eamag/protocols-with-steps huggingface dataset:
TITLE: DAB Detection of Biocytin Labeled Tissue
AUTHORS: Allen Institute for Brain Science

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the process for diaminobenzidine (DAB) detection of biocytin filled cells.  This protocol is optimized for use with brain slices cut at 350 µm thick, in which cells are first filled with biocytin (i.e., post-electrophysiological recording), fixed in 4% PFA/2.5% glutaraldehyde, and transferred to PBS until ready to stain.</div><div class = "text-block"><span style = "font-weight:bold;">Note</span><span>: 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.</span></div></div>

[STEPS]
TITLE: Growth curve for Chlamydomonas reinhardtii
AUTHORS: Joao Vitor Molino

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocols describe the steps required for obtain a growth curve of </span><span style = "font-style:italic;">Chlamydomonas reinhardtii </span><span>and fluorescent protein expression of mVenus and mCherry. </span></div></div>

[STEPS]
?. [Material   ]
TAP media or other (How to prepare TAP media here)Erlenmeyer flaskOrbital shakerLight source96 well plate, Black Frame, Clear bottom (Ex:  )
?. [Inocullum]
Innoculate  of the cells from a culture in stationary phase ( to )in an  erlenmeyer flask containing  of TAP media.Place the flask in a  with   of incident white light (   to  works)Take a initial sample  and measure it in the plate reader according to the settings above.During   take samples at least once a day. Example of DCW protocol.
1 mL
100 mL
50 mL
25 33
80
60
120
[of culture]
Frequent sampling increase data quality, but it is advice to not remove more than 10% of culture in sampling during the entire procedure. Technical replicates are advice for each time point. All culturing conditions are set initially, and can be change accordingly to the experiment goal.
{"blocks":[{"key":"c8og5","text":"This protocols describe the steps required for dry cell weight measurements using microcentrifugal tubes. ","type":"unstyled","depth":0,"inlineStyleRanges":[],"entityRanges":[],"data":[]}],"entityMap":[]}
?. [Plate reader Settings]
Reading are performed in a Black 96 well plate with clear bottom. Absorbance set to  .Fluorescence set as the Table below.   ABCDE1Excitation (nm)Emission (nm)GainOptics position2Chlorophyll44068070bottom3mVenus500530120bottom4mCherry583613150bottom
750
ABCDE1Excitation (nm)Emission (nm)GainOptics position2Chlorophyll44068070bottom3mVenus500530120bottom4mCherry583613150bottom
TITLE: Terrific broth (TB) medium
AUTHORS: Andreas Sagen

[DESCRIPTION]
IBI’s Terrific Broth is used with Glycerol in cultivating recombinant strains of E. coli. Terrific broth is a highly enriched medium for improving yield in plasmid bearing E. coli. Recombinant strains have an extended growth phase in the medium. The addition of tryptone and yeast extract in the medium will allow higher plasmid yield per volume. Glycerol is used as a carbohydrate source in this formulation. Unlike glucose, glycerol is not fermented to acetic acid.

[BEFORE_START]
Prepare glassware by cleaning it, and ensure that scale is sufficiently calibrated

[GUIDELINES]
Follow step by step, unless stated otherwise. Equipment needed should be standard to a microbiology lab.

[STEPS]
SECTION: 500 mL Terrific broth
1. Create a base solution consistent of Tryptone, Yeast extract, Potassium phosphate monobasic and Potassium phosphate dibasic in a 500 mL Reagent Bottle
SECTION: 500 mL Terrific broth
1.1. Fill the bottle with 300 mL double-distilled water
SECTION: 500 mL Terrific broth
1.2. Measure 11800 mg Yeast extract, 5900 mg Tryptone, 1100 mg Potassium phosphate monobasic and 4700 mg Potassium phosphate dibasic

Powdered compounds:
 
 
 
 
SECTION: 500 mL Terrific broth
1.3. Add powdered solids into bottle, and use a magnetic mixer with a stir bar to mix for 5 min
SECTION: 500 mL Terrific broth
2.2. Add 4 mL Glycerol and mix solution well

Liquid compounds:
 
SECTION: 500 mL Terrific broth
1.5. Autoclave liquid at 121 °C for 15 min
SECTION: 500 mL Terrific broth
1.4. Adjust pH while mixing to pH 7.2 using concentrated sodium hydroxide
SECTION: 500 mL Terrific broth
3.2. Add sterile water to a total of 500 mL
 

SECTION: 500 mL Terrific broth
0.18. 
SECTION: 500 mL Terrific broth
2. Create a carbon solution consistent of glycerol in a 100 mL Reagent Bottle
SECTION: 500 mL Terrific broth
2.1. Fill the bottle with 60 mL double-distilled water
SECTION: 500 mL Terrific broth
2.3. Adjust pH while mixing to pH 7.2 using concentrated sodium hydroxide
SECTION: 500 mL Terrific broth
2.5. Autoclave liquid at 121 °C for 15 min
SECTION: 500 mL Terrific broth
3. After having prepared a base solution and carbon solution, combine the sterile solutions. All steps from this point take place in a LAF bench, to prevent contamination
 

SECTION: 500 mL Terrific broth
2.4. Add double-distilled water to a total of 100 mL
SECTION: 500 mL Terrific broth
3.1. Add 100 mL carbon solution to base solution, and mix well
TITLE: The effects of antibiotics for Helicobacter pylori eradication or dapsone on chronic spontaneous urticaria: A systematic review and meta-analysis (protocol)
AUTHORS: Jun Watanabe, Junya Shimamoto, Kazuhiko Kotani

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Background</span><span>: Chronic spontaneous urticaria (CSU) is a mast cell-driven disease with impaired quality of life. Some drugs, especially antibiotics for</span><span style = "font-style:italic;"> Helicobacter pylori</span><span> (</span><span style = "font-style:italic;">H. pylori</span><span>) eradication and a sulfone antibiotic, dapsone, may be the candidates for treatment at CSU. The purpose of the study will be to assess the efficacy of the antibiotic therapies on CSU.</span></div><div class = "text-block"><span style = "font-weight:bold;">Methods</span><span>: Databases (MEDLINE, the Cochrane Central Register of Controlled Trials, EMBASE, the World Health Organization International Clinical Trials Platform Search Portal and ClinicalTrials.gov) will be searched. Study selection, data abstraction and quality assessment will be independently performed using Grading of Recommendations Assessment, Development and Evaluation approach. The outcomes will be remission of CSU-related symptoms, activities, and adverse events by antibiotics for </span><span style = "font-style:italic;">H. pylori</span><span> eradication or dapsone.</span></div></div>

[STEPS]
TITLE: Radiolabeled spermine uptake in cells
AUTHORS: Stephanie Vrijsen, Marine Houdou, Nathalie Jacobs, Peter Vangheluwe

[DESCRIPTION]
This protocol provides a technique to determine radiolabeled spermine uptake in cells, via the acquisition of counts per minute (CPM) using a Liquid Scintillation Counter. 

[GUIDELINES]
Proper guidelines for working with radiolabeled materials should be followed at all times. 

[STEPS]
1. Cells are seeded in 12-well plates, such that 70-80% confluency is reached on the day of the assay. Seed out 2 'treatment' wells and 1 'background' well per cell line. 


2. Remove the culture medium from all wells.  

4. Incubate 37 °C 30 min 

5. Aspirate the medium. 

6. Wash wells 2x with 1 mL PBS (-/-). 

7. Remove the last wash, then add 200 µl RIPA buffer to the wells. 

8. Incubate 10 min at Room temperature . 


9. Scrape the cells and pipette the lysates into scintillation vials, that are filled with 7 mL of scintillation fluid (Ecolite (+), MP). Rinse each well with 200 µL  PBS (-/-) and pipette into the respective scintillation vial. 

10. Mix scintillation vials well prior acquisition of counts per minute (CPM) in the Liquid Scintillation Counter. 
3. In the treatment wells: add 300 µL of medium, containing 5 µM radiolabeled spermine. 
In the background wells: add 300 µL of medium, containing 5 µM radiolabeled spermine and 100 µM unlabeled (cold) spermine.
TITLE: Whole-body clearing of beetles by successive treatment of hydrogen peroxide and CUBIC reagents
AUTHORS: Monto Kuroda, Shinya Kuroda

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Internal tissues of multicellular organisms cannot directly be seen because they contain pigments. For this reason, whole-body clearing methods have been developed and applied to mammals such as mice. Insects such as beetles, however, cannot be cleared by the mammalian method because of pigments such as melanin in their exoskeletons. In this study, we tried to develop a whole-body clearing method for large beetles. We first bleached the exoskeleton using a hydrogen peroxide treatment, and applied the the advanced Clear, Unobstructed Brain/Body Imaging Cocktails and Computational analysis (CUBIC) reagents to make the internal tissues transparent. The combined method of hydrogen peroxide and the advanced CUBIC allowed us to successfully perform whole-body clearing of the large beetles.</div></div>

[STEPS]
TITLE: Human Pancreas Biopsy Collection, ex vivo
AUTHORS: James Lyon, Patrick MacDonald, Jocelyn Manning Fox

[STEPS]
?. This protocol is associated with Isolation of Human Pancreatic Islets of Langerhans for Research step 7.
?. Label a 15ml conical tube with the internal identifier number (Rxxx) and “biopsy”.
?. Following pancreas perfusion, use surgical scissors to excise a 5mm cubic piece of tissue from the tail of the pancreas.
?. Transfer into a 15ml conical tube using forceps.
?. Add 5ml Z-fix into the conical tube, and cap the tube.
?. Store biopsy tube @4°C.
?. After 24hrs in fixative the biopsy should be transferred into PBS and can be submitted to the Histology Core for processing into paraffin blocks and cut for slide preparation. Record the sample in the Histology Library Record and on REDCap.sample Histology Library Record:  ABCDEFGHIJK1Isolation Number
&nbsp;
2&nbsp;
Pancreas Biopsy
Post-isolation
Pre-distribution
Pre-cryopreservation
Post-cryopreservation
3&nbsp;
Blocks
Slides
Blocks
slides
Blocks
slides
Blocks
slides
Blocks
slides
4R001
1
4
1
4
1
4
1
4
1
4
5R002
1
4
1
4
1
4
1
4
1
4
6R003
1
4
1
4
1
4
1
4
1
4
7R004
1
4
1
4
1
4
1
4
1
4
8R005
1
4
1
4
1
4
1
4
1
4
9R006
1
4
1
4
1
4
1
4
1
4
10R007
1
4
1
4
1
4
1
4
1
4
TITLE: Protocol   Griess Test
AUTHORS: Tamiris Silva, Carolina de Oliveira Rodini, Sandra Kalil Bussadori, Kaline de Brito Sousa, Kristianne Porta Santos Fernandes

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">To assess nitrite levels in individuals with relapsing-remitting multiple sclerosis, the Griess test was performed. A collection of 10 mL of peripheral blood was performed. Nitrite is the only stable end product of nitric oxide self-oxidation in aqueous solution. A high correlation has been established between endogenous NO production and plasma, serum and urine nitrite / nitrate levels. Therefore, the measurement of these levels provides a reliable and quantitative estimate of the nitric oxide output. Serum nitrite levels are measured by reacting the samples with the 96 well microplate Griess reagent. The total nitrite will be analyzed by reacting the samples with 50 μl Griess reagent. Total nitrite is estimated from a standard absorbance curve on a 592 nm reader.</div></div>

[STEPS]
TITLE: Tyler Perry CBD Gummies Review: Steve Harvey CBD Gummies Fake Or Trusted?
AUTHORS: Uly  CBD Gummies

[DESCRIPTION]
Tyler Perry CBD Gummies Review: Steve Harvey CBD Gummies Fake Or Trusted?

[STEPS]
SECTION: Tyler Perry CBD Gummies Review: Steve Harvey CBD Gummies Fake Or Trusted? Kelly Clarkson CBD Gummies- The Purely Concentrated CBD Product to Lose Pains!  Kelly Clarkson CBD Gummies Reviews- The verity that the true wealth we&#x27;ve is our health is known to numerous, but many know the true meaning of it and realize it in the true sense of the word. What causes so important joint pain is sheer negligence, and the causes of common pain are frequently right in front of us and we do ignore them. The right time to heal off pain is moment and does so with the right product.  The verity that the true wealth we&#x27;ve is our health is known to numerous, but many know the true meaning of it and realize it in the true sense of the word. What causes so important joint pain is sheer negligence, and the causes of common pain are frequently right in front of us and we do ignore them. The right time to heal off pain is moment and does so with the right product.  The health mystifications bear mending with the right medium from one right product, and in this case, it&#x27;s just the Kelly Clarkson CBD Gummies. The supplement has been tested, audited, and vindicated and claims to be the stylish among all. You too have the absolute right to live your life in a effortless way and your task is opting the right product right moment with no complacency.  What&#x27;s The all recently Clarkson CBD Gummies pain relief supplement?  These hemp gummies have been precisely finagled and manufactured using advanced technology, incorporating several of the finest sauces and herbal maquillages for deep relief. The medicinal value of each excerpt has been tested and used only after its safety has been impeccably guaranteed. For the FDA to certify this supplement was a robotic thing because the composition is in itself herbal and leaves no room for any dubitation.   Official Website: https://www.outlookindia.com/outlook-spotlight/kelly-clarkson-cbd-gummies-reviews-does-tyler-perry-cbd-gummies-real--news-203904 https://urbanmatter.com/tyler-perry-cbd-gummies-reviews-is-it-fake-or-trusted/ https://urbanmatter.com/ree-drummond-cbd-gummies-reviews-is-martha-maccallum-cbd-gummies-fake/ https://www.homify.in/ideabooks/8852992/tyler-perry-cbd-gummies-review-steve-harvey-cbd-gummies-fake-or-trusted https://tyler-perry-cbd-gummies-review-1.jimdosite.com/ https://educatorpages.com/site/sofo74/pages/tyler-perry-cbd-gummies-review-steve-harvey-cbd-gummies-fake-or-trusted https://promosimple.com/ps/20827/tyler-perry-cbd-gummies-review-steve-harvey-cbd-gummies-fake-or-trusted https://www.pinterest.com/pin/981784787490993211/
1.
TITLE:  Isolation of Salmonella pathogens from oysters
AUTHORS: Sade Aisha Folashade John, Patrick E. Akpaka, Chandrashekhar Unakal, Arvind Kurhade, Angel Justiz-Vaillant

[STEPS]
?. The filtered homogenate was streaked using standardized loops on Salmonella Shigella agar (selective and differential media for Salmonella and Shigella); the loops were flamed periodically to ensure sterility. This was done in duplicate. The plates were then incubated at 34°C. After an overnight incubation at 34°C, the plate with the best significant and adequate colonies was used to test for the presence of Salmonella Those colonies that were morphologically characteristic for Salmonella are gram stained:
?. Each slide was labelled according to location and given a number. A circle using a wax pencil was drawn on the underside of each slide.
?. Drop of sterile saline solution was placed into the circle and using a sterile loop, a single colony from the plate was taken and mixed into it.
?. The smear was allowed to air dry and then heat fixed by holding the slide on one side with a sterile forcep and passing the entire slide through the flame of a Bunsen burner two or three times with the smear side up. Making sure that overheating does occur.
?. The heat fixed slide was placed on a straining tray.
?. The slide was gently flood with crystal violet and left to stand for 1 minute.
?. Using a wash bottle of distilled water, the slide was tipped slightly andmgently rinsed.
?. Then using Gram's iodine, the slide was gently flood and let stand for 1 minute.
?. The slide was tipped slightly and gently rinsed with distilled was using a wash bottle.
?. 95% ethyl alcohol was used to decolorize the smear by for 5-10 seconds.
?. The slide was then immediately rinsed with water.
?. Using Safranin, the slide was gently flood to counterstain and let stand for 45 seconds.
?. The slide was tipped slightly and gently rinsed with distilled was using a wash bottle.
?. The slide was then blot dry ice with bibulous paper.
?. Using a light microscope under oil immersion, the smear was observed to the determine whether the colonies were gram negative or gram positive.
?. This was done per presumptive Salmonella colony observed on each plate.
?. A single colony of presumptive Salmonella was then subcultured on SS agar and incubated at 34°C to purify the culture. A single colony was later gram stained prior to biochemical testing in order to ensure the culture's purity. The pure single colonies were further analysed via biochemical tests (Indole, Citrate, Urease, Motility and Triple Sugar Iron Agar) together with a control Salmonella colony taken from the laboratory in order to make a comparison. A single colony of the organism was then saved in a cryovial containing Nutrient Agar at-70 °C. This was done per Salmonella spp. isolate found.
TITLE: PCR Prep from Glycerol Stock for IVT Reactions
AUTHORS: Allen Institute for Brain Science

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol is used for the PCR reaction from clone templates in glycerol stocks generating transcript templates ready for IVT reaction.</div><div class = "text-block"><span style = "font-weight:bold;">Note</span><span>: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number 1U19MH114830-01. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health</span></div></div>

[STEPS]
TITLE: transformation of E.coli DH5α with plasmid DNA
AUTHORS: iGEM Dusseldorf

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">common transformation of E.coli DH5α with plasmid DNA</div></div>

[STEPS]
?. thaw competent cells on ice
?. add 1 µl plasmid DNA to cells
?. incubate cells on ice
?. cool on ice
?. add 700 µl LB  without antibiotics to the cells
?. incubate at 37°C (with shaking)
?. plate 100 µl on antibiotic plates with Drigalski spatula
?. incubate over night at 37°C
?. heat shock cells at 42°C
TITLE: The methodological quality of physical therapy articles published in open access and subscription journals: A cross-sectional meta-epidemiological study
AUTHORS: Takashi Ariie, Yusuke Tsutsumi, Shunsuke Taito

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Objective:</div><div class = "text-block">The aim of this meta-epidemiological study will be to compare the methodological quality of randomized clinical trials  published in subscription based journals with those published in open access journals in the field of physical therapy.</div><div class = "text-block">Methods:</div><div class = "text-block">We will include randomized controlled trials. We will use the PEDro database to identify relevant physical therapy trials published in subscription based journals and open access journals. We will search the database in May 2021. </div><div class = "text-block">We will exclude trials awaiting for rating PEDro score. We will use following variables; the name of journals, the name of the first author, PEDro score, publication year, publication language, endorsement of consolidated standards of reporting trials, intervention types, subdiscipline, types of publication and the impact factor. We will use descriptive statistics to summarize data. Variables will be compared using unpaired t tests, chi-squared test and multivariable analysis as appropriate. Two-tailed p values will be considered statistically significant if less than 0.05.</div></div>

[STEPS]
TITLE: Tissue perfusion parameter-guided initial resuscitation in adult patients with sepsis or septic shock: A systematic review and network meta-analysis
AUTHORS: Tomoki Kuribara, Tetsuya Yumoto, Kohei Yamada, Takehito Sato, Shigeru Koba, Kenichi Tetsuhara, Masahiro Kashiura, Masaaki  Sakuraya,MD, MPH

[DESCRIPTION]
Background: Hemodynamic management is crucial in treating patients with sepsis or septic shock. To date, several tissue perfusion parameters have been suggested, however; the optimal parameter is not well defined.

Objective: This study aims to examine whether and which tissue perfusion parameter-guided therapy during initial resuscitation in adult patients with sepsis or septic shock improved patients’ outcomes. 

Design: Systematic review and network meta-analysis.

Data sources: We will search the following electronic bibliographic databases: Cochrane Central Register of Controlled Trials (CENTRAL) in the Cochrane Library, MEDLINE via PubMed, Web of Science, and Igaku-Chuo-Zasshi. We will also search the World Health Organization International Clinical Trials platforms Search Portal (ICTRP) and ClinicalTrials.gov. for ongoing trials. There will be no language restriction.

Analysis: We will have two types of meta-analysis planned. First, direct pairwise meta-analysis will be conducted using random effect models. Second, network comparison meta-analysis will be conducted using a frequentist approach with multivariate random effect meta-analysis.

[STEPS]
TITLE: Neural rosette banking
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh

[STEPS]
?. Make 2x stock of serum-free neural freezing medium by adding of sterile DMSO to  of sterile KOSR into a 50 ml conical tube. Mix by inverting 3-4 times. Store at for up to 4 weeks.
10 ml
40 ml
?. Aspirate supernatant from 15mL conical tube containing 1 well of neural rosette clusters. See protocol below.
?. Add of neural induction media supplemented with of 2x neural freezing medium to the single well collection of neural rosette clusters. Gently mix solution and distribute 1 mL into sterile cryovials.
1 ml
1 ml
?. Store cryovials at  for at least  then transfer to liquid nitrogen for long-term storage.