eamag/protocols-with-steps huggingface dataset:
TITLE: Neuropathy Phentoyping Protocols - Basic Breeding to Harvest
AUTHORS: Eva Feldman

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Summary:</span></div><div class = "text-block"><span style = "font-weight:bold;">Phenotyping of Rodents for the Presence of Diabetic Neuropathy </span></div><div class = "text-block">In man, the development of diabetic neuropathy is dependent on both the degree of glycemic control and the duration of diabetes. Diabetic neuropathy is a progressive disorder, with signs and symptoms that parallel the loss of nerve fibers over time. Consequently, assessments of neuropathy in mice are not performed at one time point, but are characterized at multiple time points during a 6 month period of diabetes. The degree of diabetes is evaluated in 2 ways: tail blood glucose measured following a 6 hour fast and glycated hemoglobin levels. The initial degree of neuropathy is screened using the methods discussed below. Detailed measures of neuropathy are employed when the initial screening instruments indicate a profound or unique phenotypic difference. This document contains protocols used by the DiaComp staff to examine and measure diabetic neuropathy at the whole animal, tissue and cellular levels.</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/bimz4kcn.jpg" /></div></div>

[STEPS]
?. Basic breeding scheme is harem breeding: 2 females, 1 male per cage.
?. At least 3 breeding trios are active and are replaced every 6 months.
?. Tail biopsies are collect at 3-4 weeks of age for genotyping.
?. Fasting blood glucose tests are performed every 4 weeks.
?. Body weights are recorded every 4 weeks at same time as glucose test.
?. In animals not spontaneously diabetic, diabetes is induced by STZ injections at 8 weeks. 40mg/kg for 5 consecutive days.
?. Urine is collected at 12 and 24 weeks. (24 week time point is a 24 hour collection)
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
This medium is for growing <em>Chlorella variabilis</em> NC64A, <em>Chlorella heliozoae</em> SAG 3.83, and <em>Coccomyxa</em> C-169.

[GUIDELINES]
<p><strong>BBM Stock Solutions</strong></p>
<ol>
<li> 25.0 gm NaNO<sub>3</sub> per liter d-H<sub>2</sub>O</li>
<li> 2.5 gm CaCl<sub>2</sub><sup>.</sup>2H<sub>2</sub>O per liter d-H<sub>2</sub>O</li>
<li> 7.5 gm MgSO<sub>4</sub><sup>.</sup>7H<sub>2</sub>O per liter d-H<sub>2</sub>O</li>
<li> 7.5 gm K<sub>2</sub>HPO<sub>4</sub> per liter d-H<sub>2</sub>O</li>
<li> 17.5 gm KH<sub>2</sub>PO<sub>4</sub> per liter d-H<sub>2</sub>O</li>
<li> 2.5 gm NaCl per liter d-H<sub>2</sub>O</li>
<li> 50.0 gm disodium EDTA, 31.0 gm KOH per liter d-H<sub>2</sub>O</li>
<li>4.98 gm FeSO<sub>4</sub><sup>.</sup>7H<sub>2</sub>O per liter acidified H<sub>2</sub>O (Acidified H<sub>2</sub>O is 999.0 mL d-H<sub>2</sub>O + 1.0 mL concentrated H<sub>2</sub>SO<sub>4</sub>)</li>
<li>11.42 gm H<sub>3</sub>BO<sub>3</sub> per liter d-H<sub>2</sub>O</li>
<li> 8.82 gm ZnSO<sub>4</sub><sup>.</sup>7H<sub>2</sub>O, 1.44 gm MnCl<sub>2</sub><sup>.</sup>4H<sub>2</sub>O, 0.71 gm MoO<sub>3</sub>, 1.57 gm CuSO<sub>4</sub><sup>.</sup>5H<sub>2</sub>O, and 0.49 gm Co(NO<sub>3</sub>)<sub>2</sub><sup>.</sup>6H<sub>2</sub>O per liter d-H<sub>2</sub>O</li>
</ol>
<p>Note: Stock solution 10 takes weeks for all of the salts to dissolve.  Use as suspension until then.<br /><br /></p>
<p><strong>BBM Preparation</strong></p>
<p>to 950 mL of d-H<sub>2</sub>O add:</p>
<p>   10.0 mL of stock solutions 1, 2, 3, 4, 5 and 6</p>
<p>   1.0 mL of stock solutions 7, 8 and 9</p>
<p>   2.0 mL of stock solution 10</p>
<p> <br /><strong>MBBM Preparation</strong></p>
<p>to 950 mL of d-H<sub>2</sub>O add:</p>
<p>   10.0 mL of stock solutions 1, 2, 3, 4, 5 and 6</p>
<p>   1.0 mL of stock solutions 7, 8 and 9</p>
<p>   2.0 mL of stock solution 10</p>
<p>   1.0 gm of bacto-peptone</p>
<p>   5.0 gm of sucrose</p>
<p> <br />Tetracycline (filter sterilized, 10 µg/mL final concentration) is added after the media is autoclaved and cool.<br /><br />For MBBM plates, agar is added to 1.5% before autoclaving.<br /><br />For MBBM soft agar (for titering), agar is added to 0.75% before autoclaving. </p>

[STEPS]
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This is a modified protocol for extracting DNA from fungal myelium using the Sigma-Aldrich Extract-N-Amp Plant Kit published by J.M. U'Ren et al. (2016) Contributions of North American endophytes to the phylogeny, ecology, and taxonomy of Xylariaceae (Sordariomycetes, Ascomycota). <em>Molecular Phylogenetics and Evolution</em> 98: 210-232.</p>
<p> </p>

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

[DESCRIPTION]
Another convenient way to screen larger sample volumes is to perform liquid enrichment cultures (Suttle 1993). By this approach, larger volumes of water samples can be screened for cyanophages, thus enabling detection of “rare” viruses. Similar to the use of enrichment cultures for bacteriophages, the disadvantages include the fact that lysis of the host cells are not always obvious, especially if the initial titer is low or if the host culture is not clonal or unialgal.

[GUIDELINES]
If low titers are expected, the viruses in the sample can be concentrated via TFF to make a virus concentrate (VC) (Suttle et al. 1991; Wommack et al. 2010, this volume). To increase the detection limit, several different VCs can be combined and added to the same culture. Another convenient way to screen larger sample volumes is to perform liquid enrichment cultures (Suttle 1993). By this approach, larger volumes of water samples can be screened for cyanophages, thus enabling detection of rare viruses. Similar to the use of enrichment cultures for bacteriophages, the disadvantages include the fact that lysis of the host cells are not always obvious, especially if the initial titer is low or if the host culture is not clonal or unialgal. Also, more steps are required to dilute out nonreplicating viruses to obtain pure clonal isolates. Because it is an end-point dilution assay, only the most abundant phages will be isolated. The principle is the same as for the isolation of bacteriophages mentioned earlier except that the sample volumes screened are in the order of liters instead of milliliters.

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?.
TITLE: Microscopy-based bead protein-protein interaction assay
AUTHORS: Chunmei  Chang

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">An assay to study protein-protein interaction</div></div>

[STEPS]
?. Wash glutathione sepharose beads (GE Healthcare) with the reaction buffer (20 mM HEPES at pH 8.0, 200 mM NaCl and 1 mM TCEP) three times.
?. Make a mixture of  0.5 µM GST or GST tagged cargo receptors and different ATG proteins.
?. Incubate the protein mixture with 10 µL washed glutathione sepharose beads at room temperature  for 1 h.
?. Wash the beads three times with reaction buffer.
?. Suspend the beads with 120 µL reaction buffer and transfer the beads to the observation chamber.
?. Acquire images on a Nikon A1 confocal microscope with a 63 × Plan Apochromat 1.4 NA objective.
TITLE: German Glühwein and Kinderpunsch
AUTHORS: Anita Broellochs

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Glühwein (Mulled wine) is a hot spiced wine beverage which is a traditional drink during the winter in Germany and is served at Christmas markets in Europe. The non-alcoholic version is called "Kinderpunsch" which is made with juices instead of wine and is suitable for kids. </div></div>

[STEPS]
?. Please choose between: 1. Glühwein - alcohol containing 2. Kinderpunsch - non-alcoholic
?. Pour the  into a medium sized pot.
[bottle of dry red wine]
?. Add the following ingredients to the pot: Optional:
[cinnamon sticks]
[whole star anise]
[whole cloves]
[capsules of Cardamom]
[sliced organic orange (with peel) ]
[vanilla pod]
?. Turn on the heat and let the wine and spices warm up for about .
IMPORTANT: Do not let the wine boil or you will boil off the alcohol!
?. Serve hot. Optional garnishes to place in each mug include orange slices, cloves, a star anise or cinnamon stick.
?. Add the following ingredients to a medium sized pot:
[orange juice]
[apple juice]
[cherry juice]
?. Add the following ingredients to the pot: Optional:
[cinnamon sticks]
[whole star anise]
[whole cloves]
[capsules of Cardamom]
[sliced organic orange (with peel) ]
[vanilla pod]
?. Turn on the heat and bring the juices and spices mixture to a boil.
?. Serve hot. Optional garnishes to place in each mug include orange slices, cloves, a star anise or cinnamon stick.
?. Reduce the heat, cover and simmer for .
TITLE: Mapeamento de literatura sobre mulher preta na Ciência da Informação no Brasil
AUTHORS: Gabriele  Rodrigues Pereira, Zaira  Regina Zafalon

[DESCRIPTION]
Pesquisa sobre identificação de estudos sobre mulher preta na Ciência da Informação no Brasil, desenvolvida por Gabriele Rodrigues Pereira como parte da pesquisa desenvolvida no curso de mestrado em Ciência da Informação junto à Universidade Federal de São Carlos, sob orientação da Profa. Dra. Zaira Regina Zafalon.

[STEPS]
TITLE: Multimodal imaging pipeline for molecular and cellular characterization of Liver tissue - HuBMAP TTD-Columbia/PSU
AUTHORS: Presha  Rajbhandari, Hua  Tian, Aubrianna Decker, Taruna Neelakantan, Brent R Stockwell

[DESCRIPTION]
We have developed a workflow to assess the spatial organization of liver tissue with regard to its cellular and metabolic heterogeneity at tissue and single cell level resolution - by performing multimodal imaging on consecutive tissue sections using H&E staining, DESI,  (H2O)n-GCIB-SIMS, C60-SIMS, and RNAscope.

This document provides the collection of protocols within the multimodal imaging workflow implemented by Columbia University/Pennsylvania State University Transformative Technology Development Center as a part of Human Biomolecular Atlas Program (HuBMAP, NIH).

[STEPS]
1. Acquire human tissue blocks.
dx.doi.org/10.17504/protocols.io.rm7vzy5wrlx1/v1
2. Prepare tissue sections for multimodal imaging on appropriate substrates.
dx.doi.org/10.17504/protocols.io.e6nvwjmjzlmk/v1
3. H&E staining is performed using standard protocol.
4. DESI-IMS is performed as described here.
dx.doi.org/10.17504/protocols.io.ewov1nze7gr2/v1
5. (H2O)n-GCIB-SIMS-IMS is performed as described here.
dx.doi.org/10.17504/protocols.io.81wgbyynovpk/v1
6. C60-SIMS for multiplexed antibody staining is performed as described here.
dx.doi.org/10.17504/protocols.io.b5qmq5u6
7. RNAScope imaging is performed as described here.
dx.doi.org/10.17504/protocols.io.kqdg3p3e7l25/v1
TITLE: Installing FIJI and SynBot (Mac Version)
AUTHORS: Justin T Savage

[DESCRIPTION]
Video instructions for installing FIJI and the software needed for SynBot on MacOS.

[STEPS]
1. 
 

SECTION: Install SynBot
4. 1:11-1:56 Download code from the SynBot GitHub repository https://github.com/Eroglu-Lab/Syn_Bot .
SECTION: Install FIJI
3. 0:30-1:11 Give Mac permission to open FIJI since it is from an outside developer.
SECTION: Install FIJI
2. 0:00-0:30 Download FIJI from https://fiji.sc .
SECTION: Install SynBot
5. 1:56-2:39 Move SynBot java plugins (JAR files) to the FIJI plugins folder. The ilastik4ij_Syn_Bot-1.8.2-SNAPSHOT.jar and SynQuantExtra-1.2.9.jar files are required for running SynBot.
SECTION: Run SynBot
6. 2:39-3:00  Launch FIJI and open SynBot by dragging the SynBot.ijm file into FIJI.
SECTION: Run SynBot
7. 3:00-3:11  Prepare your image folder. Create a folder for your experiment with subfolders for experimental groups. Each experimental group folder should contain only image files. Multiple experimental groups are not required, but your files must follow the Experiment/Group/Image structure. 
SECTION: Run SynBot
8. 3:11-4:53 Run SynBot (see the SynBot manual thresholding protocol for more information).
SECTION: Run SynBot
9. 4:53-5:04 View results in Summary.csv file.
TITLE: IB BIO SL IA M23 - A study on the conditions that affect yeast fermentation 
AUTHORS: Marcy Roca Cugat

[DESCRIPTION]
This protocol is designed to aid me in the research for my International Baccalaureate Biology Internal Assignment

[GUIDELINES]
None

[STEPS]
SECTION: Preparation
1. Check that all reagents and materials are ready.
SECTION: Preparation
2. Assemble the instrumentation
SECTION: Preparation
2.1. One end of the flask must be plugged with a holed stopper and a thermometer.
The other end should be plugged with a holed stopper and a glass tube.
The middle opening should be covered with plastic and secured with a rubber band.
SECTION: Preparation
2.2. A long and shallow recipient must be filled with water as much as possible. The gas recovery flask should also be filled with water as much as possible. Then, the latter should be inverted and suspended inside the former.
SECTION: Preparation
2.3. The tube should be connected from the glass tube to the gas recovery flask. 
SECTION: Preparation
3. The block of compressed yeast must be cut in 4 parts
SECTION: Processing
4. Several factors must be checked and accounted for: pressure, temperature and initial weight of the full gas recovery flask (GRF). To check the ambiental conditions, we will use a thermometer and the Google Science Notebook (discontinued) phone application, which uses the phone's integrated barometer to tell the pressure. To measure the GRF weight we will use a scale.

SECTION: Processing
5. One quarter of the yeast block must be dissolved in sugary water (concentration undetermined, volume undetermined, temperature undetermined). This should then be placed in the flask.

SECTION: Processing
6. Wait for fermentation: 30 min 

SECTION: Processing
7. Weigh the GRF. The difference from the first measurement is the gas generated. Convert it to moles of CO2+H2O for a universal measurement that is constant through different temperatures and pressures.
SECTION: Processing
8.
TITLE: HubMap UF TMC Tissue Dissociation to Single Cell
AUTHORS: Marda Jorgensen, Maigan Brusko

[STEPS]
?. [Preparation]
To make ACK Lysis Buffer:
?. [Preparation]
Add 8.02 grams of NH4Cl, 0.84 grams of NaHCO, and 5uL of 0.5M EDTA into 1000mL of deionized water.
?. [Preparation]
Filter buffer through 22um PES Filter. Aliquot in 50mL conicals and store at room temperature for long-term storage.
?. [Preparation]
To make the cDMEM:
?. [Preparation]
Add 50mL of FBS, 10mL of Penicillin/Streptomycin to 440mL of DMEM.
?. [Procedure]
Obtain 1cm x 1cm x1cm tissue cube (thymus and spleen) or whole/partial lymph node from organ dissection protocol. Place in 15mL conical tube with 5mL cDMEM, retain on ice.
?. [Preparation]
Filter through a filter flask and store at 4℃.
?. [Procedure]
Prepare 10mL digest mix using 1mL of 10x Collagenase/Hyaluronidase in DMEM and 9mL dMEM with 5% FBS. Warm to 37C in water bath.
?. [Procedure]
Mince tissue crosswise with two scalpels in sterile petri dish until tissue fragments are approximately 2 mm in all dimensions.
?. [Procedure]
Transfer tissue fragments to C tube, incubate at 37℃ in shaking incubator for 30 minutes.
?. [Procedure]
Place C tube on gentleMACS dissociator, run protocol mspln0201.
?. [Procedure]
Transfer cell suspension to 50 ml conical over 500 uM mesh filter and wash over filter with DMEM until tube is full. Centrifuge 350 x g for 10 minutes beginning at RT, step down to 8℃.
?. [Procedure]
Discard supernatant. Resuspend cell pellet in cold cDMEM, decant over 100 uM filter into new conical tube. Centrifuge 350 x g for 10 minutes, 8℃.
?. [Procedure]
Discard supernatant and retain cell pellet. Resuspend in 10 ml cold HBSS, decant over 40 uM filter into new conical tube. Retain cell suspension on ice while performing cell count.
?. [Procedure]
Take a 20ul aliquot for counting on a Nexcelom Cellometer.
?. [Procedure]
Add 20ul of Viastain AO/PI to aliquot and mix thoroughly with pipette. Add 20ul to counting slide and count with “immune cells low RBC” with dilution factor 2.0. Record total yield and viability in case worksheet.
?. [Procedure]
Centrifuge remaining cell suspension at 350 x g for 10 minutes at 8℃. Decant supernatant and dissociate cell pellet. Resuspend dropwise in Cryostor 10 at 25 million cells/ml.
?. [Procedure]
Aliquot suspension to labeled cryovial and place in CoolCell. Transfer to -80℃ freezer for 18-24 hours prior to transfer to liquid nitrogen cryounit.
TITLE: Colonic Migrating Motor Complexes
AUTHORS: Jessica Griffiths, Bryan Yoo, Sarkis Mazmanian

[DESCRIPTION]
Protocol used in "Peripheral Neuronal Activation Shapes the Microbiome and Alters Gut Physiology"

[STEPS]
SECTION: Sample Preparation
1. Intact colons were dissected from cervically-dislocated mice.

SECTION: Sample Preparation
2. Colons were flushed and placed in pre-oxygenated (95% O2, 5% CO2)
Krebs-Henseleit solution at RT
SECTION: Sample Preparation
3. Proximal and distal ends were cannulated to 2 mm
diameter tubes and secured in the center of an organ bath with continuously
oxygenated Krebs-Henseleit solution at 37 ºC. 
SECTION: Sample Preparation
4. Syringe pumps were connected to the
inlet and outlet tubes to maintain a flow of solution at a rate of 500 µL/min
through the colon. 
SECTION: Sample Preparation
5. The system was allowed to equilibrate for 30 minutes before
recording. 
SECTION: Data Aquisition
6. Baseline recordings were taken for 30 minutes, then the Krebs
solution in the organ bath was briefly removed, mixed with C21 to a final
concentration of 2 µM, and replaced in the organ bath. Recordings were taken
for another 30 minutes.
TITLE: Biohazard Garbage Protocol: Autoclave Biohazard Waste
AUTHORS: Steven Wilhelm, Gary LeCleir

[STEPS]
?. Locate Biohazard garbage.
?. If the waste container is > ¾ full, then it needs to be processed for autoclaving.
?. Autoclave the processed waste on gravity cycle.
?. Instructions on cycle times based on the amount of trash you are autoclaving are on the autoclave.
?. 
?. Transfer bag into a wide autoclavable tray.
Tray will have PP on bottom. Don't use HDPE! It will MELT!
?. Pour  di water into bag containing trash.
100 ml
?. Pour  di water into tray.
100 ml
Between the container and the bag.
?. Close bag loosely put a strip of autoclave tape on bag.
?. Write “Wilhelm” on the autoclave tape.
?. After autoclaved waste has cooled, put the autoclaved waste into designated trash bin next to autoclave.
?. Transfer sharps container into a wide autoclavable tray.
Tray will have PP on bottom. Don't use HDPE! It will MELT!
?. Pour  water into interior of the sharps container.
100 ml
?. Close lid until it snaps shut and put autoclave tape on lid.
?. Write “Wilhelm” on the autoclave tape.
?. After autoclaved waste has cooled, put the autoclaved waste into designated trash bin next to autoclave.
TITLE: Krim Asli Artropant - (Hoax atau Sah) Benar-benar Berfungsi!
AUTHORS: Artropant

[DESCRIPTION]
Artropant adalah Orinial Cream yang membantu dalam pengurangan ketidaknyamanan sendi. beli krim alami harga terbaik periksa komposisi & manfaat, ulasan!

https://www.artropant.site/
https://www.agcef.org/artropant-asli/?lang=id
https://www.ulasanpro.com/id/artropant-cream/
https://www.artropant.site/get-artropant

[STEPS]
TITLE: Highway carbon unlocking efficiency study based on super-efficiency SBM-Malmquist
AUTHORS: Yun Chen, Qi Luo, machongsen

[DESCRIPTION]
Carbon neutrality and sustainable development goals (SDGs), as new requirements for global development at this stage, have raised higher requirements for achieving the coordination of economic efficiency and ecological development of transportation infrastructure, especially highways. To promote the achievement of SDGs and carbon neutrality goals, this research intends to investigate the carbon unlocking efficiency of highways. In this paper, we take China as an example, use the data of 18 listed highway companies and their provinces from 2010-2019 to conduct the study, measure the static carbon unlocking efficiency by using the super-efficiency SBM model with undesirable outputs, combine with the Malmquist index model for the decomposition of the efficiency and the dynamic analysis, and use the Tobit panel model to analyze the factors affecting the carbon unlocking efficiency of the highway. The results show that (1) From a static perspective, the carbon unlocking efficiency of China's highways has been inefficient in general. (2) From a dynamic perspective, the carbon unlocking efficiency of China's highways shows a trend of decreasing first and then developing steadily, with noticeable differences between carbon unlocking in the East, Central, and West. The carbon unlocking efficiency change index is in the rising stage overall. (3)The regional economic level, industrial structure, and urbanization level have a significant positive correlation with carbon unlocking efficiency, while the level of scientific and technological development and the level of opening up have a negative effect.

[STEPS]
1.
TITLE: Protocols for Image Capture and Data Recording in the Field
AUTHORS: Richard Levy

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">In effort to increase usefuleness of images that we capture in the field, Denver Botanic Gardens Research and Conservation has implemented this protocol to record information about photographs taken in the field. Photographers record information about the subjects of their photographs in a separate notebook. The information cooresponds to specimen and site data. The end goal (not outlined in this protocol) is to embed specimen and site data into the image file's XMP metadata, thus making links to shared data easier to make.</div></div>

[STEPS]
TITLE: Preparation of 1M  magnesium sulfate solution (MgSO4)
AUTHORS: Alid  Al-Asmar, Alfonso   Pérez Escudero, gabrielmadirolas  

[DESCRIPTION]
Original source of the protocol: WormBook Methods http://www.wormbook.org/chapters/www_strainmaintain/strainmaintain.html
This protocol is for making 1M magnesium sulfate solution, which is used in the preparation of worm media, like NGM (Nematode Growth Medium). 

[STEPS]
1. Weigh 12.3 g of magnesium sulfate heptahydrate (MgSO4·7H2O), and add it to a 100 mL measuring cylinder.
2. Add ~40 mL of milliQ water.
3. Add a clean stirring magnet, and leave it on a stirrer until all crystals are dissolved.
4. Remove the stirring magnet: To prevent touching the solution, use another magnet from the outside of the measuring cylinder to slide the stirring magnet out of the cylinder.
5. Fill up to 50 mL with milliQ water

6. Filter-sterilize.
7. Store at 4°C. 
We usually use it without problem for up to at least a year after preparation.