Isotopes and Isotope Batch¶
Isotope¶
Isotopes can be an important step in the identification process of missing persons. If your project chooses to use Isotope analysis as part of your identification process then you have come to the right place. Here you will learn more about the Isotope module in CoRA. A critical first step is to cut a sample of the specimen for Isotope analysis and then assign a sample number to it for tracking purposes and after you get results from your Isotope lab you can capture Isotope information here to create a Isotope Profile for further analysis.
Create a Isotope Sample¶
The Isotope sample and Profile are associated with a specimen, so you must first choose a specimen for which you want to create a Isotope sample for. You can choose a specimen by navigating to the specimen screen from either the specimen search results screen or from any data table row that has a specimen link on it. All search and reports screens have specimen links on them. Simply click these links to navigate to the specimen view/edit screen. Once on the specimen screen you can navigate to the Specimen Action or Details, and then to the Isotope Profile menu.
CoRA's intellisense will automatically take you to the Create Isotope sample screen, if this is the first Isotope sample you are trying to create for this specimen or will take you to the Isotope list screen if a Isotope Sample was previously created for this specimen. Note you can create multiple Isotope samples for a specimen.
Tip
CoRA allows you to create multiple Isotope samples for a specimen. If you have multiple isotope samples, CoRA will create a Consensus Isotope Profile for you with data from the multiple samples. Consensus Isotope Profile is a powerful feature of CoRA.
The screen fields are shown below. Fields in bold are required.
| Attributes | Data Type | Size | Validation Rule | Required/Optional |
|---|---|---|---|---|
| Sample Number | Alphanumeric | 8 chars | can only contain letters and numbers | Required |
| Lab | Id | id | valid labs via dropdown setup for the org | Required |
| External Case Number | String | 32 chars | Optional |
Clicking Save will take you to the Isotope Profile screen. You can visit the Isotope Profile screen once you have received data from your Isotope processing lab to enter Isotope related data.
Edit Isotope Profile¶
Specimens which have had a Isotope sample successfully created will have an associated Isotope Profile. The Isotope profile contains all the relevant Isotope attributes and are editable via action (user must have appropriate role and permissions).
You can visit the Isotope Profile screen once you have received data from your Isotope processing lab to enter Isotope related data to build the Isotope Profile for the specimen. On this screen click the pencil icon on the top right corner to edit the Isotope profile.
The screen fields are shown below. Fields in bold are required.
| Attributes | Data Type | Size | Validation Rule | Required/Optional |
|---|---|---|---|---|
| Sample Number | Alphanumeric | 8 chars | can only contain letters and numbers | Required |
| Lab | Id | id | valid labs via dropdown setup for the org | Required |
| External Case Number | String | 32 chars | Optional | |
| Isotope Batch Number | Number | valid numeric value | Optional | |
| Results Status | String | 32 chars | valid results status via dropdown | Optional |
| Sample Cleaned Weight | Decimal | Optional | ||
| Demineraliing Start Date | Date | Optional | ||
| Demineraliing End Date | Date | Optional | ||
| Sample Vial and Lid Weight | Decimal | Optional | ||
| Weight Collagen | Decimal | Optional | ||
| Yield Collagen | Decimal | Optional | ||
| Collagen Weight used for Analysis | Decimal | Optional | ||
| Analysis Requested | String | Optional | ||
| Well Location | String | Optional | ||
| Carbon Delta | Decimal | Optional | ||
| Carbon Weight | Decimal | Optional | ||
| Carbon Percentage | Decimal | Optional | ||
| Nitrogen Delta | Decimal | Optional | ||
| Nitrogen Weight | Decimal | Optional | ||
| Nitrogen Percentage | Decimal | Optional | ||
| Carbon/Nitrogen Ratio | Decimal | Optional | ||
| Oxygen Delta | Decimal | Optional | ||
| Oxygen Weight | Decimal | Optional | ||
| Oxygen Percentage | Decimal | Optional | ||
| Carbon/Oxygen Ratio | Decimal | Optional | ||
| Sulphur Delta | Decimal | Optional | ||
| Sulphur Weight | Decimal | Optional | ||
| Sulphur Percentage | Decimal | Optional |
Click on Save if any of the fields were updated
Tip
The Isotope profile has attributes to track Carbon, Nitrogen, Oxygen, Sulphur and respective deltas, weight, percentage and relevant ratios for further analysis.
Isotope Batch¶
A new isotope batch can be created by navigating to Left Sidebar Menu -> Isotope -> New Isotope Batch.
This will allow an Isotope Analyst to first create an isotope batch with a batch number and then associate specimen isotope samples that belong to that batch. After all the isotopes samples are added to the batch we can start processing the isotope batch. The isotope batch will step through multiple processing steps which as detailed below.
We can track the progress throughout the processing cycle of an isotope batch. This functionality will allow the Isotope Analyst digitally document at which step the Isotope Batch is currently in and tracks its' progress and status.
Tip
You must be logged in as an Isotope Analyst in order to create a new isotope batch.
The screen fields are shown below. Fields in bold are required.
| Attributes | Data Type | Size | Validation Rule | Required/Optional |
|---|---|---|---|---|
| Batch Number | Alphanumeric | 8 chars | can only contain letters and numbers | Required |
| Lab | Id | id | valid labs via dropdown setup for the org | Required |
| External Case Number | String | 32 chars | Optional |
Clicking Save will create the isotope batch in the database and will allow you to now associate isotope samples to this batch
Associate Isotopes Samples¶
Once an isotope batch has been created the user will be allowed to associate isotope samples to this batch. In order to associate isotope samples to this batch the user must first select the project, this will then show you all the specimen isotope samples that are available to be added to this batch. Selecting the isotope sample and clicking the associate button will move the sample into the associated isotopes list, meaning that the sample has now been added to this batch.
The screen fields are shown below. Fields in bold are required.
| Attributes | Data Type | Size | Validation Rule | Required/Optional |
|---|---|---|---|---|
| Project | Id | id | valid projects via dropdown setup for the org | Required |
| Isotopes Sample | String | 32 chars | Required | |
| Associated Samples | String | 32 chars | Required |
Note
An isotope batch must have at least one isotope sample associated with it.
Start Batch Processing¶
The start processing button will be enable once isotope samples are associated with the isotope batch. The batch processing has multiple steps and the following sections describe each of these steps in the order they are to be performed. You cannot move forward unless all the tasks in a given step are completed, you can move back to look the data in the previous steps. Only when all steps have been completed can you close out the batch processing. Lets begin by following the steps below.
Note
Each of these steps might take anywhere from a few minutes to multiple hours.
Cleaning¶
Click the pencil icon on the top right corner to edit the fields in this step.
Each toggle switch must be enabled before moving forwards to the next tab (Demineralizing)
Toggles must be enabled for the following processes: - Label Tubes and Caps - Remove all visible signs of surface contamination using rotary tool - Rinse samples w/dH20 - Sonicate samples with dH20 - cycle 1 - Sonicate samples with dH20 - cycle 2 - Sonicate samples with 95% ethanol - Sonicate samples with 100% ethanol - Dry samples in oven
Click Save
After the toggles have been enabled and saved, you will see "Start Date" for Sonicate samples with dH20 - cycle 1, Sonicate samples with 95% ethanol, Dry samples in oven, Sonicate samples with dH20 - cycle 2, Removed cooled samples from tubes, weigh, and return.
Note: Dates cannot be edited, the dates are taken from when the toggle switch was enabled.
After you save the above one new field will appear, enable this toggle once completed and then click save
- Remove cooled samples from tubes, weigh, and return
Click Save
If you are not able to go to the next tab, please check and ensure all fields and toggles are filled out properly
Demineralizing¶
Click the pencil icon on the top right corner to edit the fields in this step.
Each toggle switch must be enabled before moving forwards to the next tab (Remove Humic Acid)
Toggle must be enabled for: - Treat samples with 40ml 0.25 M hydrochloric acid until spongy. Change acid every 2-4 days. Treat until there are no hard spots; test with dental pick. Discard waste appropriately.
click Save
Two new fields will appear, click the pencil icon again to edit to enable the toggle switches
Toggles must be enabled for: - Treatment of samples with 40ml 0.25 M hydrochloric acid complete
Note: Dates cannot be edited, the dates are taken from when the toggle switch was enabled.
Click Save
One new field will appear, click the pencil icon again to edit to enable the toggle switch
Toggles must be enabled for: - Rinse demineralized samples 3x with dH20
Click Save
You will be moved to the next tab, "Remove Humic Acid", if you are not able to go to the next tab, please check and ensure all fields and toggles are filled out properly
Remove Humic Acid¶
Click the pencil icon on the top right corner to edit the fields in this step.
Each toggle switch must be enabled before moving forwards to the next tab (Solubilizing).
Toggles must be enabled for:
- Treat samples with 40ml 0.125 M sodium hydroxide for 24 hrs. Discard waste appropriately. Rinse samples 5x with dH20.
- Rinse 1 Start
- Rinse 1 End
- Rinse 2 Start
- Rinse 2 End
- Rinse 3 Start
- Rinse 3 End
- Rinse 4 Start
- Rinse 4 End
- Rinse 5 Start
- Rinse 5 End
Click Save
One new field will appear, click the pencil icon again to edit to enable the toggle switches.
Note: Dates cannot be edited, the dates are taken from when the toggle switch was enabled.
- Treatment and Rinse Completed
Click Save
You will be moved to the next tab, "Solubilizing", if you are not able to go to the next tab, please ensure all fields and toggles are filled out properly
Solubilizing¶
Click the pencil icon on the top right corner to edit the fields in this step.
Each toggle switch must be enabled before moving forwards to the next tab (Freeze Drying).
Toggle must be enabled and fields entered for:
- Clean vials and lids. Label.
- Add 15ml pH 3 dH20 to samples and cover tubes with double layer of plastic wrap. Cap tightly.
- Place capped tubes in oven for 24 hours.
- Centrifuge tubes and transfer supernatant into PTFE beakers. Place beakers in oven to evaporate
- Number of Acid-Heat Treatments
- Number of Collagen Transfers
- Close vials and freeze until solid. Tilting vials while freezing can help prevent cracking.
Click Save
You will be moved to the next tab, "Freeze Drying", if you are not able to go to the next tab, please ensure all fields and toggles are filled out properly.
Freeze Drying¶
Click the pencil icon on the top right corner to edit the fields in this step.
Each toggle switch must be enabled before moving forwards to the next tab (Collagen Yield).
Toggles must be enabled for:
- Turn on freeze-dryer. Replace vial lids with Kimwipe caps. Ensure samples are frozen solid.
- Freeze-dry samples - this may take 1 - 3 days. Once collagen is dry, cap vials tightly.
- Freeze-dry samples step completed
Click Save
Note: Dates cannot be edited, the dates are taken from when the toggle switch was enabled.
You will be moved to the next tab, "Collagen Yield", if you are not able to go to the next tab, please ensure all fields and toggles are filled out properly.
Collagen Yield¶
Click the pencil icon on the top right corner to edit the fields in this step.
Each toggle switch must be enabled before the Isotope Batch can be saved.
Toggle must be enabled for:
- Weigh dry samples in vials with lids and record combined weight.
Click Save
You should see "Result Status" field on the top showing that it is Completed.
Isotope Batch Fields¶
The screen fields are shown below. Fields in bold are required.
Tip
dH2O is Distilled Water
| Attributes | Data Type | Size | Validation Rule | Required/Optional |
|---|---|---|---|---|
| Lab | Id | id | Can choose from the option available | Required |
| External Case # | Alphanumeric | 32 chars | Can only contain letters and numerals | Optional |
| Isotope Batch Number | Alphanumeric | 32 chars | Can only contain letters and numerals | Required |
| Status | String | 32 chars | valid statuses are Open, Associating Isotopes, Cleaning, Demineralizing, Removal Humic Acids, Solubilizing, Freeze Drying Collagen, Determining Collagen Yield and closed | Required |
| Cleaning start date | Date | Required | ||
| Label tubes and caps | Boolean | true/false toggle | Required | |
| Remove all visible signs of surface contamination | Boolean | true/false toggle | Required | |
| Rinse sample with dH2O | Boolean | true/false toggle | Required | |
| Sonicate samples with dH2O-cycle1 | Boolean | true/false toggle | Required | |
| Sonicate samples with dH2O-cycle1 Start Date | Date | Required | ||
| Sonicate samples with dH2O-cycle2 | Boolean | true/false toggle | Required | |
| Sonicate samples with dH2O-cycle2 Start Date | Date | Required | ||
| Sonicate samples with 95% ethanol | Boolean | true/false toggle | Required | |
| Sonicate samples with 95% ethanol Start Date | Date | Required | ||
| Sonicate samples with 100% ethanol | Boolean | true/false toggle | Required | |
| Sonicate samples with 100% ethanol Start Date | Date | Required | ||
| Dry samples start | Boolean | true/false toggle | Required | |
| Dry sample start date | Date | Required | ||
| Dry samples end | Boolean | true/false toggle | Required | |
| Dry sample end date | Date | Required | ||
| Cleaning initials | Alphanumeric | 32 chars | Can only contain letters and numerals | Required |
| Demineralizing Treatment Start | Boolean | true/false toggle | Required | |
| Demineralizing Treatment End | Boolean | true/false toggle | Required | |
| Demineralizing Treatment Start Date | Date | Required | ||
| Demineralizing Treatment End Date | Date | Required | ||
| Rinse Demineralized Samples | Boolean | true/false toggle | Required | |
| Removal Humic Acids treatment start | Boolean | true/false toggle | Required | |
| Removal Humic Acids treatment End | Boolean | true/false toggle | Required | |
| Removal Humic Acids treatment start Date | Date | Required | ||
| Removal Humic Acids treatment End Date | Date | Required | ||
| Removal Humic Acids treatment rinse 1 start | Boolean | true/false toggle | Required | |
| Removal Humic Acids treatment rinse 1 End | Boolean | true/false toggle | Required | |
| Removal Humic Acids treatment rinse 1 start Date | Date | Required | ||
| Removal Humic Acids treatment rinse 1 End Date | Date | Required | ||
| Removal Humic Acids treatment rinse 2 start | Boolean | true/false toggle | Required | |
| Removal Humic Acids treatment rinse 2 End | Boolean | true/false toggle | Required | |
| Removal Humic Acids treatment rinse 2 start Date | Date | Required | ||
| Removal Humic Acids treatment rinse 2 End Date | Date | Required | ||
| Removal Humic Acids treatment rinse 3 start | Boolean | true/false toggle | Required | |
| Removal Humic Acids treatment rinse 3 End | Boolean | true/false toggle | Required | |
| Removal Humic Acids treatment rinse 3 start Date | Date | Required | ||
| Removal Humic Acids treatment rinse 3 End Date | Date | Required | ||
| Removal Humic Acids treatment rinse 4 start | Boolean | true/false toggle | Required | |
| Removal Humic Acids treatment rinse 4 End | Boolean | true/false toggle | Required | |
| Removal Humic Acids treatment rinse 4 start Date | Date | Required | ||
| Removal Humic Acids treatment rinse 4 End Date | Date | Required | ||
| Removal Humic Acids treatment rinse 5 start | Boolean | true/false toggle | Required | |
| Removal Humic Acids treatment rinse 5 End | Boolean | true/false toggle | Required | |
| Removal Humic Acids treatment rinse 5 start Date | Date | Required | ||
| Removal Humic Acids treatment rinse 5 End Date | Date | Required | ||
| Solubilizing clean vials and lids | Boolean | true/false toggle | Required | |
| Solubilizing clean vials and lids date | Date | Required | ||
| Solubilizing add soluble | Boolean | true/false toggle | Required | |
| Solubilizing place in oven | Boolean | true/false toggle | Required | |
| Solubilizing centrifuge tubes | Boolean | true/false toggle | Required | |
| Solubilizing num acid heat treatment | Number | 32 chars | numeric | Required |
| Solubilizing num collagen transfers | Number | 32 chars | numeric | Required |
| Solubilizing freeze vials | Boolean | true/false toggle | Required | |
| Solubilizing freeze vials date | Date | Required | ||
| Freeze Drying Collagen on | Boolean | true/false toggle | Required | |
| Freeze Drying Collagen Start | Boolean | true/false toggle | Required | |
| Freeze Drying Collagen End | Boolean | true/false toggle | Required | |
| Freeze Drying Collagen Start Date | Date | Required | ||
| Freeze Drying Collagen End Date | Date | must be greater than start date | Required | |
| Combined Sample Weight | Boolean | true/false toggle | Optional | |
| Notes | String | 256 chars | Can contains a string alphanumeric values | Optional |
Created: 2023-12-22