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

[DESCRIPTION]
<p>This protocol has been tested by me on human adult colon samples and given good results for scRNAseq. I suggest that you do an enrichment step afterwards, because the dissociation can be quite variable results in terms of the fraction of immune vs non-immune cells that are retreived.</p>

[STEPS]
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TITLE:   ELISA for quantification of IL-9 in human serum or plasma.
AUTHORS: Angel  Justiz-Vaillant

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Interleukins (IL) are a type of cytokine first thought to be expressed by leukocytes alone but have later been found to be produced by many other body cells. They play essential roles in the activation and differentiation of immune cells, as well as proliferation, maturation, migration, and adhesion. They also have pro-inflammatory and anti-inflammatory properties. The primary function of interleukins is, therefore, to modulate growth, differentiation, and activation during inflammatory and immune responses. Interleukins consist of a large group of proteins that can elicit many reactions in cells and tissues by binding to high-affinity receptors in cell surfaces. </div><div class = "text-block"><span>Th9, Th2, Th17, mast cells, NKT cells, and regulatory T cells produce interleukin-9. It enhances T-cell survival, mast cell activation and synergy with erythropoietin.</span><a href="https://www.ncbi.nlm.nih.gov/books/NBK499840" style = "text-decoration:underline;color:blue;cursor:pointer;"><span style = ":;">[1]</span></a></div><div class = "text-block">Reference</div><div class = "text-block"><span>1. Justiz Vaillant AA, Qurie A. Interleukin. In:</span><span style = "font-style:italic;">StatPearls</span><span>. Treasure Island (FL): StatPearls Publishing; June 12, 2019.</span></div></div>

[STEPS]
?. An anti-human IL-9 coating antibody is adsorbed onto microwells by incubation overnight at 4°C.
?. Add 50 µl  of human serum. Human IL-9 present in the serum sample binds to antibodies adsorbed to the microwells.
?. The microplate is blocked with 3% non-fat milk-PBS buffer and later wash to remove unbound proteins.
?. Fifty (50) µl of biotin-conjugated anti-human IL-9 antibody is added. The optimal dilution must be investigated.
?. The microplate is rewashed with PBS-Tween 20 buffer, pH 7.4.
?. One hundred µl of streptavidin-HRP conjugate is added and it binds to the biotin-conjugated anti-human IL-9 antibody. The optimal dilution of this conjugate must be investigated.
?. The plate is washed following incubation to remove the unbound Streptavidin-HRP.
?. Add 100 µl of 3,3',5,5'- tetramethylbenzidine (TMB; Sigma-Aldrich) to each well.
?. Incubate the microwells in the dark for 15 min.
?. A colored product is formed in proportion to the quantity of human IL-9 present in the sample or standard.
?. The reaction is terminated by addition of 100 µl 3M H2SO4  and absorbance is measured at 450 nm.
?. A standard curve is made from 7 human IL-9 standard dilutions and the human IL-9 sample concentration determined.
?. For better results place the microplate on a plate shaker in every incubation.
TITLE: Oplexx Keto Reviews How Does It Helps in Weight Loss?
AUTHORS: greendolphinummiereviews  

[DESCRIPTION]
Oplexx Keto Reviews How Does It Helps in Weight Loss?


[STEPS]
1. Oplexx Keto Reviews How Does It Helps in Weight Loss?
Oplexx Keto Reviews 
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That's why numerous people are turning to keto diet tablets to help them go into ketosis and lose weight. Ketosis requires a month or further of violent exercise and complete elimination of carbohydrates from the diet. As a result, the request for keto-friendly foods and supplements is now booming. Then at Oplexx Keto, we've experts that have done expansive exploration and have discovered the most effective combination. It helps with weight loss by raising fat burning rates and, as a consequence, enhancing overall health. This product doesn't need any salutary changes or emphatic exertion. 
As a result, the great maturity of us choose this option to stay in shape on a regular base. The each-natural constituents in this mix help with fat reduction and body sculpturing for a more seductive appearance. It boosts a person’s energy situations and assists in weight reduction without causing any unwanted side goods. As a consequence, the vulnerable system is strengthened, and illness is avoided. Visit the company’s website to read what others have to say about the product. It improves overall health by reducing inflammation in the body. 
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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
This protocol describes how to recrystallize <span style="font-weight: 400;">dimethylglyoxime in order to purify it for use in measuring total dissolved and labile cobalt using cathodic stripping voltammetry. This procedure makes a 0.1 mol L<sup>-1 </sup>DMG solution.</span>

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TITLE: SOP for RT (Reverse Transcription) Promega kit
AUTHORS: Malu G Tansey

[DESCRIPTION]
SOP for RT (Reverse Transcription) Promega kit

[STEPS]
SECTION: SOP:
2. Prepare per sample: 

 

SECTION: SOP:
3. Heat samples at 70°C for 5 min (prepare mix for step 4).
SECTION: SOP:
4. Snap freeze samples at +4°C or on ice for a minimum of 5 min.
SECTION: SOP:
5. Prepare RT mix (vol per samples, calculate for all your samples + 1):


 

SECTION: SOP:
6. Brief centrifugation.
SECTION: SOP:
7. RT program 	

 

SECTION: SOP:
8. Add 30 ul of H2O to bring volumne to 50 ul.
SECTION: SOP:
9. Once it is done, cDNA can be stored at -20°C
SECTION: Before:
1. Take from the kit: OligodT, RT buffer (5x), MgCl2, dNTP mix, and H2O to thaw- you can keep them on ice or at RT for a little while.
TITLE: Eye scan pattern 
AUTHORS: Christophe Lounis

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of this study is to evaluate the expertise of certified pilots vs. novice on visual behavior strategies and performances. This study focuses mainly on the visual strategies used in the transition from one instrument to another.</div><div class = "text-block">An eye-tracking study was conducted while pilots (n = 16) and novices (n = 16) performed a manual landing task. During this task, pilots performed twice three different randomized manual landing scenarios. Scenario 1 corresponded to a nominal manual landing. In the two others landings scenarios, pilots were asked to perform a supplementary monitoring task (double-task).The monitoring task consisted in read aloud the distance in nautical miles (Nm) between the aircraft and a designed radio beacon. The pilots were asked to call out the distance either every 0.5Nm (scenario 2) or every 0.2 Nm (scenario 3). Furthermore, the pilot had to comply some specific instructions related to the flight plan such as maintain a speed of 130 knots, a vertical speed between +500 ft/min and -800 ft/min, which corresponds to a usual landing according to Toulouse-Blagnac Airport. A Smart Eye system recorded eye movements of the pilots. The cockpit has been divided into several Areas Of Interest, corresponding to the flight instruments. </div><div class = "text-block">We are looking for invariants in pilots in the way to explore flight instruments that we do not expect to find in novices. In addition, we expect to find better flight performance among certified pilots. Finally, we expect that finding some patterns in scenario 1, still present among pilots in scenarios 2 and 3, we do not expect to find these results among novices.</div><div class = "text-block">A homemade algorithm was used to compare the patterns from two to eight consecutive AOIs between groups and between conditions.</div></div>

[STEPS]
?.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<span class="cit-title">This protocol is based on one described by Li et al. (2010) and has been modified to work in a college laboratory setting. The protocol is from:<br />James <span class="cit-auth cit-auth-type-author">M. Burnette III</span><span class="cit-sep cit-sep-two-item-separator"> and</span> <span class="cit-auth cit-auth-type-author">Susan R. Wessler (2013) <a href="http://www.genetics.org/content/193/2/367.full" target="_blank">Transposing from the Laboratory to the Classroom to Generate Authentic Research Experiences for Undergraduates</a></span></span><span class="cit-auth cit-auth-type-author"> </span><em>Genetics</em><span class="cit-print-date"> </span><span class="cit-vol">193<span class="cit-sep cit-sep-after-article-vol">:</span></span><span class="cit-pages"><span class="cit-first-page">367</span><span class="cit-sep">-</span><span class="cit-last-page">375</span></span><span class="cit-sep cit-sep-after-article-pages">; </span><span class="cit-doi"><span class="cit-sep cit-sep-before-article-doi">doi:</span>10.1534/genetics.112.147355<br /><br />Students need approximately 1.5 hours to extract DNA from up to five samples and the protocol can be carried out over several class periods by stopping at steps 6 and 9. Please see the <a href="http://www.genetics.org/content/193/2/367.full" target="_blank">full manuscript</a> for additional details.<br /></span>

[GUIDELINES]
This protocol is based on one described by LI et al. (2010) and has been modified to work in a college laboratory setting. Students need approximately 1.5 hours to extract DNA from up to five samples and the protocol can be carried out over several class periods by stopping at steps 6 and 9.<br /><br /><strong>Materials list:</strong><br />Extraction Buffer (100 mM Tris, pH 8.0, 50 mM EDTA and 500 mM NaCl)<br />10% SDS (sodium dodecyl sulfate)<br />5M KOAc (Potassium Acetate)<br />1 5 cm by 5 cm piece of Miracloth (Calbiochem, La Jolla, CA)<br />100% Isopropanol<br />70% Ethanol<br />Sterile water<br />Ice<br />Liquid nitrogen<br />65˚C heating block<br />Sterile 1.5 ml tubes (2 for each prep)<br />Mortar and pestle<br /><br />All chemicals were purchased from Fisher Scientific.

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TITLE: Protein interaction network analysis for Mendelian diseases
AUTHORS: Nikoleta Vavouraki, James E. Tomkins, Eleanna Kara, Henry Houlden, John Hardy, Marcus J. Tindall, Patrick A. Lewis, Claudia Manzoni

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This protocol describes the steps to use experimentally validated human data to create a protein-protein interaction network (PPIN) based on disease causative genes. Network analysis (combination of topological functional analyses) will lead to the identification of biological processes relevant for disease and disease endophenotypes.</div></div>

[STEPS]
?. [Generation of PPI network]
Select the protein products of genes relevant for disease (seeds).
?. [Generation of PPI network]
Use the selected seeds as input to query the PINOT webtool  (Tomkins et al., 2020) [http://www.reading.ac.uk/bioinf/PINOT/PINOT_form.html] or any  other webtool that retrieves protein interactions from literature.
?. [Generation of PPI network]
Screen the PPIs (protein-protein interactions) provided from PINOT to remove PPIs with a final score
?. [Generation of PPI network]
Score each node in the network based on the number of seeds to which it connects.
?. [Generation of PPI network]
Select all nodes interacting with more than one seed.
?. [Generation of PPI network]
Extract a subnetwork composed of the nodes selected in step 5. and all the connected seeds.
?. [Enrichment analyses]
Evaluate the functions associated with the PPIN using Gene Ontology terminology (Biological Processes [BPs] and Cellular Components [CCs] Gene Ontology [GO] annotations).
?. [Enrichment analyses]
Group the enriched BP and CC GO terms by semantic similarity into semantic classes.
?. [Enrichment analyses]
Remove the GO terms classified in the semantic classes “general” and “metabolism” as they refer to GO terms that provide limited functional specificity to the analysis.
?. [Enrichment analyses]
Cluster the semantic classes into functional blocks and location blocks, respectively.
?. [Enrichment analyses]
Evaluate the consistency of the results using 3 independent online tools, g:Profiler (RRID:SCR_006809)[https://biit.cs.ut.ee/gprofiler/gost], Gene Ontology using Panther’s tool (RRID:SCR_004869) [http://pantherdb.org/] and WebGestalt ( RRID:SCR_006786) [http://www.webgestalt.org/].
?. [PCA & Hierarchical clustering]
In order to compare functional enrichment profiles, retrieved for different parts of the network, reduce data dimension for example conducting Principal Component Analysis (PCA) through R (RRID:SCR_001905, v. 4.0.2) using the prcomp() function of the stats package.
?. [PCA & Hierarchical clustering]
Conduct the hierarchical clustering using the hclust() function (R stats package) using Euclidean as a distance measure for row clustering.
?. [PCA & Hierarchical clustering]
Choose the best fit for the number of clusters derived from Hierarchical clustering based on the Silhouette method (Rousseeuw, 1987) and the Multiscale bootstrap resampling method (Suzuki and Shimodaira, 2006) (R package “pvclust”).
TITLE: No Title
AUTHORS: 

[GUIDELINES]
<p><strong>Materials:</strong><br /><br /></p>
<ol>
<li>Virus prep.</li>
<li>Lysing Solution (LS).</li>
<li>5M Sodium Perchlorate (SP).</li>
<li>Mercaptoethanol.</li>
<li>Ethanol 76% &amp; 95%.</li>
<li>Phenol – [Chloroform: isoamyl alcohol (25:1)] in the proportion equal to 1:1 .</li>
<li>TE : (10mM Tris-Hcl,1mM EDTA, pH 8.0 in 100ml water).</li>
<li>3M or 5M Sodium Acetate.</li>
</ol>
<p><strong><strong><br />Solutions:</strong></strong></p>
<p><strong><strong><br /></strong></strong>Sodium Perchlorate , 5. M</p>
<p>In 70ml water : Dissolve anhydrous perchlorate (NaClO4; 61.2g/100ml)</p>
<p>Or monohydrate (NaClO4 H2O; 70.0g/100ml)</p>
<p>Bring to 100ml with water.</p>
<p>Make fresh for each use.</p>
<p> </p>
<p>Lysing Solution (2x) (100mM Tris-HCl, 0.3 M NaCl, 20mM EDTA,</p>
<p>And 2 % (w/v) SDS,pH 8.0)</p>
<p>In 50ml of water :</p>
<p>Add 10ml of 1.0 M Tris-HCl (pH 8).</p>
<p>Add 20ml of 0.1M EDTA (pH 8).</p>
<p>Dissolve 1.8 g NaCl.</p>
<p>Dissolve 2.0g SDS (Sodium Dodecyl Sulfate).</p>
<p>Bring to 100ml with water. Store at 4ºC.</p>
<p><br />Ethanol, 76% (80% [v/v] aqueous solution made up using 95% ethanol)<br /><strong><br /></strong></p>
<p>Sodium Acetate, 3.0 M (pH 6.0)</p>
<p>In 80ml water ;</p>
<p>Dissolve 40.8g Trihydrate (NaC2H3O2 3H2O ) or 24.6g Anhydrous (NaC2H3O2)</p>
<p>Adjust pH to 6.0</p>
<p>Bring to 100ml with water.</p>
<p><br /><br />Isopropyl alcohol, 99%<br /><br />Phenol-Chloroform (1:1 v/v)</p>
<p>1 volume Tris-HCl – saturated phenol (Fisher BP17501-400/BP1750B-26;</p>
<p>pH 6.6 + /-0.2 saturated with 1.0 M Tris-Hcl and 1mM EDTA)</p>
<p>! volume chloroform : isopentyl alcohol (25:1) Note : isopentyl alcohol = isoamyl alcohol.</p>
<p><br /><strong><br /></strong></p>

[STEPS]
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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>A protocol for quantification of circulating microRNA using droplet digital PCR with TaqMan assays.</p>
<p>MicroRNAs are purified from platelet-poor plasma using Nucleospin columns</p>
<p>During the purification step samples are spiked with cel-miR-39 as a mean of technical normalization</p>
<p>Normalization are performed by calculating the relative concentration of the target microRNA and the reference.</p>

[BEFORE_START]
<p>We recommend to use a few samples to test if the volume of spike-in added during microRNA purification is adequate before purifing all your samples.</p>
<p>The concentration of the spike-in and the target miRNA should be within the same range, otherwise adjust the volume of spike-in added during miRNA purification.</p>

[GUIDELINES]
<p>Blood samples should be obtained using a minimum of venous stasis and with discard of the first 3 mL of blood.</p>
<p>Platelet-poor plasma should be prepared within 2 hours from blood sampling</p>

[STEPS]
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TITLE: Data analysis
AUTHORS: geoffrey.pages  

[DESCRIPTION]
This data analysis was used for the study.

[STEPS]
1. Statistical analysis for PreTPA was performed using ANOVA measures.

Statistical analysis for PostTPA, ReTPA, ModTPA, and bone healing was performed using non-parametric Friedman’s test.

Interobserver variability was estimated by the standard deviation of the observers’ mean measurements of TPA per dog.

Statistical analysis for SSI was performed using Fisher’s exact test.

Statistical significance was set at p < 0.05
TITLE: Vagus Nerve Recordings Using Carbon Fiber Microelectrode Array (CFMA)
AUTHORS: Ahmad  Jiman, Elissa Welle, Paras Patel, David Ratze, Elizabeth Bottorff, Julianna Richie, Zhonghua Ouyang, Dongxiao Yan, John Seymour, Cynthia Chestek, Tim Bruns

[DESCRIPTION]
The carbon fiber microelectrode array (CFMA) has demonstrated promising results in recording single-unti neural activity. This protocol is for obtaining CFMA recordings from the cervical vagus nerve of rats in response to the application of potassium chloride (KCl) on the vagus nerve. 

[STEPS]
SECTION: Potassium Chloride Solution
1. 0.3 mL of potassium chloride (KCl) solution is prepared at a concentration of 2 mEq/mL.  

SECTION: Anesthesia
2. The animal (Sprague-Dawley female rat) is anesthetised with an intraperitoneal injection of ketamine (90 mg/kg) and xylazine (10 mg/kg). Anesthesia is maintained with a ketamine (30 mg/kg) injection approximately every hour.  
SECTION: Surgical Preparation
3. A midline cervical incision is made to access the left cervical vagus nerve. Under a dissection microscope, the vagus nerve is isolated (5-7 mm) from the carotid artery and surrounding tissue and placed on a custom 3D-printed nerve holder. 
SECTION: CFMA Insertion
4. The Carbon Fiber Microelectrode Array (CFMA) is connected to a neural interface processor (Grapevine, Ripple) through a front-end headstage (Nano 2, Ripple). The headstage is controlled by a micromanipulator for accurate insertion of CFMA fibers into the vagus nerve. A small camera (MS100, Teslong) is positioned in the surgical opening to visulaize the alignment and insertion of CFMA fibers into the vagus nerve. 
SECTION: Experiment
5. Once the CFMA fibers are inserted, a recording trial is intitiated. Forty seconds into the recording trial, 0.3 mL of KCl (2 mEq/mL) is applied on the vagus nerve.  
SECTION: Data Analysis
6. Recorded signals are sorted for spikes using Plexon Offline Sorter and analyzed using MATLAB to calculates peak-to-peak voltage of spikes, conduction velocity and noise floor.
TITLE: Kelly Clarkson CBD Gummies- The Purely Concentrated CBD Product to Lose Pains!
AUTHORS: kellyclarksongummiesread  , Cannaleafz  CBD Gummies

[DESCRIPTION]
Kelly Clarkson CBD Gummies- The Purely Concentrated CBD Product to Lose Pains! 

[STEPS]
SECTION: Kelly Clarkson CBD Gummies- The Purely Concentrated CBD Product to Lose Pains!  Kelly Clarkson CBD Gummies Reviews- The verity that the true wealth we&#x27;ve is our health is known to numerous, but many know the true meaning of it and realize it in the true sense of the word. What causes so important joint pain is sheer negligence, and the causes of common pain are frequently right in front of us and we do ignore them. The right time to heal off pain is moment and does so with the right product.  The verity that the true wealth we&#x27;ve is our health is known to numerous, but many know the true meaning of it and realize it in the true sense of the word. What causes so important joint pain is sheer negligence, and the causes of common pain are frequently right in front of us and we do ignore them. The right time to heal off pain is moment and does so with the right product.  The health mystifications bear mending with the right medium from one right product, and in this case, it&#x27;s just the Kelly Clarkson CBD Gummies. The supplement has been tested, audited, and vindicated and claims to be the stylish among all. You too have the absolute right to live your life in a effortless way and your task is opting the right product right moment with no complacency.  The health mystifications bear mending with the right medium from one right product, and in this case, it&#x27;s just the Kelly Clarkson CBD Gummies. The supplement has been tested, audited, and vindicated and claims to be the stylish among all. You too have the absolute right to live your life in a effortless way and your task is opting the right product right moment with no complacency.  What&#x27;s The all recently Clarkson CBD Gummies pain relief supplement?  These hemp gummies have been precisely finagled and manufactured using advanced technology, incorporating several of the finest sauces and herbal maquillages for deep relief. The medicinal value of each excerpt has been tested and used only after its safety has been impeccably guaranteed. For the FDA to certify this supplement was a robotic thing because the composition is in itself herbal and leaves no room for any dubitation.   Official Website: https://www.outlookindia.com/outlook-spotlight/kelly-clarkson-cbd-gummies-reviews-does-tyler-perry-cbd-gummies-real--news-203904 https://urbanmatter.com/tyler-perry-cbd-gummies-reviews-is-it-fake-or-trusted/ https://urbanmatter.com/ree-drummond-cbd-gummies-reviews-is-martha-maccallum-cbd-gummies-fake/
1.