eamag/protocols-with-steps huggingface dataset:
TITLE: Cost of a Renewable Micro Grid in Moorea
AUTHORS: clairewiegand

[DESCRIPTION]
Moorea is an island in French Polynesia that depends on imported fossil fuels to meet the community's energy demands, which leads to high costs and high carbon dioxide emissions. The implementation of a renewable energy microgrid may provide a solution to reducing Moorea’s carbon footprint and energy bills. This protocol aims to assess the technical and economic feasibility of implementing a microgrid in Moorea and estimate the corresponding costs.
 

[BEFORE_START]
Before starting, familiarize yourself with microgrids, island energy production, and solar panels.  

[GUIDELINES]
Carry field notebook and camera at all times to document findings. 

[STEPS]
SECTION: Cost of a Renewable Microgrid in Moorea, French Polynesia
1. Conduct a comprehensive scientific literature review on microgrids, renewable energy, and their use in island communities. 30240 min  .Write high level notes as you read to provide a general overview of the energy landscape in Moorea.  

SECTION: Cost of a Renewable Microgrid in Moorea, French Polynesia
3. Conduct site visits to research energy infrastructure, surrounding land, and other relevant factors. During site visits, take photos and write notes if energy infrastructure relies on fossil fuels or renewable sources. 
SECTION: Cost of a Renewable Microgrid in Moorea, French Polynesia
2. Interview key stakeholders, including the local government, energy provider (Électricité De Tahiti), and community members in various parts of Moorea to gather information on their perspectives on the implementation of a renewable microgrid system in Moorea. 
SECTION: Cost of a Renewable Microgrid in Moorea, French Polynesia
4. Calculate the cost of implementing a renewable flexible grid in Moorea. Calculate this cost by adding the fixed cost of building this infrastructure and variable cost of maintenance. 
SECTION: Cost of a Renewable Microgrid in Moorea, French Polynesia
5. Conduct cost benefit analysis of continuing current energy consumption by analyzing economic, environmental, and social costs of a continued reliance on fossil fuels for Moorea. Document high level findings.
SECTION: Cost of a Renewable Microgrid in Moorea, French Polynesia
6. Summarize all findings in the Results section of the research project. Highlight any patterns, trends, or outliars in the data. 
SECTION: Cost of a Renewable Microgrid in Moorea, French Polynesia
7. Analyze results and write Discussion section of research project. In the Discussion section, explain why these results were obtained, discuss any issues with the project, and propose future research questions to further the study.   
SECTION: Cost of a Renewable Microgrid in Moorea, French Polynesia
8. Publish final report to an online academic journal.
TITLE: No Sew Face Mask in 10 Steps
AUTHORS: Julia Borden

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes how to make a face mask out of a t-shirt in 10 easy steps, no sewing required!</div></div>

[STEPS]
?. [Face Mask in 10 Steps]
Lay out a clean t-shirt with a circular collar.
?. [Face Mask in 10 Steps]
Cut off the tag, if there is one.
?. [Face Mask in 10 Steps]
Flip over the shirt so the back is facing you. Measure ~6 inches from the center of the collar. This will cover from the top of your nose to your chin, so the length may vary for each person.
?. [Face Mask in 10 Steps]
Draw a line at the 6 inch mark across the shirt and sleeves.
?. [Face Mask in 10 Steps]
Measure out ~4 inches from the collar across the shoulder.
?. [Face Mask in 10 Steps]
Draw a curved line from the 4-inch shoulder mark to about 1 inch from the top of the line on the sleeve from step 4.
?. [Face Mask in 10 Steps]
Flip over the shirt so the front is facing you. Mark ~2 inches below the center of the collar.
?. [Face Mask in 10 Steps]
Draw a curved line from the 2-inch mark to the 4-inch marks on the shoulders.
?. [Face Mask in 10 Steps]
Cut along the marked lines.
?. [Face Mask in 10 Steps]
You now have a finished mask!
?. [Optional Additions]
Optional: Cut out a 4 inches x 5 inches piece of fabric and place it in the center of the facemask, with the top almost touching the top of the collar.
?. [Optional Additions]
Sew this pocket onto the facemask. You can now fill it with extra layers of fabric or filters.
?. [To Wear]
Place the back collar over your nose, with the front collar hugging the back of your head. You may need to use a pin or rubber band to tightly secure the collar on the back of your head. Pull the two flaps tightly around your chin and secure on the top of your head with a knot.
?. [To Clean]
Place in boiling water for 10 minutes to sterilize
TITLE: Liver tissue staining with multiple lanthanides-tagged antibodies 
AUTHORS: Hua  Tian

[DESCRIPTION]
Imaging mass spectrometry (IMS) is able to image the multiple lanthanides-tagged antibodies (up to 40) simultaneously at a subcellular resolution on a single tissue section. This protocol is developed for optimized immunostaining of frozen-hydrated tissue with antibodies cocktail (10-25 Abs), which produces consistent antibody affinity and improved IMS image quality using C60-secondary ion mass spectrometry (C60-SIMS).

[STEPS]
1. Cut the fresh frozen sections at 5µm using a cyromicrotome and mount them on Au-coated silicon slides
2. Place the slides at -20 ◦C for 1h and then at 4 ◦C for 30 min for temperature equilibrium
3. Fix the tissue slides in 1% PFA for 5 min at 4 ◦C, then in prechilled methanol for 5 min at -20 ◦C
4. Wash the slides twice for 5 min in a glass petri dish by submerging the slides in 25 ml wash buffer, following by rehydrating the slides for 5 min in a glass container with 25ml DPBS and rinsing the slides for 5 min in a glass container with 25ml wash buffer
5. Use the Liquid-Repellent Slide Marker Pen to draw a circle around the tissue section to create a barrier to contain the solutions on the tissue sections
6. Apply 100 µl 3% goat serum solution to each slide for 1 h at RT and then remove excess block solution by tapping on a tissue
7. Prepare the antibody cocktail. Vortex all the antibodies for 15 s and then centrifuge at 12,000G for 2 min, followed by diluting the upper liquid of each antibody in 0.5% PBS as desired concentration
8. Add 100 µl of the antibody cocktail to each section and incubate overnight at 4◦C in a sealed glass petri dish in a fridge
9. After the incubation, wash the sections two times for 5min in a glass petri dish with 5 ml wash buffer with slow agitation
10. Incubate the slides with 100 µl 1:100 dilution of Intercalator-Ir in DPBS for 30 min at RT
11. After nuclei staining, wash the slides for 5 min in a glass container with 5 ml DPBS
12. Quickly dip the slides in a container with 5 ml DI water for 15 s, repeat three times
13. Dry the slides in a fume hood at RT for 20 min
14. Store the slides at 4◦C until C60-SIMS imaging.
TITLE: Species-specific quantitative PCR (qPCR) protocol developed to identify Haplosporidium pinnae
AUTHORS: Monserrat López-Sanmartín, Gaetano Catanese, Amalia Grau, Jose María Valencia, Jose Rafa García-March, José Ignacio Navas

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>The aim of this study has been to develop species-specific quantitative PCR (qPCR) protocol carrying out a fast, specific and effective molecular diagnose of </span><span style = "font-style:italic;">Haplosporidium pinnae</span><span>. In this sense, the detection limit for qPCR was equal to 30 copies of SSU rDNA / ng of DNA using plasmid alone and when 100ng DNA of non-infected oyster were added. </span></div></div>

[STEPS]
?. The qPCR assay for H. pinnae detection and quantification was carried out in duplicate using the species-specific primer pair (HpF3/HpR3) in a Mx3000P Thermocycler (Agilent).
?. Amplification reactions were performed in a total volume of 10 µl comprising:
?. 2 µl of genomic DNA (100 ng),
?. 5 µl of PowerUpTM SYBRTM Green Master Mix (Applied Biosystems),
?. 0.2 µM each specific primer and
?. adjusted to 10µl with distilled water.
?. Negative control (without DNA or with H. pinnae non-infected fan mussel DNA, previously confirmed by qPCR),
?. positive controls (samples with positive cPCR amplification for H. pinnae) and
?. standard curve (plasmid HpF3/HpR3) were included in each qPCR assay.
?. After testing various annealing temperature, the final qPCR program was: 1 cycle for 2 min at 50ºC; 1 cycle for 2 min at 95ºC, 40 cycles of amplification at 95ºC for 15 s, 60ºC for 18 s and 72ºC for 1 min and followed by a dissociation stage for determining the melt curve (Quantitative SYBR Green with dissociation curve).
?. Two standard curves were calculated using serial dilutions of the plasmid and plasmid diluted with DNA of fan mussel;
?. the efficiency (E) was from the slope of the standard curve following formula [11] E=10-1/slope-1.
?. Melting curve was generated with temperatures increments of 0.5ºC s-1 starting at 60ºC and ending at 95ºC in order to ensure that a single PCR product was amplified for the primers.
?. Amplification was also confirmed by electrophoresis on 2% agarose gels, in 1% TAE (Tris acetate EDTA buffer), stained with Red Safe (Nitron Biotechnology) and scanned in a GelDoc-It Imagen System Ultraviolet Transilluminator (BioImaging Systems).
TITLE: UPitt TriState SenNet TMC Heart Procurement
AUTHORS: John Sembrat, Marta Bueno, Alison Morris, koenigshoffm, Oliver Eickelberg

[DESCRIPTION]
This document outlines the request for specimen procurement before arrival at the TriState SenNet TMC Biospecimen Core at the University of Pittsburgh, as part of the Cellular Senescence Network Program (SenNet).

[STEPS]
SECTION: Requested processing protocol for Donation following Brain Death Declaration (DBD)
1. Organ Procurement Organization Recovery Team prepares for organ recovery as consistent with organ transplant protocol with cross clamp and in situ cold flush body cooling with minimal warm ischemic time.
SECTION: Requested processing protocol for Donation following Cardiac Death /Arrest(DCD)
4. Organ Procurement Organization / Recovery Team prepares for organ recovery as quickly following Cardiac Arrest while in comfort care as authorized by next of kin.
SECTION: Requested processing protocol for Donation following Cardiac Death /Arrest(DCD)
5. Remainder of organ / tissue recovery should be as consistent with organ transplant protocol (section above) as possible.


Includes organ flush with Perfadex or similar organ transplant buffer until solution runs clear.

SECTION: Requested processing protocol for Donation following Cardiac Death /Arrest(DCD)
6. All warm ischemic time is to be minimized and reported. Tissues may be accepted up to 6 hours WIT.  Other WIT may be evaluated depending of the circumstances.
SECTION: Requested processing protocol for Donation following Brain Death Declaration (DBD)
2. Heart retrieval: The superior caval vein is ligated. The inferior caval vein is opened and the left atrium is vented, in order to prevent left ventricular distension. The ascending aorta is subsequently cross clamped and cold cardioplegia is administered via the aortic root to achieve hypothermic diastolic arrest.
SECTION: Requested processing protocol for Donation following Brain Death Declaration (DBD)
3. Place Heart in a Specimen Bag and submerge with chilled Perfadex or similar. Triple bag the tissue. (if recover with lungs)

if retrieved alone, heart is packed in one or two litres of cardioplegia and placed in an ice box for transport.
TITLE: RNA isolation of Pinctada fucata martensii
AUTHORS: Xiong Xinwei

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol provides details on RNA isolation of the tissue of Pinctada fucata martensii.</div></div>

[STEPS]
?. Incubate for 5 minutes to permit complete dissociation of the nucleoproteins complex.
?. Add a steel ball to each tube and then flacker for 3 min by TissueLayer 2. The frequency is 26 (1/S). Repeat this step one time.
?. Centrifuge the lysate for 15 minutes at 12,000 × g at 4 ℃, then transfer the aqueous phase containing the RNA (~500 ul) to a new 1.5 mL tube.
?. Take 50-100 mg of tissue to 2.0 mL tube, then add 1 mL of TRIzol™ Reagent per 50–100 mg of tissue to the tube.
?. Add 200 ul Chloroform (4 ℃ pre-cooling), then securely cap the tube and shake for 1 min to mix it completely. Then incubate for 10 min at 4 ℃.
?. Add 0.5 mL of isopropanol to per 0.5 mL aqueous phase, then mix it gently.
?. Incubate 10 min at 4 ℃. Then centrifuge for 10 minutes at 12,000 × g at 4 ℃.
?. Remove the supernatant as much as possible. Centrifuge for 1 minute at 12,000 × g at 4 ℃ to remove the supernatant completely if necessary.
?. Resuspend the pellet in 1 mL of 75% ethanol per 1 mL of TRIzol™ Reagent used for lysis.
?. Centrifuge for 5 min at 12,000 × g at 4 ℃, then discard the supernatant. Repeat step 9 and step 10 for one time.
?. Air-dry the RNA pellet for 5 min at 4 ℃.
?. Resuspend the RNA pellet in 20–50 ul of RNase-free water.
?. Measuring the concentration of RNA by the instrument of SimpliNano and detecting RNA integrity using a 1% agarose gel.
?. RNA sample stored at -80 ℃.
TITLE: Adverse drug reactions associated with the use of biological agents
AUTHORS: Jorge Machado Alba, Luis Valladales, Yadira Parrado

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:justify"><span style = "font-style:italic;">Introduction:</span><span> 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.</span></div><style>
							  .justify:after {
							    content: "";
							    display:inline-block;
							    width: 100%;
							  }
							</style></div><div class = "text-block"><div class = "justify" style = "text-align:justify"><span style = "font-style:italic;">Methods:</span><span> 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.</span></div><style>
							  .justify:after {
							    content: "";
							    display:inline-block;
							    width: 100%;
							  }
							</style></div><div class = "text-block"><div class = "justify" style = "text-align:justify"><span style = "font-style:italic;">Results:</span><span> 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%).</span></div><style>
							  .justify:after {
							    content: "";
							    display:inline-block;
							    width: 100%;
							  }
							</style></div><div class = "text-block"><div class = "justify" style = "text-align:justify"><span style = "font-style:italic;">Conclusions:</span><span> 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.</span></div><style>
							  .justify:after {
							    content: "";
							    display:inline-block;
							    width: 100%;
							  }
							</style></div></div>

[STEPS]
TITLE: Protein Purification ( Column Cromotography)
AUTHORS: Sevval Uysalcan, Rengin Yamur Akbiyik

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"> It is very difficult to purify a desired protein from a cell and tissue in a pure state. If the concentration of this protein is low, it is necessary to select the purification techniques appropriate for this protein to separate it from thousands of different proteins and to obtain it in pure form. The methods used in the purification of proteins are quite advanced.</div><div class = "text-block"> Today, many enzymes and non-enzyme proteins have been isolated in pure and crystalline form. To study the amino acid composition and sequence, molecular weight, and other physical properties of a protein, it is first necessary to purify the protein. In order to isolate proteins from a group of tissues and cells, there are certain procedures that should be done first. In the first stage, the tissue or cell group where the protein we want to work at most is selected. The tissue and cells are homogenized by using buffer solutions to keep the protein we are interested in. The cell membrane and the nucleus membrane must be broken down. This homogenate is then subjected to centrifugation at certain rates to remove cell particles. The resulting protein mixture is then removed in the supernatant state to purify the proteins in pure form using one or more of the purification methods.</div></div>

[STEPS]
?. 2 ml of resin (Ni-beads) should be put onto columns. Wash column with double distilled water before using resin.
[Resin]
?. 1X Binding Buffer should be added until fill the whole column.
?. When all Binding Buffer is leaked, samples should be put into columns.
?. Wash columns and sample until all residues are gone. In the washing step take  from sample and from bradford and put into 96 well plate.
[sample]
[Bradford]
?. As a last step, to keep the protein that is purified from samples, Elution Buffer is added andtransferred to new centrifuge tubes.
[Elution Buffer]
TITLE: Electrocompetent Agrobacterium transformation
AUTHORS: Magdalena Julkowska

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Standard protocol for Agrobacterium transformation</div></div>

[STEPS]
?. Add a small amount of plasmid DNA (
?. Pipette Agro cells with DNA into a chilled 0.2 cm electroporation cuvette.Shake cells to bottom of cell
?. Pulse cells at 2.5kV.
?. Add 1 ml YEP (of LB) media to cuvette, mix, and immediately transfer cells into sterile test tubes.
?. Allow cells to shake at 28°C for 2-4 hours.
?. Plate 10 μl and 100μl on selective media. Put the plates at 28°C.
?. Select positive cultures after 48h. If you use multiple antibiotics for selection, you might have to wait even longer.
TITLE: Objectives (Part 2 of Safety and Efficacy of Imatinib for Preserving Beta-Cell Function in New-onset Type 1 Diabetes Mellitus)
AUTHORS: Stephen.Gitelman , Jeffrey A. Bluestone

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is Part 2 of "Safety and Efficacy of Imatinib for Preserving Beta-Cell Function in New-Onset Type 1 Diabetes Mellitus".</div><div class = "text-block">This clinical study is supported by JDRF. The aim of the collection is to determine whether imatinib will slow the progression of the autoimmune destruction of ß cells and lead to the preservation of C-peptide secretion in T1DM and to assess Diabetes-related objectives and safety of Imatinib in new-onset type 1 diabetes mellitus".</div></div>

[STEPS]
TITLE: No Title
AUTHORS: 

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?.
TITLE: Preparation of 1M calcium chloride solution (CaCl2)
AUTHORS: Alfonso  Pérez Escudero, Alid  Al-Asmar, gabrielmadirolas  

[DESCRIPTION]
Original source of the protocol: WormBook Methods http://www.wormbook.org/chapters/www_strainmaintain/strainmaintain.html
This protocol is for making 1M calcium chloride solution, which is used in the preparation of worm media, like NGM (Nematode Growth Medium). 

[STEPS]
1. Weigh 7.4 g of calcium chloride dihydrate (CaCl2·2H2O).

2. Dissolve it in ~40 mL of milliQ water in a 100mL measuring cylinder.
5. Fill up to 50 mL. 
6. Filter-sterilize.
7. Store at 4°C. 
We usually use it without problem for up to at least a year after preparation.
3. Add a clean stirring magnet, and leave it on a stirrer until all crystals are dissolved.
4. Remove the stirring magnet: To prevent touching the solution, use another magnet from the outside of the measuring cylinder to slide the stirring magnet out of the cylinder.
TITLE: Labeling lysosomes in the adult Drosophila brain using LysoTracker
AUTHORS: Mel Feany

[DESCRIPTION]
This protocol describes the labeling and quantification of Lysosomes in the adult Drosophila brain using the LysoTracker dye

[STEPS]
1. Prepare the working solution, 0.05 μM LysoTracker Green DND26, using 1X PBS
2. Brains from 10-day-old animals are dissected in ice-cold 1X PBS
3. The dissected brain is transferred to a glass slide, and the excess 1X PBS removed
4. The brains are re-incubated with 0.05 μM LysoTracker for 5 min at Room temperature

5. After 5 minutes, the excess solution is removed, a drop of DAPI Fluoromount added, and the brain mounted with a coverslip
6. Brains re imaged immediately using a Zeiss confocal microscope under a 63X objective lens
7. The number of puncta per 1000 μm2 is counted in Zen software
TITLE: Quick saag paneer/tofu
AUTHORS: Lenny Teytelman

[DESCRIPTION]
(Based on the NYT recipe https://cooking.nytimes.com/recipes/1021954-saag-paneer)


My kids don't like fried onion, and one of them doesn't like paneer. So this is a very quick saag with onion powder and tofu instead.

[STEPS]
1. Mince the spinach in a food processor. Do not overprocess into a puree.
2. Heat ghee on medium-low
3. Fry garlic and ginger for 1 min or less

4. Add spinach
5. Add   cup of water
6. Raise the heat to medium and add coriander, cumin, onion powder, salt, pepper.
7. Cook for 5 min

8. Add cubed tofu and cook another 2-3 minutes until the water is absorbed
9. Add whipping cream. Turn off the heat and mix.