eamag/protocols-with-steps huggingface dataset:
TITLE: Determination of lignin in lignocellulosic biomass
AUTHORS: Magdiel Lainez

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>Explanation of NREL/TP-510-42618</span><span style = "vertical-align:super;">1</span><span> laboratory analytical procedure.</span></div><div class = "text-block"><span style = "vertical-align:super;">1</span><span>A. Sluiter, B. Hames, R.O. Ruiz, C. Scarlata, J. Sluiter, D. Templeton, D. Croker, Determination of Structural Carbohydrates and Lignin in Biomass, Biomass Analysis Technology Team Laboratory Analytical Procedure, National Renewable Energy Laboratory Golden, CO, 2010 NREL/TP-510-42618. </span></div></div>

[STEPS]
?. [Preparation of biological material]
First, mill the material until reaching a particle size between  and   for better results.If previously it's necessary to wash the material use distiller water. Do this with the objective to remove starch, gums, and non-structural carbohydrates. Then dry the biomass.
0.25
0.425
?. [Characterization of lignin]
Weight  of dry biomass into an assay tube. Be accurate!
300 mg
?. [Characterization of lignin]
Add   of 72% H2SO4 to the assay tube and put into a water bath at  during Use a glass rod or magnetic stirrer to homogenize the mix.
3 mL
30 °C
?. [Characterization of lignin]
Transfer the mix to a glass bottle. Add  of distiller water to dilute at 4% H2SO4.Take care to add only . You can do this using an analytical balance. The total weight of biomass and 4% H2SO4 will be  . See the calculations in the file attached
84 mL
84 mL
89.19 g
?. [Characterization of lignin]
Autoclave the material at  during
121 °C
?. [Characterization of lignin]
Filter the material autoclaved using the glass Gooch crucible, previously record its weight. Take a sample of the filtered for subsequent analysis and then wash the lignin to remove the residual acid solution.Can be used  MCE membrane filter. Lignin will be retained into the glass Gooch crucible.Carbohydrates will be soluble in the filtered. To determinate the carbohydrate concentration [To calculate cellulose and hemicellulose content], the sample should be analyzed by HPLC.
0.45
?. [Preparation of biological material]
Take ready a glass Gooch crucible. Dry  until constant weight a glass Gooch crucible of pore fine [type F].
?. [Characterization of lignin]
Dry until constant weight a glass Gooch crucible [or MCE membrane filter] with lignin. Determine lignin content by the difference in weight.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
This section outlines the analyses we used in our replication cycle section of our report. We first predict how many contigs are potentially of the temperate replication cycle and display this information using a Euler diagram. We then use a relative abundance approach by visualizing the percent of temperate phages present at each site. We end by visualizing the relative abundances of bacteria annotations of the phage contigs. Based on methods from the following publication:<br /><br />Hannigan, Geoffrey D., et al. "The Human Skin Double-Stranded DNA Virome: Topographical and Temporal Diversity, Genetic Enrichment, and Dynamic Associations with the Host Microbiome." <em>mBio</em> 6.5 (2015): e01578-15.<br /><br /><br />

[BEFORE_START]
Supplemental information available at:<br /><br /><a href="https://figshare.com/articles/The_Human_Skin_dsDNA_Virome_Topographical_and_Temporal_Diversity_Genetic_Enrichment_and_Dynamic_Associations_with_the_Host_Microbiome/1281248" target="_blank">https://figshare.com/articles/The_Human_Skin_dsDNA_Virome_Topographical_and_Temporal_Diversity_Genetic_Enrichment_and_Dynamic_Associations_with_the_Host_Microbiome/1281248</a>

[GUIDELINES]
<span class="identifier">sessionInfo</span><span class="paren">(</span><span class="paren">)<br /><br />## R version 3.2.0 (2015-04-16) <br />## Platform: x86_64-apple-darwin13.4.0 (64-bit) <br />## Running under: OS X 10.10.4 (Yosemite) <br />## ## locale: <br />## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 <br />## <br />## attached base packages: <br />## [1] stats graphics grDevices utils datasets methods base <br />## <br />## loaded via a namespace (and not attached): <br />## [1] magrittr_1.5    formatR_1.2    tools_3.2.0    htmltools_0.2.6 <br />## [5] yaml_2.1.13    stringi_0.4-1    rmarkdown_0.7    knitr_1.10.5 <br />## [9] stringr_1.0.0    digest_0.6.8    evaluate_0.7</span>

[STEPS]
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TITLE: 10x v3.1 HT Genomics Sample Processing Protocol
AUTHORS: Allen Institute

[DESCRIPTION]
Protocol is used for rapid generation of 3’ transcriptomic-NGS-ready- single-cell-libraries from pools of cells. Doubling the capacity of the original 10xv3.1 protocol, allowing for a capture of ~20,0000 cells instead of ~10,000 cells per port.

Note: Research reported in this publication was supported by the National Institute Of Mental Health of the National Institutes of Health under Award Number 
1U01MH114812-01
1U19MH114830-01. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

[STEPS]
TITLE: Isolation and detection of CTCs in HCC pat
AUTHORS: Linda Riegelbauer

[STEPS]
?. -  Blood from Cellsave Preservative Tubes was transferred into 50 ml tubes and made up to the 15 ml mark with PBS (without Ca2+ and Mg2+)
?. - this was transferred to the filter of the OncoQuick tube.
?. - Centrifuge this OncoQuick tube for 20 minutes at 1600g and +4 °C. The acceleration as well as the deceleration of the centrifuge were set to level five (medium) as specified by greiner bio one. The pipette and a 50 ml tube were moistened with the FACS buffer to minimize the binding of tumor cells to the walls of these materials. This step was also called "pre-wetting".
?. - The supernatant from the centrifuged Oncoquick tube was carefully pipetted off completely and transferred with the moistened pipette to the 50 ml tube that had also been prepared. The walls of the Oncoquick tube were washed again with 5 ml FACS buffer by gentle swiveling during pipetting in order to transfer any adherent tumor cells. The same 5 ml FACS buffer was then added to each 50 ml tube.
?. - The first washing of the resulting sample was performed by refilling to the 50 ml mark with FACS buffer and swivelling the tube five times. The tubes were then centrifuged for 10 min at 200 g and +4 °C. The acceleration and deceleration were set to the highest level (nine).
?. - Pipette 45 ml of the solution washed in step 5, leaving the cells at the bottom of the tube undisturbed.
?. - For the second wash, the same tube was refilled to the 50 ml mark with FACS buffer and swivelled five times. The tube was then centrifuged again for 10 min at 200 g and +4 °C.
?. - The air bubbles formed on the surface of the sample were then removed using a Pasteur pipette and the tube decanted.
?. - Finally, the remaining sample was carefully mixed using the pipette and all remaining liquid (including the remaining cells at the bottom of the tube) was transferred to a FACS tube.
?. - After decanting the sample, ideally mainly CTCs have remained at the bottom of the tube. The leucocytes still within the sample could be separated from the CTCs in flow cytometry.
?. - Immediately after tumor cell isolation the liquid in the FACS Tubes was stained with the mixture of the fluorescence labeled antibodies.
?. - 30 min incubation of the antibodies at +4 °C in the dark
?. - a wash cycle was performed to eliminate unbound antibodies
?. - 1 ml FACS buffer was added to each sample
?. – it was centrifuged for 5 min at 1500 g and at room temperature.
?. - Finally, the samples were filled up with 500 µl FACS buffer each.
?. -To detect the fluorescent antibodies and thus the tumor cells, the samples were measured with the BD FACSAria Fusion Flow Cytometer of the Flow Core Unit (FCU) in the Georg-Speyer-Haus at the University Hospital Frankfurt am Main, Germany, and then analyzed with the FACS Diva Software.
0 µl
TITLE:   Universal sandwich enzyme linked immunosorbent assay for investigating   protein-LG (SpLG)  interactions with immunoglobulins using a SpA-HRP conjugate.
AUTHORS: Angel  Justiz-Vaillant, Norma McFarlane-Anderson

[DESCRIPTION]
<div class = "text-blocks"></div>

[STEPS]
?. This ELISA is used to study the interaction of a protein-LG (SpLG) with different immunoglobulin preparations from mammalian species.
?. The 96 well microtitre plate is coated overnight at 4°C with 2 µg/µl per well of a mixture of protein-L and protein-G in carbonate-bicarbonate buffer pH 9.6.
?. Then plate is treated with bovine serum albumin solution and washed 4X with PBS-Tween.
?. 50 µl of  animal serum (1 mg/ml) is added and incubated for 1h at room temperature and the microplate is rewashed 4X with PBS-Tween.
?. Then 50 µl of peroxidase-labeled SpA conjugate diluted 1:5000 in PBS-non-fat milk is added to each well and  incubated for 1h at RT. The plate is washed 4X with PBS-Tween.
?. 50 µl of 4 mg/ml o-phenylenediamine solution (OPD) is added and the plate is incubated 15 minutes at RT in the dark.
?. The reaction is stopped with 50 µl of 3M H2SO4 solution.
?. The plate is visually assessed for the development of colour and read in a microplate reader at 492 nm.
?. A cut-off point should be calculated as the mean of the optical density of negative controls x 3. The higher the OD value the higher will be the affinity of SpLG to mammalian immunoglobulins.
TITLE: No Title
AUTHORS: 

[BEFORE_START]
<p>Clean the benches and all the material that will be used with alcohol 70. </p>
<p>Use tips with filter. </p>
<p>Cool the centrifuge to 4°C.</p>

[STEPS]
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TITLE: The Preemie-Test for the assessment of the newborn skin maturity
AUTHORS: Zilma Reis, Gabriela Luiza Nogueira Vitral, Rodney Nascimento Guimarães, Regina Amélia P L de Aguiar, Roberta Maia C Romanelli

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The authors describe the skin reflection measurement, obtained using a handheld optoelectronic device, to estimate gestational age of a newborn. The prototype unit of measurement and process of gestational age estimation were patented under number BR1020170235688 (CTIT-PN862)  PCT/IB2017/056786 (WO2018083602). </div><div class = "text-block">The Preemie-Test device was developed to detect the preterm newborns by analyzing the photobiological properties of the newborn's skin. This noninvasive and non-ionizing technology features a probe containing light emitters and receivers that is brought in contact with the newborn’s foot and, using mathematical algorithms, provides an estimated dating within seconds </div><div class = "text-block">The device provides automatic data acquisition with minimum operator influence and stores values in an electronic database. No values will be displayed on the device screen, thereby blinding the users to the results obtained at the time of acquisition.</div></div>

[STEPS]
?. The foot of the newborn examination:Expose the newborn's foot gently. Do not raise the lower limb to perform the exam.Do not handle the newborn. Instead, examine the child where he is being cared for: inside the incubator, warm crib or mother's lap.
?. Determining the position of the skin assessment:The Preemie-Test should be performed on the skin of the posterior portion of the sole of the foot (Figure 1). Imagine two diagonal lines running through the child's sole region and choose the central area where these lines meet.
?. Position of the sensor during the assessment:Touch the skin with the sensor should perpendicularly (90 degrees - Figure 2)
?. Performing the test:Follow the instructions according to the messages that will appear on the Preemie-Test display.Repeat the assessment three times in the same site of the skin foot.
TITLE: Rotarod test for assessing motor coordination and balance (Rat)
AUTHORS: devilbiss

[DESCRIPTION]
This is a variant of the published Med-Associates protocol used to study the effects of mild TBI on motor performance and balance. The original manual/protocol can be found here: https://med-associates.com/wp-content/uploads/2022/09/DOC-056-R2.2-ENV-577-ROTA-ROD-TREADMILLS.pdf

In these experiments, animals were trained/acclimated to the Rotarod for 3 consecutive days (9 trials total) prior to induction of TBI. Post-injury, animals were re-tested on days 1, 3, and 5 to assess sensorimotor performance and balance improvements over time.  

[STEPS]
SECTION: Daily testing on Rotarod
1. Setup Rotarod for daily use
SECTION: Daily testing on Rotarod
1.1. Turn on Rotarod and sanitize with an IACUC-approved method (e.g. https://peroxigard.com/product-information/wipes/)
SECTION: Daily testing on Rotarod
1.2. Verify Rotarod is set to accelerate from 4-40 RPM over 5 Min
(Setting #9 on ENV-577; Med-Associates. Inc.)
SECTION: Daily testing on Rotarod
1.3. Reset all photobeams and counters
SECTION: Daily testing on Rotarod
2. Start the Rotorod at a fixed rotational speed.
(Push the toggle switch down to the RESET position and release)
SECTION: Daily testing on Rotarod
3. Test animal's ability to remain on accelerating Rotarod
SECTION: Daily testing on Rotarod
3.1. Place animal(s) on rod (facing away from you).
(animals will walk in a forward motion).
SECTION: Daily testing on Rotarod
3.2. Allow animal(s) a 5 sec. to acclimate to task.
SECTION: Daily testing on Rotarod
3.3. Start acceleration of rod rotation and timer
(Move switch to ON/ACCEL position)
SECTION: Daily testing on Rotarod
3.4. Record time (in sec.) when 
1) animal falls (breaks IR beam) or 
2) maintains grip for a full rotation of rod or 
3) 300 sec has passed
(remove animal from testing lane as each one completes task and return to home cage)
SECTION: Daily testing on Rotarod
4. Allow animals 15 min inter-trial interval rest in home cage.
SECTION: Daily testing on Rotarod
5.   


SECTION: Daily testing on Rotarod
6. Average times across each of the 3 trials.
TITLE: Effect of Optimal Movement, Stretching and Strengthening Exercise to Prevent Shoulder Pain of Paraplegic Spinal Cord Injury Patient.d protocol
AUTHORS: Nadia Afrin Urme

[DESCRIPTION]
This study was conducted to determine and compare the effect of optimal movement, stretching, and strengthening exercises with usual care to prevent shoulder pain in paraplegic SCI patients. Researchers used a Single blinded (assessor), Randomized control trial study (CTRI/2020/04/025628) design. Based on eligibility criteria, 80 participants were recruited from the inpatient SCI unit, CRP-Bangladesh, by hospital randomization technique. After that participants were allocated into an experimental group and a control group (40 vs 40) by computer generated randomization table. Primary outcome measurement was pain during functional activities by Wheelchair User’s Shoulder Pain Index (WUSPI) and secondarily muscle strength by Manual Muscle Testing (MMT) and demographic and injury-related information. Pre-test data were taken 1 week after using the wheelchair and post-test data after 8 weeks (6 sessions/ week) of treatment. 

[STEPS]
TITLE: siRNA Transfection of Dispersed Islet Cells
AUTHORS: Amanda Gomes, Xiong Liu, Xiaoqing Dai

[DESCRIPTION]
siRNA Transfection of Dispersed Islet Cells

[BEFORE_START]
Reconstitute your siRNA to a 20 μM working solution with nuclease-free water. 

Work in a cell culture hood, in an RNAse-free environment, and keep the hood light off. 

Clean the cell culture hood, turn the UV light on, and thaw reagents on ice. 

[STEPS]
6. After 2-3 days, perform desired experiment and add 0.5 -1 mL of Trizol to the extra dishes. Freeze cells with Trizol in the -80°C freezer until RNA extraction. 

5. Wait 4-6h, and add 2 ml of human media (DMEM) to the dishes. 
4. Add 103 μL of transfection reagents to each dish with 100 μL of media with dispersed cells.
2. For each control dish (calculate the volume of reagents according to the number of dishes you wish to make):
Tube 1:  50 μL OptiMem media + 3 μL Lipofectamine RNAiMAX Transfection Reagent
Tube 2: 50 μL OptiMem media + 0.6 μL control siRNA + 0.4 μL dye indicator (Silencer‱ FAM-labeled Negative Control)

For each dish with the target gene silenced:
Tube 3: 50 μL OptiMem media + 3 μL Lipofectamine RNAiMAX Transfection Reagent
Tube 4: 50 μL OptiMem media + 0.6 μL target siRNA + 0.4 μL dye indicator (Silencer‱ FAM-labeled Negative Control)

Wait 5 minutes after making the 4 tubes.  
3. Mix tubes 1 and 2, and tubes 3 and 4. Wait 15 minutes.
1. Disperse islets, and resuspend cells in Opti-Mem media after centrifugation. Distribute 100 μL of media with cells per 35 mm dish.

Remember to make extra dishes for qPCR to test the efficiency of the transfection.
TITLE: Protocol for scoring animal calls on structural acoustic features prevalent in human music 
AUTHORS: David Schruth

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">The following protocol was developed using ethnomusicological universals rhythm, tone, interval, repetition, transposition, and syllable diversity in order to look for them in animal calls. The literal feature definitions themselves are merged from various musical dictionary sources. And the spectrographic examples are from bird calls and songs. </div></div>

[STEPS]
?. [For trainer]
Sample spectrographic repertoires from the literature
?. [For trainer]
Screen capture or scan each figure and name it systematically e.g. genus-species-voc#-name-author-year-figure.png
?. [For trainer]
Generate a list of vocalizations (in rows) from literature for recording info above (in columns)
?. [For trainer]
Give each vocalization a globally unique identifier (e.g. 3 digits for hundreds of calls)
?. [For trainer]
Create a scoring table for each of your scorers using the following: a. use the list of vocalizations but add a uniquely randomized score id column b. sort the table by this new, randomized score id column. c. add feature columns across the top for structural acoustic features you would like to score d. hide the columns relating to genus, species, name, author, & year
?. [For trainer]
Use these new scoring tables to generate a new directories for each vocalization (titled by score id))
?. [For trainer]
Gather training materials from literature and reference texts; make these tangible via screenshots or via print outs of definitions (table) and example spectrograms (figure)
?. [For trainer]
Post these on screen at a computer lab where training and scoring take place
?. [For trainer]
Pass out printed or digital copies of these for reference during the remainder of the scoring session
?. [For trainer]
Answer any clarifying questions before the session starts
?. [For scorer]
Read the instructions for scoring (step 7) as well as printed or digital definitions (table and figure)
?. [For scorer]
Iterate through each vocalization (do each of the following for each vocalization in your spreadsheet) a. rate, on a scale of 1-10, how tonal, intervalic, rhythmic, etc. each vocalization type is and enter it b. count the number of different types of syllables or shapes and enter this in the syllables column
TITLE: Donor Acceptance Criteria for GE/UPitt HuBMAP Inclusion
AUTHORS: Ho, Jonhan

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">This document outlines the required criteria for donor inclusion of skin specimens in the Human BioMolecular Atlas Program (HuBMAP). The study intends to be as inclusive as possible of race and ethnicity, dependent only on the consent for donor tissue for research. Disease known at the time of donation or later identified during the research will not necessarily exclude the sample from the research program.</div></div>

[STEPS]
?. [DONOR SELECTION]
Specimens used will be residual skin from clinical excision procedures. A search in the UPMC laboratory information system for excision specimens from adults in sun-exposed sites and non- sun exposed sites will be performed. Blocks and unstained slides will be created from archived formalin fixed paraffin embedded tissue from patients that have had prior skin excisions.Tissue selected will be waste tissue that is not required for patient care. Slides and blocks will be de-identified by the investigator who has normal access to the identifiable specimens/records.
?. [DONOR SELECTION]
Blocks and slides will be examined for adequate tissue.
?. [DONOR SELECTION]
Once deemed adequate, de-identified blank slides and blocks will be created.
?. [INCLUSION AND EXCLUSION CRITERIA]
Inclusion Criteria:  Age: Adulthood -Young through middle age and early senior years (approx. 18 to 70 years)All sex, gender, race, ethnicity are eligibleKnown state of health and diagnoses
?. [INCLUSION AND EXCLUSION CRITERIA]
Exclusion Criteria: Unknown time of deathProlonged Warm Ischemic Time –preferred to be less than 5-10 minutes as per transplant organ recovery protocols but may accept up to 6 hours after cardiac arrest, with knowledge and discretion of the investigator.Known disease including congenital anomaly or inborn error unsuitable for HuBMAP researchInfection with high-level organism representing risk in processing and shipment
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p><span style="font-weight: 400;">We developed a bioinformatic two-step pipeline, so called "MetaMap" pipeline,  to screen human RNA-seq datasets for the presence of microbial and viral reads by re-inspecting the non-human-mapping read fraction.</span></p>
<p><span style="font-weight: 400;">In the first step, reads are aligned against the human genome with STAR (version 2.5.2) and subsequently </span><span style="font-weight: 400;">the non-human-mapping reads are subjected to metatgenomic classification using CLARK-S (version 1.2.3).</span></p>

[STEPS]
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