eamag/protocols-with-steps huggingface dataset:
TITLE: How does long term exposure to low levels of radiation affect prenatal health in the Marshall Islands?
AUTHORS: slicata

[DESCRIPTION]
The purpose of this research proposal is to investigate the public health issues inflicted on women and children following the period of nuclear testing in French Polynesia, specifically in communities descending from victims of direct impact in the Marshall Islands. This research may give insight into the intergenerational transmission of potential health defects resulting from nuclear exposure, which may aid in creating a humanitarian solution to such a health crisis. 
Through a multi-method approach involving the analysis of health history and engagement with the Marshall Island residents, this research aims to understand the modern implications of radiation exposure on prenatal and reproductive health.


[BEFORE_START]
Prepare a data extraction template for health and birth records to report information and occurrences of reproductive health complications, prenatal health complications, and birth defects for the quantitative portion of this study. Prepare a guided interview question sheet for the qualitative portion of this study. 

[GUIDELINES]
The information involved in this study is highly personal to the individual. It is important to respect the sensitivities of the participant and share all data and outcomes while observing participant confidentiality. 

[STEPS]
SECTION: Quantitative Data Collection
1. Obtain birth and health records from individuals living and originating from Northern Marshallese populations (study group) in the Kwajalein Atoll, Enewetak Atoll, Utrik Atoll, Roungelap Atoll, and Bikini Atoll beginning in 1980.
SECTION: Quantitative Data Collection
2. Obtain birth and health records from individuals living and originating in Southern Marshallese populations (control group) in the Majuro Atoll beginning in 1980.
SECTION: Quantitative Data Collection
3. Consolidate health file pool by searching for key words related to prenatal health, birth defects, and reproductive health.
SECTION: Quantitative Data Collection
4. Extract information based on the data extraction template in the relevant pool of study files. 
SECTION: Quantitative Data Analysis
5. Calculate summary statistics for each group.
SECTION: Quantitative Data Analysis
6. Compare statistics and conduct a T test. 
SECTION: Quantitative Data Analysis
7. Present data in a table with T-values. 
SECTION: Qualitative Data Collection
8. Partner with the World Health Organization and Community Health Councils in the Marshall Islands to engage with local health centers and communities in the Kwajalein Atolls, Utrik Atolls, Enewetak Atolls (in the North) and the Majuro Atoll (in the South).
SECTION: Qualitative Data Collection
9. Visit each health center and connect with individuals willing to engage in this research. Use the guided interview sheet to lead conversations around their experiences and observations. 
SECTION: Qualitative Data Analysis
10. Create a write up of reports to supplement the quantitative data.
TITLE: Pure CBD Gummies Dr OZ
AUTHORS: health 

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Official Website@>> </span><a href="https://timesofcbd24x7.com/pure-cbd-gummies-dr-oz" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-weight:bold;">https://timesofcbd24x7.com/pure-cbd-gummies-dr-oz/</span></a></div><br/><div class = "text-block"><a href="https://timesofcbd24x7.com/pure-cbd-gummies-dr-oz" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-weight:bold;">Pure CBD Gummies Dr OZ</span></a><span style = ":;font-weight:bold;">:</span><span> Take a wreck from the quest and pay attention this guide first.Cannabidiol (CBD) has end up a famous alternative to prescription drugs. It is likewise the number one promoting natural complement detail in 2019, topping turmeric, elderberry and wheatgrass. With the quantity of a fulfillment instances in treating joint and irritation-associated worries, restlessness and anxiety increasing by the usage of the second, it comes of no surprise that one’s curiosity about CBD-rich hashish oil will were inspired.</span></div><br/><div class = "text-block"><span style = "font-weight:bold;">Facebook Page@>> </span><a href="https://www.facebook.com/Pure-CBD-Gummies-Dr-OZ-107426194960653" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-weight:bold;">https://www.facebook.com/Pure-CBD-Gummies-Dr-OZ-107426194960653</span></a></div><br/><div class = "text-block"><span style = "font-weight:bold;">Facebook Page@>> </span><a href="https://www.facebook.com/Pure-CBD-Gummies-Dr-OZ-110114441354479" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;font-weight:bold;">https://www.facebook.com/Pure-CBD-Gummies-Dr-OZ-110114441354479</span></a></div></div>

[STEPS]
TITLE: Effectiveness of rehabilitation for osteoarthritis of the knee associated with isolated meniscus injury: a scoping review protocol V2
AUTHORS: Masateru  Hayashi, Shusaku Koga, Takashi  Kitagawa

[DESCRIPTION]
⮚ Objective: The purpose of this scoping review is to examine whether there are differences in rehabilitation according to the degree of damage to the isolated medial and lateral meniscus and to determine whether it is of value to conduct a systematic review in the future.
⮚ Introduction: The prevalence of meniscus injuries in middle-aged and elderly people (>50 years) is 31%, and they occur more frequently in medial meniscus injuries than in lateral meniscus injuries (28%＞12%). The treatment of meniscus injuries consists of conservative therapy and surgery, and the benefit of combining surgery with rehabilitation has become clear. However, the effectiveness of rehabilitation alone, according to the degree of isolated meniscus injury, has not been clarified.
⮚ Eligibility criteria: The review will be a scoping review of the effectiveness of rehabilitation for osteoarthritis of the knee with unilateral or bilateral isolated meniscus injuries in patients over 40 years of age. Outcomes will be pain, function, and re-injury. All types of research will be accepted without restrictions as to location, race, gender, or language of the original article. ⮚ Methods: A systematic search of PubMed, Cumulative Index to Nursing and Allied Health Literature (CINAHL), Web of Science, and Physiotherapy Evidence Database (PEDro) databases using the keywords "meniscus" and "physical therapy" will be conducted during September 2021. In addition, we will not limit the language of the search, in order to include all studies.
Data extraction tools will be used to specifically show findings in extracted articles related to participants, concepts, context, research design, and review questions. Outcomes should be pain, function, and re-injury, and results should be specified for each outcome.

[STEPS]
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>1. Draw a circle (c1).</p>
<p>2. Within that circle, about a third of the way from the top draw two points.</p>
<p>3. Another third of the way draw a semicircle (starting at the top and curving down, then back up).</p>
<p>4. from the bottom of the circle extend a line (L1) down, roughly twice the diameter of circle C1.</p>
<p>5. from the center of line L1, draw two lines extending up, at roughly 45 degrees from each other and centered on the orginal line.</p>
<p>6. from the end of line L1, draw two lines again with roughly 45 degrees between them, centered on the original line.</p>
<p>7. next to the right bottom line, draw another circle C2 (similar size to  circle C1).</p>
<p>8. Within this circle draw 4 pentagons, one near the top, one near the bottom, one near the left, and one near the right, having them almost touch each other.</p>
<p>9. Shade in these pentagons.</p>
<p>10. further to the right draw a line (L2) (parallel to the L1, starting at the same height as circle C1 and ending at the same bottom point as the circle C2.</p>
<p>11. from the bottom of line L2, draw a perpendicular line (L3) to the right, about 1/2 the length of L2</p>
<p>12. Connect the top of L2 with the end of line L3 with an arc.</p>
<p>13. Add some medium cross hatching to this shape. (cross hatching is perpendicular lines that fill the interior of the shape).</p>

[STEPS]
TITLE: General Microtome Sectioning of Formalin-Fixed Paraffin Embedded (FFPE) blocks
AUTHORS: Toby J Curless, Zane Jaunmuktane

[DESCRIPTION]
This protocol describes the steps for the sectioning of formalin-fixed paraffin embedded blocks in preparation for further tissue processing such as immunohistochemistry.

[BEFORE_START]
Check all equipment, supplies and consumables
Set-up water bath to required temperature
Ensure blade is fit-for-purpose and clean
Label/barcode SuperFrost Plus slides

[STEPS]
SECTION: Preparation
1. Check all equipment, consumables and supplies are in place.
SECTION: Sectioning
5. Once both block and water are at the correct temperature, insert the block into the chuck of the microtome.
SECTION: Sectioning
6. Adjust the levers on the microtome to position the face of the block parallel with the blade.


SECTION: Preparation
2. Place a clean blade into the blade holder of the microtome.
SECTION: Preparation
3. Place the FFPE block onto ice, with the face of the block on the surface of the on ice until the block is cold through.

SECTION: Preparation
4. Heat 1 L distilled H2O to40 °C in a water bath.

SECTION: Sectioning
7. Lower the block until it is level with the blade and move the block closer to the blade using the handle on the microtome.
SECTION: Sectioning
8. Select the thickness of choice on the microtome (usually  .

SECTION: Sectioning
9. Section and trim into the block until the whole tissue cross-section is present in the sections.
SECTION: Sectioning
10. Using tweezers or a fine paintbrush, gently pull sections down until a ribbon of tissue sections has formed. 

SECTION: Sectioning
11. Pick up the ribbon with tweezers and place into the water bath to allow wrinkles to disappear from the tissue.  

SECTION: Sectioning
12. Separate sections using tweezers and collect individual sections on SuperFrostTM charged microscope slides.
SECTION: Sectioning
13. Allow slides to drain and air dry vertically at Room temperature for > 720 min prior to further processing.
TITLE: Western Blot Analysis
AUTHORS: michela.deleidi, Federico   Bertoli

[DESCRIPTION]
Western blot protocol

[STEPS]
1. Wash cells 1X in PBS.
2. Detach cells using Accutase for 5 minutes at 37°C and collect them.
3. Spin cells in a centrifuge at 250g for 5 minutes at room temperature.
4.  Remove the supernatant.
5. Lyse cells in 1% TBS + 0.5% NP40 + PI/PHI (Pierce #A32959).
6. Determine protein concentration was determined using the Pierce BCA Protein Assay Kit (Thermo Fisher Scientific).
7. Dilute samples in 6x Laemmli buffer containing 12.5% β-mercaptoethanol.
8. Boil samples 5 minutes at 95°C in a thermoblocker.
9. Load protein in a self-casted 7.5-15% acrylamide gel or in precast NuPage 4-12% Bis-Tris Protein gel.
10. Run gel at 100V for 30min-2h.
11. Transfer proteins to PDVF membrane via wet transfer (20% methanol) overnight at 20V at 4°C.
12. Block membrane in TBS 0.1% Tween containing 5% milk or 5% bovine serum albumin.
13. Incubate primary or secondary antibodies in 5% Roche Block solution or 5% BSA in TBS-T supplemented with 0.04% sodium azide.
TITLE: Plasmid Isolation: Miniprep (Protocol for GeneJET Plasmid Miniprep Kit)
AUTHORS: Alba Balletbó

[STEPS]
?. Centrifuge overnight culture at 4700rpm for 5 minutes and discard the supernatant.
?. Add 250 µL Resuspension solution and resuspend the cells in this. Transfer the mix to an Eppendorf tube.
?. Add 250 µL Lysis solution and invert the tube 4-6 times.
?. Add 350 µL Neutralization solution and invert the tube 4-6 times.
?. Centrifuge for 5 minutes and transfer the supernatant to a GeneJET spin column tube.
?. Centrifuge for 1 minute. Empty the flowthrough and place the column back in the collection tube.
?. Add 500 µL Wash buffer and centrifuge for 1 minute. Discard the flowthrough and place the column back.
?. Repeat step 7.
?. Centrifuge for an additional minute to remove all residual ethanol. Place the column in a fresh Eppendorf.
?. Add 25-50 µL of either Elution buffer or MilliQ to the column and incubate at room temperature for 1 minute.
?. Centrifuge the column for 1 minute.
?. Discard the column and store the purified DNA in -20ºC.
TITLE: Chelex DNA isolation for quick plant genotyping
AUTHORS: Magdalena Julkowska

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Quick and dirty, but very very fast protocol for DNA isolation. It works beautifully if you have plenty of lines to genotype - example T-DNA insertion lines for validation of your favourite gene. </div></div>

[STEPS]
?. Grind tissue in liquid N2 (1 leaf should be enough)If you collect the tissue in a tube containing glass beads (1-2 mm diameter) you can put the frozen tissue samples in the tissue grinder. This is by far the most efficient method to gind large quantities of various samples.
?. Add 200μl 10% Chelex (in MilliQ)
?. Vortex
?. Incubate 15min @ 95 degrees in shaker
?. Vortex
?. Spin 15min @ max RPM
?. Use (2μl) supernatant for PCR (optional: transfer supernatant to fresh tube for storage at -20C)
?. [Genotyping PCR (DreamTaq)]
step 1 94 degrees 4minstep 2  94 degrees 45s step 3 50 degrees 45s (try higher temp for more specificity) step 4 72 degrees 1:20min (depending on size insert)step 5 repeat 35x step 3step 6 72 degrees 10min step 7 16 degrees 10min
?. [Run the gel]
Run 20uL of the PCR product on the 1% agarose gel
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Protocol for heatshock transforming E.coli competent cells, from strains such as DH5-alpha. These can be made competent in-house or bought from various suppliers.</p>
<p> </p>
<p>Transformations are essential to using the DNA Distribution Kits: resuspend the DNA sample in a well, transform the DNA into competent cells, and select single colonies. However, transformations can also be one of the more fickle laboratory techniques.</p>
<p> </p>
<p>Read through the entire protocol before starting!</p>
<p> </p>
<p>If you have issues with transformations, read through the Troubleshooting page for help.</p>
<p> </p>
<p> </p>
<p>(adapted from http://parts.igem.org/Help:Protocols/Transformation)</p>

[STEPS]
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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This protocol decribes how to make 1 L of Luria-Bertani agar (also known as LB agar) for the culturing of bacteria on plates. </p>

[GUIDELINES]
<p>1 L of LB agar makes ~20 plates. </p>
<p>At 4 °C unused plates can be stored for around 2 weeks prior to use.</p>
<p>Once used, LB agar plates containing bacterial colonies can be stored in air-tight container/bag at 4 °C for a maximum of 2 weeks.</p>
<p>Prior to disposal, plates containing bacterial colonies must be wrapped in Parafilm and autoclaved.</p>

[STEPS]
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?.
TITLE: Oceanit Lateral Flow Assay (LFA) Protocol
AUTHORS: proposals , Dexter Poon

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This experiment uses infectious WA1 strain of SARS-CoV2 and is conducted in a qualified BSL3 facility at the University of Hawaii John A Burns School of Medicine (Honolulu, Hawaii).</div></div>

[STEPS]
?. [Oceanit Lateral Flow Assay (LFA) Protocol]
Prepare Serial DilutionThis experiment uses infectious WA1 strain of SARS-CoV2 and is conducted in a qualified BSL3 facility at the University of Hawaii John A Burns School of Medicine (Honolulu, Hawaii).
?. [Oceanit Lateral Flow Assay (LFA) Protocol]
Aliquot diluent solution into centrifuge tubesDiluent solution is cell growth media supplemented with 10% FBS.
?. [Oceanit Lateral Flow Assay (LFA) Protocol]
Prepare lysis buffer with LFA capture moleculeLysis buffer containing LFA capture molecule is Oceanit’s proprietary formulation.
?. [Oceanit Lateral Flow Assay (LFA) Protocol]
Virus stock (4 x 10e7 pfu/mL)Virus stock 10-fold serial dilutions.
?. [Oceanit Lateral Flow Assay (LFA) Protocol]
10-fold serial dilutions and control tubesa.Tube 1 – Neat (4e7 pfu/mL); pfu = plaque forming unitsb.Tube 2 – 10e-1c.Tube 3 – 10e-2d.Tube 4 – 10e-3e.Tube 5 – 10e-4f.Tube 6 – 10e-5g.Tube 7 – 10e-6h.Tube 8 – 10e-7i.Control – no virus
?. [Oceanit Lateral Flow Assay (LFA) Protocol]
Add lysis buffer to dilutionsAdd prepared lysis buffer to labeled individual LFA cassettes. Test and control lines are Oceanit’s proprietary molecules.
?. [Oceanit Lateral Flow Assay (LFA) Protocol]
Incubate 5 minutes
?. [Oceanit Lateral Flow Assay (LFA) Protocol]
Add to labeled individual LFA cassettes.Add 250uL of the corresponding sample to individual LFA cassettes.
?. [Oceanit Lateral Flow Assay (LFA) Protocol]
Record results with photography:A.Amount: B.Concentration: Virus stock and dilution range from 4 x 10e7 pfu/mL to 0 virus added.C.Temperature: Virus stocks are stored at -80C; assay is performed at room temperature.D.Duration of the experiment: 1 hour elapsed time.E.Equipment: BSL3 containment, Class II biological safety cabinet, autoclave, pipette and disposable tips, disposable tubes, dedicated camera. F.Reagents: Vero E6 cell culture growth media supplemented with 10% FBS, Oceanit lysis buffer + capture molecule (proprietary), LFA embedded test and control line molecules (proprietary)
TITLE: Mitomycin C inactivation of mouse embryonic fibroblasts (MEFs) for hPSC cultures
AUTHORS: Hanqin  Li, Oriol Busquets, Steven Poser, Dirk Hockemeyer, Frank Soldner

[DESCRIPTION]
This protocol describes the process of using Mitomycin C to inactivate mouse embryonic fibroblasts (MEFs), which can then be used as feeder cells for human pluripotent stem cell (hPSC) culture.


General notes
1. Throughout this protocol, the term hPSC is used to collectively refer to both hiPSCs and hESCs. All described procedures have been tested and work equally well for hiPSCs and hESCs.
2. MEFs were obtained as described in Manipulating the Mouse Embryo: A Laboratory Manual, Third Edition (ISBN: 0879695919)
 




[STEPS]
1. Grow MEFs to 90-95% confluency in 15-cm cell culture dish
2. Aspirate the medium and add 15 ml of Mitomycin C solution to cover the surface
3. Incubate in Mitomycin C for 150 min 37 °C 

4. Aspirate Mitomycin C solution from the plates and wash 4 times with DPBS (with Ca/Mg) and final wash with DPBS (w/o Ca/Mg).
5. Add Trypsin and incubate in 37°C; 5% CO2 for 5 min 

6. Add MEF medium to neutralize the Trypsin and collect the solution into a conical tube.
7. Centrifuge the cell suspension at 250 x g, 10 min 

8. Discard supernatant and re-suspend the cells in fresh MEF medium
9. Count cells using trypan blue solution
10. Mitomycin C treated cells can be either freshly plated as feeder cells for hPCS cultures or frozen as Mitomycin C inactivated stocks at 10x106 cells/vial. 

A protocol on freezing MEFs can be found in the collection "Maintenance and inactivation of mouse embryonic fibroblasts (MEFs) as feeder cells for human pluripotent stem cell culture." A link to this collection can be found in the title section of this protocol, located above
6.1. MEF medium
TITLE: Hematoxylin and Eosin Stain - FOR PARAFFIN-EMBEDDED TISSUE SECTIONS
AUTHORS: Michael X. Henderson

[DESCRIPTION]
This protocol details Hematoxylin and Eosin Stain for paraffin-embedded tissue sections.

[GUIDELINES]
Results:

1. Nuclei are stained blue.
2. Cytoplasm stained various shades of pink, identifying different morphologic tissue components.

[STEPS]
SECTION: Hematoxylin and Eosin Stain
1. Deparaffinize slides and hydrate to ddH2O: 

 

SECTION: Hematoxylin and Eosin Stain
2. Filter undiluted Harris Hematoxylin and Eosin using Whatman #4 filter paper.
SECTION: Hematoxylin and Eosin Stain
3. Immerse sections in filtered Harris Hematoxylin for 5 min.

SECTION: Hematoxylin and Eosin Stain
4. Rinse in 2 changes of ddH2O.
SECTION: Hematoxylin and Eosin Stain
5. Differentiate in 0.1% acid alcohol solution:

 

SECTION: Hematoxylin and Eosin Stain
6. Rinse in tap H2O for 10- 15 min or until sections turn bright blue.

SECTION: Hematoxylin and Eosin Stain
7. Immerse in Eosin for 1 min.

SECTION: Hematoxylin and Eosin Stain
8. Briefly rinse in tap H2O.
SECTION: Hematoxylin and Eosin Stain
9. Dehydrate in:

 

SECTION: Hematoxylin and Eosin Stain
10. Coverslip with Cytoseal.
TITLE: Operating Procedures: Ring Infiltrometer
AUTHORS: USDA Usda

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Operating procedure for using the ring infiltrometer.</div></div>

[STEPS]
?. Fill up your containers with water. Make sure that the water that will be going into the mariotte device has as little dissolved gas in it as possible.Well water is often supersaturated with CO2, and when the gas bubbles come out of solution they can interfere with flow from the Mariotte to the infiltrometer ring. (St. Paul tap water worked well for us).
?. Bring all of the equipment to the infiltration site.
?. Place the ring over the infiltration site. Clear obstructions from beneath it.
?. Place the durable wood on top of the ring, and use the sledgehammer to drive the ring into the ground (by hitting the wood). Every so often, check to make sure that the ring is level.
?. When the ring has been inserted about 2.5-5cm into the ground, stop.
?. Using the shovel, clear a level surface to place the scale on.
?. Place the scale (on the flat plywood) on the now level surface and hook it up to the computer. You will need to connect the two scale parts as well.
?. Set the shovel on the ground with the head resting in the ring.
?. Begin pouring water gently into the ring, using the head of the shovel to disperse the flow.For this part you can use well water.
?. When the ring is almost full, stop. Determine how quickly the water is draining. The goal is to achieve a near steady-state in the ring where the water level decreases very slowly. Add more water as necessary.
?. When the water level seems relatively stable, fill the mariotte device with tap water.
?. Turn on the scale and zero it.
?. Start up the ADAM DU software following its operating procedures.
?. Place the mariotte device on the scale.
?. Take the rubber top off the device and open the valve at the base. Water should begin to flow out of the tubing rapidly.
?. Reinsert the rubber top.
?. Put one finger on the end of the tubing, blocking the flow.
?. Place the end of the tubing under water in the ring and remove your finger.
?. Attach the c-clamp over the rim of the ring, to help hold the tubing in place.
?. Inspect the tubing for bubbles.
?. Make sure the ADAM DU software is collecting data.
?. Wait until the weight loss of the Mariotte becomes linear, and confirm that the water level in the ring is steady.
?. Use the meter stick to find the head height of the water in the ring. A good way to do this is to measure the height of the water from one side, the middle, and the other side, then calculate the mean height.
?. In a notebook, record the height of water in the ring and the depth of insertion of the ring.
?. Stop the data collection.
?. Clean up.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Before starting, please visit the <a href="http://earthcube.org/group/ecogeo" target="_blank">ECOGEO website</a> for more information on this 'Introduction to Environmental 'Omics' training series. The site contains a pre-packaged virtual machine (developed by <a href="https://www.protocols.io/researchers/benjamin-tully" target="_blank">Dr. Benjamin Tully</a>, USC) that can be downloaded and used to run all of the protocols in this protocols.io collection. In addition to the VM, the website contains videos and presentations from our initial 'Introduction to Environmental 'Omics' workshop held at the Univ. of Hawai'i at Manoa on 25-26 Jul 2016.<br /><br />Please email ‘ecogeo-join@earthcube.org’ to join the ECOGEO listserv for future updates.</p>
<p> </p>
<p>Attached documentation includes an informational flyer, workshop agenda and participant list.</p>

[STEPS]
?.