[Babase] Wounds&Path and white infants - was Censoring +
Alto's split
Niki Learn
nlearn at princeton.edu
Fri Oct 16 16:06:03 EDT 2009
> Code 7 - Limp, no wound visible
> Code 10 - Malaise, weakness, stiffness in absence of wound
> Code 14 - Other pathology
>
Susan wrote:
So, my main question about your next very useful 4 paragraphs is, I
assume we are going to ask the team to implement the recommendations
you make (which I agree with), rather than letting them do whatever,
and then do the interpretation here in the lab, right? I think it
makes sense to tell them about WMS (Jeanne has presumably talked with
them at some length about it already, I have mentioned it at least)
and explain that when they see " the walk" they should use 10 and make
a note that this looks like "that infant disease" or "that infant walk
that goes with white fur" or "possibly white monkey syndrome" or
something. If they see white fur they should record it as a separate
thing. Is everyone agreed? If so, Jeanne, can you (or have you
already) have this conversation with them?
Niki writes:
Certainly the team should be informed that this is the way we would like it
coded. As for what they want to call it, I'm fine with "that stiff walk"
but something referring in some way to white fur or white monkey syndrome is
fine. Sometimes when they write a note for white fur they'll say something
like, no sign of the stiff walk yet. A few of the cases do have both the
stiff walk and the white fur but for those that just have the stiff walk if
they want to make a similar note like, So and so is developing the stiff
walk but does not have white fur, that works for me too.
> I would not advise using code 7 for the stiff walk. This is the
> most frequently used code and it already has some irregularities
> that should probably be addressed. [Essentially, limp has changed
> from time to time on the datasheets, sometimes being listed simply
> as limp or even as limp from wound but usually as "limp, no wound
> visible" - sometimes it is marked along with wounds that could
> obviously be causing a limp, particularly in older data where the
> name may not match up with the code's name. Recent data (2000
> onward) is fairly consistent in not checking code 7 if there is a
> limp-causing wound. This is fine because there is also the column
> for checking whether the wound "impairs locomotion" which SHOULD
> always be checked when code 7 is used and whenever a limp-causing
> wound is evident. It also often marked with code 10 when the
> stiffness or weakness impairs locomotion.]
>
> Code 10 is mostly used in the following cases: To indicate slowing
> by older baboons (rheumatism, stiffness, slowing down, etc.), to
> indicate infants that are not thriving (can't cling, etc.), and for
> cases where a baboon has been badly wounded or is very sick and so
> is weak/in a state of malaise. The large outbreak of Coxsackie
> mentioned earlier was coded as 10, as are two cases that seem
> similar where 3 or 4 baboons simultaneously had stiff walks/stiff
> sacral regions for a short period of time.
>
> Code 14 is mostly used for really bizarre things that nobody knows
> where else to put and for more extreme cases where baboons become
> very thin (I found several cases of thinning that were flagged "low
> body weight" in the notes - I similarly flagged Liberty and can flag
> any other individuals that I actually get wounds & pathologies
> sheets for).
>
> That said it sounds like 10 is the best existing code to use.
> Possibly if we think they are white monkey cases we could flag them
> "possible white monkey syndrome" in the notes? Of course, right now
> there are four tables, three of which have notes. I'll have to see
> how Karl wants to arrange everything in babase since these sheets
> were designed with a different database system in mind; babase
> usually designated ids but these have predesignated ids (with many
> gaps) to allow the information in the four tables to be aligned with
> each other.
>
> It appears that wounds and pathologies mentioned solely in
> demography notes (of which I think there are many) do not appear in
> the existing wounds and pathologies tables. For example, surely
> there were cases of white monkey syndrome before 2003 but they were
> not given wounds sheets and so cannot be easily located. Is this
> something we need to remedy?
>
Susan wrote:
We started using wounds sheets in the 1980's. Before then, all W&Ps
were in demog notes. Starting in the early 1980's, all W&Ps should
have been written on the wounds sheets. Are you saying that you have
found a lot of W&P notes in demog notes from the 80's, 90's, and 00's
that have no wounds sheets? I am assuming not, but am just clarifying.
Also, I do think it is possible that there was no (or very little)
white monkey syndrome before 2002. I know that Jeanne and Stuart saw
white-furred infants in the 1960's, not sure if those infants had a
locomotor problem. My understanding is that they did not see it in the
1970's, I certainly never saw it in the 1980's. It may have appeared
in the 1990's (and it sounds like we have one possible record of it,
with SCI's infant), but it sounds like you have looked in the 1990's
wounds sheets and not seen anything? Or, maybe the team was not
identifying this as a pathology and so they would take demog notes
about it but no path notes. This is definitely possible, and may
explain your earlier comment about W&Ps in the demog notes -- yes?
But, I think it is also plausible that TOF was the first (or, YUM,
FIT, COD or FAM).
Niki writes:
I think I have noticed some mentions of wounds or illnesses with no wounds
sheet - I wouldn't say a lot. I am not sure how widespread this phenomenon
is and some of those sheets may yet be forthcoming.
Scion's white infant does not have a wounds sheet but the group was only
vaguely being monitored at the time and, as you say, it may not have
occurred to the team then that this was from an illness and should get a
sheet. No, I have not come across any other white infant cases in the
1990s, but there could be more in the demography notes, especially if the
team was not recognizing it as a pathology during those years.
It has been somewhat difficult to track whether a wound or illness gets a
wounds sheet since the sheets often come one or more months after any
related demography note. Now that I have the wounds and pathologies tables
up to date I will update that information regularly along with other update
files, which should make it easier to track wounds and see how we are doing
with getting sheets for all wounds that are mentioned. I have been trying
to do this over the past couple months by marking on the monthly checklist
that I am expecting a wounds sheet for so and so and then inquiring about it
if it doesn't come the following month. Sometimes the team follows up on a
baboon for several months though (particularly with white monkeys and badly
injured or very sick baboons) so some sheets take a long time to show up
here. Many other wounds and pathologies are never mentioned in demography
notes so I have no way of knowing if and when such sheets will arrive. A
good many of those that came in August were unexpected while some of the
ones I knew should be coming soon were not there - hopefully they are on
their way with the September data, especially for those (like Gypsy and
Vohani) who appear to have died.
With the updated wounds tables in hand I could compare them to demog notes
over the past couple years and see if it looks like we're getting wounds
sheets for all cases that are mentioned in demog notes.
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