Monthly Archives: February 2024

Me vs Peak Valley Detection Template xlsx

There are many things i dont understand about peak and valley detection using functions.

I would have to test out whether the lag and amplitude and influence of the detection works against having a tiny peak detected next to a high peak by plotting this same trimer of surfactant protein D up, down, rotated and mirrorred to figure out how to have it see what I see: that would be to include a tiny peak before the glycosylation peak, and eliminate a much less obvious peak in the middle of the series of peaks that follow the glycosylation peak. I know these things can be selected and I can choose whether to change the parameters.  I am trying to eliminate not induce bias. I like the first lines by this blogger, yes i agree, the human mind is very unique.

This is a real handicap to detection of relevant grayscale peaks in a plot of the length of SP-D trimers. I could of course change the smoothing and other factors but then I end up with a rediculous number of peaks and it no longer is relevant.
Case in point… plots from ImageJ that I selected peaks on (which are in line with the vast number of plots from which a mean number of peaks along each trimer was established. (peaks on the left, valleys on the right, top row of plots) versus what i find with smooth 11 using (what i think is one of the best peak and valley finding templates around (easy to use, output can be edited like any excel plot as opposed to those that come out of octave functions for finding peaks which are, as vector illustrations, total nighmares to work with). The bottom set is what I get from PeakValleyDetectionTemplate.xlsx offered by Tom O’Haver – thank you). The trimer plotted is from an image by Raquel Arroyo et al – thank you).
The plots are virtually identical in peak number, width, height and valley EXCEPT for the two tiny peaks, one lost and one added.

Verge of a Dream: Picture of you

You are not the
Sky unable to decide to
Drop its grey clouds to
Just below the edge of
The planet. You are not the
Planet with plates
Cracking, I think I mean
Laughing at feet above
that won’t
Maintain their balance
And monuments shed
Their riders in the
Middle of a park once
So peaceful in a
Month ending summer.
You are not a burning
Need to have crowds
In awe though they
Gasp at you and
How you wake each
Sunrise only to create.
A piece of van gogh’s afterlife
Or wish to say in words
But cannot, what
You are. Anyone
Can reach for an
Expletive in frustration
At a missing piece in
The picture of you.
Anyone can search
For a figure of
Speech that has
Not been heard
On the runway and
Dance floor. Anyone
Can hope to sit
Not caring if
The world spins
lawless
Or if the movie at
The drive in ends.

Verge of a Dream: A gentle tumble of pins

Life, it started
Not in a burst
But in a gentle
Tumble of pins
A click, not a
Crack.
It was as
you straightened
My collar
The feeling
Of light rippling
On the spine.
As you stood
Close to me
Behind.
Life, of it,
Less is known
If seen close in
Place and time.
Looking for
Meaning,
The meaning is
Clear of your wave
Despite any dust
In the way
As the
Observation car
Disappears from
Sight.

AFM: one limitation affecting peak number of SP-D dodecamers

AFM: one limitation affecting peak number of SP-D dodecamers, could be what I found on a website. “Due to the nature of AFM probes, they cannot normally measure steep walls or overhangs“. This quote is from a website that is mostly in chinese so I didnt bother to read or translate. BUT it is clearly what I have seen as I search for peak number in SP-D molecules (whether trimers, hexamers dodecamers, or higher order multimers).

Case in point is how many times the “tiny peak” which I have noted dozens and dozens of times as a small in height, narrow peak right near the base of the N term peak. It seems to be missed a lot of the time, there are other times when it is very obvious. A couple reasons for its intermittent appearance in AFM could actually be because of the very steep wall on the downslope of the N term peak before the glycosylation peak.

In terms of “overhang” this might also apply to the blending and disappearance of the neck area which is sometimes covered in the CRD peaks which flop around visibly lying over the neck domain.

Quilts forgotten:

This will be a different kind of a post. It reflects my own “terror” of being old and “being forgotten” maybe even more, the total loss of anything I did in my life as meaningful. I have tried to be kind, thrifty towards myself, generous to my family, and others, but nothing I have done would seem to have had much impact on the planet, on life, on the present, or on the hereafter, whatever the hereafter is.

I like to quilt. I quilt with scraps, tiny scraps (down to 1.5in square). Its like putting together something organized out of something lost in entropy, destined for land fill in some foreign country, saving grief from the world wide land fill.

I like putting the scraps of “nothing” together into something orderly. I don’t quilt all the time, incessantly, but about one or two quilts per year, using my old (now ailing) green metal singer sewing machine. Many quilts I made had clothes from my three children, boy scout color light brown blocks from their shirts, and pink glossy fabric from my daughter’s play dress up dresses. Fabrics from PolyFlinders left over boxes of cutter’s scraps… 7 dollars for several pounds of stacks of cute ginghams, flower prints, delicate little girl fabrics and sometimes yard goods, ribbons, thread etc. (They were on 8th street i believe, in cincinnati in the 1980s). I enjoy quilting.

I have a colleague who offered me a bag of fabric scraps, since they knows I quilt with scraps. These scraps were presumably from a family member no longer with them.  It was a heavy bag of scraps, I could see from the outside that some piece work was there.

I was not prepared for what was inside. Nine (9) finished quilt tops, varying sizes, all waiting to be quilted into bedspreads, or coverlets.  I was full of grief: for that woman who’s last dozen years were spent hand piecing these precious gifts for her children, grandchildren and friends and they were never finished, never given as treasured gifts, and then “pitched” to an unknown friend of a friend, as if the thousands of hours of hand piecing these quilt tops was “nothing” “nada” “rien” “zilch” “zero” “trash”.  It grieved me so much.  They went back to the giver. Hopefully with instructions on where to find someone who will add batting and a back, and finish what this woman can give her children and friends.

There were three quilts i suspect were for three little boys, in particular, maybe one for her grandson, they looked pretty much alike. I hope when i return them, they are finished by a professional and given to individuals, just where they were intended, as finished works, they can ask her who was to get which.

I was totally grieved.  For her yes: for myself yes, as I know beyond hope, that because I have not completed my own grandmothers, necktie quilt, whose silk is shreding from a 100 years of age, that the quilts i have made will be similarly “pitched” as will my grandmothers quilt.  I dont find those thought entertiaining at all, i find them totally depressing.  And in fact, there is nothing new in my thoughts….. dust to dust and there is nothing then to remember, to treasure, to feel proud of, to hand out as a legacy. That is just how this journey works.   See pix below…. all 9 of that grandmother’s hand work, tossed, but maybe saved and given as gifts.

So this also begs the question, why were these quilt tops NOT finished. I suspect the reasons are just like my quilting. Not perfectly straight, there will be lumps in the quilting with puckers in the fabric, no straight corners, some colors showing through to the front. The backing and quilting the whole quilt is really a hard part.  I know. I have one pieced currently waiting to be finished.

Kudos to this woman, whose fingers didn’t stop when she got old.

Bobbin, sometimes called boobin…LOL

Bobbin, sometimes called boobin…LOL

While checking to find the part number for the motor belt on my old Singer sewing machine, i saw this typo for the bobbin winding belt.

This is one of the funnier typos online that i have found recently.  And no, Boobin is not the way bobbin is spelled in german.  I checked.

Surfactant protein D, peak plots from AFM images

Last couple months I have been plotting individual trimers of SP-D to determine if number of peaks, peak heights, a valleys using the same 6 methods used on dodecamers produces the same results. The same 6 functions were use on trimers as on dodecamers (See list of image and signal processing functions used — at the end of this post).

There is clearly a smaller N term peak (N) in the trimers than the dodecamers where four N term peaks are “piled” or “linked” together. Other peaks do not change much, which is a good thing.

The plot immediately below shows just the peaks plotted for just one trimer (kind of a perfect one), and immediately below that plot shows mean peak height, width, and variation for 6 dodecamers (24 trimers, 368 trimer plots),  and the third plot down is 14 dodecamers (56 trimers, 897 trimer plots) and the line graph below that is the plot from Arroyo et al, 2018 in which she identifies the N peak (peachie orange), the Gly peak (light green), and the CRD peak (orange) ONLY. My purpose was to show that there are at least 8 prominent, consistenly found peaks per trimer, not just three.

So many different images analyzed from different publications with Arroyo as author, are shown, ploted as dodecamers (6 or 14 individual dodecamers) or single trimer, there seem to be 8 peaks per trimer. Widest peaks are indeed the N, Gly and CRD, next widest and most consistend are peaks 4 and 6, the yellow peak (coiled coil neck domain) is infrequent, and during preparation for AFM is typically covered by the CRD domains flopping around, and also infrequent are the small peak called “tiny” because it is both thin and low (but consistently on the down slope of the N term peak) and peak 4 which is broad and rolling like the GLy peak, and a low and thin peak (pink), and a broad low peak before the coiled coil neck.

So after more than a thousand plots, I think I am pretty sure these peaks are part of the molecule and can perhaps contribute to creating a complete protein model of SP-D (which do date has not been done).

https://imagej.nih.gov/ij/
https://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm#ipeak
https://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm#findpeaksx
https://terpconnect.umd.edu/~toh/spectrum/PeakFindingandMeasurement.htm#Spreadsheet (s)
https://docs.scipy.org/doc/scipy/reference/generated/scipy.signal.find_peaks.html
https://stackoverflow.com/questions/22583391/peak-signal-detection-in-realtime-timeseries-data/22640362#22640362 (version: 2020-11-08)

Verge of a Dream: Two letters

There were two letters
You had never shown
To me. Two letters
On the back of a
Charm I guess
You’d say. I don’t know
The names of ornaments.
Of gold pieces worn on
A gold string of links.
A rosette fairly finely
Made with two letters
On back of the
Rose to
Lay
flat below the
Neck and above
All, the heart.
The letters
Began a name.
It is too clear
To ask how
Despondency
Comes from
The heart with
Sense unengaged.
The name,
from
The two letters
Engraved upon
A heart that
Was never shown to me.

RLB 02-08-2024

Verge of a dream: from that day forward

At work everyday,
almost, the
Tie you bought
I wear
Though there is
No reason to
Believe but it is hope
Which Has no equivalent.
That you will like
me more.
A clip for the
Tie, I’d ask for
Just ask, nothing
Is less useful
Than to beg but
It must be
Unquestioned of
Weight and
Solid gold.
So pure no one
Would try and
Scratch their
Way between us.
Or a pearl shirt
I wanted,
For you to
Give
made from
finest cloth
And though from
The loom it
Was unmarked.
I wash anyway
The bleach
Undoes the past
And there
my care
is sure that
You may like me
each fresh warm
tropical morning
Worn for you
From that day forward

RLB 02 06 2024