eamag/protocols-with-steps huggingface dataset:
TITLE: Body composition assessment and sarcopenia in patients with biliary tract cancer: A systematic review and meta-analysis (protocol)
AUTHORS: Jun Watanabe, Ryota Matsui, Hideki Sasanuma, Kazuhiko Kotani, Naohiro Sata

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The purpose of the study will be to assess the impact of assessment of body composition in patients with biliary tract cancer.</div></div>

[STEPS]
TITLE: Biochemical Measures of Neuropathy - DHE
AUTHORS: Eva Feldman

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block">Oxidative stress is highly correlated with the metabolic changes caused by hyperglycemia. Increased levels of glucose overload mitochondria and result in the production of reactive oxygen species (ROS). In addition, the flow of excess glucose through cellular pathways decreases the cell’s normal ability to detoxify ROS. As a result, the neurons and axons of the peripheral nervous system contain increased levels of ROS and decreased antioxidant capacity. The following assays are used to measure these changes in rodent models of diabetic neuropathy. </div><div class = "text-block"><span style = "font-weight:bold;">Diabetic Complication:</span></div><div style = "text-align :; float : ;"><img style = "" src = "https://s3.amazonaws.com/pr-journal/bivb4kcn.jpg" /></div></div>

[STEPS]
?. Open Fluoroskan and choose open under the file menu. Scroll down and select DHE.sed. Set up your plate layout. Save your layout as DHxxxxxx.sed with xxxxxx being yy/mm/dd.
?. *Treat cells per experimental paradigm.Note: *As an alternative, cells can be pre-loaded with DHE- do steps 3, 4, 5, 2, then 5.
?. 15 minutes prior to reading, gently rinse cells once with HBSS.
?. Apply 3 μΜDHE in HBSS and leave on for 15 minutes.
?. Rinse cells and add HBSS.
?. Place plate into Fluroskan holder and click START.
?. Take readings using 485 nm ex, 612 nm em filter pairs for ethidium and 355 nm ex, 430 nm em for DHE.
?. Save both sheets with .xls extension into the DHE data folder or your own folder. Use the naming convention DHXXXX.xls, where XXXX is the date in mmdd format and add a r for the red reading and b for the blue reading.
TITLE: C+ Kapseln Kaufen, Test, Preis, Bewertung or Erfahrung
AUTHORS: Health

[DESCRIPTION]
C+ Kapseln Kaufen - Sie müssen schnell handeln. Viel mehr Männer kennen die Hauptvorteile des allgemeinen Ausstellung Verstärkers ohne Drogen. Darüber hinaus verwenden sie C+ Kapseln Kaufen Pillen. Daher könnte ein Teil dieser Behälter zur Neige gehen. C+ Kapseln Kaufen Der Verlust der sexuellen Kraft im Bett könnte zu unbefriedigenden Ergebnissen führen, die die meisten Frauen fürchten. Mit den Anforderungen Ihres Partners Schritt zu halten, kann eine echte Herausforderung sein, da Sie nicht immer bereit sind, Leistung zu erbringen. Wir verstehen dieses Gefühl wirklich, da Sie die Angst vor unbefriedigenden Ergebnissen überwinden müssen. Um die Leistung zu erbringen, können Sie Ihre Leistung leicht steigern, indem Sie eine härtere Erektion, längere Ausdauer und explosive Energie ermöglichen. Um eine solche Männlichkeit zu erreichen, brauchen Sie eine perfekte Transformationsformel, die Ihnen bei Ihrem Sexualleben hilft. Das versuchen wir zu tun. Die Idee des Geschlechtsverkehrs ist vertraut mit gegenseitigem Verständnis, um die Bedürfnisse des anderen richtig zu befriedigen. Sowohl Männer als auch Frauen sind bestrebt, ihr Sexualleben in vollen Zügen zu genießen. Einen perfekten Partner zu finden, ist das, was im Leben einer Frau wirklich zählt, aber wenn ein Mann seine Frau auf dem Bett nicht befriedigen kann, dann beginnen die Dinge zu fallen, da die Frauen anfangen, weniger Interesse an ihnen zu zeigen. Es gibt ein Geheimnis, wie man einer Frau gefällt, wenn sie dich am meisten braucht. Lass sie niemals erkennen, wo deine Grenze im Bett liegt. Es bringt Frauen immer dazu, sich nach mehr und mehr von ihnen zu sehnen. Wenn Sie damit Schritt halten, können Sie mit Hilfe von C+ Kapseln Kaufen natürlich den Moment mit dem besten Leistungsfaktor intensivieren. Hier ist eine Liste von Zutaten, die Ihre Männlichkeit in jedem Alter leicht neu erfinden könnten Ein natürliches Aphrodisiakum, das für seine traditionelle Verwendung als Arzneimittel bekannt ist, das das sexuelle Ansehen und die Leistungsfähigkeit von Männern erhöht. Offizielles Internet: https://filmdaily.co/obsessions/c-testosterone/

[STEPS]
TITLE: Enzymatic fingerprinting of AX and  mixed-linked BG
AUTHORS: Alison Lovegrove

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Lab protocol for: Enzymatic fingerprinting for arabinoxylan and mixed-linked beta-glucan in wheat flour by HPAEC-PAD. Based on Ordaz-Ortiz and Saulnier, 2005 J. Cereal Sci. 42. 119-125. and Odaz-Ortiz et al., 2005 J. Ag Food Chem. 53. 8349-8356.</div></div>

[STEPS]
TITLE: Optimization of blood pressure management after acute ischemic stroke and its prognostic significance: Prospective, randomized, open, blinded outcome evaluation, and feasibility Trial
AUTHORS: Beom Joon Kim

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Optimization of blood pressure management after acute ischemic stroke and its prognostic significance: Prospective, randomized, open, blinded outcome evaluation, and feasibility Trial [BOSS trial]; NCT03024476</div><div class = "text-block">A phase II clinical trial protocol written in Korean language. Apologize not providing a translation. </div></div>

[STEPS]
TITLE: Nucleic acids extraction from single cell using MasterPure Complete DNA purification (Epicenter)
AUTHORS: Sarah Romac

[DESCRIPTION]
Radiolaria are protists which can't be cultivated. These microoganisms have to be isolated by single-cell for genetic identification and it can be difficult to get clean DNA.
Here we optimized a DNA extraction protocol from protist single-cell.
It works very well on single-cell Radiolaria, Foraminifers, but also Ciliates, Dinoflagelletes, Diatoms.

[BEFORE_START]
Prepare Ethanol 70% from absolute Ethanol : Mix 35 mL of absolute Ethanol with 15 mL nuclease-free water in a Falcon 50mL Store at -20°C.

[STEPS]
SECTION: 1.    Cell Isolation
1. Isolate individually protist cells (at least 50µm in length) using a glass bent micropipette under a binocular microscope. 

SECTION: 1.    Cell Isolation
2. Wash each cell in three successive baths of 0.22µm-filtered and sterile seawater. 
SECTION: 1.    Cell Isolation
3. Transfer subsequently cells in a 1.5mL sterile microtube.
SECTION: 1.    Cell Isolation
4. Add 30 μL of lysis buffer (Tissue and Cell Lysis Solution from MasterPureTM DNA and RNA Purification Kit, Epicenter) and store at -20°C.
SECTION: 2.	Cell lysis
5. Pellet cells by centrifugation (2 min at Vmax), throw the supernatant, let ~25-30 µL of liquid.

SECTION: 2.	Cell lysis
6. Dilute 1 µL of Proteinase K in 300 µL de lysis solution Tissue et Cellule for each sample. Vortex 10 sec for resuspending cells (facultative).
SECTION: 2.	Cell lysis
7. Add 300 µL of mix Proteinase K + lysis solution Tissue et Cellule in each sample. Vortex.
SECTION: 2.	Cell lysis
8. Incubate 15 min at 65°C , 1000 rpm. Put samples in ice 3-5 min.
SECTION: 3.	Total nucleic acids precipitation
9. Add 150 µL MPC reagent to 300 µL of lysed sample. Vortex.
SECTION: 3.	Total nucleic acids precipitation
10. Spin 10 min at 11 000 g, 4°C. If there is no pellet, add more 25 µL MPC buffer and spin again 10 min at 11 000 g, 4°C.
SECTION: 3.	Total nucleic acids precipitation
11. Transfer the supernatant ion a new clean microtube (1,5 mL), discard the pellet.
(To keep the squeletton, keep the tube with the pellet, add 500 µL MilliQ Water and store at -20°C).
SECTION: 3.	Total nucleic acids precipitation
12. Add 500 µL of Isopropanol. Mix per inversion. Spin 10min at Vmax, 4°C.
SECTION: 3.	Total nucleic acids precipitation
13. Discard the supernatant with precaution, without touching the pellet.
SECTION: 3.	Total nucleic acids precipitation
14. Add 500 µL of Ethanol 70%. Don’t vortex, mix gently the support. Spin 5min at Vmax ;at 4°C.
SECTION: 3.	Total nucleic acids precipitation
15. Discard a maximum of supernatant with precaution, without touching the pellet.
SECTION: 3.	Total nucleic acids precipitation
16. Let dry 5-10 min at room temperature. The pellet should become transparent.
SECTION: 3.	Total nucleic acids precipitation
17. Elute in 25 µL of TE1x buffer.
Vortex and spin shortly.
Store at - 80°C.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
This is the correct protocol if you are using the C3019H cells. If you are using the C3019I cells, please refer to <a href="High-Efficiency-Transformation-Protocol-using-NEB-imstq5" target="_blank">this protocol</a>.

[GUIDELINES]
<strong>Transformation Protocol Variables</strong><br /><br /><strong>Thawing</strong>:&nbsp;Cells are best thawed on ice and DNA added as soon as the last bit of ice in the tube disappears. Cells can also be thawed by hand, but warming above 0&deg;C will decrease the transformation efficiency.<br /><br /><strong>Incubation of DNA with Cells on Ice</strong>:&nbsp;For maximum transformation efficiency, cells and DNA should be incubated together on ice for 30 minutes. Expect a 2-fold loss in transformation efficiency for every 10 minutes this step is shortened.<br /><br /><strong>Heat Shock</strong>:&nbsp;Both the temperature and the timing of the heat shock step are important and specific to the transformation volume and vessel. Using the transformation tube provided, 30 seconds at 42&deg;C is optimal.<br /><br /><strong>Outgrowth</strong>:&nbsp;Outgrowth at 37&deg;C for 1 hour is best for cell recovery and for expression of antibiotic resistance. Expect a 2-fold loss in transformation efficiency for every 15 minutes this step is shortened. SOC gives 2-fold higher transformation efficiency than LB medium; and incubation with shaking or rotating the tube gives 2-fold higher transformation efficiency than incubation without shaking.<br /><br /><strong>Plating</strong>:&nbsp;Selection plates can be used warm or cold, wet or dry without significantly affecting the transformation efficiency. However, warm, dry plates are easier to spread and allow for the most rapid colony formation.<br /><br /><strong>DNA Contaminants to Avoid</strong><br /><table width='468'><tbody><tr><td><strong>Contaminant</strong></td><td><strong>Removal Method</strong></td></tr><tr><td>Detergents</td><td>Ethanol precipitate</td></tr><tr><td>Phenol</td><td>Extract with chloroform and ethanol precipitate</td></tr><tr><td>Ethanol or Isopropanol</td><td>Dry pellet before resuspending</td></tr><tr><td>PEG*</td><td>Column purify or phenol/chloroform extract and ethanol precipitate</td></tr><tr><td>DNA binding proteins (e.g. Ligase)</td><td>Column purify or phenol/chloroform extract and ethanol precipitate</td></tr></tbody></table><br /><em>* Ideally, DNA for transformation should be purified and resuspended in water or TE. However, up to 10 &micro;l of DNA directly from a ligation mix can be used with only a two-fold loss of transformation efficiency. Where it is necessary to maximize the number of transformants (e.g. a library), a purification step, either a spin column or phenol/chloroform extraction and ethanol precipitation should be added.&nbsp;</em>

[STEPS]
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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Contact Dr. Steven Wilhelm (wilhelm@utk.edu) or Robbie Martin (rmarti49@vols.utk.edu) for additional information regarding this protocol.</p>

[STEPS]
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TITLE: Carver et al, Aged Brain Spatial Profiling  - CosMx
AUTHORS: Chase Carver

[DESCRIPTION]
This protocol provides the process for spatial molecular imaging using the Nanostring CosMx platform used in
Carver et al., "Senescent- and disease-associated microglia are modifiable features of aged brain white matter".

[STEPS]
SECTION: CosMx Slide Preparation
1. Using FFPE sections, follow the protocol found in the document  

SECTION: CosMx Instrument run
2. Follow the protocol found in the document  
for imaging of flow cells, FOV selection, and running spatial molecular imaging on the instrument.
The Cell Segmentation Profile used for mouse brain RNA is Configuration B. Cell overlay files are generated with the completion of the CosMx imaging and are used to segment 2D cell areas to be used in conjunction with transcript localization data.
TITLE: ADP Glo Max measuring ATP13A2 ATPase activity in microsomes
AUTHORS: Sue  Sim, eunyong_park  

[DESCRIPTION]
Measuring ATP13A2 ATPase activity in microsomes using commercial luminescence-based ADP detection assay (ADP Glo Max; Promega)

[STEPS]
1. Thaw microsomes on ice
2. Use 1 μg microsomes per reaction (1 µL of 5 mg/mL stock)
3. Dilute to 4 µL in Reaction Buffer at 4C
4. Equilibrate microsomes in reaction buffer for 90 min on ice and for 10 min at 37 °C

5. Add 1 µL of 25 mM ATP (final concentration 5 mM ATP) to start reaction (total reaction volume 5 µL)
6. Incubate for 15 min at 37 °C upon addition of ATP

7. Terminate reaction by heating samples for5 min at 80 °C

8. Mix with 5 µL of ADP-Glo Reagent for 60-80 min at23 °C

9. Mix with 10 uL of ADP-Glo Max Detection Reagent for 60 min

10. Measure luminescence in 384 multi-well plate using a luminometer (NOVOstar; BMG Labtech)
TITLE: Using Github to create a eNotebook
AUTHORS: Alise J J. Ponsero

[DESCRIPTION]
Instructions to create a Github Account and your first repository.

[STEPS]
SECTION: Create an account
1. Browse to the Github website
https://github.com/
SECTION: Create an account
2. Click on the Sign-up button on the right corner of the screen.
SECTION: Create an account
3. Follow the instructions to create your account.

To the Qestion 1, answer that you are working alone and that you are a student.

  

SECTION: Create an account
4. In the recommended pricing plan, select "Continue for free".

This will lead you to this home interface: 

  

SECTION: Create a first repository
5. Now that you have an account, let's create the repository you'll need for this CURE class.

Click on the green button on the left corner "Create repository"

  

SECTION: Create a first repository
6. First, create the name of the repository to be "CURE2022_{YOUR INITIALS AND NAME}"

Then fill the description to be "BAT 102 - CURE class repository 2022"

Leave the repository as "Public"

  

SECTION: Create a first repository
7. Click the tick box "Add a README.md" and select the licence as "MIT license"

  

SECTION: Create a first repository
8. Now click the green button "Create repository". Congratulations, you have created your first repository!

Your interface should now look like this:

  

SECTION: Adding a Wiki
9. We will use the wiki function of the Github repository as a eNotebook.

On the top of the screen, click on the "Wiki" tab, and create the first page. You should see this interface:

   

SECTION: Adding a Wiki
10. You can now fill your first entry of your lab Notebook. Paste the following text:


 


Note that in Markdown, the "#" sign signals a header. You can see a preview of your page by clicking on the tab "Preview".

  

You can now click on the button "Create page" to save the first entry of your Notebook!
SECTION: Adding a Wiki
11. You are now done with creating your notebook and your first entry. If you notice a mistake or want to correct something , you can modify the page you created using the button "edit".
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Cluster genomes is script that clusters genomes at a set nucleotide identity and coverage length. Additonally, it offers the ability to cluster sequences whose ends may not align correspondingly, i.e. the special cases of assembled, circular viral genomes that are treated as 'linear' by other sequence-clustering software (that can "miss" the ends).</p>
<p> </p>
<p>This is 'beta-like' software that has been vetted, though has not been as thoroughly tested as other widely-recognized clustering tools, such as CD-HIT, UCLUST, etc... As with all software, please examine the final results to see if they make sense.</p>

[BEFORE_START]
<p>To run this protocol, users must first <a href="https://user.iplantcollaborative.org/register/" target="_blank">register</a> for Cyverse account. All data (both inputs and outputs) are available within Cyverse's data store at /iplant/home/shared/iVirus/ExampleData/</p>
<p> </p>
<p>All source code is available at the Sullivan lab bitbucket repository, <a href="https://bitbucket.org/MAVERICLab/" target="_blank">MAVERICLab</a> - at <a href="https://bitbucket.org/MAVERICLab/stampede-clustergenomes" target="_blank">stampede-clustergenomes</a>.</p>

[STEPS]
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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
A short and relatively cheap method for non-homologous nuclear transformation of Chlamydomonas reinhardtii. Works best with linearized DNA. Requires 500 micron glass beads for DNA transformation.

[STEPS]
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TITLE: Macroalgae Analysis
AUTHORS: Nohea Rodriguez, Kai Bloom, Mistie Tran

[DESCRIPTION]
Determine the abundance and biomass of the invasive macroalgae species, Turbinaria and Sargassum. Then, identify marine species located on random samples of each species. Turbinaria decreases fish abundance and biodiversity, competing with native algae and coral for space and resources. Determine the effect on biodiversity if Turbinaria were to be removed from an ecosystem entirely. Under the guidance of Mayalen, the ISP class will conduct transect data collection in Baie Vaiori, located in Mo'orea. The objective is to gather data on the spatial occupancy of algae. Additionally, algae will be gathered to bring back to the lab where they will be examined for any residing organisms.

[BEFORE_START]
Make sure participants are well equipped with proper snorkel gear. Before getting in water, have data table written out on slate clipboard for convience.

[STEPS]
SECTION: Algae Transect Survey
1. Split into five groups of four people.
SECTION: Algae Transect Survey
3. Swim to the group's transect location, approximately 5 meters apart.
SECTION: Algae Transect Survey
4. Begin 30 meter transect along reef crest, parallel to the shore.
5. Swim along transect tape and record the presence of rock, coral, Turbinaria, or Sargassum for every 10 centimeters of the transect. Take photos along the transect for later reference. (300 observations per 30m)
SECTION: Sample Inspection
8. Gather samples of Turbinaria and Sargassum into ziploc bags filled with seawater. Bring sample bags into dirt lab
SECTION: Sample Inspection
9. Dump out contents into a plastic tub, and strain water from algae into a colander.
6. Move 5 meters towards the shore, and repeat Step 4 and 5.
7. Repeat Step 6 (until you have three 30 m transects).
SECTION: Sample Inspection
10. Carefully inspect macroalgae bunches, searching for organisms.  
 

SECTION: Algae Transect Survey
4.1. Tie down transect tape to coral or rock and map out the transect trajectory and distance. Tie to the 1 meter mark so that your first observation is at 1 meters.


 


5.1.  
 
 
 

5.2. Record the species of coral if possible
SECTION: Algae Transect Survey
3.1. Groups should have received the location of their transect areas on shore
SECTION: Algae Transect Survey
2. Gather materials - Transect tape, slate clipboard, snorkel gear
SECTION: Sample Inspection
11. Photograph any organisms next to a ruler, against your white background

 

SECTION: Sample Inspection
12. Record the weight of each algae bunch, number, size, and type of critters present, stem length of each bunch
SECTION: Sample Inspection
13. Record field and lab data in separate spreadsheets
TITLE: DNA extraction and precipitation
AUTHORS: Marco  Cacciabue, María Ines Gismondi

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Briefly, the DNA solution is extracted with phenol / chloroform / isoamyl alcohol in a ratio of 25/24/1 to remove protein contaminants and then precipitated with 100% ethanol or isopropanol. It is then washed with 70% ethanol to remove remaining organic molecules and the pellet is resuspended in a volume of interest.</div></div>

[STEPS]
?. Add 1 volume of 25/24/1 phenol / chloroform / isoamyl alcohol.
?. Mix by vortexing for or more at  .
Centrifuge: 13000 33, 15 s
0 Room temperature
?. Take the aqueous phase (the upper one) using a  pipette; transfer to new tube.
200 µl
?. Add 1/10 of 3M sodium acetate,. And mix by vortexing or tapping. An alternative way is to extract using chloroform / isoamyl alcohol, this serves to prevent phenol residues, which is not important if you wash well with 70% ethanol.
?. Add 2 or 2.5 vol of  100% Ethanol. Mix well and leave at freezer. (minimum , one hour preferrable)
0 °C
-20 °C
?. and discard the supernatant.
Centrifuge: 13000 33, 5 min
?. Add 70% ethanol (RNase Free)  at , invert several times and microcentrifuge as in step 6.
1 mL
0 Room temperature
?. Discard the supernatant and dry for  at(repeat)
37 °C
?. Resuspend the pellet in water.
TITLE: Purification and quantification from  PCR amplification protocol
AUTHORS: Rene Flores Clavo, Nataly Ruiz Quinones, Cristian Daniel Asmat Ortega

[STEPS]
?. [Purification steps]
Prepare collection tubes for each sample with their corresponding columns
?. [Purification steps]
Add 500 μL of capture buffer on each column
?. [Purification steps]
Add 25 μL of PCR-amplified DNA
?. [Purification steps]
Slowly mix the solution using a micropipette.
?. [Purification steps]
Centrifuge for 1 min at 16000 g
?. [Purification steps]
Keep the DNA in the column and discard the flow through on the tube
?. [Purification steps]
Add 500 μL of washing buffer on the column
?. [Purification steps]
Centrifuge for 1 min at 16000 g
?. [Purification steps]
Incubate for 1 min at room temperature
?. [Purification steps]
Transfer the column into a new tube
?. [Quantification]
To visualize the amplified products, put 2 μL of the PCR product with 2 μL of loading buffer dye in agarose gel electrophoresis with 1X TBE stained with SYBER safe at 1:10000.
?. [Quantification]
To compare, add 1 μL of 1kb DNA ladder (final concentration 0,5 ng/μL) and observe a band of 1500 pb approximately.
?. [Purification steps]
Add 10 μL of elution buffer
?. [Purification steps]
Incubate for 2 min at room temperature
?. [Purification steps]
Centrifuge for 2 min at 16000 g
?. [Purification steps]
Repeat step 11
?. [Purification steps]
Repeat step 12
?. [Purification steps]
Discard the columns and keep the tubes with purified DNA at 4 °C until visualization
?. [Purification steps]
Repeat step 13
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
These laboratory protocols contain more detailed information on the experimental methods of study 1 and 2 of the paper Dual Pathways to Voice Quality.  

The paper investigates the involvement of Working Memory Capacity (WMC, the cognitive resource necessary for controlled elaborate thinking) in voice behavior (speaking up with suggestions, problems, and opinions to change the organization). 

The methods are designed to capture voice behavior in the laboratory.

[STEPS]
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>In this paper, an adaptive fractional order sliding mode control (AFSMC) scheme is designed for the current tracking control of the Boost-type converter in a Battery/Supercapacitor hybrid energy storage system (HESS). In order to stabilize the current, the adaptation rules based on state-observer and Lyapunov function are being designed. A fractional order sliding surface function is defined based on the tracking current error and adaptative rules. Furthermore, through fractional order analysis, the stability of the fractional order control system is proven, and the value of the fractional order (λ) is being investigated. In addition, the effectiveness of the proposed AFSMC strategy is being verified by numerical simulations. The advantages of good transient response and robustness to uncertainy are being indicated by this design, when compared with a conventional integer order sliding mode control system.</p>

[STEPS]
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