eamag/protocols-with-steps huggingface dataset:
TITLE: Deep Cleaning Bacteria Incubator
AUTHORS: Kenneth Schackart

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol details how to deep-clean the bacteria incubator (Fisher Scientific Isotemp 637F). This cleaning should be performed at least every 4 months during regular usage, more frequently under heavy usage. Full Owner's Manual is attached to this protocol as a link (I do not claim any credit in the development of that document; it is for reference only)</div></div>

[STEPS]
?. [Disassemble]
Before beginning any work on the incubator, turn off the power using the switch at the bottom.
?. [Disassemble]
Remove incubator door:Loosen the screws on the inside of the hinges (hold the door so it doesn't fall when released).Slide door out of the hinges by pulling outward.The hinge on the top will fall out when the door is removed, or come off with the door.Each hinge has a small plastic bushing the goes between the hinge and the incubator; do not lose these bushings.Set aside for now on lab bench.
?. [Disassemble]
Remove rack shelving by pulling straight outward. Set aside for now on lab bench.
?. [Disassemble]
Remove the shelf holders:Make note of the placement of each shelf at this time.Each horizontal shelf holder can be removed by lifting up, rotating the bottom up/out, then sliding the top downward and out.Set aside for now on lab bench.
?. [Disassemble]
Remove vertical mounts:Make note of the orientation of the mounts at this time.Remove the screws holding the mount in place; 2 screws per mount.Set aside for now on lab bench.
?. [Disassemble]
Remove the bottom tray:Undo the 2 screws holding the tray in place.Lift the tray straight up to remove (this may be assisted by inserting a small curved metal pick into the holes to help lift the back end up).Set aside for now on lab bench.
?. [Wash]
Using a sponge, wash all interior surfaces of the incubator with VersaClean solution (or other laboratory cleaner - do not use bleach on stainless steel).My recommendation is to dip the sponge in cleaner, and scrub one surface (e.g. the top) with VersaClean, then wring sponge into a waste container and rewipe surface. This should leave the surfaces only slightly damp, not wet.Work from the top-down: top, sides, then bottom last.Avoid the mechanical moving parts on the bottom, or be cautious in washing them.
?. [Wash]
Spray all interior surfaces with EtOH and wipe with paper towels, but avoid directly spraying the mechanical moving parts on the bottom.
?. [Wash]
Using a sponge with VersaClean, wash the door and all interior parts including the rack mounts, racks, and shelf holders. Spray with EtOH to disinfect just prior to reinstalling.
?. [Reassemble]
Reassemble the incubator by reversing the disassembly instructions.
?. [Reassemble]
Allow the incubator to completely dry before closing door or powering on, especially since ethanol vapor is flammable!
TITLE: Step 1: Swab sample collection
AUTHORS: Peter H L Krijger, Tim A Hoek, Sanne Boersma, Lieke I P M Donders, Maaike M C Broeders, Mark Pieterse, Pim W Toonen, Ive Logister, Bram M P Verhagen, Marjon J A M Verstegen, Thomas W van Ravesteyn, Rene J T M Roymans, Francesca Mattiroli, Jo Vandesompele, Monique Nijhuis, Stefan Meijer, Anton van Weert, Edwin Dekker, Fred J Dom, Rob Ruijtenbeek, Lieven B J van der Velden, Jeroen H B van de Bovenkamp, Martijn Bosch, Wouter de Laat, Marvin E Tanenbaum

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">One of the most critical innovations within STRIP is the collection of samples in small tubes (0.8 ml compared with 5–15 ml in standard diagnostics) with virus-inactivating and RNA-stabilizing lysis buffer (InActiv Blue) spiked with a control RNA (PDV). The use of small tubes enables the collection of sample tubes in small 96-tube boxes at sample collection sites. These 96-tube boxes are directly compatible with automated sample processing in the lab without slow and often laborious transfer of samples from collection tubes to plates that are compatible with robotics.</div><br/><br/><br/><br/><br/></div>

[STEPS]
?. [Sample collection]
Person 1 scans the 2D barcode at the bottom of a 0.8 ml Micronic tube prefilled with 0.4 ml virus transport buffer and places it in a Micronic tube rack (tube rack A).
?. [Sample collection]
Person 1 removes cap from the Micronic tube using the manual recapping device (cap stays on the recapping device).
?. [Sample collection]
After instructing the patient to blow their nose, the naso- oropharyngeal swab specimen is collected by person 2 using 1 flocked swab using standard procedures. Importantly: Make sure no mucus is attached. Repeat swab collection when needed.
?. [Sample collection]
Person 2 places the swap in the tube placed in tube rack A, rotates the swab 10 times between thumb and index finger, and trashes the swab.
?. [Sample collection]
Person 1 close the tube with the cap and transfers the tube to a new tube collection rack (tube rack B).
?. [Sample collection]
Store at room temperature until shipment to the RNA extraction site. Samples are processed as soon as possible after arrival at the lab. Samples are regularly processed within 24h but can be stored up to 72h if required.
TITLE: Rotarod test
AUTHORS: Chuyu Chen

[DESCRIPTION]
Motor learning was assessed with an accelerating rotarod. 

[STEPS]
1. The task was done using a rotarod apparatus (Panlab) equipped with a mouse rod (3 cm diameter) and set to 4–40 rpm acceleration over 300 seconds. 
2. The task consisted of daily sessions (five trials per session; intertrial-interval = 15 s, max trial duration = 300 s)
3. Mice were placed on the accelerating rotarod. The time of mouse fell from the rod was recorded. The mean of 5 trials is used for the final analysis
TITLE: SPARC Cat - Sham Control Chronic Cat 1 Day 30
AUTHORS: Brett           Hanzlicek, Anna Rietsch, Margot Damaser

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This is a procedure for a sham control chronic cat experiment (Day 30-terminal) for cystotomy (bladder surgery).  The cystotomy is performed without UroMOCA implantation.  The cat is observed daily and imaged on day 0, 14 and 30 to track changes to the bladder and overall cat health in response to the cystotomy.  This protocol  incudes urodynamics and imaging for Day 30 in the chronic experiments.</div></div>

[STEPS]
?. [Transport Cat]
Transport cat from housing site to surgery site.
?. [Animal Prep and catheter placement]
Animal is anesthetized and abdomen is shaved by the vet team.  The cat is then moved into the surgery room and attached to monitors by the vet team.
?. [Animal Prep and catheter placement]
Drape animal and perform betadine scrub on abdomen and genitals.
?. [Animal Prep and catheter placement]
Put surgilube on 3.5Fr catheter and insert into bladder through the urethra.  Advance the catheter until resistance is met, then pull back 2-3cm.
?. [Animal Prep and catheter placement]
Use gentle suction with syringe to withdraw urine from bladder through the catheter.  Measure the volume and save the urine for urinalysis.  urine removed
15 mL
?. [Cystogram - DYNA CT]
Use 1:5 dilution of contrast to saline to visualize bladder.Fill the bladder with   contrast and take a single CT image.Add   more to bladder (total of 20ml) and take single CT imageAdd   more to bladder (total of 30ml) and take single CT imageTake a 3D CT image with 30ml contrast:saline in the bladder
10 mL
10 mL
10 mL
?. [Cystogram - DYNA CT]
Empty Bladder
?. [Urodynamics/Cystometry 1]
Performed after cat is transferred from Isoflurane to propofol anesthetic.
Fill rate is 2ml saline/minute using syringe pump.
Data is recorded using Labview software.
Pressure is recorded using an external pressure transducer connected to syringe pump on one end and tubing that leads to the catheter on the other end.
?. [Urodynamics/Cystometry 1]
Fill bladder with saline and record pressure using pressure transducer connected to  LabViewFill to  ; Peak pressure around 20 cmH2OFill to  ; Peak pressure around 34 cmH2OTug on catheter after filling to visualize contraction in Labview software
13.9 mL
20 mL
?. [Urodynamics/Cystometry 1]
Empty Bladder
?. [Urodynamics/cystometry 2]
Fill bladder with saline at 2ml/min
?. [Urodynamics/cystometry 2]
Fill to  ; End round 2 urodynamics
15 mL
Appears bladder capacity is around 15-20 ml
?. [Euthanasia]
Cleveland Clinic animal team euthanizes the animal
?. [Dissection/Histology]
Bladder is removed, examined and placed in formalin for histological analysis
TITLE: URMC TriState SenNet TMC Mouse Donor Selection Criteria
AUTHORS: Gagandeep Kaur, Irfan Rahman

[DESCRIPTION]
This document outlines the required criteria for donor inclusion of mouse lung specimens in the TriState SenNet TMC Biospecimen Core at the University of Rochester, as part of the Cellular Senescence Network Program (SenNet). 
The study intends to outline the effect of age on the cellular senescence in mice and intends to describe the translatability of obtained results. 

[STEPS]
SECTION: Inclusion Criteria
1. Age: Adult mice. Two age ranges: 
                                                        Young Adults : 2-6 months
                                                         Old adults (geriatric) : 18-24 months
SECTION: Inclusion Criteria
2. Sex: Both sexes were included.
SECTION: Inclusion Criteria
3. Strain: C57Bl/6J mice were procured from Jackson Laboratory. Mice were housed for 1 week at the University of Rochester Vivarium with a 12-hour light/12-hour dark cycle. 
SECTION: Inclusion Criteria
4. Health Status: No known health issues or abnormalities approved by the Veterinary staff at the University of Rochester Vivarium facilities.
SECTION: Exclusion Criteria
5. Infection/Disease: The animals were housed in a Helicobacter- and pathogen-free facility. Necessary precautions (use of microisolator technique, one-way MIT rooms) were taken to ensure that the study animals did not have any infection or disease state prior to conducting of experiments.
TITLE: SOP – 2-step protein fractionation (Triton) from fly heads
AUTHORS: ALFONSO.M.PENA

[DESCRIPTION]
SOP – 2-step protein fractionation (Triton) from fly heads

[STEPS]
SECTION: Protocol
4. Collect 20-40 fly heads via Snap Freeze method into a Biomasher tube and transfer tubes to CTRND on dry ice.
SECTION: Protocol
5. Turn on Sorvall ultracentrifuge and set temperature to 4degC, place rotor inside and turn on vacuum to allow internal temperature to set.
SECTION: Protocol
6. Add 50uL (2.5uL/fly head) of 1% TritonX-100 with PPI to heads in Biomasher II tube and homogenize for 1.5 min with a hand-held automatic homogenizer and Biomasher pestles.
SECTION: Protocol
7. Briefly spin down in tabletop centrifuge to get the liquid to the bottom of the tube.
SECTION: Protocol
8. Sonicate at 35% with 5 one-second pulses for tissue to break down/dissolve. Skip this step for ‘non-sonicated’ extractions.
SECTION: Protocol
9. Clarify by centrifugation in a tabletop centrifuge (2,100g) for 15 seconds.
SECTION: Protocol
10. Move entire liquid sample into ThermoScientific    1.5ml microtube WX und MX (Cat #314352H01) before centrifuging
SECTION: Protocol
11. Centrifuge the supernatant at 100,000 g (29,900 rpm) for 30 min at 4°C using the chilled rotor.
SECTION: Protocol
12. Remove and save Supernatant into new labeled collection Eppendorf (soluble fraction).
SECTION: Protocol
13. Wash the pellet by adding 50uL of TritonX-100 with PPI and centrifuging at 100,000 g for 15 min at 4°C. Discard the supernatant.
SECTION: Protocol
14. Resuspend pellet in 50ul (2.5ul/fly head) in TritonX-100 with PPI by sonication with 3 one-second pulses or until it is fully resuspended. Label and save (insoluble fraction)
SECTION: Protocol
15. Perform BCA. If strapped on time, samples can wait to be quantified and stored at -80C.
SECTION: Reagents Needed:
1.  Protease and Phosphatase Inhibitors (cOmplete 04 693 124 001, PhosphoSTOP 04 906 837 001)
SECTION: Reagents Needed:
2. Triton X-100 (Millipore Sigma, Cat# T9284)
SECTION: Reagents Needed:
3. NaF (Sigma-Aldrich, Cat# S7920)
SECTION: Reagents Needed:
3.1.
TITLE: XPRIZE SANATA Protocol for Saliva LFIA Test
AUTHORS: Mario Thomas, Jasmine Sollen, Natalia Ivanova, Michelle Feng, Reda Fayek, Heidi Abdilla, Stephanie Lim, Amanda Naaum, Holly  Rumery, Mario Escobar

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This procedure outlines the protocol for testing for SARS-CoV-2 using a saliva sample collected from an individual. The purpose of this test is to detect low levels of SARS-CoV-2 antigen at a higher sensitivity. Precision Biomonitoring Inc. developed an ultra-rapid digital, disposable, highly-sensitive and inexpensive testing device used for screening purposes. The mobile app complementary to this medical device is connected through Bluetooth. Using this innovation, the user can be tested at point-of-care (POC) by a health care professional, and obtain qualitative results. </div></div>

[STEPS]
?. [Setting up the test]
Refrain from consuming food or beverage (including water) for 30 minutes before providing a saliva sample.
Ensure the smartphone is fully charged and Bluetooth on the smartphone is turned on. The mobile app should be downloaded and ready to run.
When working with human saliva and other human bodily fluids, pathogens may be present. Wear gloves and wash your hands immediately after removing the gloves.
?. [Preping ingredients]
Collect saliva in
?. [Preping ingredients]
Transfer   of saliva into the using the
1 mL
?. [Preping ingredients]
Mix the saliva-buffer mixture using the by squeezing the bulb of the pipette 10 times slowly in the Saliva Lysis Tube from Step 3.
?. [Preping ingredients]
Let saliva-buffer mixture sit at   for   before transferring mixture to LFA Device.
0 Room temperature
?. [Using the Testing device ]
Using the Apply  of the saliva-buffer mixture into the sample port of the
100 µl
?. [Using the Testing device ]
Place the device on a flat surface. Let the sample mixture run undisturbed for  at  .
0 Room temperature
?. [Using the Testing device ]
Ensure the smartphone is connected to the testing device through Bluetooth and read the results using the mobile phone app.
The result will appear on screen as positive, negative, or inconclusive. If the result is inconclusive, conduct another test with a new device.
TITLE: Efficacy of proton pump inhibitor (PPI) therapy in treating sleep disturbances in patients with gastroesopahgeal reflux disease (GERD): a systematic review and meta-analysis
AUTHORS: Yeseong  Kim, Fahmi Shibli, Takafumi Kubota

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The review question: What is the clinical effectiveness of proton pump inhibitor (PPI) therapy on sleep</div><div class = "text-block">disturbances in patients with gastroesophageal reflux disease (GERD)?</div><div class = "text-block">The following databases should be use: CENTRAL; MEDLINE; EMBASE; WHO-ICTRP; ClinicalTrials.gov.</div><div class = "text-block">Types of study to be included: Prospective, randomized controlled trials describing PPI therapy for patients with GERD and sleep disturbances will be assessed for eligibility. Crossover studies, cluster</div><div class = "text-block">randomized studies, will be excluded. Studies conducted by quasi-experimental methods will be excluded. Retrospective studies will be excluded. No exclusion will be made for observation periods.</div><div class = "text-block">Main outcome(s): Change in sleep time and quality.</div><div class = "text-block">Additional outcome(s): Change in pH impedance parameters (acid exposure, number of refluxes episodes); Change in reflux symptoms; All adverse events: Proportion of people who developed an adverse event according to the original author's definition.</div><div class = "text-block">We will perform meta-analysis of the above outcomes using random effect models.Besides, we will assess heterogeniety and publication bias.</div></div>

[STEPS]
TITLE: TS Procure 812 - primary fixation Karnovsky&#39;s - tissue (TM - 013)
AUTHORS: sandra.crameri

[DESCRIPTION]
The method is used to process conventionally EM fixed 1mm3 tissues to Procure 812 resin blocks. 

[GUIDELINES]
Sample is not optimal for EM, best to dissect and use only the outer 2mm of tissue mass. Sample is usually derived from histology.

[STEPS]
SECTION: HEADER
1. SAN:




SPEC No:




OPERATOR & STEPS:




OPERATOR & STEPS:
SECTION: Conventional
2. Karnovsky's fixative: 2.5 % volume   and 4 % volume   in 0.1 Molarity (M) Sorenson's Phosphate buffer (pH 7.2, 300mosmol/kg) for at least 40 min  or overnight

SECTION: Conventional
3. 0.1 Molarity (M) buffer 15 min 

SECTION: Conventional
4. 1 % volume   in buffer 60 min 

SECTION: Conventional
5. 70 % volume   for at least 20 min  or overnight

SECTION: Conventional
6. 95 % volume    20 min 

SECTION: Conventional
7. 100 % volume    20 min 

SECTION: Conventional
8. 100 % volume    dried with molecular sieve 20 min 


SECTION: Conventional
9. 50 % volume   50 % volume   20 min 

SECTION: Conventional
10. 100 % volume   20 min 

SECTION: Conventional
11. 50 % volume   50 % volume Procure 812


SECTION: Conventional
12. 100 % volume Procure 81220 min 

SECTION: Conventional
13. 100 % volume Procure 812 60 min 

SECTION: Conventional
14. Embed & polymerise overnight in oven at 60 °C
TITLE: UC Davis - Lipoprotein Binding Protein (LBP)-Endotoxemia Assay
AUTHORS: Trina Knotts

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary: </span></div><div class = "text-block">Plasma samples will be assayed for lipopolysaccharide binding protein (LBP) as surrogate for bacterial LPS/measure of endotoxemia via ELISA.</div></div>

[STEPS]
?. Prepare kit reagents.
?. Dilute mouse plasma or serum samples 1:800.
?. Add 100 μl of standards (50, 25, 12.5, 6.25, 3.12, 1.56 ng/ml) or diluted samples in duplicate into the corresponding wells of the precoated modules and incubate for one hour at room temperature and shaking (300rpm).
?. Wash 3X with Wash Buffer.
?. Add 100 μl detecting antibody to each well and incubate at room temperature for 1 hour at shaker.
?. Wash 3X with Wash Buffer.
?. Add 100 μl Substrate solution to each well. Incubate 12-14 min in the dark at room temperature without shaking.  Cover with foil during incubation or place in drawer.
?. Add 100 μl stopping solution to each well. Tap gently to mix.
?. Read absorbance at 450 nm (reference wave length 620 nm)
?. Calculate the LBP concentration by first plotting the OD means of standards (y-axis) and the LBP concentration (x-axis). Calculate the LBP concentration from the mean OD of samples from the standard curve and multiply with dilution factor.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This protocol describes how to make chemically competent <em>Escherichia coli</em> cell.</p>
<p>For the protocol <em></em><em>E. coli</em> strain NEB Tubo was taken.</p>

[BEFORE_START]
<p>Make sure you have the following solutions:</p>
<p> </p>
<ul>
<li><strong>TYM</strong>
<ul>
<li>Bacto-tryptone 20g/L</li>
<li>Yeast extract 5g/L</li>
<li>NaCl 100mM</li>
<li>MgSO<sub>4</sub> 10mM</li>
</ul>
</li>
<li><strong>TfB1</strong><br />
<ul>
<li>KAc 30mM (pH5.8)</li>
<li>KCl 100mM</li>
<li>CaCl<sub>2</sub> 10mM</li>
<li>Glycerol 15%</li>
<li>(Add after autoclaving 5% vol. MnCl<sub>2</sub> 1M)</li>
</ul>
</li>
<li><strong>TfB2</strong>
<ul>
<li>Na-MOPS 10mM</li>
<li>CaCl<sub>2</sub> 75mM</li>
<li>KCl 10mM</li>
<li>Glycerol 15%</li>
<li>Adjust pH 6.8 - 7.0</li>
</ul>
</li>
</ul>

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

[DESCRIPTION]
<p>For promoting the successful aging of elderly residents of Chang Gung Silver Village in Taiwan, five interactive exergames were developed to promote the well-being of the elderly. The exergames included both physical games and cognitive games and were implemented using various computer-based technologies in the Chang Gung Silver Village. The exergames were trialed by 39 elderly residents (15 male, 24 female; mean age 79.5 ± 17.5 years) of Chang Gung Silver Village. Following the trials, the participants were requested to complete a Technology Acceptance Model 2 (TAM2) questionnaire. The results showed that the perceived playfulness and perceived usefulness of the exergames were significantly related to the users’ usage behavior and intention to use for both the physical games and the cognitive games. However, a relationship between the output quality of the game and the usage behavior was apparent only in the case of the cognitive exergames. Finally, the impact of social influence on the intention to use and the usage behavior was more pronounced for the physical exergames. Overall, the results revealed that the acceptance of exergames by the elderly depends not so much on the awareness of fun in using the game, but the perceived usefulness of the related physical and cognitive abilities.</p>

[BEFORE_START]
<p><span lang="EN-US" style="color: red;">They signed the inform-concern to know that they could discontinue the tests if discomfort developed including dizziness. We provided an assistant for each elder to protect and prevent injury.</span></p>

[GUIDELINES]
<p>Participates have enrolled from Chang Gung Silver Village participated in this study. All of them are walking and living independently without physical or cognitive impairment. Those with the neuromuscular or musculoskeletal disease, permanent impairment of cardiopulmonary function, poor balance, frailty, and poor vision people were excluded in this study.</p>

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

[DESCRIPTION]
<p>The Modified Ziehl-Neelsen stain (mZN stain) is a type of differential bacteriological stain used to identify acid-fast organisms, mainly <em>Mycobacteria</em>. Acid fast organisms are those which are capable of retaining the primary stain when treated with an acid (<em>fast=holding capacity</em>). Members of the Actinomycetes, genus <em>Nocardia</em> (N. <em>brasiliensis</em> and N. <em>asteroides </em>are opportunistic pathogens) are partially acid-fast. Oocysts of coccidian parasites, such as <em>Cryptosporidium</em> and <em>Isospora</em>, are also acid-fast. Hence they can also be detected and identified through mZN staining procedure.</p>

[STEPS]
?. 
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?. 
?. 
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?. 
?. 
?. 
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