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Authors: Olivier George, Lieselot Carrette, Francisco Ramirez
Group: George Lab

Proper citation: Olivier George, Lieselot Carrette, Francisco Ramirez 2021. Western for Brain Punches. protocols.io https:// Copy   

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Authors: Juanita Hoe, Gill Livingston, Sergi Costafreda, Nomi Weberloff, Gianluca Biao, Helen Souris, Emily van de Pol
Summary: Around 850 000 people live with dementia in the UK and this is expected to almost triple by 2050, due to the welcome reduction in premature mortality. Approximately 70% of people with dementia live at home and are supported mainly by their families, but because of complex needs, including comorbid physical illness, they also use both health and social care service. A policy priority is to find the best ways to help people with dementia to live well at home. .justify:after { content: ""; display:inline-block; width: 100%; } Part of the initial assessment of all people with dementia is to evaluate and manage risk, to enable people with dementia to live safely and well at home. As cognition deteriorates, people with dementia become vulnerable through self-neglect, accidents and greater risk of abuse and exploitation. Society places a high ethical value on autonomy. Trying to avoid risk altogether can lead to excessive restrictions. Therefore, risk management must balance the rights of a person with dementia with those of society and families’ usually beneficent wishes to reduce risks. Risk enablement aims to find the right balance by protecting autonomy as much as possible. However, there is no validated tool available to assess or manage and re-assess risk in dementia to enable this to happen consistently and to allow evaluation of risk enablement. The Islington Dementia Navigator Risk Assessment Tool is used to generate a plan for people with dementia and stratifies the level of risk to inform frequency and method of follow-up. We intend to evaluate its validity, the feasibility of the risk management plans derived from it, their acceptability and outline costs. .justify:after { content: ""; display:inline-block; width: 100%; } We will examine .justify:after { content: ""; display:inline-block; width: 100%; } Validity - How well the tool identifies risks (compared to gold standard semi-structured clinical assessments) Feasibility - Whether the plan derived after using the tool is implemented over the subsequent 6 months. Acceptability - What people with dementia, family carers and workers think of the process and how it can be improved? We aim to provide a validated, valuable tool for use by professional and support staff working with people with dementia throughout the UK. If shown to be effective in practice, it would promote positive risk enablement, offering a tailored approach to the management of risk and support person-centred care in people with dementia living at home. This is consistent with best practice and is relatively inexpensive and translatable to wider clinical settings. .justify:after { content: ""; display:inline-block; width: 100%; } .justify:after { content: ""; display:inline-block; width: 100%; }

Proper citation: Juanita Hoe, Gill Livingston, Sergi Costafreda, Nomi Weberloff, Gianluca Biao, Helen Souris, Emily van de Pol 2019. Risk Assessment and Increasing Safety in Dementia – RAISe-Dementia study. protocols.io https://dx.doi.org/10.17504/protocols.io.2uzgex6 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. B lymphocytes mainly produce IL-39. It acts on neutrophils inducing their differentiation or expansion. [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-39 in human serum.. protocols.io https://dx.doi.org/10.17504/protocols.io.bj4ekqte Copy   

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Authors: Jason Kim
Group: Mouse Metabolic Phenotyping Centers
Summary: This experiment provides the quantification of multiple cytokines and chemokines using multiplexed-Luminex technology based on beads containing specific antibodies. Serum cytokine levels reflect chronic or acute inflammation, and circulating cytokines and chemokines are altered in obesity. Cytokines Panel I include IL-1α, IL-1β, IL-2, IL-3, IL-4, IL-5, IL-6, IL-7, KC (IL-8 homologue), IL-9, IL-10 (interleukin-10), IL-12 (p40), IL-12 (p70), IL-13, IL-15, IL-17A, TNFα (tumor necrosis factor alpha), IFNγ (interferon gamma), IP-10 (interferon gamma-induced protein 10; CXCL-10), Eotaxin (CCL-11), G-CSF (granulocyte colony stimulating factor), GM-CSF (granulocyte macrophage colony stimulating factor), LIF (leukemia inhibitory factor), LIX (LPSinduced CXC chemokine), MCP-1 (monocyte chemotactic protein-1; CCL-2), M-CSF (macrophage colony stimulating factor), MIG (monokine induced by gamma interferon; CXCL9), MIP-1α (macrophage inflammatory protein alpha; CCL-3), MIP-1β (macrophage inflammatory protein beta; CCL-4), and MIP-2/RANTES (macrophage inflammatory protein 2alpha; CXCL-2). A service can be requested for all or any combination of listed cytokines/chemokines for customized multiplexed Luminex assay.

Proper citation: Jason Kim 2019. U Mass - Gamma-glutamyl Transferase. protocols.io https://dx.doi.org/10.17504/protocols.io.xwzfpf6 Copy   

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Authors: John Stack, Gary Cline
Group: Mouse Metabolic Phenotyping Centers
Summary: Procedure used to determine the concentration of magnesium in blood, serum, and plasma. Magnesium is measured as the chlorophosphonazo III complex (addition of EGTA prevents calcium interference) and monitored at 600 nm.

Proper citation: John Stack, Gary Cline 2019. Yale - Magnesium. protocols.io https://dx.doi.org/10.17504/protocols.io.y3zfyp6 Copy   

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Authors: Angel Justiz-Vaillant, Norma McFarlane-Anderson
Group: University of the West Indies, [email protected]

Proper citation: Angel Justiz-Vaillant, Norma McFarlane-Anderson 2020. Universal sandwich enzyme linked immunosorbent assay for investigating Staphylococcal protein-A (SpA) interactions with immunoglobulins using a SpLG-HRP conjugate.. protocols.io https://dx.doi.org/10.17504/protocols.io.bjpwkmpe Copy   

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Authors: Josh Quick
Group: ARTIC, Coronavirus Method Development Community, COG-UK
Summary: ARTIC amplicon sequencing protocol for MinION for nCoV-2019

Proper citation: Josh Quick 2020. nCoV-2019 sequencing protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bbmuik6w Copy   

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Authors: New England Biolabs
Summary: This is the protocol for the Q5® Site-Directed Mutagenesis Kit (E0554)

Proper citation: New England Biolabs 2020. Q5® Site-Directed Mutagenesis (E0554). protocols.io https://dx.doi.org/10.17504/protocols.io.besrjed6 Copy   

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Authors: David S. Booth, Heather Middleton, and Nicole King
Group: King Lab, Protist Research to Optimize Tools in Genetics (PROT-G)
Summary: This collection of protocols describes the preparation of reagents for transfecting DNA into the choanoflagellate Salpingoeca rosetta using a Nucleofector 4d Device and SF kit from Lonza. Plasmids that use S. rosetta promoters and regulatory elements to drive the expression of luciferase and fluorescent protein reporters are being deposited at Addgene. Acknowlegements: Arielle Woznica and Laura Wetzel for meticulous editing of protocol and clarifying steps in the procedure. The Gordon and Betty Moore Foundation for supporting this research.

Proper citation: David S. Booth, Heather Middleton, and Nicole King 2018. Transfection of Salpingoeca rosetta. protocols.io https://dx.doi.org/10.17504/protocols.io.h8bb9sn Copy   

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Authors: Salvatore D Morgera, Tiffany Miller, Arash Takshi, Stephen E Saddow, Matthew Palm
Group: Coronavirus Method Development Community, Front Line Technologies
Summary: The magnitude of how rapidly the COVID-19 virus could spread and infect others facilitated the need for a rapid COVID-19 test, accessible and affordable for both children and adults worldwide. As a result, an infected patient can quickly quarantine and isolate to slow the spread. Our research group has determined VOCs associated with COVID-19 and has built a prototype gas analysis system similar to a breathalyzer for detecting gasses of COVID-19. Some of the symptoms like headaches, coughing, and diarrhea result in an inflammatory response to create a unique variety of gasses like acetone, hydrogen, and carbon monoxide that can be detected when they are exhaled through a person’s breath. A sample of a person’s breath is first collected in a chamber when a patient breaths into the valve, the gas sensors then detect a voltage change when they contact a COVID-19 target gas. The concentration in parts-per-million is calculated based on the non-linear resistance ratio of the target gas and clean air. Log-based scale calculations and post-data processing calibrate the sensors to increase the accuracy and selectivity. Finally, the voltages and PPM of the target gas concentration data is stored in a computer database and sensor coding reveals the resulting breath pattern signature of COVID-19. At just under $15.00 United States Dollars (USD), test results are just a breath away, within seconds of taking the test and even before leaving the doctor’s office. Although, this system may also be modified to sniff out other pathogens of disease, spoiled meats, and ripened fruit, we are dedicated to build a gas sensor platform for low cost, noninvasive, and rapid detection of the breath pattern signature of COVID-19, in an attempt to slow the spread of the global health threat of infection and in turn to help save lives.Breath analysis systems serve as a noninvasive means for disease screening. Our objective is to utilize this prototype to obtain a database of H2, CO, NO, Acetone and Alcohol concentrations, whereby, COVID patient breath samples are compared to healthy individual breath samples using our breath analysis system prototype. This system is configured for measuring the aforementioned gas concentrations in ppm and recording the data to a text file in a computer database for subsequent analysis. The data obtained from this study is critical to the development of this system.

Proper citation: Salvatore D Morgera, Tiffany Miller, Arash Takshi, Stephen E Saddow, Matthew Palm 2020. Breath Analysis System for Detecting Breath Pattern Signature of COVID-19 . protocols.io https://dx.doi.org/10.17504/protocols.io.bpcqmivw Copy   

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Authors: Lenny Teytelman, protocols.io team, Anita Broellochs
Group: protocols.io news, protocols.io Ambassadors
Summary: protocols.io offers extensive flexibility in entering and presenting detailed methods. However, simple suggestions in here can help to make your protocol more useful to you and others. Importantly, easy steps outlined here can greatly increase the visibility of your protocol and ensure that scientists who need can find it.If you have any questions, please feel free to reach out to the protocols.io team by e-mailing us at  info [at] protocols.io. 

Proper citation: Lenny Teytelman, protocols.io team, Anita Broellochs 2020. How to make your protocol more reproducible, discoverable, and user-friendly. protocols.io https://dx.doi.org/10.17504/protocols.io.bnknmcve Copy   

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Authors: Omar Valencia
Summary: PCO plot based on gobies fish incidence data. All marine ecoregions and provinces were grouped sensu Spalding et al. (2007). Jaccard similarity was used as a resemblance measure of species composition.

Proper citation: Omar Valencia 2018. Gamma-diversity partitioning of gobiid fishes (Teleostei: Gobiidae) ensemble along of Eastern Tropical Pacific: biological inventory, latitudinal variation and species turnover. protocols.io https://dx.doi.org/10.17504/protocols.io.sbceaiw Copy   

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Authors: Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wenwei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhaopeng Yang, Feng Mu, Shangxian Gao
Group: BGI, GigaScience Press

Proper citation: Jie Huang, Xinming Liang, Yuankai Xuan, Chunyu Geng, Yuxiang Li, Haorong Lu, Shoufang Qu, Xianglin Mei, Hongbo Chen, Ting Yu, Nan Sun, Junhua Rao, Jiahao Wang, Wenwei Zhang, Ying Chen, Sha Liao, Hui Jiang, Xin Liu, Zhaopeng Yang, Feng Mu, Shangxian Gao 2020. BGISEQ-500 Sequencing. protocols.io https:// Copy   

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Authors: Jorge Machado Alba, Luis Valladales, Yadira Parrado
Summary: Introduction: Biotech drugs open new possibilities to treat diseases for which drug therapy is limited, but they may be associated with serious adverse drug reactions (ADRs). The objective was to identify the ADRs associated with the use of biotech drugs in Colombia. .justify:after { content: ""; display:inline-block; width: 100%; } Methods: This was a retrospective study of ADR reports from 2014 to 2019, contained in the database of the pharmacovigilance program of Audifarma SA. The ADRs, groups of associated drugs and affected organs were classified. .justify:after { content: ""; display:inline-block; width: 100%; } Results: A total of 5,415 reports of ADRs associated with biotech drugs were identified in 78 Colombian cities. A total of 76.1% of the cases corresponded to women. The majority were classified as type A (55.0%) and B (28.9%), and 16.7% were serious cases. The respiratory tract was the most commonly affected organ system (16.8%), followed by the skin and adnexa (15.6%). Antineoplastic and immunomodulatory drugs accounted for 70.6% of the reports, and the drugs related to the greatest number of ADRs were adalimumab (12.2%) and etanercept (11.6%). .justify:after { content: ""; display:inline-block; width: 100%; } Conclusions: There has been an incremental increase in the reporting of ADRs associated with the use of biotech drugs in the pharmacovigilance program, related to the strengthening and appropriation of the patient safety culture and improvement in the quality of the generated information. It is important to empower physicians and entire health teams to ensure the traceability of ADRs and to perform interdisciplinary interventions derived from pharmacovigilance at the individual and population levels. .justify:after { content: ""; display:inline-block; width: 100%; }

Proper citation: Jorge Machado Alba, Luis Valladales, Yadira Parrado 2020. Adverse drug reactions associated with the use of biological agents. protocols.io https://dx.doi.org/10.17504/protocols.io.bkcfkstn 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.grgbv3w Copy   

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Authors: Matthew Sullivan
Group: VERVE Net, Sullivan Lab
Summary: The usefulness of cesium chloride (CsCl) step gradients and continuous gradients for the separation of viruses is based on the differing buoyant densities of viruses, bacteria, and extracellular debris. This protocol provides a method for Cesium Chloride and DNA Extraction for Viruses (See guidelines for DNA Extraction).

Proper citation: Matthew Sullivan 2016. Cesium Chloride Gradients. protocols.io https://dx.doi.org/10.17504/protocols.io.c7dzi5 Copy   

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Authors: Bao Thai
Group: Stephen Floor Lab

Proper citation: Bao Thai 2019. Cas9/sgRNA ribonucleoprotein nucleofection using Lonza 4D nucleofector with lower amount of RNP (final best version-tested). protocols.io https://dx.doi.org/10.17504/protocols.io.2ijgccn Copy   

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Authors: Max Marrone
Group: Coronavirus Method Development Community, Opentrons COVID-19 Testing

Proper citation: Max Marrone 2020. Opentrons COVID-19 testing (Zymo, station B, 48 samples). protocols.io https://dx.doi.org/10.17504/protocols.io.bestjeen Copy   

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Authors: Monica Accerbi, Vinay K Nagarajan, Kathryn Coyne, Pamela J Green
Summary: This protocol was developed for isolating high quality genomic DNA from Heterosigma akashiwo for the purpose of Next generation sequencing technologies. We successfully repeated this protocol to obtain genomic DNA.  

Proper citation: Monica Accerbi, Vinay K Nagarajan, Kathryn Coyne, Pamela J Green 2017. Modified genomic DNA extraction method for Heterosigma akashiwo. protocols.io https://dx.doi.org/10.17504/protocols.io.himb4c6 Copy   

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Authors: Adolfo Maria Tambella, Stefano Martin, Luca Omini, Cecilia Vullo, Anna Rita Attili
Summary: This protocol describes a validation procedure to assess the diagnostic accuracy of a radiographic method using a simple device, specifically designed to quantify the cranial tibial translation in dogs. .justify:after { content: ""; display:inline-block; width: 100%; } This protocol was used in the following publication: .justify:after { content: ""; display:inline-block; width: 100%; } https://doi.org/10.1371/journal.pone.0228621 .justify:after { content: ""; display:inline-block; width: 100%; } Tambella AM, Omini L, Attili AR, Vullo C, Martin S (2020) Evaluation of cranial tibial translation in dogs: Diagnostic accuracy of radiographic method using a simple device. PLoS ONE 15(2): e0228621. (ISSN: 1932-6203) (DOI: 10.1371/journal.pone.0228621) .justify:after { content: ""; display:inline-block; width: 100%; }

Proper citation: Adolfo Maria Tambella, Stefano Martin, Luca Omini, Cecilia Vullo, Anna Rita Attili 2020. Diagnostic accuracy of a radiographic device to assess cranial tibial translation in dogs: validation protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.bdczi2x6 Copy   

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