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scinote-web/app/assets/templates/experiment_440/experiment.json
Oleksii Kriuchykhin 244c003137 Prettify template JSON files [SCI-3988]
2019-11-18 14:26:38 +01:00

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{
"experiment": {
"id": 440,
"name": "Microbiological sampling_QA",
"description": "This template will guide you on how to do monitor microbiological contamination with contact plates, settle plates and swabs. Quality assurance (QA) is a process, where primarily concerns are controls of errors in the performance of tests and verification of test results. All materials, equipment and procedures must be adequately controlled. \r\nThe objectives of microbiological sampling are to allow statements of density, types and locations of microorganism which reside on different surfaces.",
"project_id": 223,
"created_by_id": 202,
"last_modified_by_id": 202,
"archived": false,
"archived_by_id": null,
"archived_on": null,
"restored_by_id": null,
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"created_at": "2018-11-15T09:56:28.245Z",
"updated_at": "2019-02-19T14:12:34.714Z",
"uuid": "c35c71c3-2f8b-45fb-8064-f14e5d4cc724"
},
"my_modules": [
{
"my_module": {
"id": 2192,
"name": "Plate preparation",
"due_date": null,
"description": "",
"x": 0,
"y": 16,
"my_module_group_id": 1250,
"created_at": "2018-11-15T09:56:30.961Z",
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"nr_of_assigned_samples": 0,
"workflow_order": 0,
"experiment_id": 440,
"state": "uncompleted",
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},
"outputs": [
{
"id": 6284,
"input_id": 2188,
"output_id": 2192
},
{
"id": 6285,
"input_id": 2190,
"output_id": 2192
},
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}
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"name": null,
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"created_at": "2018-11-15T09:56:31.020Z",
"updated_at": "2019-01-31T09:33:37.119Z",
"published_on": null,
"nr_of_linked_children": 0
},
"protocol_protocol_keywords": [],
"steps": [
{
"step": {
"id": 4533,
"name": "Examine the plates",
"description": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body><p>Follow the guidelines bellow. </p></body></html>",
"position": 0,
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"user_id": 202,
"created_at": "2018-11-15T09:56:31.091Z",
"updated_at": "2018-12-24T08:23:09.402Z",
"last_modified_by_id": 202,
"protocol_id": 3548
},
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"checklist": {
"id": 924,
"name": "Guideline:",
"step_id": 4533,
"created_at": "2018-12-12T07:16:14.619Z",
"updated_at": "2018-12-24T08:23:09.400Z",
"created_by_id": null,
"last_modified_by_id": null
},
"checklist_items": [
{
"id": 3812,
"text": "Monitor refrigerator temperature and record it in Results.",
"checked": false,
"checklist_id": 924,
"created_at": "2018-12-12T07:16:14.622Z",
"updated_at": "2018-12-12T07:16:14.622Z",
"created_by_id": null,
"last_modified_by_id": null,
"position": 0
},
{
"id": 3813,
"text": "Contact plates and/or Settle plates are taken to the room temperature. They will be used depending on the surface of the sampling.",
"checked": false,
"checklist_id": 924,
"created_at": "2018-12-12T07:16:14.634Z",
"updated_at": "2018-12-12T07:16:14.634Z",
"created_by_id": null,
"last_modified_by_id": null,
"position": 1
},
{
"id": 3814,
"text": "Examine the plates for contamination prior to use. If any plates are contaminated they should be discarded according to protocol.",
"checked": false,
"checklist_id": 924,
"created_at": "2018-12-12T07:16:14.641Z",
"updated_at": "2018-12-12T07:16:14.641Z",
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"position": 2
}
]
}
],
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{
"step": {
"id": 4535,
"name": "Preincubation",
"description": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body><p>Preincubate the empty plates in incubator <strong>30°C-35°C</strong> for <strong>48 hours</strong> to check for any accidental contamination. Check for contamination again. If there is contamination record it and discard according to appropriate procedures. Take contamination-free plates to room temperature an hour before exposure.<br><br></p></body></html>",
"position": 1,
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"created_at": "2018-11-15T09:56:31.144Z",
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}
]
}
],
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},
{
"my_module": {
"id": 2200,
"name": "Counting colonies and recording data",
"due_date": null,
"description": null,
"x": 103,
"y": 16,
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"created_at": "2018-11-15T09:56:33.039Z",
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"created_at": "2018-11-15T09:56:33.091Z",
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"published_on": null,
"nr_of_linked_children": 0
},
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"steps": [
{
"step": {
"id": 5174,
"name": "Discarding plates",
"description": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body><p>All samples (contaminated or not) should be disposed of according to procedures.</p></body></html>",
"position": 2,
"completed": false,
"completed_on": null,
"user_id": 202,
"created_at": "2018-12-12T11:23:59.242Z",
"updated_at": "2018-12-12T11:24:31.752Z",
"last_modified_by_id": 202,
"protocol_id": 3564
},
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{
"step": {
"id": 5173,
"name": "Counting colonies and recording",
"description": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body><p>After appropriate incubation microbiological contamination should grow into discrete macroscopic colonies that can be enumerated and the number of discrete colonies forming units (CFU) can be counted on each sample. <br>Record the number (per unit surface area) on the results tab. Separate colony counts may be tabulated for mould and bacteria.<br><br>Colony types may be identified if this is considered appropriate.</p></body></html>",
"position": 0,
"completed": false,
"completed_on": null,
"user_id": 202,
"created_at": "2018-12-12T11:21:40.888Z",
"updated_at": "2019-02-19T14:27:48.440Z",
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},
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"estimated_size": 10556538,
"lock": null,
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"asset_blob": {
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}
}
],
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{
"step": {
"id": 4567,
"name": "Action to be taken",
"description": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body>\n<div style=\"text-align: justify;\">Recording of data provides oversight for microbiological cleanliness. In order for results to provide meaningful data, it is of key importance that alert and action limits are established. <em><strong>Alert levels ensure that any excursion of the parameter can be detected early. Action levels deviate more from the standard. If the alert level is exceeded repeatedly, this is considered equivalent to exceeding the action level.</strong></em> In practice, several statistical methods including normal, Poisson, and negative binomial modelling have been routinely used to set these limits. <br><br>Exceeding action levels on isolated occasions may not require more action than an examination of control systems. However, the frequency of exceeding the limit should be examined and should be low. <strong>If the frequency is high or shows an upward trend then action should be taken which may include an increase in the frequency of testing, observation of operator technique or investigation of cleaning procedures.<br><br></strong>\n</div>\n<div style=\"text-align: justify;\">Identification of the causative microorganism(s) may aid tracing the <strong>source of the contamination</strong>. Successive results greater than the action levels demand that appropriate action is taken to reduce contamination to within limits. Where a problem has been observed the contaminating microorganisms should be identified. Isolated instances require no more action than an examination of control systems. If repeated contamination appears an investigation into the problem should take place and<strong> corrective action should be carried out which will rectify the problem</strong>. The corrective action should investigate the root cause of the problem and identify steps, with the timescale, that will be taken to reduce the contamination levels to \"normal\". A record of all action taken should be made in an \"Abnormal Event Log\".</div>\n<div style=\"text-align: justify;\">The following areas should be examined where action levels are repeatedly breached:<br><br><strong>Identify:</strong>\n</div>\n<ul>\n<li>Possible cause</li>\n<li>Contaminating microorganisms</li>\n</ul>\n<strong>Investigate:</strong><br>\n<ul>\n<li>Whether an isolated sample or whole area involved</li>\n<li>Personnel - operator status (grade), level of training, health, technique, wash up</li>\n<li>Cleaning procedures</li>\n<li>Changing procedure</li>\n<li>HEPA filter integrity of room/clean air device</li>\n<li>Processes carried out</li>\n<li>Previous test results for trends or other identified problems.</li>\n</ul>\n<strong>Liase with:</strong> <br>\n<ul>\n<li>Aseptic personnel</li>\n<li>Microbiology personnel</li>\n<li>QA/QC personnel</li>\n</ul>\n</body></html>",
"position": 1,
"completed": false,
"completed_on": null,
"user_id": 202,
"created_at": "2018-11-15T09:56:33.108Z",
"updated_at": "2019-01-28T09:02:38.188Z",
"last_modified_by_id": 202,
"protocol_id": 3564
},
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}
]
}
],
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},
{
"my_module": {
"id": 2190,
"name": "Sampling of uneven surfaces",
"due_date": null,
"description": "A method using swabs that makes microbiological load visible on uneven surfaces.",
"x": 34,
"y": 33,
"my_module_group_id": 1250,
"created_at": "2018-11-15T09:56:30.349Z",
"updated_at": "2019-02-19T14:12:22.366Z",
"archived": false,
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},
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"output_id": 2190
}
],
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},
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{
"step": {
"id": 5448,
"name": "Labeling of plates",
"description": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body>\n<p>Assemble the plates required and label them. Ensure that correct information about sampling is written on the base of the plate with a permanent ink marker.<br>The following sampling details should be recorded on the plate:<br><br></p>\n<ul>\n<li>Initials of a person who is sampling</li>\n<li>Sampling location code</li>\n<li>Date and time of the day of sampling/plating </li>\n</ul>\n</body></html>",
"position": 3,
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"created_at": "2019-01-25T12:11:53.234Z",
"updated_at": "2019-01-25T12:18:18.027Z",
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},
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{
"step": {
"id": 4523,
"name": "Collect all the swabs",
"description": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body><p>After all the samples are taken, collect all sample swabs together, remove them from the sampling area and plate them as directed in the next step. Complete and enclose all the necessary documentation in <span class=\"atwho-inserted\" contenteditable=\"false\" data-atwho-at-query=\"#countin\">[#Counting and recording...~tsk~ZU]</span>.</p></body></html>",
"position": 2,
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"created_at": "2018-11-15T09:56:30.601Z",
"updated_at": "2019-01-25T12:40:08.288Z",
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"protocol_id": 3544
},
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},
{
"step": {
"id": 4521,
"name": "Sampling with a swab",
"description": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body><p><strong>Sampling:</strong> Wipe the swab over the sample area in close parallel streaks, using firm even pressure and rotating the swab between fingers to maximise sample pick-up. The swab should be held at a <strong>30°</strong> angle to the contact surface. With the same swab, repeat this process at right angles to the first streaks to ensure that the entire sample area is swabbed. Replace swab into transport tube ensuring that swab comes into contact with the transport medium by pushing down hard. Clean the surface tested with disinfectant.</p></body></html>",
"position": 1,
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"created_at": "2018-11-15T09:56:30.480Z",
"updated_at": "2019-02-19T14:13:06.622Z",
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},
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"checklist": {
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"name": "Sample locations:",
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{
"id": 3405,
"text": "Filling needle",
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"position": 0
},
{
"id": 3406,
"text": "Interior of the stopper chute",
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{
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}
]
}
],
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},
{
"step": {
"id": 5172,
"name": "Plating of swabs",
"description": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body><p>Follow the guidelines below for plating of swabs.</p></body></html>",
"position": 4,
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},
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"name": "Guidelines:",
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"created_by_id": null,
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},
"checklist_items": [
{
"id": 3906,
"text": "Prepare a safe and sterile workspace: Sterilize all instruments, solutions, and media prior to using them for plating procedures. Clear away all materials cluttering your work area on the laboratory bench. Clean work area with disinfectant to minimize possible contamination.",
"checked": false,
"checklist_id": 952,
"created_at": "2018-12-21T06:58:27.770Z",
"updated_at": "2018-12-21T06:58:27.770Z",
"created_by_id": null,
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"position": 0
},
{
"id": 3907,
"text": "Set up a Bunsen burner: Work slowly, carefully, and deliberately within the sterile field area created by the updraft of the flame.",
"checked": false,
"checklist_id": 952,
"created_at": "2018-12-21T06:58:27.777Z",
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"created_by_id": null,
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"position": 1
},
{
"id": 3908,
"text": "Prepare lab equipment and settle plates.",
"checked": false,
"checklist_id": 952,
"created_at": "2018-12-21T06:58:27.784Z",
"updated_at": "2018-12-21T06:58:27.784Z",
"created_by_id": null,
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"position": 2
},
{
"id": 3909,
"text": "Arrange all the supplies needed for the procedure on the laboratory bench near the sterile field. Make sure all the materials are properly labelled.",
"checked": false,
"checklist_id": 952,
"created_at": "2018-12-21T06:58:27.791Z",
"updated_at": "2018-12-21T06:58:27.791Z",
"created_by_id": null,
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"position": 3
},
{
"id": 3910,
"text": "Carefully open the lid of the plate. A standard streaking out method should be used when plating out the swab. The method should ensure that the swab is rotated as it is run over the surface of the media to ensure that any microorganisms recovered from the surface sample are deposited onto the surface of the plate.\r\nReplace the lid.",
"checked": false,
"checklist_id": 952,
"created_at": "2018-12-21T06:58:27.797Z",
"updated_at": "2018-12-21T06:58:27.797Z",
"created_by_id": null,
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"position": 4
},
{
"id": 3911,
"text": "Complete and enclose all the necessary documentation.",
"checked": false,
"checklist_id": 952,
"created_at": "2018-12-21T06:58:27.804Z",
"updated_at": "2018-12-21T06:58:27.804Z",
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"position": 5
}
]
}
],
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},
{
"step": {
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"name": "Preparation of swabs before sampling",
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"id": 4135,
"text": "Cover the smear with 3% v/v acid alcohol for 5 minutes or until the smear is sufficiently decolorized, i.e. pale pink.",
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"id": 4137,
"text": "Cover the smear with methylene blue dye for 1–2 minutes.",
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"id": 4139,
"text": "Wipe the back of the slide clean, and place it in a draining rack for the smear to air-dry (do not blot dry).",
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"id": 4140,
"text": "Examine the smear microscopically, using the 100 X oil immersion objective.",
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"step": {
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"description": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body><p>Follow the guidelines below.</p></body></html>",
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"id": 4124,
"text": "Flood air-dried, heat-fixed smear of cells for 1 minute with crystal violet staining reagent. Please note that the quality of the smear (too heavy or too light cell concentration) will affect the Gram Stain results.",
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"id": 4125,
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"id": 4126,
"text": "Flood slide with the mordant: Gram's iodine. Wait 1 minute.",
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"id": 4128,
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"id": 4129,
"text": "Flood slide with counterstain, safranin. Wait 30 seconds to 1 minute.",
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"id": 4131,
"text": "Observe the results of the staining procedure under oil immersion using a Brightfield microscope. At the completion of the Gram Stain, gram-negative bacteria will stain pink/red and gram-positive bacteria will stain blue/purple.",
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"description": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body>\n<p>Reagents bellow can be made or purchased.<br><strong><br>Crystal Violet Staining Reagent:<br></strong><span style=\"text-decoration: underline;\"><br>Solution A for crystal violet staining reagent</span></p>\n<ul>\n<li>Crystal violet (certified 90% dye content), 2g </li>\n<li>Ethanol, 95% (vol/vol), 20 mL</li>\n</ul>\n<span style=\"text-decoration: underline;\">Solution B for crystal violet staining reagent<br></span>\n<ul>\n<li>Ammonium oxalate, 0.8 g</li>\n<li>Distilled water, 80 mL</li>\n</ul>\nMix A and B to obtain crystal violet staining reagent. Store for<strong> 24 h</strong> and filter through paper prior to use.<br><br><strong>Gram's Iodine:<br></strong><br>\n<ul>\n<li>Iodine, 1.0 g</li>\n<li>Potassium iodide, 2.0 g</li>\n<li>Distilled water, 300 mL</li>\n</ul>\nGrind the iodine and potassium iodide in a mortar and add water slowly with continuous grinding until the iodine is dissolved. Store in amber bottles.<br><br><strong>Safranin:<br><br></strong><span style=\"text-decoration-line: underline;\">Stock solution:</span><br>\n<ul>\n<li>2.5g Safranin O</li>\n<li>100 ml 95% Ethanol</li>\n</ul>\n<p><span style=\"text-decoration: underline;\">Working Solution:</span></p>\n<ul>\n<li>10 mL Stock Solution </li>\n<li>90 mL Distilled water</li>\n</ul>\n</body></html>",
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"step": {
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"step": {
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"description": "<!DOCTYPE html PUBLIC \"-//W3C//DTD HTML 4.0 Transitional//EN\" \"http://www.w3.org/TR/REC-html40/loose.dtd\">\n<html><body>\n<p>Heat fixing kills the bacteria in the smear, firmly adheres the smear to the slide, and allows the sample to more readily take up stains.<br>Allow the smear to air dry. After the smear has air-dried, hold the slide at one end and pass the entire slide through the flame of a Bunsen burner <strong>two to three times with the smear-side up.</strong></p>\n<p> </p>\n<p> </p>\n</body></html>",
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"x": 34,
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"step": {
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