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Authors: Phase Diagnostics
Group: Coronavirus Method Development Community, Phase Diagnostics

Proper citation: Phase Diagnostics 2020. INDICAID Rapid Point-of-Care Test for SARS-CoV-2 Antigen. protocols.io https://dx.doi.org/10.17504/protocols.io.bkt4kwqw Copy   

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Authors: Lusajo Mwakibete, Cristina Tato, Vida Ahyong, Amy Kistler, Manu Vanaerschot, Angela Detweiler, Michelle Tan
Group: Chan Zuckerberg Biohub, Coronavirus Method Development Community

Proper citation: Lusajo Mwakibete, Cristina Tato, Vida Ahyong, Amy Kistler, Manu Vanaerschot, Angela Detweiler, Michelle Tan 2021. ARTIC-NEB: SARS-CoV-2 Library Prep. protocols.io https:// Copy   

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Authors: Elizabeth Fozo

Proper citation: Elizabeth Fozo 2021. NAO staining. protocols.io https:// Copy   

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Authors: Bonnie Poulos
Group: VERVE Net, Sullivan Lab
Summary: Purpose: to measure the infective titer (number of infective elements per mL) of from 1-5 viral samples in a quick and efficient manner.

Proper citation: Bonnie Poulos 2016. Most Probable Number (MPN) Counts of Cyanophages. protocols.io https://dx.doi.org/10.17504/protocols.io.ddb22m Copy   

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Authors: María Dolores Rojo-Martín, Germán Peñalva, Carmen Pinto, Inmaculada Salcedo, Rocío Fernández-Urrusuno, José Cabeza, Juan de Dios Alcántara, Olaf Neth, Paloma Porras, Javier Bautista, José Garnacho-Montero, Rafael Sierra, Ángel Estella, Carmen Lupión, Elena Hevia, Arantxa Irastorza, José Luis Márquez, María Luisa García-Gestoso, Álvaro Pascual, Jesús Rodríguez-Baño, Raquel Valencia, María Antonia Pérez-Moreno, José Miguel Cisneros, on behalf of the PIRASOA programme group
Summary: BackgroundAntimicrobial Stewardship Programmes (ASPs) and Healthcare-associated Infections (HAIs) Programmes are recommended by scientific societies as a key intervention to fight against antimicrobial resistance (AMR), but their implementation and sustainability are not easy to achieve. Spain is among the European countries with the highest antimicrobial consumption, as well as high AMR rates; despite this fact, development of ASPs is scarce. In this scenario, we designed and implemented a long-term comprehensive Institutional Programme for the Prevention and Control of Healthcare-associated Infections and Appropriate Use of Antimicrobials (PIRASOA) in both inpatient and outpatient care covering the whole Public Healthcare System of Andalusia, which is the most populated autonomous region in Spain with 8.4 million inhabitants.Methods/designThis protocol describes the design, structure, organisation and indicators of the PIRASOA programme, as well as the methodology for its implementation development, data collection, assessment, feedback and continuity over time.This education-based multifaceted programme with institutional support is divided into two sub-programmes integrated into daily clinical practice: the HAIs sub-programme, aimed at hospitals, and the ASP sub-programme, applied to both hospitals and primary care.ConclusionsThe PIRASOA programme is the first institutional comprehensive education-based programme integrated into daily clinical practice to prevent and control HAIs and to optimise the use of antimicrobials implemented in the entire public healthcare system of an autonomous region in Spain, being among the first integral regional programmes in Europe. The assessment of antimicrobial consumption, clinical and microbiological indicators and reports are performed on a quarterly basis and are available for assessment and feedback in near real-time with only a three-month delay. The programme started on 1 January 2014, has been adequately implemented in all public centres of Andalusia and it is committed to be integrated into daily clinical practice. Data collection is ongoing. Long-term results will be analysed and published from 2018 onwards.

Proper citation: María Dolores Rojo-Martín, Germán Peñalva, Carmen Pinto, Inmaculada Salcedo, Rocío Fernández-Urrusuno, José Cabeza, Juan de Dios Alcántara, Olaf Neth, Paloma Porras, Javier Bautista, José Garnacho-Montero, Rafael Sierra, Ángel Estella, Carmen Lupión, Elena Hevia, Arantxa Irastorza, José Luis Márquez, María Luisa García-Gestoso, Álvaro Pascual, Jesús Rodríguez-Baño, Raquel Valencia, María Antonia Pérez-Moreno, José Miguel Cisneros, on behalf of the PIRASOA programme group 2018. The PIRASOA programme: design, structure, organisation and indicators of a comprehensive regional Institutional Programme for the Prevention and Control of Healthcare-associated Infections and Antimicrobial Stewardship for hospitals and primary care settin. protocols.io https://dx.doi.org/10.17504/protocols.io.r3bd8in Copy   

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Authors: Kirsten Abbot-Smith, Franklin Chang, Caroline Rowland, Heather Ferguson, Julian Pine
Summary: Permutation analysis for eyetracking study

Proper citation: Kirsten Abbot-Smith, Franklin Chang, Caroline Rowland, Heather Ferguson, Julian Pine 2017. Permutation Analysis: Two and three year old children use an incremental first-NP-as-agent bias to process transitive sentencee. protocols.io https://dx.doi.org/10.17504/protocols.io.ju6cnze Copy   

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Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. They play essential roles in the activation and differentiation of immune cells, as well as proliferation, maturation, migration, and adhesion. They also have pro-inflammatory and anti-inflammatory properties. The primary function of interleukins is, therefore, to modulate growth, differentiation, and activation during inflammatory and immune responses. Interleukins consist of a large group of proteins that can elicit many reactions in cells and tissues by binding to high-affinity receptors in cell surfaces. Regulatory B cells mainly secrete IL-35. One of the primary functions of this interleukin is its involvement in lymphocyte differentiation. It exhibits an immune-suppressive effect. [1]Reference1. Justiz Vaillant AA, Qurie A. Interleukin. In:StatPearls. Treasure Island (FL): StatPearls Publishing; June 12, 2019.

Proper citation: Angel Justiz-Vaillant 2020. ELISA for quantification of IL-35 in human serum.. protocols.io https://dx.doi.org/10.17504/protocols.io.bj37kqrn Copy   

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Authors: Kelsey Knight
Group: BioLegend

Proper citation: Kelsey Knight 2018. T Cell Activation with anti-CD3 Antibodies Protocol - Mouse. protocols.io https://dx.doi.org/10.17504/protocols.io.tnaemae Copy   

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Authors: Mark Kelly LAT, Timothy P. Fitzgibbons
Group: Mouse Metabolic Phenotyping Centers
Summary: Summary: This is a mouse model of acute myocardial infarction. This protocol is suitable for studying mouse models thought to be relevant to coronary ischemia or the development of congestive heart failure.

Proper citation: Mark Kelly LAT, Timothy P. Fitzgibbons 2019. U Mass - Coronary Artery Ligation. protocols.io https://dx.doi.org/10.17504/protocols.io.56kg9cw Copy   

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Authors: Allen Institute for Brain Science
Group: BICCN, Allen Institute for Brain Science
Summary: This SOP provides instructions to prepare Internal Solution II used for simultaneous patch clamp electrophysiology experiments to probe circuit connectivity.Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number U19MH114830. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

Proper citation: Allen Institute for Brain Science 2020. Electrode Internal Solution with Biocytin II. protocols.io https://dx.doi.org/10.17504/protocols.io.bdn8i5hw Copy   

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Authors: JCPrice
Group: Chemistry 586 Advanced Biochemical Methods

Proper citation: JCPrice 2020. Transfection with PEI . protocols.io https:// Copy   

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Authors: Peng Wang, Hongjian Ni, Ruihe Wang

Proper citation: Peng Wang, Hongjian Ni, Ruihe Wang 2018. Fig 4. Weight on bit for the various vibration manners. protocols.io https://dx.doi.org/10.17504/protocols.io.ke5ctg6 Copy   

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Authors: Jamie Allen, Elizabeth Neumann, Maya Brewer, Jeff Spraggins, Danielle Gutierrez, Mark De Caestecker
Group: VU Biomolecular Multimodal Imaging Center, Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: Scope: Extract RNA for RIN and DV 200 Assessment.Expected Outcome: RIN and DV 200 measurements for tissue quality assessment.

Proper citation: Jamie Allen, Elizabeth Neumann, Maya Brewer, Jeff Spraggins, Danielle Gutierrez, Mark De Caestecker 2020. RNA Extraction for RIN and DV 200 Analysis. protocols.io https://dx.doi.org/10.17504/protocols.io.86nhzde Copy   

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Authors: Christa Smith
Group: Moran Lab, PriME

Proper citation: Christa Smith 2018. MBM Vitamin Supplement. protocols.io https://dx.doi.org/10.17504/protocols.io.jwkcpcw Copy   

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Authors: Sam Li
Group: BioLegend
Summary: Product description and procedure summary: Target cells are positively selected or depleted by incubating the sample with an anti-human PE conjugated antibody, followed by incubation with magnetic anti-PE Nanobeads. The magnetically labeled fraction is retained by the use of a magnetic separator. These are the PE+ cells, do not discard them if those are the cells of interest. Some of the downstream applications include functional assays, gene expression, phenotypic characterization, etc. Note: This procedure is optimized for the isolation of 107 to 2 x 108 cells per tube. If working with fewer than 107 cells, keep volumes as indicated for 107 cells. For best results, optimize the conditions to your specific cell number and tissue. Prepare fresh MojoSort™ Buffer solution by diluting the 5X concentrate with sterile distilled water.Scale up volumes if using 14mL tubes and Magnet, and place the tube in the magnet for 10 minutes.

Proper citation: Sam Li 2019. MojoSort™ Mouse anti-PE Nanobeads Protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.7xshpne Copy   

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Authors: LI-COR Biosciences
Group: LI-COR Biosciences
Summary: This protocol describes a method to determine optimal blocking conditions for NIR Western blot detection with the Odyssey family of Imagers. It is for use with the Millipore Immobilon®-FL PVDF membrane.

Proper citation: LI-COR Biosciences 2017. Odyssey Western Blot Blocker Optimization for Near-Infrared (NIR) Detection (PVDF membrane). protocols.io https://dx.doi.org/10.17504/protocols.io.g7qbzmw Copy   

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Authors: Manuela De Las Casas, Laura Sánchez
Group: AEGIS - Madrid iGEM 2019
Summary: The aim of this protocol is to separate the aptamers that bind to the cells from the ones that don't. The cells used have a histidin tag that attaches to the beads' streptavidin tag. The beads will then pull the cells and the complex will precipitate. Since the aptamers have high specifity and affinity for particular sequences, those able to recognice the cells will bind to them, being part of the complex. The aptamers that don't recognice the cells, won't bind. This protocol enables to separate aptamers based on their affinity using the target cells.The Dynabeads His-Tag Isolation and Pulldown from ThermoFisher is an already proven system to separate and isolate proteins. We have automatised the system with the Opentrons to separate cells and it worked succesfully. But if you don't have an Opentrons machine, it is also possible to perform a manual protocol as described here.

Proper citation: Manuela De Las Casas, Laura Sánchez 2019. Dynabeads™ Cell Separation. protocols.io https://dx.doi.org/10.17504/protocols.io.8h6ht9e Copy   

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Authors: Ian Mackay, Judy Northill
Group: Public Health Virology, Forensic and Scientific Services
Summary: This protocol aims to amplify enterovirus (EV) D68 viruses but not other viruses.This protocol is modified from a previously published method cited below. Details of the modification are included in the method.The oligonucleotides target the 5'UTR noncoding region. This is a qualitative test for investigating EV-D68 infection of humans.The test has identified both the historical EV-D68 strains and contemporary strains which has been confirmed by subgenomic sequencing of partial 5'UTR-VP2 and partial VP1 regions. Culture of the virus is not required as this assay is capable of detecting EV-D68 direct from extracted clinical samples.

Proper citation: Ian Mackay, Judy Northill 2019. Enterovirus (EV) D68 real-time RT-PCR (EV-D68-TM2018). protocols.io https://dx.doi.org/10.17504/protocols.io.xb4fiqw Copy   

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Authors: Brandon M. Satinsky, Scott M. Gifford, Byron C. Crump, Christa Smith, Mary Ann Moran
Group: Moran Lab

Proper citation: Brandon M. Satinsky, Scott M. Gifford, Byron C. Crump, Christa Smith, Mary Ann Moran 2015. In vitro transcription mixture, Moran Lab. protocols.io https://dx.doi.org/10.17504/protocols.io.dx37qm Copy   

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Authors: Cortina Chen, Iman Mali, Florian T Merkle
Group: Neurodegeneration Method Development Community
Summary: This protocol is about Differentiation of hPSCs to hypothalamic neurons.

Proper citation: Cortina Chen, Iman Mali, Florian T Merkle 2020. Differentiation of hPSCs to hypothalamic neurons. protocols.io https://dx.doi.org/10.17504/protocols.io.bn8qmhvw Copy   

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