract	Surveillance screening at scale to identify people infected by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) prior to extensive transmission is key to bringing an end to the coronavirus disease 2019 (COVID-19) pandemic, even though vaccinations have already begun. Here we describe Corona Detective, a sensitive and rapid molecular test to detect the virus, based on loop-mediated isothermal amplification, which could be applied anywhere at low cost. Critically, the method uses freeze-dried reagents, readily shipped without cold-chain dependence. The reaction detects the viral nucleocapsid gene through a sequence-specific quenched-fluorescence readout, which avoids false positives and also allows multiplex detection with an internal control cellular RNA. Corona Detective can be used in 8-tube strips to be read with a simple open-design fluorescence detector. Other methods to use and produce Corona Detective locally in a variety of formats are possible and already openly shared. Detection specificity is ensured through inclusion of positive and negative control reactions to run in parallel with the diagnostic reactions. A simple user protocol, including sample preparation, and a bioinformatics pipeline to ensure that viral variants will still be detectable with SARS-CoV-2 primer sets complete the method. Through rapid production and distribution of Corona Detective reactions, quite inexpensive at scale, daily or weekly surveillance testing of large populations, without waiting for symptoms to develop, is anticipated, in combination with vaccination campaigns, to finally control this pandemic.
MeSH term(s)	COVID-19 ; Humans ; Molecular Diagnostic Techniques ; Nucleic Acid Amplification Techniques ; RNA, Viral/genetics ; Reverse Transcription ; SARS-CoV-2 ; Sensitivity and Specificity
Chemical Substances	RNA, Viral
Language	English
Publishing date	2022-01-13
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2116011-9
ISSN	1943-4731 ; 1943-4731
ISSN (online)	1943-4731
ISSN	1943-4731
DOI	10.7171/jbt.21-3203-003
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Participatory research to monitor lake water pollution

Rachel Aronoff / Anna Dussuet / Roger Erismann / Shannon Erismann / Luc Patiny / Carlos Vivar‐Rios

Ecological Solutions and Evidence, Vol 2, Iss 3, Pp n/a-n/a (2021)

2021

Abstract: Abstract A participatory research team, concerned about water quality around Lake Geneva, particularly in the Montreux Bay region where some were lifeguards, ran sampling campaigns to determine summertime levels of lake water pollution. The participants ... ...

Abstract	Abstract A participatory research team, concerned about water quality around Lake Geneva, particularly in the Montreux Bay region where some were lifeguards, ran sampling campaigns to determine summertime levels of lake water pollution. The participants were brought together serendipitously through a course organized by academic researchers and ‘biohackers’ from the community laboratory, Hackuarium. After discussion about lifeguards’ gastrointestinal and dermatological ailments each season, the decision to pursue this participatory research project was made. In order to assess water quality, thereby testing the hypothesis that unsuspected pollution enters the lake each summer season, microbiological plating of water samples was proposed. Volunteers collected and analysed water samples over summer seasons (8 weeks in 2016, 2017 and 2020) from three sites around Montreux Bay, with tap and local river water samples as controls. Contamination of lake water was measured using standard microbiological methods, with growth media allowing quantitative assessment of abundance of several bacterial species. In particular, the focus was to quantify Escherichia coli, the classic bioindicator organism for raw sewage contamination. These open science data reveal peaks of bioindicator and other bacterial pollution in lake water samples during all sampling years. For the initial two sampling campaigns, increased microbial burdens occurred during a popular music festival, and were not simply dependent upon rainfall. In contrast, only scattered, lower level bioindicator pollution events occurred across the sampling period during the pandemic summer of 2020, when the festival was cancelled. This study confirms the power of participatory research: dedicated people on a budget can do meaningful environmental monitoring. These analyses suggest that better management, both to support water quality monitoring and for event organization, is essential, as sewage treatment facilities near many popular festivals, internationally, may need ...
Keywords	bioindicator ; citizen science ; Do‐It‐Together (DIT) research ; environmental monitoring ; microbiology ; water sampling ; Environmental sciences ; GE1-350 ; Ecology ; QH540-549.5
Subject code	333
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	Wiley
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Out of the Laboratory and Into the Field: Validation of Portable Cell Culture Protocols.

McDade, Thomas W / Aronoff, Jacob E / Leigh, Adam K K / Finegood, Eric D / Weissman-Tsukamoto, Rachel M / Brody, Gene H / Miller, Gregory E

Psychosomatic medicine

2021 Volume 83, Issue 3, Page(s) 283–290

Abstract: Objective: Field-based research on inflammation and health is typically limited to baseline measures of circulating cytokines or acute-phase proteins, whereas laboratory-based studies can pursue a more dynamic approach with ex vivo cell culture methods. ...

Abstract	Objective: Field-based research on inflammation and health is typically limited to baseline measures of circulating cytokines or acute-phase proteins, whereas laboratory-based studies can pursue a more dynamic approach with ex vivo cell culture methods. The laboratory infrastructure required for culturing leukocytes limits application in community-based settings, which in turn limits scientific understandings of how psychosocial, behavioral, and contextual factors influence the regulation of inflammation. We aim to address this gap by validating two "field-friendly" cell culture protocols, one using a small volume of venous whole blood and another using finger-stick capillary whole blood. Methods: We evaluated the performance of both protocols against a standard laboratory-based protocol using matched venous and capillary blood samples collected from young adults (n = 24). Samples were incubated with lipopolysaccharide and hydrocortisone, and the production of proinflammatory cytokines interleukin 1β, interleukin 6, and tumor necrosis factor α was measured in response. Results: Comparisons indicate a high level of agreement in responses across the protocols and culture conditions. The overall correlation in results was 0.88 between the standard and small-volume protocols and 0.86 between the standard and capillary blood protocols. Repeatability for the small-volume and capillary blood protocols was high, with mean coefficients of variation across five replicates of 6.2% and 5.4%, respectively. Conclusions: These results demonstrate the feasibility of culturing cells and quantifying the inflammatory response to challenge outside the laboratory, with a wide range of potential applications in biobehavioral research in community-based and remote field settings.
MeSH term(s)	Cell Culture Techniques ; Cytokines ; Laboratories ; Lipopolysaccharides ; Tumor Necrosis Factor-alpha
Chemical Substances	Cytokines ; Lipopolysaccharides ; Tumor Necrosis Factor-alpha
Language	English
Publishing date	2021-02-04
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	3469-1
ISSN	1534-7796 ; 0033-3174
ISSN (online)	1534-7796
ISSN	0033-3174
DOI	10.1097/PSY.0000000000000923
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Article ; Online: Defining Key Performance Indicators for the California COVID-19 Exposure Notification System (CA Notify).

Aronoff-Spencer, Eliah / Nebeker, Camille / Wenzel, Alexander T / Nguyen, Kevin / Kunowski, Rachel / Zhu, Mingjia / Adamos, Gary / Goyal, Ravi / Mazrouee, Sepideh / Reyes, Aaron / May, Nicole / Howard, Holly / Longhurst, Christopher A / Malekinejad, Mohsen

Public health reports (Washington, D.C. : 1974)

2022 Volume 137, Issue 2_suppl, Page(s) 67S–75S

Abstract: Objectives: Toward common methods for system monitoring and evaluation, we proposed a key performance indicator framework and discussed lessons learned while implementing a statewide exposure notification (EN) system in California during the COVID-19 ... ...

Abstract	Objectives: Toward common methods for system monitoring and evaluation, we proposed a key performance indicator framework and discussed lessons learned while implementing a statewide exposure notification (EN) system in California during the COVID-19 epidemic. Materials and methods: California deployed the Google Apple Exposure Notification framework, branded CA Notify, on December 10, 2020, to supplement traditional COVID-19 contact tracing programs. For system evaluation, we defined 6 key performance indicators: adoption, retention, sharing of unique codes, identification of potential contacts, behavior change, and impact. We aggregated and analyzed data from December 10, 2020, to July 1, 2021, in compliance with the CA Notify privacy policy. Results: We estimated CA Notify adoption at nearly 11 million smartphone activations during the study period. Among 1 654 201 CA Notify users who received a positive test result for SARS-CoV-2, 446 634 (27%) shared their unique code, leading to ENs for other CA Notify users who were in close proximity to the SARS-CoV-2-positive individual. We identified at least 122 970 CA Notify users as contacts through this process. Contact identification occurred a median of 4 days after symptom onset or specimen collection date of the user who received a positive test result for SARS-CoV-2. Practice implications: Smartphone-based EN systems are promising new tools to supplement traditional contact tracing and public health interventions, particularly when efficient scaling is not feasible for other approaches. Methods to collect and interpret appropriate measures of system performance must be refined while maintaining trust and privacy.
MeSH term(s)	Humans ; COVID-19/epidemiology ; SARS-CoV-2 ; Disease Notification ; Contact Tracing/methods ; California/epidemiology
Language	English
Publishing date	2022-10-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	120953-x
ISSN	1468-2877 ; 0033-3549
ISSN (online)	1468-2877
ISSN	0033-3549
DOI	10.1177/00333549221129354
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Article ; Online: Empowering grassroots innovation to accelerate biomedical research.

Greshake Tzovaras, Bastian / Rera, Michael / Wintermute, Edwin H / Kloppenborg, Katharina / Ferry-Danini, Juliette / Aidelberg, Guy / Aronoff, Rachel / Lindner, Ariel / Misevic, Dusan

PLoS biology

2021 Volume 19, Issue 8, Page(s) e3001349

Abstract: The purpose of biomedicine is to serve society, yet its hierarchical and closed structure excludes many citizens from the process of innovation. We propose a collection of reforms to better integrate citizens within the research community, reimagining ... ...

Abstract	The purpose of biomedicine is to serve society, yet its hierarchical and closed structure excludes many citizens from the process of innovation. We propose a collection of reforms to better integrate citizens within the research community, reimagining biomedicine as more participatory, inclusive, and responsive to societal needs.
MeSH term(s)	Biomedical Research ; Citizen Science ; Inventions
Language	English
Publishing date	2021-08-09
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2126776-5
ISSN	1545-7885 ; 1544-9173
ISSN (online)	1545-7885
ISSN	1544-9173
DOI	10.1371/journal.pbio.3001349
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Article ; Online: Empowering grassroots innovation to accelerate biomedical research.

Bastian Greshake Tzovaras / Michael Rera / Edwin H Wintermute / Katharina Kloppenborg / Juliette Ferry-Danini / Guy Aidelberg / Rachel Aronoff / Ariel Lindner / Dusan Misevic

PLoS Biology, Vol 19, Iss 8, p e

2021 Volume 3001349

Abstract	The purpose of biomedicine is to serve society, yet its hierarchical and closed structure excludes many citizens from the process of innovation. We propose a collection of reforms to better integrate citizens within the research community, reimagining biomedicine as more participatory, inclusive, and responsive to societal needs.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Empowering grassroots innovation to accelerate biomedical research

Bastian Greshake Tzovaras / Michael Rera / Edwin H. Wintermute / Katharina Kloppenborg / Juliette Ferry-Danini / Guy Aidelberg / Rachel Aronoff / Ariel Lindner / Dusan Misevic

PLoS Biology, Vol 19, Iss

2021 Volume 8

Abstract	The purpose of biomedicine is to serve society, yet its hierarchical and closed structure excludes many citizens from the process of innovation. We propose a collection of reforms to better integrate citizens within the research community, reimagining biomedicine as more participatory, inclusive, and responsive to societal needs.
Keywords	Biology (General) ; QH301-705.5
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Layer, column and cell-type specific genetic manipulation in mouse barrel cortex.

Aronoff, Rachel / Petersen, Carl C H

Frontiers in neuroscience

2008 Volume 2, Issue 1, Page(s) 64–71

Abstract: Sensory information is processed in distributed neuronal networks connected by intricate synaptic circuits. Studies of the rodent brain can provide insight into synaptic mechanisms of sensory perception and associative learning. In particular, the mouse ... ...

Abstract	Sensory information is processed in distributed neuronal networks connected by intricate synaptic circuits. Studies of the rodent brain can provide insight into synaptic mechanisms of sensory perception and associative learning. In particular, the mouse whisker sensorimotor system has recently begun to be investigated through combinations of imaging and electrophysiology, providing data correlating neural activity with behaviour. In order to go beyond such correlative studies and to pinpoint the contributions of individual genes to brain function, it is critical to make highly controlled and specific manipulations. Here, we review recent progress towards genetic manipulation of targeted genes in specific neuronal cell types located in a selected cortical layer of a well-defined cortical column of mouse barrel cortex. The unprecedented precision of such genetic manipulation within highly specific neural circuits may contribute significantly to progress in understanding the molecular and synaptic determinants of simple forms of sensory perception and associative learning.
Language	English
Publishing date	2008-07-07
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2411902-7
ISSN	1662-453X ; 1662-4548
ISSN (online)	1662-453X
ISSN	1662-4548
DOI	10.3389/neuro.01.001.2008
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Layer- and column-specific knockout of NMDA receptors in pyramidal neurons of the mouse barrel cortex.

Aronoff, Rachel / Petersen, Carl

Frontiers in integrative neuroscience

2007 Volume 1, Page(s) 1

Abstract: Viral vectors injected into the mouse brain offer the possibility for localized genetic modifications in a highly controlled manner. Lentivector injection into mouse neocortex transduces cells within a diameter of approximately 200mum, which closely ... ...

Abstract	Viral vectors injected into the mouse brain offer the possibility for localized genetic modifications in a highly controlled manner. Lentivector injection into mouse neocortex transduces cells within a diameter of approximately 200mum, which closely matches the lateral scale of a column in barrel cortex. The depth and volume of the injection determines which cortical layer is transduced. Furthermore, transduced gene expression from the lentivector can be limited to predominantly pyramidal neurons by using a 1.3kb fragment of the alphaCaMKII promoter. This technique therefore allows genetic manipulation of a specific cell type in defined columns and layers of the neocortex. By expressing Cre recombinase from such a lentivector in gene-targeted mice carrying a floxed gene, highly specific genetic lesions can be induced. Here, we demonstrate the utility of this approach by specifically knocking out NMDA receptors (NMDARs) in pyramidal neurons in the somatosensory barrel cortex of gene-targeted mice carrying floxed NMDAR 1 genes. Neurons transduced with lentivector encoding GFP and Cre recombinase exhibit not only reductions in NMDAR 1 mRNA levels, but reduced NMDAR-dependent currents and pairing-induced synaptic potentiation. This technique for knockout of NMDARs in a cell type, column- and layer-specific manner in the mouse somatosensory cortex may help further our understanding of the functional roles of NMDARs in vivo during sensory perception and learning.
Language	English
Publishing date	2007-11-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2452962-X
ISSN	1662-5145 ; 1662-5145
ISSN (online)	1662-5145
ISSN	1662-5145
DOI	10.3389/neuro.07.001.2007
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