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Authors: Maysa Silva, Maryana Branquinho, Maria Cármen Sales

Proper citation: Maysa Silva, Maryana Branquinho, Maria Cármen Sales 2018. Qiagen - RNeasy mini kit for cells. protocols.io https://dx.doi.org/10.17504/protocols.io.ssbeean Copy   

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Authors: Jose Mendoza-Sanchez
Summary: Multicriteria desicion analysis (MCDA) is a tool used to perform quantitative benefit-risks assessment (BRA) anlysis in drugs, procedures and devices in health. It allows comparisons in the same indication, that allows quantitative BRA balances, is useful to shows results in a transparency and consistency manner and also to communicate easily to the stakeholders.MCDA has emerged as a promising tool in the decision context for drugs, although its use has been relegated to assess drugs in the context of medicine reimbursment and a few for benefits, risks and others assessments in medicines for a particular indication. One of the major advantages of MCDA is the inclusion of criterian weights that is "preferences". this roadmap to formulate a MCDA compile the recomendations of IMI-PROTECT and ISPOR task force to easy, explicit and transparent election of criteria included in a MCDA.

Proper citation: Jose Mendoza-Sanchez 2018. Roadmap to formulate a Multicriteria Decision Analysis (MCDA). protocols.io https://dx.doi.org/10.17504/protocols.io.mwgc7bw Copy   

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Authors: Lele Sun, Xiujun Cheng, Hong Liu, Furen Zhang

Proper citation: Lele Sun, Xiujun Cheng, Hong Liu, Furen Zhang 2019. ddPCR. protocols.io https://dx.doi.org/10.17504/protocols.io.v4ze8x6 Copy   

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Authors: DAVID DUNIGAN AND IRINA AGARKOVA
Group: VERVE Net
Summary: For use in Polyacrylamide Gel System For Electrophoresis Of Proteins.

Proper citation: DAVID DUNIGAN AND IRINA AGARKOVA 2016. Running gel buffer (10X). protocols.io https://dx.doi.org/10.17504/protocols.io.ercbd2w Copy   

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Authors: Marda Jorgensen, Jerelyn Nick
Group: Human BioMolecular Atlas Program (HuBMAP) Method Development Community
Summary: This is an appendix diagram for spleen tissue cutting.

Proper citation: Marda Jorgensen, Jerelyn Nick 2020. Appendix for Spleen SOP. protocols.io https://dx.doi.org/10.17504/protocols.io.bbcviiw6 Copy   

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Authors: Tobias von der Haar
Summary: This method is based on that originally described by Hanahan et al (1991), with the difference that we grow cells faster at a higher temperature (this works fine for us).

Proper citation: Tobias von der Haar 2019. Preparation and Transformation of Competent E. coli cells (CCMB80 Method). protocols.io https://dx.doi.org/10.17504/protocols.io.hayb2fw Copy   

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Authors: Benjamin Bolduc
Group: Sullivan Lab, iVirus
Summary: Preparing data for use in vContact by using VirSorted Ocean Sampling Day (2014) contigs, using tools available in Cyverse. This protocol creates a BLAST DB, BLASTs sequences, and creates a gene-to-contig mapping file. Results from this protocol are suitable for vContact-PCs.

Proper citation: Benjamin Bolduc 2018. Preparing Data for vContact from Proteins (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.wigfcbw Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab

Proper citation: Matthew Sullivan 2016. YTSS Medium. protocols.io https://dx.doi.org/10.17504/protocols.io.dbq2mv Copy   

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Authors: Stepan Feduniw, Jan Modzelewski, Dorota Sys, Sebastian Kwiatkowski, Anna Kajdy
Group: Department of Reproductive Health, Centre od Postgraduate Medical Education
Summary: Introduction. The article presents a rapid systematic review protocol. The aim is to assess the current studies about the influence of exposure to a natural disaster or catastrophic event on the prevalence of anxiety among pregnant women worldwide. We hope that this knowledge will provide better understanding of the current situation related to the COVID-19 pandemic. There are more than 30 million coronavirus infection cases worldwide, and many countries have declared states of a natural disaster. Therefore, we believe that experiences from previous natural disasters on maternal anxiety could be an important lesson for planning intervention in this group of patients. Methods and Analysis. For the purpose of this systematic review the following databases will be screened Pubmed / MEDLINE, Web of Science, Cochrane Library, EMBASE, Google Scholar. This literature review will compare the prevalence of anxiety among pregnant women during a catastrophic event including and pregnant women with pregnancy studied in a naturally stable setting. Exposure to natural disasters or other catastrophic events onmaternalanxiety. The risk of bias will be assessed independently during the data extraction process by at least two researchers using the Newcastle-Ottawa Scale.Ethics and Dissemination. A manuscript will be prepared for submission to a peer-reviewed journal. The current protocol is made using PRISMA-P guidelines and were registered in PROSPERO with ID-number: CRD42020178944.

Proper citation: Stepan Feduniw, Jan Modzelewski, Dorota Sys, Sebastian Kwiatkowski, Anna Kajdy 2021. Anxiety of pregnant women in time of catastrophic events, including COVID-19 pandemic – a systematic review and metanalysis protocol.. protocols.io https://dx.doi.org/10.17504/protocols.io.bq9zmz76 Copy   

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Authors: Angel Justiz-Vaillant
Group: Carbon
Summary: This ELISA was used to study the interactions between Peptostreptococcal protein-L (SpL) and protein LAG (PLAG) with different immunoglobulin preparations from mammalian and avian species.

Proper citation: Angel Justiz-Vaillant 2021. Peptostreptococcal protein L and a Chimeric Protein-LAG sandwich ELISA. protocols.io https://dx.doi.org/10.17504/protocols.io.bta6nihe Copy   

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Authors: Yaowu Yuan
Group: Mimulus

Proper citation: Yaowu Yuan 2019. CTAB DNA Extraction for genotyping. protocols.io https://dx.doi.org/10.17504/protocols.io.3rrgm56 Copy   

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Authors: Janet Keast, Peregrine Osborne
Group: SPARC
Summary: This protocol is used for studies of neurons containing retrograde tracer dye in adult rat dorsal root ganglia (DRG) or pelvic ganglia (PG; synonym, major pelvic ganglia). Cryosections of ganglia are mounted directly on slides for immunohistochemical staining. Antibodies have been selected to distinguish different neurochemical classes of PG neurons or to specifically identify subclasses of sensory neurons that are myelinated (immunoreactive for NF200 [neurofilament, 200 kD]) or nociceptive (immunoreactive for TRPV1).

Proper citation: Janet Keast, Peregrine Osborne 2019. Immunohistochemical analysis of ganglion neurons innervating the lower urinary tract [keast-001-stage03]. protocols.io https://dx.doi.org/10.17504/protocols.io.w3efgje Copy   

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Authors: New England Biolabs
Group: New England Biolabs (NEB)
Summary: T7 Endonuclease I recognizes and cleaves non-perfectly matched DNA. This protocol describes how to determine genome targeting efficiency by digesting annealed PCR products with T7 Endonuclease I. In the first step PCR products are produced from the genomic DNA of cells whose genomes were targeted using Cas9, TALEN, ZFN etc. In the second step, the PCR products are annealed and digested with T7 Endonuclease I. Fragments are analyzed to determine the efficiency of genome targeting.

Proper citation: New England Biolabs 2015. Determining Genome Targeting Efficiency using T7 Endonuclease I (M0302). protocols.io https://dx.doi.org/10.17504/protocols.io.cqpvvm Copy   

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Authors: Roscoff Culture Collection
Group: Roscoff Culture Collection
Summary: Medium used for cyanobacteria based on artificial seawater (ASW)

Proper citation: Roscoff Culture Collection 2019. ASW+NO3 medium. protocols.io https://dx.doi.org/10.17504/protocols.io.s5zeg76 Copy   

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Authors: Rosa Leon
Group: Leon Zayas Lab
Summary: This protocol series will guide students through the experience of analyzing metagenomic data. 

Proper citation: Rosa Leon 2018. BIOL 354W - Research Methods in Advance Microbiology. protocols.io https://dx.doi.org/10.17504/protocols.io.m5xc87n Copy   

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Authors: Margaret Kalacska, J. Pablo Arroyo-Mora, Raymond Soffer, Kathryn Elmer
Group: Canadian Airborne Biodiversity Observatory
Summary: The following protocol describes best practices for collecting field spectrometer measurements with an ASD Fieldspec 3 spectroradiometer. In order to determine absolute reflectance users are urged to follow the calibration and analytical theory described in Soffer et al (2019). Processing of the files collected by the ASD following the theory presented in Soffer et al. (2019) can be carried out with the ASDtoolkit (Elmer et al. 2019).Soffer R., Ifimov G., Arroyo-Mora J.P., Kalacska M. 2019 Validation of Airborne Hyperspectral Imagery from Laboratory Panel Characterization to Image Quality Assessment: Implications for an Arctic Peatland Surrogate Simulation Site. Canadian Journal of Remote Sensing. DOI: 10.1080/07038992.2019.1650334Elmer K, Soffer R, Kalacska M, Schaaf ES, Arroyo-Mora JP. (2019) ASDtoolkit for reflectance measurements dx.doi.org/10.17504/protocols.io.6pahdie

Proper citation: Margaret Kalacska, J. Pablo Arroyo-Mora, Raymond Soffer, Kathryn Elmer 2019. ASD FieldSpec3 field measurement protocols. protocols.io https://dx.doi.org/10.17504/protocols.io.qu7dwzn Copy   

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Authors: Angel Justiz-Vaillant
Group: University of the West Indies, [email protected]
Summary: Protein LA, a novel hybrid protein, structurally contains 4 of the Ig Fc-binding and 4 of the Ig Fab binding regions on SpA with 4 of kappa light chain-binding sites of protein L. It has a MW of 65 kDa. Protein LA combines the binding properties of the both SpL and SpA and in some cases, give higher binding affinity than either protein alone. The binding of an Ig to SpL does not interfere with binding of another Ig molecule to the SpA domains and vice versa. Protein LA has been shown to bind effectively to immunoglobulins and their fragments from many species of animals [1]. Reference1. Justiz-Vaillant AA, Akpaka PE, McFarlane-Anderson N, Smikle MF. Comparison of techniques of detecting immunoglobulin-binding protein reactivity to immunoglobulin produced by different avian and mammalian species.West Indian Med J. 2013;62(1):12-20.

Proper citation: Angel Justiz-Vaillant 2020. Preparation of a protein-LA conjugated to horseradish peroxidase by the periodate method.. protocols.io https://dx.doi.org/10.17504/protocols.io.bjkzkkx6 Copy   

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Authors: Lauren Segers, Kendall Morris, Donald Bolser
Group: SPARC

Proper citation: Lauren Segers, Kendall Morris, Donald Bolser 2020. Morris USF Lab protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bci8iuhw Copy   

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Authors: Diep Ganguly
Group: Pogson Genomics Group
Summary: This protocol (based on the BigDye® Terminator v3.1 Cycle Sequencing Kit) is for performing terminator cycling sequencing reactions for Sanger sequencing of amplified PCR products or plasmid DNA on the 3130X genetic analyser (Applied Biosystems).

Proper citation: Diep Ganguly 2019. Dye-terminator DNA sequencing. protocols.io https://dx.doi.org/10.17504/protocols.io.baq7idzn Copy   

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Authors: David Dunigan and Irina Agarkova
Group: VERVE Net

Proper citation: David Dunigan and Irina Agarkova 2016. Restriction Endonuclease Purification From Virus Infected Chlorella. protocols.io https://dx.doi.org/10.17504/protocols.io.errbd56 Copy   

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