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| Quantitative Sensory Testing (QST) is a set of standardized psychophysical assays that assess how pain is processed. In A2CPS, we use QST to characterize each participant's pain-processing "profile" before surgery, on the hypothesis that these profiles help predict who goes on to develop chronic post-surgical pain. | ||
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| A2CPS collects three complementary QST assays, and each one is tested at both a surgical **index site** (near where surgery will occur, i.e., the knee for the TKA cohort and the chest for the thoracic cohort) and a **remote site** (the contralateral deltoid, which serves as a control location): |
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It would be great to have a citation for each of the measurements, if one exists. That could either look like a historical review paper, or even an "original" reference for the method. Here's one candidate:
McDaniel, A. L., Dimitrov, T. N., Bruehl, S. P., Monroe, T. B., Failla, M. D., Cowan, R. L., ... & Anderson, A. R. (2023). Psychophysics of pain: A methodological introduction. Pain Management Nursing, 24(4), 442-451.
Alternatively, is there something like a QST lecture that could be linked to?
Those kinds of links are especially helpful for people who have never worked with the data before.
| - **Mechanical Temporal Summation (MTS)**: the increase in pain over a train of ten identical pokes delivered at 1 Hz with a Neuropen. MTS captures *pain facilitation*, i.e., the tendency of the central nervous system to amplify repeated input. **Higher MTS means greater facilitation.** | ||
| - **Conditioned Pain Modulation (CPM)**: the change in PPT after a conditioning cold-water hand immersion. CPM captures *descending inhibition*, i.e., the "pain inhibits pain" mechanism. **Negative CPM scores indicate that inhibition is present.** | ||
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| For each assay, the cleaning workflow computes a **primary** and a **secondary** outcome, and for PPT and MTS these are reported at both the index and the remote site. The exact definitions follow the A2CPS Manual of Procedures: |
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By "outcome," do you mean the same thing as "biomarker"? For example, some readers could be left wondering whether "Primary Outcome" and "Primary Biomarker" are the same thing.
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| | PPT | Mean PPT at the **index** site | Mean PPT at the **remote** site | | ||
| | MTS | Mean of 3 difference scores (Max minus initial) | Mean of 3 wind-up ratios, (Max + 1)/(initial + 1) | | ||
| | CPM | % change: (pre minus post)/pre × 100 | Difference: pre minus post | |
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Are these equations defined anywhere else? For example, in a publicly available data dictionary?
| The files are plain CSVs, and here we use the [`tidyverse`](https://www.tidyverse.org/). We focus on the TKA cohort. | ||
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| ```{r setup} | ||
| library(tidyverse) |
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Could you move this to the top of the file? That'd be more consistent with the others. Also, in the other kits, we've loaded individual packages rather than pulling in the whole tidyverse.
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| The eight derived biomarker columns for the TKA cohort follow a consistent naming scheme: `primary_` or `secondary_`, then the assay (`ppt`, `ts`, `cpm`), and for PPT and MTS the site (`index` or `remote`). | ||
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| ```{r peek} |
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Are you able to get prek working? That would apply some formatting and linting rules to harmonize the style. I have just now added a section to the contributing.md file about this: https://github.com/a2cps/starterkits?tab=contributing-ov-file#pre-commit-hooks
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| ``` | ||
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| ### Data Quality |
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The template was ambiguous, but there was meant to be a difference between Data Quality and Quality Control. It sounds like you're describing things that have already been done to the data, which I would take to mean Quality Control.
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| ### Data Generation | ||
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| QST is administered in person by trained study staff, following the A2CPS Manual of Procedures, which specifies the algometer and Neuropen procedures, the cold-water CPM protocol, the index and remote testing locations, and the double entry of every pain rating. Raw responses are captured in REDCap. The steps that turn the REDCap export into the reformatted files (filtering, deduplication, error checking, and computing the PPT, MTS, and CPM biomarkers) are documented in the cleaning workflow that comes with the release (`QSTCRF_data_quality_checks_and_reformat.html`). |
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You can link directly to the rendered version of this document so people go straight to the appendix. See: https://quarto.org/docs/authoring/cross-references.html#sections.
Just a reminder for later: at a meeting earlier this week, we discussed updating the appendix to take the NDA download as input and produce data in the format expected by this QST starter kit. You can link directly
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| - **Directionality matters.** Higher PPT means less sensitivity, higher MTS means more facilitation, and negative CPM points to inhibition. A flipped sign quietly reverses a result, so the table above is a handy reference. | ||
| - **MTS and WUR are non-negative by construction.** The difference and wind-up scores use `max(final, initial)` in place of the recorded maximum, so they never fall below 0 (difference) or 1 (wind-up ratio). This includes a handful of records where the recorded maximum was below the initial rating, but it is worth knowing when reproducing the values. | ||
| - **Cohort-specific field names.** The TKA and thoracic files use different underlying REDCap field names (for example, the double-entry suffixes differ), and the thoracic cohort also includes a Dynamic Mechanical Allodynia assessment. The biomarker columns are harmonized across cohorts, so they tend to be the easier starting point when comparing the two. |
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Many readers won't know how REDCap relates to the data. I'd replace REDCap for "raw," or maybe "raw (REDCap exported)"
| - **Directionality matters.** Higher PPT means less sensitivity, higher MTS means more facilitation, and negative CPM points to inhibition. A flipped sign quietly reverses a result, so the table above is a handy reference. | ||
| - **MTS and WUR are non-negative by construction.** The difference and wind-up scores use `max(final, initial)` in place of the recorded maximum, so they never fall below 0 (difference) or 1 (wind-up ratio). This includes a handful of records where the recorded maximum was below the initial rating, but it is worth knowing when reproducing the values. | ||
| - **Cohort-specific field names.** The TKA and thoracic files use different underlying REDCap field names (for example, the double-entry suffixes differ), and the thoracic cohort also includes a Dynamic Mechanical Allodynia assessment. The biomarker columns are harmonized across cohorts, so they tend to be the easier starting point when comparing the two. | ||
| - **Quality control.** The biomarker code has been reviewed and independently derived from the raw pain ratings, and the error report shows which records were flagged during cleaning. |
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While this is true, it may leave readers wondering what you mean by "review" and "flagging," specifically. What about linking to your preprint for the app?
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