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Authors: Luciano Martelotto
Group: Human Cell Atlas Method Development Community
Summary: This protocol is an adaptation and extension of the 'Frankenstein' protocol – originally developed for nuclei isolation from fresh and frozen tissue for snRNA-Seq – in order to perform snATAC-Seq on the same nuclei prep. It has been successfully applied to fresh, snap/flash and cryopreserved frozen cell lines as well as to tissue derived from solid tumours and other tissues such as pancreas adenocarcinoma (PDAC), breast cancers, pheochromocytomas/paragangliomas, normal paraganglia, brain organoids, PDAC organoids, ovary, fallopian tube, mouse brain and sperm using the Chromium Platform (10x Genomics).

Proper citation: Luciano Martelotto 2020. Protocol for nuclei isolation from fresh and frozen tissues for parallel snRNA-Seq and snATAC-Seq on 10x ChromiumTM platform using the same nuclei preparation (UPDATED version). protocols.io https://dx.doi.org/10.17504/protocols.io.bdeni3de Copy   

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Authors: Michelle Altemara
Summary: Zebrafish (Danio rerio) are a popular animal model used in a variety of research areas. As with all animal models, husbandry conditions, including environmental parameters, nutrition, and exposure to pathogens can affect research results. Additionly, zebrafish are tolerant of a wide range of environmental parameters, which has led to wide variation in husbandry practices across facilities around the world. The lack of standard conditions across zebrafish laboratories may play a role in irreproducible experiments. Therefore, a summary of these conditions for the year 2017 have been compiled for the Zebrafish Aquaculture Core (ZAC) facility at the University of North Carolina (UNC) Chapel Hill with the aim to have this data included in research articles published using our fish. As more institutions publish husbandry protocols, standard husbandry practices may emerge.

Proper citation: Michelle Altemara 2019. UNC Chapel Hill Zebrafish Aquaculture Core (ZAC) Environmental Summary. protocols.io https://dx.doi.org/10.17504/protocols.io.3chgit6 Copy   

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Authors: Hari Mohan Saxena, Sugandha Raj
Summary: A protocol for preparing phage lysate of Brucella organisms employing a lytic brucellaphage is given here.

Proper citation: Hari Mohan Saxena, Sugandha Raj 2017. Generation of phage lysates of Brucella using Brucellaphage. protocols.io https://dx.doi.org/10.17504/protocols.io.matc2en Copy   

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Authors: Allen Bennett
Summary: Platelets are the primary cellular mediator of thrombosis. This protocol allows for the preparation of washed human platelets. These platelets can then be stimulated or cultured for various purposes. 

Proper citation: Allen Bennett 2018. Human platelet isolation. protocols.io https://dx.doi.org/10.17504/protocols.io.pymdpu6 Copy   

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Authors: Kirstie Whitaker

Proper citation: Kirstie Whitaker 2017. UCHANGE structural neuroimaging pipeline. protocols.io https://dx.doi.org/10.17504/protocols.io.eu5bey6 Copy   

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Authors: Katherine Santostefano, Jared Taylor, Naohiro Terada, Mark Wallet
Group: Human Islet Research Network, Consortium on Modeling Autoimmune Interactions
Summary: This protocol is a modification of a previously published method by Wilgenburg et al (PLoS One, 2013) to obtain monocytes and macrophages from induced Pluripotent Stem Cells (iPSCs) lines. 

Proper citation: Katherine Santostefano, Jared Taylor, Naohiro Terada, Mark Wallet 2018. The production of monocytes and macrophages from human iPSCs. protocols.io https://dx.doi.org/10.17504/protocols.io.m8kc9uw Copy   

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Authors: Chen Chen, Lilan Hao, Weixia Wei, Fei Li, Liju Song, Xiaowei Zhang, Juanjuan Dai, Zhuye Jie, Jiandong Li, Xiaolei Song, Zirong Wang, Zhe Zhang, Liping Zeng, Hui Du, Huiru Tang, Tao Zhang, Huanming Yang, Jian Wang, Susanne Brix, Karsten Kristiansen, Xun Xu, Ruifang Wu, Huijue Jia
Group: GigaScience Press, BGI
Summary: Human urine is traditionally considered to be sterile, and whether the urine harbours distinct microbial communities has been a matter of debate. Potential links between female urine and reproductive tract microbial communities is currently not clear. Here, we collected urine samples from 147 Chinese women of reproductive age and explored the nature of colonization by 16S rRNA gene amplicon sequencing, quantitative real-time PCR, and live bacteria culture. To demonstrate the utility of this approach, the intra-individual Spearman's correlation was used to explore the relationship between urine and multiple sites of the reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. Streptococcus-dominated, Lactobacillus-dominated, and diverse type were the three most common urinary bacterial community types in the cohort. Detailed comparison of the urinary microbiota with multiple sites of the female reproductive tract microbiota demonstrated that the urinary microbiota were more similar to the microbiota in the cervix and uterine cavity than to those of the vagina in the same women. Our data demonstrate the potential connectivity among microbiota in the female urogenital system and provide insight and resources for exploring diseases of the urethra and genital tract.

Proper citation: Chen Chen, Lilan Hao, Weixia Wei, Fei Li, Liju Song, Xiaowei Zhang, Juanjuan Dai, Zhuye Jie, Jiandong Li, Xiaolei Song, Zirong Wang, Zhe Zhang, Liping Zeng, Hui Du, Huiru Tang, Tao Zhang, Huanming Yang, Jian Wang, Susanne Brix, Karsten Kristiansen, Xun Xu, Ruifang Wu, Huijue Jia 2020. Protocols for "The female urinary microbiota in relation to the reproductive tract microbiota.". protocols.io https://dx.doi.org/10.17504/protocols.io.bp3wmqpe Copy   

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Authors: Ida Barlow
Group: Behavioural Genomics
Summary: This protocol is for obtaining synchronised populations of C. elegans. Eggs are harvested from gravid hermaphrodites and allow to grow to L1 arrest for 12-120 hours (0.5-5days). L1 larvae are then fed and left to develop to the appropriate developmental stage

Proper citation: Ida Barlow 2019. Bleach synchronisation of C. elegans. protocols.io https://dx.doi.org/10.17504/protocols.io.2bzgap6 Copy   

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Authors: Hirotaka Mori, Masahiko Fukatsu, Hiroshi Ohkawara, Yuka Oka, Yuki Kataoka, Shunsuke Taito, Takayuki Ikezoe
Summary: IntroductionThe differential diagnosis of plasmablastic lymphoma (PBL) form plasmablastic myeloma (PBM) is sometime very difficult. In such cases, the diagnosis of plasmablastic neoplasm (PBN) is acceptable. But clinicians face the question whether chemotherapies for PBL, PBM or others are effective for PBN and the question increases the diagnosis dilemma. Although evidence on the differential diagnosis and treatment of those three entities is compiling, there is no scopingreview of different diagnosis and treatment for PBL, PBM, and PBN to answer those questions. The aim of this study is to develop an a priori protocol to undertake a scoping review of the available evidence on the reproducibility of differential diagnosis and the treatment of PBL, PBM, and PBN. Methods and analysisFor the conducting the scoping review protocol, we will use an scoping review methodology established in the Joanna Briggs Institute manual. This methodology has a five-stage approach: (1) identify the research question; (2) identify relevant studies; (3) select studies; (4) chart the data and (5) collating, summarize and report the results. We also will use the Preferred Reporting Items for Systematic Reviews and Meta-Analyses Extension for Scoping Reviews to assess the results.Ethics and disseminationSince this is a review of the literature, ethics approval is not indicated. We will disseminate the findings from this study in publications in peer-reviewed journals.

Proper citation: Hirotaka Mori, Masahiko Fukatsu, Hiroshi Ohkawara, Yuka Oka, Yuki Kataoka, Shunsuke Taito, Takayuki Ikezoe 2020. Diagnosis and treatment of plasmablastic lymphoma, plasmablastic myeloma and plasmablastic neoplasm: protocol for a scoping review. protocols.io https://dx.doi.org/10.17504/protocols.io.beyzjfx6 Copy   

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Authors: Deepak Ravi

Proper citation: Deepak Ravi 2020. Using rhythmic auditory stimuli to modulate resilience to perturbations during walking in healthy young adults. protocols.io https://dx.doi.org/10.17504/protocols.io.bmu3k6yn Copy   

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Authors: Benjamin Bolduc
Group: Sullivan Lab
Summary: Identifying putative viral sequences from SPAdes-assembled data from the Ocean Sampling Day (2014) metagenomic datasets using VirSorter.

Proper citation: Benjamin Bolduc 2016. Identifying Viral Sequences Using VirSorter (Cyverse). protocols.io https://dx.doi.org/10.17504/protocols.io.ev2be8e Copy   

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Authors: Ben Matthews
Summary: This protocol details the steps necessary to generate injection mixes (comprised of plasmid DNA for integration and transposase mRNA) for transposon-mediated integration into Aedes aegypti and other insects. It has been empirically tested in Ae. aegypti embryos with piggyBac transposase. In our hands, using mRNA as a source of transposase instead of a helper plasmid increases transformation rates substantially.

Proper citation: Ben Matthews 2019. Transposase injection mix protocol. protocols.io https://dx.doi.org/10.17504/protocols.io.4a6gshe Copy   

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Authors: Angel Justiz-Vaillant
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. Bone marrow stromal cells and fibroblasts produce IL-11. The IL-11 principal targets are hemopoietic progenitors and osteoclasts. The IL-11 primary effects include osteoclast formation, colony stimulating factor, raised platelet count in vivo, and inhibition of pro-inflammatory cytokine production. [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-11 in human serum.. protocols.io https://dx.doi.org/10.17504/protocols.io.bj3akqie Copy   

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Authors: Sonia García-Ruiz
Group: Ryten Laboratory

Proper citation: Sonia García-Ruiz 2021. How to expose existing R code as a web service. protocols.io https:// Copy   

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Authors: James R. Collins, Krista Longnecker, Helen F. Fredricks, Benjamin A. S. Van Mooy
Group: Van Mooy Lab @ WHOI
Summary: The protocols in this collection were original created by Krista Longnecker and Jamie Collins for creating lipsomes to be used in lipid photo-oxidation experiments. The results of these experiments are detailed in Chapter 4 of:Collins, J. R. 2017. The remineralization of marine organic matter by diverse biological and abiotic processes. Ph.D. thesis. Cambridge, Massachusetts: Massachusetts Institute of Technology, 300 pp; doi:10.1575/1912/8721A manuscript of the chapter is forthcoming.

Proper citation: James R. Collins, Krista Longnecker, Helen F. Fredricks, Benjamin A. S. Van Mooy 2017. Two-step protocol: Preparation and extrusion of phospholipid liposomes. protocols.io https://dx.doi.org/10.17504/protocols.io.haub2ew Copy   

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Authors: Courtney Comrie
Summary: Organization is important in the IPA and MSBIL

Proper citation: Courtney Comrie 2019. Organization for Lab Data using Bash. protocols.io https://dx.doi.org/10.17504/protocols.io.7h4hj8w Copy   

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Authors: Teris Cheung, Paul H. Lee, Paul S.F. Yip
Summary: AbstractBackgroundThis paper describes the association between workplace violence and job satisfaction among physicians and nurses in Macau. It further examines the risk factors for intrinsic and extrinsic job satisfaction among these professionals.MethodsConvenience sampling was sourced from six health centers supervised by the Macau Health Bureau, namely, the Coloane Health Center, Coloane Shek Pai Wan Temporary Health Center, Taipa Elderly Macau University of Science and Technology Hospital, Macau Sino-Portuguese Nurses Association, Macau Association of Medical Volunteers and the Macau Surgical Association. Design: This study uses a cross-sectional self-administrative survey. Instruments: The study used case studies research instruments for workplace violence in the health sector by country (from the ILO, ICN, WHO, PSI) and the Minnesota Satisfaction Questionnaire and Perceived Stress Scale. The data collection period spanned from August to December, 2014. Data analysis: Multiple logistic regression examines levels of intrinsic and extrinsic satisfaction in physicians and nurses and significant correlates affecting their job satisfaction.ResultsA total of 720 (14.9% physicians) participants were recruited. Worry about WPV, on-call duty and shift work, experience of bullying and verbal abuse and employment sector emerged as significant correlates affecting the intrinsic and extrinsic job satisfaction of physicians and nurses. Working on the frontline, being aged 30 to 39, coming from an ethnic minority, and perceived stress were significant correlates affecting nurses’ job satisfaction.ConclusionsWPV remains a significant concern in healthcare settings in Macau. Healthcare professionals should deploy protective strategies to combat the negative psychological effects of WPV. Stakeholders should legally enforce a zero-tolerance policy towards WPV within healthcare workplaces. The perpetrators of WPV should be told that violence will be deemed a violation of human rights and not tolerated, not least on account of how WPV is detrimental to healthcare professionals’ mental wellbeing, risking irreversible physical and psychological harm for its victims.Keywords: Workplace Violence, Physicians, Nurses, Job satisfaction, Occupational health, Macau

Proper citation: Teris Cheung, Paul H. Lee, Paul S.F. Yip 2018. The Association between Workplace Violence and Physicians' and Nurses' Job Satisfaction in Macau. protocols.io https://dx.doi.org/10.17504/protocols.io.tcyeixw Copy   

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Authors: Renata Alitto, Michela Borges, Letícia Dias de Oliveira, Karin Regina Seger, Luciana Bolsoni Lourenço
Summary: Using 16S and COI fragmens in Bayesian Inference, Maximum Parsimony, and Maximum Likelihood.

Proper citation: Renata Alitto, Michela Borges, Letícia Dias de Oliveira, Karin Regina Seger, Luciana Bolsoni Lourenço 2019. Phylogenetic analyses of Ophiothrix (Echinodermata: Ophiuroidea). protocols.io https://dx.doi.org/10.17504/protocols.io.wimfcc6 Copy   

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Authors: Cristian Riccio
Summary: This protocol describes how to extract total RNA from C. elegans worms starting with 3300 worms on a 90mm NGM plate

Proper citation: Cristian Riccio 2019. Extracting total RNA from Caenorhabditis elegans using phase-lock gel separation tubes. protocols.io https://dx.doi.org/10.17504/protocols.io.3pzgmp6 Copy   

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Authors: Hyunsuk Frank Roh, Chang-Guk Kim, Soon-Ho Chon, Jung Mogg Kim
Summary: Purpose:Time-to-event data of hazard ratios were used to generate a forest plot of mortality on extracorporeal membrane oxygenation (ECMO) in respiratory failure in adults.Materials and Methods:A systemic search was conducted in PubMed from 1975 to 2018. Among 4,121 articles, a total of 5 clinical reports comprising 1,014patients (333 of the patients who underwent ECMO and 681 of the patients who did not undergo ECMO) met the inclusion criteria.Results:The pooled hazard ratio of 0.64 (95% confidence interval (CI): 0.54, 0.76) suggests that the ECMO group comprising both veno-arterial (VA) type and a majority of veno-venous (VV) type was significantly associated with a reduction in mortality compared with the non-ECMO group in respiratory failure. The results of VV-ECMO alone also showed significantly improved patient survival of respiratory failure with the hazard ratio of 0.67 (0.56, 0.81).Conclusions:The results of the ECMO group with VV and VA types, or the VV type alone revealed a reduction in mortality for patients with respiratory failure based on time-to-event data.Future investigation of the efficacy of VA-ECMO alone in respiratory failure may be more enlightening.

Proper citation: Hyunsuk Frank Roh, Chang-Guk Kim, Soon-Ho Chon, Jung Mogg Kim 2020. Extracorporeal membrane oxygenation meta-analysis of time-to-event data in respiratory failure in adults. protocols.io https://dx.doi.org/10.17504/protocols.io.bb7nirme Copy   

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