eamag/protocols-with-steps huggingface dataset:
TITLE: The association between echo intensity and muscle strength or physical performance in the older population: a scoping review
AUTHORS: Takashi Kitagawa, Masatoshi Nakamura, Yoshihiro Fukumoto

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span style = "font-weight:bold;">Objective: </span><span>The purpose of this scoping review is to understand the extent and type of evidence in relation to the usefulness of muscle echo intensity using ultrasound imaging in the assessment of physical performance.</span></div><div class = "text-block"><span style = "font-weight:bold;">Introduction:</span><span> Recently, there has been an increasing number of reports on the use of ultrasound imaging to assess muscle strength or physical performance. While indices such as muscle thickness are common, reports on the relationship between muscle echo intensity and physical function have increased in the last few years. In the absence of randomized controlled trials of sufficient quantity and quality, a comprehensive summary of these studies has yet to be reported.</span></div><div class = "text-block"><span style = "font-weight:bold;">Inclusion criteria:</span><span> The participants should be healthy participants who are over 65 years old. The concept will be the investigation of the relationship between muscle echo intensity using ultrasound imaging and physical function such as muscle strength or physical performance (e.g., a sit and stand test or 6 minutes walking test). For context, only observational studies should be included.</span></div><div class = "text-block"><span style = "font-weight:bold;">Methods: </span><span>MEDLINE, CENTRAL, CINAHL, and Web of Science will be systematically searched using the keywords “echo intensity,” “ultrasound,” and “geriatrics”until March 2021. In the first screening step, two independent reviewers will review all of the titles and abstracts to exclude irrelevant articles. The second screening step will be according to the same inclusion criteria. </span></div></div>

[STEPS]
TITLE: K1 Keto Reviews Is K1 Keto Life Pills Scam Or Legit?
AUTHORS: ketoreviewsketopillsas  

[DESCRIPTION]
K1 Keto Reviews Is K1 Keto Life Pills Scam Or Legit?


[STEPS]
1. K1 Keto Reviews Is K1 Keto Life Pills Scam Or Legit?
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TITLE: Nest Building Test
AUTHORS: Valina L. Dawson, Ted Dawson, Hanseok Ko

[DESCRIPTION]
Used to assess nigrostriatal sensorimotor function in mice. Based on the Deacon 2006 protocol.

[STEPS]
1. Place 2.5 g nestlet into feeder of each cage.
2. Individually house mice must then pull the cotton nestlet from the feeder by rearing and useing complext fine motor skills.
3. Scores based on the amount of unused nestlet material were determined 16 hours after the nestlet was placed. Further details on scoring can be seen in Deacon 2006.
TITLE: Extraction of bacterial DNA using ChargeSwitch gDNA Mini Bacteria kit on KingFisher Flex robot
AUTHORS: Leyi  Wang, Carol Maddox, Melanie  Prarat, Yan  Zhang, Lifang Yan, Akhilesh Ramachandran, Sai Sankara Narayanan, Girish Patil

[DESCRIPTION]
This procedure is used to extract genome DNA of bacteria isolates using the ChargeSwitch gDNA Mini Bacteria kit on the KingFisher Flex Robot. The process consists of Sample processing, Prepare plates for Robot, and Operate on KingFisher Flex machine.

[BEFORE_START]
At the first time use, add RNase A to Resuspension Buffer (R4).

[GUIDELINES]
In the whole procedure, need wear PPE

[STEPS]
1. Sample processing
1.1. 
Bacterial Broth Culture

If using broth, pick single colony and grow in 5 ml Trypticase Soy Broth (TSB), overnight grow at 37 degree without shaking. Use 0.4 ml of the bacterial culture and centrifuge for 4min at 8000 rpm, discard supernatant and resuspend the cell pellet in 100 μL of Resuspension Buffer (R4) containing RNase A, then add 5 ul of lysozyme solution (50 mg/ML). Mix by vortexing. After adding RNase A to Resuspension Buffer (R4), store the buffer at 4 degrees Celsius. 
1.2. Bacterial Colonies in Plate

If using bacterial colonies, scoop 3 colonies into 100 μL of Resuspension Buffer (R4) containing RNase A, and then add 5 ul of lysozyme solution (50 mg/ML). Mix by vortexing.
2. Prepare plates for Robot
2.1. Load all resuspension solution prepared in 1.1. or 1.2  into 2.4 mL 96 deep well Sample plate.
2.2. Prepare Elution Plate by adding 100 ul of Elution buffer to each well of the 0.5ml 96-well plate.
2.3. Prepare 3 Wash Plates (Wash Plate 1, Wash Plate 2 and Wash Plate 3) by adding 650 ul Wash Buffer (W12) to each well of 2.4 mL 96 deep well plates.
3. Operate on KingFisher Flex machine
3.1. Install script of ChargeSwitch gDNA Mini Bacteria kit on KingFisher Flex by requesting the script through ThermoFisher and installing it using BindIt software
3.2. Select the right script/method and then click start. 
3.3. Load 0.5ml 96-well plate containing the Tip comb.
3.4. Load Elution plate.
3.5. Load Wash Plate 1, Wash Plate 2, and Wash Plate 3 one by one.
3.6. Load Sample plate. The instrument will automatically start processing the sample plate.

(While the instrument is processing the sample plate, prepare a premix of 500 ul Lysisi Buffer (L14) and 10 ul of Proteinase K solution).
3.7. 6)	After 10 mins of sample processing, there is the first pause. Once the Instrument pauses, pick up the sample plate from the instrument and add 500 ul of the premix prepared in step 5 (500 ul Lysis Buffer/Proteinase K mixture) to each sample well of Sample plate.
3.8. Then load Sample plate back into the instrument and click Start.
3.9. After 10 mins, there is a second pause, take the sample plate off the instrument and add 40 ul of Charge Switch Magnetic Beads and 300 ul Binding Buffer (B8) to each sample well, and then load the Sample plate back into the instrumentand click Start. The machine will do the remaining steps until it is done.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>This protocol explores how to run USEARCH (v11.0.667) (<a href="https://academic.oup.com/bioinformatics/article/26/19/2460/230188" target="_blank" rel="noopener noreferrer">Edgar, 2010</a>) on a 16s RNA dataset.</p>
<p> </p>
<p>USEARCH is a sequence analysis tool that offers search and clustering algorithms. Here USEARCH will be used to run a quality control on a 16S RNA dataset. This protocol uses a staggered mock community as an example (see attached files).</p>

[BEFORE_START]
<p>You need to download USEARCH on your computer. To do so, request a dowload link <a href="https://www.drive5.com/usearch/manual/install.html" target="_blank" rel="noopener noreferrer">here</a>. Once the binary is downloaded, no need to install anything, just copy the binary to a directory that is accessible from the computer where you want to run the code.</p>
<p> </p>
<p>For easier run, you can rename the binary to 'usearch' by running in your shell :</p>
<p><em>mv usearch11.0.667_i86osx32 usearch</em></p>
<p> </p>
<p>On linux and Mac-OS systems, please make sure to have the execution rights on the binary. To add execution rights, run :</p>
<p><em>chmod u+rwx usearch</em></p>
<p> </p>
<p> To run usearch, you can either add the path to the binary to your PATH variable, ou must type the full path to the file : </p>
<p><em>./YOUR/PATH/TO/usearch -cluster_fast reads.fasta -id 0.9 -uc results.uc</em></p>

[GUIDELINES]
<p>For more information on USEARCH, please read the <a href="https://drive5.com/usearch/manual/" target="_blank" rel="noopener noreferrer">dedicated documentation</a>.</p>

[STEPS]
?. 
?. 
?.
TITLE: Tunnel Slide Preparation for Motor Speed Recordings 
AUTHORS: Uriel Barboza Perez, Ekaterina Krasnopeeva, Jerko   Rosko, Teuta Pilizota

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">Preparation of our standard tunnel-slide, used for BFM speed measurements and experiments involving rapid media exchange.</div></div>

[STEPS]
?. [Tunnel Slide Making]
Take out 22x40 mm coverslips and standard microscope slides.
?. [Tunnel Slide Making]
Cut 2 pieces of Scotch sticky tape and tape them perpendicularly on the microscope slide.
The separation between the tapes should be approximately  3-4mm apart from each other.
?. [Tunnel Slide Making]
Cut the  excess tape off with a razor and place the coverslip onto  the slide gently. Use pipette tips to push it down gently and to remove air.
?. [Tunnel Slide Making]
Once finished, flip the tunnel slide so that you have the coverslip at the bottom and the tunnel entries are accessible . Note: The channel that was made on the slide has a capacity of 8-10 uL.
TITLE: User Guide for CytoFLEX S Analyzer
AUTHORS: Jamie C Tijerina

[DESCRIPTION]
This is the Caltech Flow Cytometry Facility's User Guide for the CytoFLEX S Analyzer. This guide is given to all investigators who are trained to run the CytoFLEX S in the facility. A copy is kept in a binder next to the instrument at all times along with all other CytoFLEX S related protocols. This user guide includes basic instructions for operating the instrument in both tube mode and plate mode. It also contains instructions for troubleshooting.

[BEFORE_START]
Make sure that you have checked the configuration of your instrument before purchasing reagents and preparing your samples. Before switching on the instrument, wipe down the area around the instrument with 70% ethanol or CaviWipes. Refill the sheath tank and empty the waste tank.

[STEPS]
1.  
Download the full user guide here.
TITLE:   ELISA for quantification of IL-9 in human serum.
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: No Title
AUTHORS: 

[DESCRIPTION]
<p>The biGBac system presented by Weissmann <em>et al. </em>(Weissmann <em>et al, </em>2016 and Weissmann <em>et al, </em>2018) is a modular insect cell expression system designed for expression of multi-subunit complexes. The system is very powerful, allowing up to 25 genes to be assembled into one baculo-virus expression vector, but does require a reasonable amount of cloning experience in order to attain clones in the 6 day time frame stated in the paper. This guide was written to provide a detailed explanation how the system is designed, how it can be further exploited and provide in-depth practical information that even a novice cloner can follow.</p>

[STEPS]
TITLE: RNA re-precipitation protocol
AUTHORS: Cristian Riccio

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block">If the RNA you have extracted is not pure and contains some residual contamination, as shown by poor Nanodrop ratios, you can reprecipitate the RNA, wash it and re-dissolve it to purify it.</div></div>

[STEPS]
?. Add 10% volume 3M sodium acetate pH 5.2 and 250% volume ethanol. So if your RNA solution is 100 ul, add 10 ul NaAc solution and 250 ul ethanol.
?. Mix well and put on dry ice for 30 min or -20 overnight
?. Centrifuge max speed 30 min at 4 C, remove supernatant
?. 3 washes with 75% ethanol kept on dry ice. For example, add 900 ul 75% ethanol, centrifuge 5 min at max speed (~ 21,000 g), remove ethanol, three times.
?. 10 min RT in hood drying
?. flick tubes for 1 minute
?. 1 min at 80 C in heat-block
?. Resuspend in DEPC water
?. Assess the quality of the RNA using Nanodrop and Qubit.
?. Make Sodium Acetate 3M, pH 5.2.
TITLE: No Title
AUTHORS: 

[DESCRIPTION]
<p>El ensayo de herida o ruptura <em>in vitro</em>, es un método fácil, de bajo costo y bien desarrollado para medir migración celular <em>in vitro</em>. Los pasos básicos implican la creación de una “herida” en una monocapa celular, capturando las imágenes al principio  y en intervalos regulares de tiempo durante la migración celular para cerrar la herida y comparar las imágenes para cuantificar la tasa migración de las células. </p>
<p> </p>
<p>La realizacion de este protocolo fue posible gracias al apoyo del departamento administrativo de ciencia tecnología e innovacion, Colciencias a traves del proyecto 111356933173 convocatoria569-2012. </p>

[BEFORE_START]
<p style="text-align: justify;">Trabajar con las células dos o tres pases depués de descongeladas. </p>
<p style="text-align: justify;">Realizar la señas en el reverso de la placa como guía de referencia para el registro fotográfico.</p>
<p style="text-align: justify;">Pretratar la placa de cultivo con colágeno un día antes de la realizar el ensayo. </p>
<p style="text-align: justify;">Preparar las soluciones a utilizar:</p>
<ul style="text-align: justify;">
<li>Fibronectina</li>
<li>Control negativo</li>
<li>Control positivo</li>
<li>Tratamientos a evaluar </li>
</ul>
<p style="text-align: justify;"> </p>
<p style="text-align: justify;"> </p>
<p> </p>
<p style="text-align: justify;"> </p>

[GUIDELINES]
<p style="text-align: justify;">Los pasos básicos implican la creación de una roptura o 'herida' en una monocapa celular, capturando las imágenes al principio y en intervalos regulares durante la migración celular hasta el cierre de la herida y comparando las imágenes para cuantificar el porcentaje de cierre.</p>

[STEPS]
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?. 
?.
TITLE: Cultivation of Seminavis robusta
AUTHORS: Lev Tsypin, Aaron Turkewitz

[DESCRIPTION]
<div class = "text-blocks"><div class = "text-block"><span>This protocol describes how we grew </span><span style = "font-style:italic;">S. robusta</span><span> and stored cultures at 4 C. Under these condtiions, the cells grow to a maximum density of 2-2.5 x 10</span><span style = "vertical-align:super;">6 </span><span>cells/mL.</span></div></div>

[STEPS]
?. [Growth]
Set up an incubator for 12 hr day-night cycling at 18 C.
?. [Growth]
Inoculate 100 mL F/2 in 175 cm2 flask with ~500,000 cells
?. [Cold storage]
Scrape a growing 175 cm2 flask
?. [Cold storage]
Mix 5 mL of scraped culture with 5 mL fresh F/2 medium in a 15 mL falcon tube
?. [Cold storage]
Wrap with foil and store flat at 4 C.
?. [Growth]
Lay flat in incubator
TITLE: Paraoxonase 1 and chronic obstructive pulmonary disease: A meta-analysis (protocol)
AUTHORS: Jun  Watanabe, Kazuhiko Kotani, Alejandro Gugliucci

[DESCRIPTION]
Introduction:Oxidative stress is a driving factor in the pathophysiology of chronic obstructive pulmonary disease (COPD). While paraoxonase 1 (PON1) is an antioxidant enzyme, a potential biomarker of this disease, data regarding the relationship of PON-1 with COPD appear to show some controversy. In this regard, to shed light on this issue, we will aim to perform a meta-analysis of data on PON1 activity in COPD.
Methods: Electronic databases (MEDLINE, Embase and CENTRAL) will be searched for available studies on PON1 activity in patients with stable COPD published before October 2021. A meta-analysis will be performed using random-effects models.

[STEPS]
TITLE: OcuPrime Vision Support Reviews: Shocking Side Effects &amp; Customer Complaints
AUTHORS: ocuprimevision  

[DESCRIPTION]
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[STEPS]
TITLE: Whitefly DNA extraction, partial mtCO1 gene amplification and gel electrophoresis
AUTHORS: Joachim Nwezeobi, Onyeyirichi Onyegbule, Chukwuemeka Nkere, Joseph Onyeka, Sharon van Brunschot, Susan Seal, John Colvin

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

[STEPS]
?. Single whitefly adults were randomly chosen from each of the 1.5 ml Eppendorf tubes containing 70% ethanol, using a sterilized entomological pin.
?. Each whitefly was transferred to a clean 1.5 ml Eppendorf tube.
?. To extract insect DNA, 50 µl of 10% Chelex was added to the tube and the whitefly was crushed using a plastic pestle until a clear homogenised mixture was obtained.
?. The mixture was then incubated at 56°C for 20 minutes and further incubated at 100°C for five minutes.
?. The mixture was then centrifuged at 13,500 g for five minutes using the Eppendorf Centrifuge 5424 R and the supernatant was collected and stored at -20°C until use.
?. Two sets of primers, with different degrees of sensitivity, were used to amplify the mtCO1 fragments, which were the: (i) African specific 2195Bt (5’-TGRTTTTTTGGTCATCCRGAAGT-3’) and C012/Bt-sh2 (5’-TTTACTGCACTTTCTGCC-3’) primers [21] and (ii) generic CI-J-2195 (5’-TTGATTTTTTGGTCATCCAGAAGT -3’) and TL2-N-3014 (TCCAATGCACTAATCTGCCATATTA -3’) primers.
?. Polymerase chain reaction (PCR) was run on an Applied Biosystems 2720 thermal cycler for 35 cycles.
?. The PCR program conditions were set at (i) initial denaturation at 94°C for 2 minutes, (ii) denaturation at 94°C for 20 seconds, (iii) annealing at 52°C for 30 seconds, (iv) extension at 72°C for one minute and (v) final extension at 72°C for five minutes.
?. Agarose gel electrophoresis (1% w/v in 0.5 X Tris/borate/EDTA buffer) was used to confirm PCR amplification.
?. The GeneJETPCR purification kit (Thermo Scientific)was used to purify amplicons of interest as described by the kit manufacturer.
TITLE: Geometric morphometrics nesomyinae rodent skulls
AUTHORS: Lea   Terray, Christiane Denys, Steven Goodman, Voahangy Soarimalala, Aude Lalis, Raphaël Cornette, christiane.denys  

[DESCRIPTION]
Here we aim to define how skull morphology in an endemic and monophyletic clade of rodents (subfamily Nesomyinae), which show considerable morphological variation and are largely forest-dwelling, has evolved and to characterize this disparity in a phylogenetical and ecological context. We performed a two-dimensional geometric morphometric analysis on 371 dorsal and 400 ventral skull images comprising all nine extant endemic genera (26 different species) and tested the influence of ecological parameters in a phylogenetic context on size and shape. 

[STEPS]