eamag/protocols-with-steps huggingface dataset:
TITLE: Protocol: A Scoping Review of the Biomechanics of the Autogenous Bone Graft Harvest from Proximal Tibia
AUTHORS: pooyan.eshkevari , riley.sumner , Robert Leon Flint, David Seligson

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Background:</span><span> The maxillofacial as well as orthopedic community have known proximal tibia bone as an abundant, reliable, and safe autogenous bone donor for reconstructive purposes. There have been reports of uncommon complications, mostly resolving seromas and hematomas, and rarely bone fractures following such procedures. </span></div><div class = "text-block"><span style = "font-weight:bold;">Objectives:</span><span> The authors aim to locate, review, and summarize the evidence concerning the biomechanics of the proximal tibial donor site following graft harvestation.</span></div><div class = "text-block"><span style = "font-weight:bold;">Methods and analysis: </span><span>Our study will follow the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) Checklist. With the help of a librarian, we will design a search strategy using Boolean features through PubMed, Embase, and Google Scholar using terms like tibia, graft, mechanical, shear, etc, restricted to English language. We will upload the results in EndNote, eliminate the duplicates, and scan the titles for potential inclusion. We will export the chosen titles into Rayyan QCRI website for abstract review and selection of articles for full text review. A summary and a critical appraisal of the extracted evidence will follow. Thestudy protocol is registered in Open Science Framework, </span><a href="https://osf.io/mequ6" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">https://osf.io/mequ6</span></a><span>. </span></div><div class = "text-block"><span style = "font-weight:bold;">Article summary: </span><span>this study maps and summarizes the available evidence on the biomechanics of donor site following proximal tibial autogenous bone graft harvest.</span></div><div class = "text-block"><span style = "font-weight:bold;">Strengths and limitations of this study</span></div><div class = "text-block"><ul style = "list-style-type:disc;"><li style = "counter-reset:ol0;list-style-type:disc;">The strength of this study relies on its systematic review of the evidence based on gold standard methods and protocol registrations. </li><li style = "counter-reset:ol0;list-style-type:disc;">This study suggests there is need for further investigation into the biomechanics of proximal tibia autogenous bone harvest.</li><li style = "counter-reset:ol0;list-style-type:disc;">This study is a scoping review and harbors the inherent limitations of such studies.</li></ul></div></div>

[STEPS]
TITLE: Coleta de dados actigráficos - ActTrust
AUTHORS: Daniel Vartanian

[DESCRIPTION]
Esta coleção reúne os protocolos do processo de coleta de dados actigráficos do Grupo Interdisciplinar de Pesquisa em Ritmos Biológicos (GIPERBIO). Esses protocolos foram desenhados para os actígrafos provenientes da companhia Condor Instruments. Algumas das configurações mencionadas podem ser específicas desses aparelhos.

Se você não é membro ou parceiro do GIPERBIO, você pode utilizar esta coleção como referência para o processamento de seus equipamentos. Neste caso, por favor, não envie os formulários mencionados nos protocolos relacionados ao processo.

Se você utilizar os protocolos do GIPERBIO em sua pesquisa, por favor considere citá-los na seção de materiais e métodos de sua estudo. Nós nos esforçamos bastante para elaborar e manter protocolos de acesso aberto à comunidade científica. Você pode encontrar a citação dos protocolos na aba metadata.

Consulte a aba Guidelines para visualizar o fluxograma do processo como um todo.

Para dúvidas ou sugestões, entre em contato pelo e-mail giperbio@gmail.com.

---

This collection gathers the protocols for the process of collecting actigraphy data from the Interdisciplinary Research Group on Biological Rhythms (GIPERBIO). These protocols were designed for actigraphs from Condor Instruments. Some of the settings mentioned may be specific to these devices.

If you are not a member or partner of GIPERBIO, you can use this collection as a reference for processing your own equipment. In this case, please do not send the forms mentioned in the protocols related to the process.

If you use GIPERBIO's protocols in your research, please consider citing them in the materials and methods section of your study. We have made a great effort to develop and maintain protocols that are open to the scientific community. You can find the citation of the protocols in the metadata tab.

Please refer to the Guidelines tab to view the process flowchart as a whole.

For questions or suggestions, please contact us at giperbio@gmail.com.

[GUIDELINES]
O processo de coleta de dados actigráficos do GIPERBIO segue o seguinte fluxograma.

  
A etapa Abordagem de voluntários não tem um protocolo geral, pois ela irá variar de acordo com o estudo.

[STEPS]
TITLE: Iso-Seq mapping to L1HS/PA2 consensus sequence
AUTHORS: Raquel Garza

[DESCRIPTION]
The protocol describes the steps to map HiFi reads to a consensus sequence and retrieve density plots

[STEPS]
SECTION: Mapping to L1HS/PA2 consensus sequence
1. A L1HS and L1PA2 consensus sequence was used to create a minimap2 (version 2.24; RRID:SCR_018550) index
 
to map FLNC reads (HiFi reads).
SECTION: Mapping to L1HS/PA2 consensus sequence
2. The density of mapped reads was visualized in the Integrative Genomics Viewer (IgV) (version 2.12.3; RRID:SCR_011793)
SECTION: Mapping to L1HS/PA2 consensus sequence
3. The number of mapped reads in the L1s 5’ UTR was retrieved using samtools view (-c) (version 1.9; RRID:SCR_002105), specifying the first 900 bp of the consensus sequence as the coordinates of interest.
TITLE: Protocol 7: Picking colonies of transformed Spizellomyces punctatus (Sp)
AUTHORS: Sarah M Prostak, Edgar M Medina, Erik Kalinka, Lillian Fritz-Laylin

[DESCRIPTION]
If transformation was successful, antibiotic-resistant Spizellomyces colonies should appear after 4-6 days of growth on selection media. These colonies should be rough, white, and opaque. When viewed under a microscope, there should be clustering of sporangia and some movement of zoospores. Picking these colonies and culturing them until there are enough cells for cryopreservation and to use in downstream molecular analysis is the last protocol in the entire transformation process. All steps here, with the exception of centrifugation steps, must be carried out in a sterile environment, either in a laminar flow hood or in the sterile area around an open flame.

[STEPS]
SECTION: Steps
1. Divide one K1 plate with selection antimicrobials into four sections using a marker on the bottom of the plate.
 

SECTION: Steps
2. Aliquot 50 µL of DS into one microcentrifuge tube per colony to be picked.

SECTION: Steps
3. Using an 18G needle, gently lift the colony of interest from the agar.
 

SECTION: Steps
4. Resuspend the colony into the appropriate tube pre-filled with DS. 
 

SECTION: Steps
5. Pipette gently to mix and break up the pellet.
SECTION: Steps
6. Pipette 50 µL of the resuspended colony onto one quadrant of the K1 plate prepared in step 1.

SECTION: Steps
7. Repeat steps 3-6 for each colony to be picked.
SECTION: Steps
8. Let the cells grow for 2-3 days before rehydrating the quadrants with 100 µL of DS and transferring each colony to its own quadrant of a new K1 selection plate. 
 

SECTION: Steps
9. After 2-4 rounds of colony expansion there is enough inoculum to transfer each isolated colony into its own plate.
SECTION: Steps
10. Continuing subculturing each colony until enough culture exists to freeze and perform downstream analyses.
TITLE: extract dropped plasmid DNA from filter paper
AUTHORS: Joseph Shenekji

[DESCRIPTION]
this is a short yet effective protocol to extract plasmid DNA on filter paper, this protocol could benefit plasmid production labs and companies and also receiving researchers or universities from underdeveloped countries.


[BEFORE_START]
STERILE EVERYTHING!! to avoid contamination, and wear gloves.

[GUIDELINES]
be fast and prepare your materials ahead in one place.

[STEPS]
SECTION: extraction of DNA from filter paper
1. locate the dropped plasmid on filter paper, it is usually circled with a marker or a pencil, it is preferable to take a photo and look at the texture if it looks "powdery" then you have a high concentration, if it looks flat then you have a low concentration and need additional time in incubation in step 4.
all steps should be sterile to the max.
SECTION: extraction of DNA from filter paper
2. Cut the desired piece of paper with a sterile surgical scalpel, try to avoid ink and not to tremble the paper, and put your elbows on a table to be more steady.  

SECTION: extraction of DNA from filter paper
3. pierce a 0.2 ml centrifuge tube with a sterile syringe from the bottom, then Place the piece of cutted paper containing the plasmid with sterile forceps the tube (you can use 0.5 tube also if 0.2 not available).
SECTION: extraction of DNA from filter paper
4. Add 30 µL  of elution buffer to the paper to absorb it (you can use TE or DH2O), you can modify the volume according to the miniprep information, it could be from 20-50 µL .

SECTION: extraction of DNA from filter paper
5. The 0.2 ml tube containing the paper is then placed in a 1.5 ml Eppendorf tube or you can place it in a 1ml tube if possible, it is necessary that the tube doesn't sink and the tip of the 0.2 tube hold steady on the edge of the 1.5 tube  

SECTION: extraction of DNA from filter paper
6. The soaked paper is incubated for 30 min 90 min at room temperature25 °C  (if the concentration is low and you want the maximum yield you can leave it 4h or overnight)

SECTION: extraction of DNA from filter paper
7. Centrifuge the tubes at 16,000 r/min for 2 minutes, but be careful that the small tube doesn't sink inside the bigger one, you can but a small sterile adhesive tape.
SECTION: extraction of DNA from filter paper
8. the hole in the 0.2 tube allows the liquid where the plasmid is dissolved in to pass to the bigger tube,  so you will get 25 ul filtrate from 30 ul original liquid, no you can take the filtrate and place it on ice for 10 min 10 minutes.

SECTION: extraction of DNA from filter paper
9. test your dissolved plasmid in nanodrop or make a quick electrophoresis to check the quality of dna.
SECTION: extraction of DNA from filter paper
10. store your dissolved plasmid in  -4 °C or -20 °C C for downstream application.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<div title="Page 55">
<div>
<div>
<p>Thrombus formation was measured by the viscoelastic test: ROTEM (Tem International GmbH c/o Dutch Affiliate, Tilburg, The Netherlands). Standard assays were used according to the manufac- turer’s recommendations: EXTEM (ref.: 503-05, Tem International GmbH c/o Dutch Affiliate, Til- burg, The Netherlands), FIBTEM (ref.: 503-06, Tem International GmbH c/o Dutch Affiliate, Til- burg, The Netherlands), and HEPTEM (ref.: 503-09, Tem International GmbH c/o Dutch Affiliate, Tilburg, The Netherlands). All samples were measured within 1 h after blood collection. Further- more, by means of EXTEM and FIBTEM results, the contribution of platelet count to the thrombus formation was calculated as the PLTEM parameter [22].</p>
</div>
</div>
</div>

[STEPS]
TITLE: transmissive blood test
AUTHORS: mbloore , marcello.manfredi 

[STEPS]
?. Collect blood with finger prick.
[2 drops]
0 Room temperature
?. Place blood in cuvette well, either directly or from a micro pipette. This image shows the same protocol being followed using human milk.
?. Slide cuvette window over well. This image shows the same protocol being followed using human milk.
?. Place cuvette in mount. This image shows the same protocol being followed using human milk..
?. Place mount in sensor. This is the Preemie-branded sensor. The COVIDTell sensor will be the same spectrometer with different branding and housing.
?. Launch COVIDTell app on mobile device at start of day.
?. Perform scan by pressing button on sensor or tapping button in app.
?. Read results on app screen.
Positive or Negative, or Failed.
?. Clean cuvette with 50% alcohol. This might be done by a second person.
?. Clear result in app before next subject arrives.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>The understanding of genome characteristics for a given new species, i.e., genome size and heterozygosity, facilitates customizing a specific sequencing and assembling strategy. Thus, the genome size was estimated using four independence methods, i.e., a script of KmerSpectrumPlot.pl in ALLPATHS-LG (version r52488), GCE (Genome Characteristics Estimation, released 20150107, ftp://ftp.genomics.org.cn/pub/gce), JELLYFISH (version 2.0) and flow cytometry.</p>

[STEPS]
?. 
?.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This is a multiplex PCR-SSP for amplification of the follow SNPs of CR1 gene:</p>
<p>rs3849266;</p>
<p>rs2274567;</p>
<p>rs4844610;</p>
<p>rs12034383.</p>

[BEFORE_START]
<p>1- Wear clean gloves;<br />2- Clean pipettes and stand with hypochlorite and 70% alcohol;<br />3- Defreeze DNA samples and reagents (exception: Taq polymerase);<br />4- Gently mix the DNA samples and pass the reagents briefly on the vortex.<br />5- Centrifuge the DNA samples and reagents with a spin;<br />6- Keep reagents on ice;<br />7- Leave microtubes ready for preparation of the mix, keep the same ones identified and on ice.<br />8- Leave application plates properly identified.</p>

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?.
TITLE: Recording Whale Watching Boat and Humpback Whale Collisions
AUTHORS: Laura Barragan

[DESCRIPTION]
The purpose of this research protocol is to record collisions caused by whale watching boat tours. We make use of remotely operated water vehicles to collect video footage of whale watching tours and analyze the footage simultaneously. This data will be taken over a five year period at multiple whale watching sites along the coast of Mo'orea, French Polynesia. 

[BEFORE_START]
- Verify all permits have been obtained
- Attempt to speak with whale watching agencies about project 


[GUIDELINES]
- Be sure you are 300 feet away from whale watching site, otherwise you would be violating federal rules
- Be sure to get proper training on operation of ROV, including deployment and retrieval

[STEPS]
SECTION: Remotely Operated Underwater Vehicle Set Up and Deployment
1. Drive ship to 300 feet distance from whale watching tour site
SECTION: Observation Methods
6. For 14 hours that ROV is underwater, monitor video footage carefully
SECTION: Closing Steps
12. 
SECTION: Remotely Operated Underwater Vehicle Set Up and Deployment
2. Equip the ROV with four video cameras and lights
SECTION: Remotely Operated Underwater Vehicle Set Up and Deployment
4. Deploy ROV to site carefully, make sure to stop at 10 feet deep
SECTION: Observation Methods
10. If you observe a collision, record it on the Google Spreadsheet
SECTION: Observation Methods
11. 
SECTION: Closing Steps
13. 
SECTION: Closing Steps
14. 
SECTION: Remotely Operated Vehicle Set Up and Retrieval
None. 
SECTION: Remotely Operated Underwater Vehicle Set Up and Deployment
3. Connect the ROV to ship with a tether
SECTION: Remotely Operated Underwater Vehicle Set Up and Deployment
5. Follow general direction of where whale watching tours go from 5am to 7pm
SECTION: Remotely Operated Underwater Vehicle Set Up and Deployment
5.1. 5am to 7pm as this is within the business hours of whale watching tour agencies
SECTION: Observation Methods
10.1. Include the following data: Date, Time, Tour Agency, Visible Injuries on Whale, Deaths (visible through whale fall)
SECTION: Observation Methods
8. If you observe a whale watching tour, record it on field notebook
SECTION: Observation Methods
7. Make sure that are multiple observers on shift observing footage from different cameras/angles
SECTION: Observation Methods
9. 
SECTION: Observation Methods
8. R
SECTION: Observation Methods
9. If you observe a collision, record it on field notebook
SECTION: Observation Methods
8.1. Include the following data: Date, Time, Agency
SECTION: Observation Methods
9.1. Include the following data: Date, Time, Agency, Approximate Speed, Injuries (if visible), Deaths (visible through whale fall)
SECTION: Observation Methods
None. 
SECTION: ROV Retrieval and Closing Steps
10. Retrieve tether and ROV from under water carefully
SECTION: ROV Retrieval and Closing Steps
11. Be sure to transfer data from field notebook onto Google Spreadsheet
TITLE: Microbiome and eDNA sampling of water using Sterivex filters
AUTHORS: Daniel S Read

[DESCRIPTION]
Protocol for field based sampling of bacterial biomass or environmental DNA (eDNA) using Sterivex filters and syringes.

[STEPS]
1. Open sampling pack and put gloves on.

  

2. Take the 60 mL syringe and Sterivex filter out of the packaging.

3. Fill the syringe with 60 mL of water to be sampled (either directly from the water source or collected in a clean sampling container that has been thoroughly rinsed with water from the sampling site).

4. Connect the syringe full of water to the luer lock end of the filter unit by twisting.
5. Use the syringe plunger to force the water through the filter unit.
 
  

 

6. Refill the syringe and repeat this process until no more water can be filtered through the unit (a reasonable pressure can be applied, but be careful to not apply excessive force). Expect between 60 mL  and 600 mL, depending on water turbidity.

7. Record the volume of water that passed through the filter in ml.
8. Fill the 60 mL syringe with air, reattach to the filter unit and expel any remaining water in the filter unit by forcing the air through. Dispose of the 60 mL syringe.

9. Add the end cap to the outlet of the filter unit by twisting it on.
11. Attach the 2.5 ml syringe to the inlet of the syringe filter and holding upright (syringe on top), add the Zymo DNA/RNA shield to the filter vial by depressing the syringe plunger. Allow the syringe to refill with air, remove and dispose of the empty syringe.

  

10. Remove the 2.5 mL syringe from its packaging and fill with Zymo DNA/RNA shield from the 5 mL vial. Dispose of the empty vial.
12. Cap the inlet of the filter unit with the other cap to seal in the preservative.

  

13. Ensure the caps are on tightly and place the filter unit in the labelled 50 ml plastic centrifuge tube.

  

14. Store the filter unit at -20 °C, or at the very least keep at 4 °C and out of direct sunlight, until returning to the laboratory. Once in the laboratory, store at -20 °C until shipping and analysis.

Shipping of samples can be performed at room temperature, although cooled (4 °C  or -20 °C  shipping is preferred.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
Experiment was conducted to determine the stage at which mutant embryos arrest their development. All Drosophila melanogaster lines were crossed to balancers with a YFP marker for unambiguous identification of mutant and non-mutant embryos. Embryos were collected on apple juice agar plates with a smear of yeast paste for 1hr and aged for 17 hours at 25&deg;C. Embryos were fixed and stained as described by Fehon et al., 1991 using a modified rotational speed of 150rpm.

[STEPS]
?. 
?. 
?. 
?.
TITLE: Splitting 96 Well Plates for gDNA Extraction and Freezing Down
AUTHORS: Celeste Karch, Rita Martinez, Jacob Marsh

[STEPS]
?. Aspirate media from original plate.
?. Wash with PBS and aspirate.
200 µl
?. Add  of 0.05% Trypsin.
25 µl
?. Incubate at  for
?. Tap to lift cells from plate.
?. Check under microscope to ensure that cells have detached from plate.
?. Add  mTesR1 to plate and tap to mix.
45 µl
?. Transfer  to a 96 well PCR plate, while maintaining the location of each sample (this plate will be used for gDNA extraction).
15 µl
?. Add  of 2X Freezing Media (20% DMSO in FBS) to cell plate and tap to mix.
50 µl
?. Wrap plate in parafilm. Add tape over parafilm. Label the plate on the outside of the tape.
?. Place plate in Styrofoam box. Fill any open areas with diapers, paper towels, or Kimwipes. Cover box and make sure that lid is closed completely.
?. Store in for up to 4 months .
TITLE: Human Pancreas Procurement and Processing of Prodo Laboratories
AUTHORS: Giray Eryilmaz

[DESCRIPTION]
Human pancreas procurement and processing as described in Advances in Human Islet Processing: Manufacturing Steps to Achieve Predictable Islet Outcomes from Research Pancreases
David W. Scharp, Jayagowri Arulmoli, Kelly Morgan, Hannah Sunshine, Ergeng Hao
Received: October 15, 2018; Published: February 26, 2019; doi:10.21926/obm.transplant.1901052

[STEPS]
SECTION: Human Pancreas Procurement and Processing of Prodo Laboratories
1. Refer to this publication:
Advances in Human Islet Processing: Manufacturing Steps to Achieve Predictable Islet Outcomes from Research Pancreases
David W. Scharp, Jayagowri Arulmoli, Kelly Morgan, Hannah Sunshine, Ergeng Hao
Received: October 15, 2018; Published: February 26, 2019; doi:10.21926/obm.transplant.1901052

Section 2.1 for Pancreas Procurement, 
Section 2.2 for Human Pancreas Processing.
TITLE: 4% PFA for fixation
AUTHORS: Martin Thomas Jahn

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Fixative for FISH and other applications</div></div>

[STEPS]
?. pour 2 g of paraformaldehyde (PFA) powder in 50 ml phosphate buffered 
saline (PBS; 130 mM NaCl, 10 mM Na 2 HPO 4 /NaH 2 PO 4 , pH 7.4)
use mask be careful with PFA
adjust to amount actually required
?. check pH and adjust to pH 7.0
?. heat to approx. 60° C (must not boil!), until suspension is clear (approx. 1/2 h); if not add some drops of 1N NaOH
?. filter through 0.2 µm filter and place on ice
TITLE: P1 20/05
AUTHORS: Maria  Gul, katarina  

[DESCRIPTION]
qa

[STEPS]
1. test 

Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Nam libero tempore, cum soluta nobis est eligendi optio cumque nihil impedit quo minus id quod maxime placeat facere possimus, omnis voluptas assumenda est, omnis dolor repellendus. Morbi imperdiet, mauris ac auctor dictum, nisl ligula egestas nulla, et sollicitudin sem purus in lacus. Nam quis nulla. Nunc auctor. Fusce wisi. Aliquam erat volutpat. Curabitur ligula sapien, pulvinar a vestibulum quis, facilisis vel sapien. Cras pede libero, dapibus nec, pretium sit amet, tempor quis. Nullam dapibus fermentum ipsum.
2. test 2

Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Nam libero tempore, cum soluta nobis est eligendi optio cumque nihil impedit quo minus id quod maxime placeat facere possimus, omnis voluptas assumenda est, omnis dolor repellendus. Morbi imperdiet, mauris ac auctor dictum, nisl ligula egestas nulla, et sollicitudin sem purus in lacus. Nam quis nulla. Nunc auctor. Fusce wisi. Aliquam erat volutpat. Curabitur ligula sapien, pulvinar a vestibulum quis, facilisis vel sapien. Cras pede libero, dapibus nec, pretium sit amet, tempor quis. Nullam dapibus fermentum ipsum.
3. test 3 

Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Lorem ipsum dolor sit amet, consectetuer adipiscing elit. Nam libero tempore, cum soluta nobis est eligendi optio cumque nihil impedit quo minus id quod maxime placeat facere possimus, omnis voluptas assumenda est, omnis dolor repellendus. Morbi imperdiet, mauris ac auctor dictum, nisl ligula egestas nulla, et sollicitudin sem purus in lacus. Nam quis nulla. Nunc auctor. Fusce wisi. Aliquam erat volutpat. Curabitur ligula sapien, pulvinar a vestibulum quis, facilisis vel sapien. Cras pede libero, dapibus nec, pretium sit amet, tempor quis. Nullam dapibus fermentum ipsum.