eamag/protocols-with-steps huggingface dataset:
TITLE: Assessment of Knowledge, Attitude and Practice toward Hepatitis B virus infection among Healthcare Providers working at sixty Public and Private Hospitals in Khartoum State Sudan 2023 
AUTHORS: essam.abuobaida

[DESCRIPTION]
Introduction: Hepatitis B infection is a major public health problem worldwide, according to the WHO (World Health Organization) statistics in 2019 it affected 296 million people and over 6 million children under the age of five,It contributed to more than 820,000 death every year(1).According to its blood borne transmission nature of the virus, HBV (Hepatitis B virus) is very common in Khartoum and more likely to be endemic, a previous study which was conducted in Khartoum citizens, it prevailed that Hepatitis B Sero-prevalence among population varied from (47%) to (78%) which is very high and hepatitis B surface antigen prevalence ranging from (6.8%) in central Sudan to (26%) in southern Sudan(2).

 Objectives: The main aim of the study is to evaluate and assess the level of (KAP) toward (HBV) among (HCWs) in 60 Public and Private hospitals in Khartoum state, Sudan.
 Specific objectives are to estimate the proportion of immunized HCWs, to estimate the proportion of needle stick injuries and their relationships with the endemic status of HBV in Khartoum.

 Methods: A  Cross sectional descriptive study will be conducted. The study will be conducted in the capital of Sudan,Khartoum state including 60 public and private hospitals that are well distributed among the tripartite metropolis capital of Sudan. From late January 2023 to late March 2023.
 population size is (21,576) Samle size will be calculated using the proportion formula of a cross sectional study (n = required sample size n = Z (α/2) 2 pq/d2).
Size of population:(21,576), P value:(0.58), q(1-0.58)= (0.42) , (95%) confidence level and (4%) error margin.
Here, n = required sample size, n = Z (α/2) 2 pp./d2, p = 0.58. This resulted in the required sample size of 569 HCWs.
A self administered questionnaire will be obtained from HCWs at the previously listed hospital.
Data will be analysed using SPSS version 20.

[STEPS]
SECTION: Research Steps
1. Writing the study protocol
SECTION: Research Steps
2.         Data collection and analysis                                    
SECTION: Research Steps
3. Writing the manuscript
SECTION: Research Steps
4. Publishing
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Contact Dr. Alison Buchan (abuchan@utk.edu) with any questions.</p>

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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
Supplement to seawater for growth of cyanobacteria.

[GUIDELINES]
<strong>Note:</strong> <br />Matt suggested higher concentrations of NH<sub>4</sub>Cl so only need to use 0.5 ml per 1 L seawater:<br />1.6 M NH<sub>4</sub>Cl    2.14g/25ml or 8.56g/100ml<br />Use 500µl per 1L seawater

[STEPS]
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TITLE: Crystallization of ATG9 HDIR-ATG101:ATG13 complex
AUTHORS: Adam  Yokom

[DESCRIPTION]
Crystallization protocol for the ATG9 HDIR-ATG101:ATG13 complex

[STEPS]
SECTION: Crystallization
1. ATG9 HDIR (828-839) fused ATG101 (1-198):ATG13 (1-197) complex was concentrated to 6 mg/ml in 25 mM HEPES pH 7.5, 150mM NaCl, 1mM MgCl2, 1mM TCEP
SECTION: Crystallization
2. Crystallization was carried out by sitting-drop vapor diffusion using an automated liquid-handling system (Mosquito, TTP LabTech, UK) at 288 K in 96-well plates
SECTION: Crystallization
3. The protein solution was mixed with the reservoir buffer composed of 0.1 M HEPES pH 7.5, 0.2 M NaCl, 12% PEG8000 with a ratio of 1:1
SECTION: Crystallization
4. Crystal trays were checked daily using a light microscopy for crystal growth
SECTION: Crystallization
5. Large crystals were obtained in 2–4 days. Crystals were cryo-protectedin 28% glycerol/reservoir buffer and frozen in liquid N2
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This protocol describes an immunoassay, originally developed to quantitate ubiquitin in mouse tissues (Oh et al., Anal. Biochem. 443, 153–155), which we adapted to <em>Drosophila melanogaster</em>. The method is suitable for the simultaneous determination of total, free and conjugated ubiquitin forms from whole protein extracts by densitometric analysis of Western blots. In this assay, endogenous deubiquitylating enzymes, DUBs, present in the lysates process all conjugated ubiquitins to monoubiquitins, therefore the total ubiquitin content of cell lysates can be determined in the form of monoubiquitins. The free monoubiquitin fraction in turn is determined from similar lysates, but supplemented with a potent DUB inhibitor, NEM. Appropriate samples of these lysates are immunoblotted together with ubiquitin standards that allow the quantification of the different ubiquitin forms by densitometric analysis of the 8,5 kDa monoubiquitin band.</p>

[BEFORE_START]
<p>Precool the centrifuge to 4 <sup>o</sup>C. Buffers F and T should be prepared prior to use and kept on ice.</p>
<p> </p>
<p><u>Buffer F:</u></p>
<p>100 mM Tris, pH 7.6</p>
<p>150 mM NaCl</p>
<p>1 mM EDTA</p>
<p>10 mM N-Ethylmaleimide (NEM)</p>
<p>20 µM MG132</p>
<p>1× EDTA-Free Complete Protease Inhibitor Cocktail</p>
<p> </p>
<p><u>Buffer T:</u></p>
<p>100 mM Tris, pH 7.6</p>
<p>150 mM NaCl</p>
<p>20 µM MG132 (Calbiochem)</p>
<p>1× EDTA-Free Complete Protease Inhibitor Cocktail (Roche)</p>
<p>2 mM DTT</p>
<p> </p>
<p><u>4 x Laemmli sample buffer:</u></p>
<p>40% glycerol</p>
<p>240 mM Tris-Hcl pH=6.8</p>
<p>8% SDS</p>
<p>0.04% Bromophenol blue</p>
<p>5 % 2-mercaptoethanol</p>
<p> </p>
<p><u>TBS:</u></p>
<p>10 mM Tris pH 8.0</p>
<p>150 mM NaCl</p>

[GUIDELINES]
<p><u>Buffers and reagents</u></p>
<p>Tris base</p>
<p>NaCl</p>
<p>Glycine</p>
<p>Tween-20</p>
<p>EDTA</p>
<p>N-Ethylmaleimide (NEM, Sigma-Aldrich)</p>
<p>MG132 (Calbiochem)</p>
<p>EDTA-Free Complete Protease Inhibitor Cocktail (Roche)</p>
<p>DTT</p>
<p>Glycerol</p>
<p>Bromophenol blue</p>
<p>2-mercaptoethanol</p>
<p>Purified ubiquitin (Sigma-Aldrich)</p>
<p>PVDF membrane (Merck Immobilon-P)</p>
<p>Tris-Glycine SDS-PAGE gel</p>
<p>30-40% Acrylamid solution (29:1 acrylamide/bis-acrylamid)</p>
<p>Non-fat milk powder</p>
<p>anti-Ub antibody (rabbit, Dako)</p>
<p>Bovine serum albumin</p>
<p>HRP conjugated goat anti-rabbit secondary antibody</p>
<p>Immobilon Western Chemiluminescent HRP Substrate (Merck)</p>
<p>X-ray films (Fujifilm)</p>
<p>Tetenal X-ray film processing developer and fixative solutions</p>

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TITLE: CD200 and CD200R  levels in psoriasis patients
AUTHORS: Carmen Farid, Aisha A. Mahmoud, Hanaa  M. Donia, Hafsa M. Ghatesh

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Serum soluble CD200 levels in psoriasis patients was measured by ELISA (Human CD200 PicoKine™ ELISA Kit, Boster Biological Technology, Pleasanton CA, USA, Catalog # EK0993)), and CD200R expression level on both peripheral blood monocytes and lymphocytes  were measured by flowcytometry using human CD200 R1 conjugated antibody(Human CD200 R1 Fluorescein-conjugated Antibody, Bio-Techne,Minneapolis, Minnesota, USA, Catalog # FAB3414F)). Cells were analyzed on a FACSCalibur flow cytometer using CellQuest pro software (BD Biosciences, San Diego, CA, USA). Membrane fluorescence intensity was estimated and expressed as mean fluorescence intensity (MFI). </div></div>

[STEPS]
TITLE: Quantitative Real‐Time Polymerase Chain Reaction (qRT‐PCR)
AUTHORS: Yingchao Xue, Xiping Zhan, Shisheng Sun, Senthilkumar S. Karuppagounder, Shuli Xia, Valina L Dawson, Ted M Dawson, John Laterra, Jianmin Zhang, Mingyao Ying

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol explains Quantitative Real‐Time Polymerase Chain Reaction (qRT‐PCR) of lines ND1014, N1, and ND27760 from </span><span style = "font-style:italic;">Synthetic mRNAs Drive Highly Efficient iPS Cell Differentiation to Dopaminergic Neurons</span><span>. </span></div></div>

[STEPS]
?. [RNA Extraction]
Extract total RNA using a RNeasy Mini Kit.
?. [qRT-PCR]
Reverse transcribe using murine leukemia virus reverse transcriptase and oligo(dT) primers.
?. [qRT-PCR]
Set up qRT-PCR using SYBR green PCR Master Mix in the IQ5 RT‐PCR detection system. Primer sequences are listed in "Guidelines".
?. [qRT-PCR]
Normalize relative expression to 18S rRNA.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Socioeconomic status (SES) predicts health, wellbeing, and cognitive ability, including executive function (EF). A body of recent work has shown that childhood SES is positively related to EF, but it is not known whether this disparity grows, diminishes or holds steady over development, from childhood through adulthood.  We examined the association between childhood SES and EF in a sample ranging from 9-25 years of age, with six canonical EF tasks.  Analyzing all of the tasks together and in functionally defined groups, we found positive relations between SES and EF, and the relations did not vary by age. Analyzing the tasks separately, SES was positively associated with performance in some but not all EF measures, depending on the covariates used, again without varying by age.  These results add to a growing body of evidence that childhood SES is associated with EF abilities, and contribute novel evidence concerning the persistence of this association into early adulthood.</p>

[STEPS]
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TITLE: Glucose Tolerance Test
AUTHORS: Sabina Marciano, Roberta Marongiu

[DESCRIPTION]
The glucose tolerance test is performed to determine how quickly the glucose is cleared from the blood. It is used to test for diabetes or insulin resistance. 

[STEPS]
1. Single cage the mice for 1 week in advance
2. Weight the mice
3. Fast mice for 360 min 

4. After fasting, measure glucose with a glucose meter
5. Perform an intraperitoneal injection of 2g / kg body weight of glucose (20% D-glucose stock solution dissolving 2g of glucose in 10ml saline and give 10ul per gram of body weight).
6.  Collect blood samples for glucose measurement at 15, 30, 45, 60, 90 and 120 min post glucose injection
TITLE: ONETAHI PLANT DISCOVERY PROTOCOL
AUTHORS: Flynn Ryan Dartland, Leilani Villasenor, Alexander Ferrera, Jacob Yinger

[DESCRIPTION]
Invasive Plant Identification On Onetahi Motu, Tetiaroa Within French Polynesia
This protocol describes a means of sampling plant species on Tetiaroa's Onetahi Motu in order to identify and address harmful invasive species impacting their environment. By dividing the island into five sections, invasive plant species can be identified using iNaturalist and cross-checking with expert Dr. Jean-Yves Meyer, an esteemed terrestrial botanist specializing in Polynesian flora.

[BEFORE_START]
Ensure that you have all of your materials, charged and loaded. 

[STEPS]
SECTION: Protocol
6. Analyze the data to see which plants are native or nonnative to Tetiaroa. If there's a need for clarification, utilize the help of local experts such as Dr. Jean-Yves Meyer. 
SECTION: Protocol
7. Distinguish which plants are most invasive, overcrowding the rest, and even potentially harmful. 
SECTION: Protocol
9. Determine which native species are the most threatened by these invasive species. 
Create an action plan to further protect such native plants species, avoiding the use of pesticides in order to protect the water and the diversity therein.
SECTION: Protocol
5. Using the data collected from your region, identify the entirety of the distribution of plant species rooting on Onetahi using all means possible (guidebooks, iNaturalist, local knowledge, etc.)
SECTION: Protocol
2. Give the groups an hour to gather as much data on the flora of their section as possible. Teams can take more time as necessary depending on their area being covered. 

SECTION: Protocol
1. Divide Onetahi (the motu with the greatest traffic) into five even sections (ex: Brando, Middle Earth, Landing Strip, Beach, Urban Jungle). Assign groups of 4 people to each of these sections.
SECTION: Expected Results
11. We expect the areas near the Brando to have higher counts of invasive species due to the planting of aesthetic, "pretty" plants there to please the guests. We also expect the areas farther away from the hotel or any other housing areas to feature less invasive species, but more native plants instead. 
SECTION: Protocol
4. With each of the plant species, note whether it is cultivated or naturalized. 
SECTION: Protocol
3. Make sure to take pictures of each different plant species and well as explore the entirety of their section.
SECTION: Protocol
8. Formulate a sustainably sound plan for the swift eradication of the most determinedly harmful plants as well as the plants with most potential for harm. 
SECTION: Protocol
10. Follow-Up: Continue monitoring to ensure that eradicated species do not grow back as well as monitor for the wellbeing of native species and their recovery. 
SECTION: Follow-Up
12. Continue regular (likely monthly) monitoring to ensure that eradicated species do not grow back. 
SECTION: Follow-Up
13. Monitor for the wellbeing of native species and their recovery, noting their reaction to our protocol and whether there's any positive growth thereafter.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
Combine:<br />150mls Ethanol<br />150mls distilled water<br />3mls Glacial Acetic Acid<br /><br />Split into 4 beakers (approx 75mls each) and add a stir bar.<br /><br />Beaker 1 - Add: 0.5g Acid Fuchsin and 1.0g Ponceau 2R<br />Beaker 2 - Add: 0.45g Light green, SF, yellowish<br />Beaker 3 - Add: 0.75g Orange G and 1.5g Phosphotungstic acid<br />Beaker 4 - Add: 1.5g Phosphomolybdic acid<br /><br />When each reagent is maximally dissolved, combine the 4 dyes and filter. Cover storage bottle in tin foil to reduce light exposure. Remake each month.

[STEPS]
TITLE: Disposal of Samples from Water Bodies with Zebra Mussels
AUTHORS: Malcolm A Barnard, Stephen Powers

[DESCRIPTION]
Zebra Mussels (Dreissena polymorpha) are a highly invasive species that have been invading water bodies around the United States and beyond. This protocol for sample disposal for sample collected from know zebra mussel infested water bodies to prevent spread though local water treatment facilities by bleaching the samples to kill any larvae or other potential zebra mussels in the sample water.

[STEPS]
SECTION: Sample Killing
1. Pour all sample water into a dish pan.
SECTION: Sample Killing
3. Add 50 mL of bleach per 1 L of sample water.
SECTION: Sample Killing
2. Save the bottles for acid washing (do not bleach as acid and bleach produce chlorine gas).
SECTION: Sample Disposal
5. Dispose of bleached sample down drain with excess water. 
4. Let the bleached sample sit for a minimum of four hours if not until the next day.
SECTION: Sample Disposal
6. Save bin for future sample disposal or bleach work.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>Purpose: The immediate purpose is to determine the maximum number of tube voltages which are useful for acquiring information in medical computed tomography (CT) along with specific linear combinations of quantities of chemical elements which are observable with the current generation of medical CT machines. The larger purpose is to encourage the development of CT reconstruction algorithms based on the material basis described herein and, ultimately, to tie the measurand of CT to the International System of Units (SI).<br />Methods and Materials: Experimentally, we scanned samples at four tube voltages, namely 80 kV, 100 kV, 120 kV, and 140 kV on a medical CT. The samples included 30 small plastic bottles of powders containing various compounds spanning the atomic numbers from 1 to 20, along with a similar bottle of water and one of air. Using the known chemical formulas and measured masses, we formed a matrix giving the number of Hounsfield units per (mole per cubic meter) at each tube voltage for each of 13 chemical elements. Theoretically, we took the XCOM cross sections, combined them with the tungsten anode spectral model using interpolating cubic splines (TASMICS), with a one-parameter filter, and a simple detector model, and created a similar matrix for the first 20 chemical elements. In the training phase, we found a best-fit parameter. We define the molar Hounsfield unit (HU) potency as the difference in HU values that an<br />added mole per cubic meter in a given voxel would add to the measured HU value. We built a matrix of molar potencies for each chemical element and tube voltage and performed a singular value decomposition (SVD) on these. In a validation phase, we compared the model predictions to Hounsfield unit measurements on three CT calibration phantoms taken from the literature.<br />Results: We found that we could predict the measured HU potency for the chemical elements within our model. The singular values and singular vectors of the model and powder measurements are in substantial agreement. Application of the Bayesian Information Criterion (BIC) shows that exactly two singular values and singular vectors describes the results over four tube voltages. We were able to give a good account of the HU values measured for the calibration phantoms at several tube voltages for several vendors within our model without<br />introducing additional parameters.<br />Conclusions: Measurements at two tube voltages are necessary and sufficient to extract the available material dependent information in medical CT. The linear combination of elements that can be observed using a medical CT have been characterized, providing a material basis for use in dual-energy reconstruction. This approach provides groundwork for improved reconstruction and for the link of Hounsfield units to the SI.</p>
<p> </p>

[STEPS]
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TITLE: No Title
AUTHORS: 

[DESCRIPTION]
Comeau, A. M., and R. T. Noble. 2010. Preparation and application of fluorescently labeled virus particles, p. 19–29. In S. W. Wilhelm, M. G. Weinbauer, and C. A. Suttle [eds.], Manual of Aquatic Viral Ecology. ASLO.<br /><br />Please see the <a href="http://www.aslo.org/books/mave/MAVE_019.pdf" target="_blank">published manuscript</a> for additional information.

[STEPS]
TITLE: Glutaraldehyde fixation 
AUTHORS: Veronika Cencen

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Fixation of adherent mammalian cells for AFM imaging </div></div>

[STEPS]
?. Rinse cells 3 times with appropriate buffer, such as PBS or Ringer's
?. Prepare  concentration glutaraldehyde in KMgH buffer (or other buffer used for your application). Pipette just enough of the dilution on top of the rinsed cells to cover the area. Let sit for
2 Mass/Volume Percent
?. Rinse at least 3 times with buffer, properly disposing of the diluted glutaraldehyde.
Glutaraldehyde is appropriate for whole and unroofed cell fixation, so up to 100% should be fixed with decent crosslinking. For thicker samples use an addition of paraformaldehyde
Use sodium hydroxide for deactivation if necessary http://msdssearch.dow.com/PublishedLiteratureDOWCOM/dh_0936/0901b80380936cd5.pdf?filepath=microbial/pdfs/noreg/253-03304.doc&fromPage=GetDoc
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This is a magnetic bead-based protocol enables the generation of high quality Illumina miRNA libraries without the need of PAGE-gel size selection.</p>
<p> </p>
<p>Our protocol enables the discovery and profiling of miRNAs from various organisms and tissues via the Illumina sequencing platform. The unique TailorMix reagents and workflow have been developed for simplicity and reproducibility without sacrificing quality or yield.</p>
<p> </p>
<h1>Features</h1>
<p> </p>
<ul>
<li>No need for PAGE-gel size selection</li>
</ul>
<ul>
<ul>
<li>Final miRNA libraries are cleaned up with magnetic bead-based protocol.</li>
</ul>
</ul>
<ul>
<li>Low input requirement</li>
</ul>
<ul>
<ul>
<li>Compatible for as little as 150ng total RNA input</li>
</ul>
</ul>
<ul>
<li>User friendly workflow</li>
</ul>
<ul>
<ul>
<li>Libraries can be prepared in a single day with less than one hour of hands on time.</li>
</ul>
</ul>
<ul>
<li>Comprehensive sample prep kit</li>
</ul>
<ul>
<ul>
<li>Most components are supplied as ready-to-use mixtures which improves consistency and reproducibility.</li>
</ul>
</ul>
<p> </p>
<p> </p>

[GUIDELINES]
<p style="text-align: center;"><strong>Figure 1 </strong>TailorMix miRNA Sample Preparation Overview</p>
<p><img id="s-mce-img" class="s-mce-img" src="https://s3.amazonaws.com/pr-journal/d2yeffe.png" width="762" height="439" data-src="https://s3.amazonaws.com/pr-journal/d2xeffe.png" data-ofn="1.png" /></p>
<p> </p>
<h1>Best Practices</h1>
<p> </p>
<ul>
<li>Always wear gloves and use sterile technique.</li>
<li>Set up reactions using sterile non-stick nuclease-free tubes.</li>
<li>Place samples and reagents on ice or on chilled cooler block at all times and avoid extended pauses.</li>
<li>Reagents should be prepared using RNAse-free components</li>
<li>Prepare an extra 10% mixture when running multiple samples.</li>
</ul>
<p>Avoid repeated freeze-thaw cycles.</p>
<p> </p>
<h1>RNA Input</h1>
<p> </p>
<p>The TailorMix Gel-Free miRNA Sample Preparation protocol has been optimized using 900 ng of purified high quality human kidney total RNA as input and confirmed with as low as 150ng RNA input.  Because miRNA populations vary among different tissue types and species, the use of total RNA from other tissue or species may require optimization.  Low yield libraries may require gel-base size selection for optimal results (See the Appendix, Table 1 for suggestions on Library Size Selection Methods).</p>
<h1> </h1>
<h1>Sample Pooling Guidelines</h1>
<p> </p>
<p>The TailorMix Gel-free mi RNA Sample Preparation kit is capable of multiplexing up to 96 samples into a single lane of an Illumina flow cell. While processing multiple samples in parallel, use a unique index primer for each sample at the PCR step. Samples can be pooled before or after the library purification step. Contact SeqMatic for more information about the 96-reaction sample preparation kit (<a href="mailto:sales@seqmatic.com" target="_blank">sales@seqmatic.com</a>). </p>
<p> </p>

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