eamag/protocols-with-steps huggingface dataset:
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>In this study, we investigate the effects of using smart wearables by patients undergoing cardiac rehabilitation. A field experiment involving 29 patients was designed and participants were either assigned to the study group (N=13 patients who finished the study and used a self-tracking device) or the control group (N=16 patients who finished the study and did not use a device). For both groups data about physiological performance during cardiac stress test was collected at the beginning (baseline), in the middle (in week 6), and at the end of the study (after 12 weeks). Comparing the physiological performance of both groups, the data showed significant differences. The participants in the study group not only maintained the same performance level as during the midterm examination in week 6, they improved performance even further during the six weeks that followed. The results provide evidence for positive effects of digital self-tracking by patients undergoing cardiac rehabilitation on performance of the cardiovascular system. In this way, our study provides novel insight about the effects of the use of smart wearables by chronic disease patients. Our findings have implications for the design of self-management approaches in a patient rehabilitation setting. In essence, the use of smart wearables can prolong the success of the rehabilitation outside of the organized rehabilitation setting.</p>

[BEFORE_START]
<p>A consent form has to be signed by the patient and the responsible author after all patient questions were answered satisfactorily; hence the patient completely understands the way in which the study will be conducted, is aware of his rights as a participant, is willing to consent to participation and confirmes that he/she had had enough time to think about whether he/she wishes to participate in the study or not.</p>

[GUIDELINES]
<p>Recruite participants from routine rehabilitation groups on the day of their baseline examination. Design the groups for the study to avoid an overlap of study and control group participants in the same routine rehabilitation group to ensure that participants of different groups could not influence each other.</p>
<p> </p>
<p>Standard diagnostic processes (in cardiology), like the exercise test for enabling determination of a participant’s maximum exercise capacity, should follow the latest Practice Guidelines for Exercise Testing which provide recommendations about the procedure of testing, the valuation of measured parameters, possible influences and interruption or termination criteria.</p>

[STEPS]
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TITLE: Modified Promega Wizard Extraction for Barcoding Macrofungi
AUTHORS: Stephen Douglas Russell

[DESCRIPTION]
'This protocol is best used when preparing macrofungal specimens for Sanger sequencing or as a secondary extraction protocol for ONT nanopore barcoding. 

The quality of a DNA extraction method is a primary limiting factor in the total number of samples that will return a result with nanopore barcoding of fungi. The "quick" extraction protocol will often yield a positive result for 80-85% of general fungal collections (less if biased with polypores and recalcitrant species). Utilizing this extraction protocol pushes that number to nearly 100%. It is more time consuming and utilizes more expensive chemicals, but may be worth considering for important specimens that fail with the quick extraction protocol.

[STEPS]
2. Add 600uL of   to 1.5mL eppi tubes containing your tissue.

1. Place tissue from your specimens into each tube using tweezers. Utilize a piece about the size of a grain of rice or smaller. It should easily drop to the bottom of the tube. The tissue can be either fresh or dried. Label the tube with the appropriate number. Wipe the tweezers off with a Kimwipe or paper towel in between each specimen. These tubes can be stored at room temperature until they are ready to be used. 
3. Grind the tissue well in each tube using a sterile pestle.
4. Heat the tubes at 65 °C for at least 15 min. It is fine to leave it in longer. I often use one hour.

5. Centrifuge the tubes for 3 min at max rpm.

6. Transfer the supernatant (liquid on top) to a new 1.5mL eppi tube. Label your tubes.

Add 200 µL of   to the tube. 

Vortex the tube for 20 s.

Centrifuge the tube for 6 min at max rpm.


7. Transfer the supernatant (liquid on top) to a new 1.5mL eppi tube. Label your tubes

Add 600 µL of 100%   to the tube.  This precipitates the DNA.
 
Centrifuge the tube for 1 min. The DNA will now be in a pellet stuck to the bottom of the tube.

Discard the supernatant. It can just be poured out of the tube into a waste container.

8. Add 600 µL of 70% ethanol to the tube.  

Centrifuge the tube for 1 min.

Discard the supernatant. It can just be poured directly out of the tube into a waste container.

Place the tube upside down on a Kimwipe for at least 15 min, or until all of the ethanol has evaporated from the tube. I usually leave the tube to dry overnight.

9. Add 30uL of molecular water to the tube.

Your DNA template is now ready for amplification.
TITLE: Planaria 2021 Environmental Summary, Reptile &amp; Aquatics, Stowers Institute for Medical Research
AUTHORS: Shane  C. Miller, M.  Shane Merryman, Diana P Baumann

[DESCRIPTION]
Planaria are an emerging model organism, and we have maintained a colony of asexual and sexual worms at the Stowers Institute for Medical Research since 2010. Their small size allows us to maintain a large census across several systems requiring a small footprint. The planaria systems at the Stowers Institute allow for standardization of husbandry and environmental parameters. Acknowledging that husbandry conditions and environmental parameters can impact research results we provide information about the housing, nutrition, maintenance, and health for our Planaria colonies. This information will be applicable to any Planaria housed in the facility in 2021.

[STEPS]
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<strong>Purpose:</strong> This protocol describes how to pellet bacterial cells onto grids and stain them so that viruses can be visualized within the cells using transmission electron microscopy. Data obtained from these grids can be used to calculate the frequency of visibly infected cells (FVIC), the frequency of infected cells (FIC), the fraction of mortality due to viral lysis (FMVL), and burst size.

[GUIDELINES]
<strong>Materials required:</strong><br />- glow discharge apparatus <br />- ultracentrifuge and rotor capable of 55000 xg <br />- pollyallomer ultracentrifuge tubes with epoxy in the bottom to provide a flat surface <br />- EM grid-grade forceps <br />- EM grids (formvar coated 200 mesh copper grids) <br />- paper dividers from between commercially packaged filters <br />- double-sided tape <br />- razor blade <br />- uranyl acetate <br />- ultra-purified water such as Milli-Q water <br />- petri dish <br />- 4x 2 ml microcentrifuge tubes with screw caps <br />- 4 ml plastic culture tube with cap <br />- small stir bar <br />- stir plate <br />- filter paper (cut into wedges) <br />- 0.02 &micro;m syringe filter and syringe (3-5 ml) <br />- lab coat, respiratory protection (mask), eye protection <br />- timer <br />- transmission electron microscope<br /><br /><strong>Applicable References:</strong> <br /><br />Proctor and Fuhrman (1990) &ndash; The original description of the FVIC method. <br /><br />Binder (1999) &ndash; The equations used to calculate FIC and FMVL, and the assumptions inherent in those equations. <br /><br />Brum et al. (2005) &ndash; An example of a use of the FVIC method to investigate viral induced mortality of bacteria in an aquatic ecosystem. <br /><br />Binder, B. (1999) Reconsidering the relationship between virally induced bacterial mortality and the frequency of infected cells. Aquatic Microbial Ecology 18: 207-215. <br /><br />Brum, J.R., Steward, G.F., Jiang, S.C., and Jellison, R. (2005) Spatial and temporal variability of prokaryotes, viruses, and viral infections of prokaryotes in an alkaline, hypersaline lake. Aquatic Microbial Ecology 41: 247-260. <br /><br />Proctor, L.M., and Fuhrman, J.A. (1990) Viral mortality of marine bacteria and cyanobacteria. Nature 343: 60-62.

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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Please contact Dr. Steven Wilhelm (wilhelm@utk.edu) for additional information regarding this protocol.</p>
<p> </p>
<p>Modified from <span style="font-family: 'Segoe UI', sans-serif; font-size: small;">Schwyn, B. &amp; Neilands, J. B. Universal chemical assay for the detection and determination of siderophores.</span><span style="font-family: 'Segoe UI', sans-serif; font-size: small;"><em>Anal Biochem</em></span><span style="font-family: 'Segoe UI', sans-serif; font-size: small;">, 160:147-156 (1987).</span></p>

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TITLE: AFOG
AUTHORS: Joana G Antunes

[DESCRIPTION]
Staining technique largely used to diagnose ischemic cardiac lesions and kidney diseases, in particular the regeneration or scarring of the lesion. The selectivity in this method is due to the different affinity degrees between dyes and the macromolecules of the tissue. A key role is played by phosphomolybdic acid, which acts as a binding agent between tissue structures (collagen, fibrils, cell membranes) and aniline blue (amphoteric dye). Orange G, which is the second component of an AFOG solution, has no affinity for phosphomolybdic acid, and this is why it is used to stain all remaining structures. Acid fuchsin, conversely, dyes any protein deposits selectively.

[STEPS]
SECTION: Preparation
1. Warm the cryosections from the -80º freezer toRoom temperature  30 min ;

SECTION: Preparation
2. If gelatin embedded tissue, incubate in   15 min 37 °C ;

SECTION: Preparation
3. Fix the slides in 4% PFA for 5 minRoom temperature
 

SECTION: Preparation
4. Wash 1x in   5 min 

SECTION: Preparation
5. Wash 2x in   5 min 

SECTION: Preparation
6. Heat   60 °C 30 min 

SECTION: Staining
7. Place the slides in Bouin’s solution for 2h at 60ºC;
SECTION: Staining
8. Continue to stain in Bouin’s solution for an additional 1h at room temp (can be reused 3 times);
SECTION: Staining
9. Wash slides with dH2O 5-6 times for 5 min until the water comes out clear;
SECTION: Staining
10. Rinse slides in 1% Phosphomolybdic acid for 5 min (can be reused 2 times);
SECTION: Staining
11. Rinse slides in dH2O for 5 min;
SECTION: Staining
12. Rinse slides in AFOG staining solution for 10min (can be reused);
SECTION: Staining
13. Rinse slides in dH2O for 2 min;
TITLE: Tissue biopsy FFPE preparation
AUTHORS: kyu sang han, peihsun.wu

[DESCRIPTION]
Creating human tissue FFPE block from excisional biopsy, and sectioning to create H&E slides.

[STEPS]
SECTION: Tissue biopsy collection
1. Take excisional biopsy of human skin in abdomen or scalp
SECTION: Tissue biopsy collection
2. After excisional biopsy from a operating room (OR), place the skin tissue into a tissue container prefilled with buffered formalin for 12-24 hours at room temperature (RT)
SECTION: Tissue biopsy collection
3. Discard formalin, rinse with PBS, refill PBS, and leave the tissue in PBS for 1 minute
SECTION: Tissue biopsy collection
4. Take tissue out on a large Petri dish and measure the tissue size
5. Label a slotted cassette with a pencil with tissue ID and place the tissue in the cassette
6. Put cassette with the tissue back into the tissue container filled with PBS
SECTION: Paraffin Embedding
8. Embed cassette paraffin at 60 deg C and store at room temperature
SECTION: Paraffin Embedding
7. Dehydrate tissue by submerging cassettes into ethanol at increasing concentrations from 70% to 99%.
SECTION: FFPE sectioning
9. Section tissue and place on water bath to expand
SECTION: FFPE sectioning
10. Place expanded tissue section on a Superfrost Plus microscope slide
SECTION: H&amp;E stain
11. Stain with Hematoxylin and Eosin    
SECTION: H&amp;E stain
12. Place coverslip
TITLE: Sonication-induced fragmentation analysis of α-synuclein fibrils
AUTHORS: Arpine Sokratian

[DESCRIPTION]
This protocol is designed to quantify the fragmentation pattern of full-length α-synuclein fibrils, induced by ultrasonic frequencies through sonication. To ensure consistency, we have adopted the indirect 
water-bath sonication method, which offers a more controlled distribution of ultrasonic waves compared to the cup-horn technique. Our protocol involves multiple time-points of sonication, specifically at 1 minute, 2 
minutes, 10 minutes, 30 minutes, and 1 hour of sonication. We recommend analyzing the sonication-induced fragmentation of α-synuclein fibrils using dynamic light scattering measurements and acquisition electron 
micrographs for quantification of fibril length and size distribution

[STEPS]
SECTION: Amplification of α-synuclein fibrils
1. Prepare α-synuclein fibrils according to the protocol attached

 


SECTION: Concentration measurements
2. Measure concentration of fibrils according to the protocol step #5 
 

SECTION: Concentration measurements
3. Dilute fibrils to the concentration 5 mg/mL in PBS
  
Use protein-low binding tubes
  

SECTION: Concentration measurements
4. Prepare 20 ul aliquots as estimated sonication time-points: three-five technical replicates for each experimental sample, three separate sonication runs.   

SECTION: Concentration measurements
5. Place first round of replicates into the tube holder for the water-bath sonicator 
 

SECTION: Concentration measurements
6. Set the amplitude to 30%, temperature to 10 °C, adjust the water level in the water tank to align the liquid level in the tubes
Set the desired time for the first time-point (for example: 2 minutes)
SECTION: Concentration measurements
7. Collect the tubes after sonication, transfer 2 uL from each sonicated/technical repeat sample into eppendorf tube and dilute 100 times, then measure size range of fibrils using DLS
Collect 30 acquisitions with the acquisition time set for 10 seconds. 
See the protocol 
 

SECTION: Concentration measurements
8. Continue collecting the samples from the remaining time-points then repeat with another set of replicates. 
SECTION: Concentration measurements
9. Analyze the size distribution of small fibrils (ranging from 10 to 100 nm) at multiple time points
TITLE: Rebel Wilson Keto Reviews - Is It Fake Or Trusted Pills?
AUTHORS: rebelwilsonketoreviews  

[DESCRIPTION]
Rebel Wilson Keto Reviews - Is It Fake Or Trusted Pills?


[STEPS]
1. Rebel Wilson Keto Reviews - Is It Fake Or Trusted Pills?
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TITLE: Biolistic Transfection in Euplotes crassus (provisional)
AUTHORS: Angela Piersanti

[STEPS]
?. 105 vegetative Euplotes crassus cells or 105 mating DP1 and DP3 E. crassus strains (50 h after mixing) were placed on a filter paper soaked with 10 mM HEPES pH 7.4.
?. Shooting conditions were set as follows in the Bio-Rad Biolistic PDS-1000/He Particle Delivery System : rupture disk 1550 psi, helium pressure 1750 psi, vacuum 26 inches Hg, gap distance ⅜ inches, 1st shelf.
?. They were shot with 0.6 μm or 1.6 μm golden nanoparticles coated with 1.25 μg of the construct containing G418  resistance gene.
?. The filter paper was then fold and placed into 50 ml of sea water. After the transfection more than 50% of the cells were alive.
?. The antibiotic selection started after 24 h; increasing concentrations of G418 were added every 4 days, from 1 mg/ml up to 10 mg/ml.
TITLE: CNO Preparation and Consumption Monitoring
AUTHORS: Victoria Vance, Katerina Rademacher, Ken Nakamura

[DESCRIPTION]
Chemogenetic models utilize the consumption of clozapine N-oxide (CNO) to activate Designer Receptors Activated Only by Designer Drugs (DREADDs) in order to modulate neuronal activity. This protocol describes the preparation of a CNO solution for consumption by mice, as well as the daily monitoring of water intake. 

[STEPS]
SECTION: Materials and Solutions
1. Materials:
Clozapine N-oxide    
Sucrose   
Autoclaved water

SECTION: Materials and Solutions
2. Making CNO and vehicle water stock stolutions

 

SECTION: Materials and Solutions
2.1. CNO Water (2% sucrose, 200 mg/L CNO):
20g sucrose and 300mg CNO in 1L autoclaved water
Carefully weigh CNO to the nearest 0.05mg, then protect from light
Slowly add CNO in small amounts to autoclaved water while stirring, then add sucrose
Wrap bottle in foil to protect from light
SECTION: Materials and Solutions
2.2. Vehicle water (2% sucrose):
20g sucrose in 1L autoclaved water
SECTION: Monitoring water intake
3. On day 0, discard the autoclaved water, and give 10mL of medicated water (e.g. CNO or vehicle water) in a water bottle per mouse. Record the time when mice were given medicated water.

  
Guardian Hamster Water Bottle (Amazon cat: B0713XMP98)


SECTION: Monitoring water intake
4. Monitor water intake at the same time every day of the experiment.  

For each cage, perform the following substeps:
SECTION: Monitoring water intake
4.1. Remove from rack and check that there is sufficient food available on cage floor. Add more if needed.
SECTION: Monitoring water intake
4.2. Use a 10 or 25 mL serological pipette to measure how much water is still left in the bottle. Record this value.
SECTION: Monitoring water intake
4.3. For single-housed cages (e.g. mice with activity wheels), if water level is below 8.0 mL, use a clean pipette to add 5 mL more from the stock. If water level is below 4.0 mL, add 10 mL more. Record how much water is added.
SECTION: Monitoring water intake
4.4. For group-housed cages, top off with enough water to ensure at least 5mL per mouse plus overage (e.g. 15mL for two mice, 35mL for 5 mice).
SECTION: Monitoring water intake
4.5. Return cage to rack and repeat for remaining cages.
SECTION: Monitoring water intake
5. Enter recorded water levels into an Excel spreadsheet to track water intake per mouse over time.
TITLE: Environmental Exposures and Craniofacial Birth Defects: A Scoping Review Protocol.
AUTHORS: Maira Alejandra Moreno Castillo, João Victor Leite Dias, Sarah Alves Auharek

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><div class = "justify" style = "text-align:left"><span style = "font-weight:bold;">Introduction: </span><span>birth defects and congenital anomalies include a variety of pathologies that affect 2-3% of all newborns, with craniofacial birth defects (CFBD) such as neural tube defects (NTD) and orofacial clefts (OFC), being some of the most prevalent congenital anomalies in children. Since an individual may be exposed to pollutants present in the workplace, and at the same time, the population may be exposed to multiple sources of environmental contamination (for example water, soil and air) and socioeconomic deprivation, assess the possible association between environmental exposures, both at the individual and area level, it could improve the understanding of how these variables would affect pregnant women and the developing fetus. To provide an overview about updated information related to those factors and its association with NTD and OFC, we consider performing a scoping review. The aim of this publication is to present a scoping review protocol about the relationship between environmental exposures and the etiology of CFBD. </span></div></div><div class = "text-block"><div class = "justify" style = "text-align:left"></div></div><div class = "text-block"><div class = "justify" style = "text-align:left"><span style = "font-weight:bold;">Methods and analysis:</span><span> the identification of the papers for this review was done through a search strategy using MeSH vocabulary, in the electronic database PUBMED MEDLINE and SCIELO. Additionally, we performed a gray literature search using Google Scholar. All the selected studies for the review were subjected to methodological quality assessment, according to the Joanna Briggs Institute protocol for scoping reviews. </span></div></div><div class = "text-block"><div class = "justify" style = "text-align:left"></div></div><div class = "text-block"><div class = "justify" style = "text-align:left"><span style = "font-weight:bold;">Ethics and dissemination:</span><span> a paper summarizing the findings from this review will be published in a peer-reviewed journal. Ethical approval is not required. </span></div></div></div>

[STEPS]
TITLE: SenNet Participant Selection Criteria for Breast Tissue
AUTHORS: kschneider

[DESCRIPTION]
SenNet Participant Selection Criteria for Breast Tissue.  Tissue was acquired from the Komen Tissue Bank: https://komentissuebank.iu.edu/donate-tissue/donation-procedure.php based on H&E slide from the KTB study (https://doi.org/10.1186/s13058-020-01322-6) and availability of frozen tissue or tissue FFPE or PFPE blocks.

[STEPS]
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Lipid peroxidation (LP) is determined by quantifying the malondialdehyde (MDA) content in the homogenate supernatant in the caudal adjacent segment to epicenter by colorimetric reaction with thiobarbituric acid (TBA) at high temperatures. Malondialdehyde is the principal and most studied product of polyunsaturated fatty acid peroxidation.</p>

[STEPS]