All posts by thankusc

Verge of a Dream: You better get a lesson –

You better get a lesson
From up that hill
From up that hill (refrain)

It all came down
Came down on me
May still come down
On you too
Still come Down
on you too

refrain

Wrap your body up
Flake’s not cold but
Won’t be one alone
Look up that hill.
At a million coming
down

refrain

What someone wise said
Wise for sure
You better better
Take what happened
To me, see that
See all that
try to listen well

refrain

It can’t be easy
Whether you make
The bread or find
Yourself in line.
Its just the same
whether
a common
bramble vine or
a soul divine.

refrain repeated

RLB 08-09-2022

Four SP-D dodecamers: more plots use to determine trimer and hexamer peak numbers

Previously counted plots included all that were available at the time (found in this link; which had about equal numbers of plots from each dodecamer (hexamer – trimer). The data on this page show just about every plot that I have ever made….. these are divided as to trimer…. so this is mean trimer peak number. The latter counts the N term peak with each trimer (even though it is shared between all the trimers…. each trimer it gets counted once.   Therefore a peak number of 8 per trimer would become peak number of 15 per hexamer owing to the N term peak being shared.  In terms of progress…. its best to assume that the more recent posts are the better data.  Every possible image and signal processing filters and algorithms are summed here. Some people counts, all counts….  this represents a huge N, in my estimation.

I think my current favorite image processing filter is still the gaussian blur, and my favorite peak counting program is PeakValleyDetectionTemplate.xlsx by Thomas O’Haver.


Peaks per hexamer were calculated four ways.  As every plot made for each of these four dodecamers. This includes hundreds of counts for one dodecamer, and between 26 and 50 hexamer plots for the other three. Certainly one carries more weight, or one would think, but the data using each of the plots separately is not different than using each of the methodologies (at an absolute minimum there were 2 image processing filters, and at least 5 signal processing algorithms for several of these image processed pictures.

Data are also given with each of the four dodecamers individually: (41_ak45; 42a_aka_44; 43; 97-1).  In addition. n, mean, sd, and other parameters were calculated from my original peak counts from just the “image”, as well as from my original peak counts from the plot generated in ImageJ.  This is in addition to the whole lot of plots subjected to signal processing.    Bottom line is that signal processing appears to increase the peak count in a significant way. Whether the signal processing is “better” (which i dont think it true” or counts from images is “better” remains to be sorted out.   Below is a comparison of the various “sorting” that I used to determine mean number of peaks per hexamer of SP-D.

Two left columns are: 1) Every plot of a hexamer separately, 2) Plots divided into each of the four dodecamers separated into groups; Two right columns are counts separated into  “image with signal processing” per dodecamer ( and separated again into, my counts of image processing plots only plus my counts of the peaks in plots made in ImageJ (that is… NO SIGNAL processing)  18+ peaks with signal processed plots, and 15+ peaks using my hand counts.  15 peaks per hexamer is in my bet for the best number.  See previous posts here.

 

Getting closer to making a “concensus SP-D LUT plot” from which to build an AI model

Getting closer to making a “concensus SP-D LUT plot” from which to build an AI model.

I had four SP-D dodecamers to work with, literally hundreds of plots, 5 different plot peak finding algorithms (apps, programs, websites), and a dozen different image processing programs, all to find the perfect peak plot for SP-D hexamers.  These molecules are bilaterally symmetrical (three identical x three identical) with the N term junction in the center.  Little is known about the central connections though the CRD and neck regions have molecular models.  Taken about 3 years to try to figure this out, input would have been (would still be) very valuable.

I am hopeful that an easy technique will be the outcome, that is an easy technique for assessing peaks in many different types of molecules (images from AFM at this point), particularly those which are bilaterally symmetrical.

Out of 7.7 billion people

Out of 7.7 billion people, I marvel that I have not found ONE single one with whom I can share my interests, not in gardening, mosaic, stained glass, polymer clay art, science, electron microscopy, pattern making, music, writing music, repairing old houses, making walkways with concrete.  You would think at least ONE person would be around to do these things with.  Dunno…  what are the odds.

Verge of a Dream: Advice

I’ve heard it said
What seems like
Good instruction
be not attached
To things. So
maybe three
times or maybe
four.
Passed it on to
Titan yet there,
throughout
all my lifetime,
it was, and is,
in orbit,
next
To Saturn.
I’ve heard it said,
And sensible it may
Be.
to forge your
Own trail cause
Convention will not
Become
The mother of
Invention. Passed it
On to my captain
Who drew new plots
And graphs found
Board our
ship discovered
somewhere
Lost at sea.
I’ve heard it said
And it seemed
The path
Of progression
to do things better,
as a gift
to the next
Generation.
And now
mostly done with
Looking I wish
I’d followed
footsteps
That connected
Me and you
much
Less to now
and
more
moored my
life to then.

RLB 7-31-2022

Temporary Lobulation in Cartilagenous Models of Long Bones

The first rhythm and order I think i found as a graduate student in anatomy (light microscopy of cartilege) was the order of the beginning of long bone development in mice.  Back then, (as in 50 years ago) many journals didn’t have cover images. At this time, dissolving all my records, publications, micrographs from the finite universe, I made this cover for one very lovely design in nature. I attach a very bad phone phot of the publication (not even I, its author, was willing to spend the highway robbery that some journal websites ask for an almost equally fuzzy scanned image of the original).

Here is my suggested cover, half century down the pike, and a free link to a terrible scanned pdf of the paper. cartilagenous models of long bones
Miller_Basom_McCuskey_Cartilage_1973

or HERE

“In truth lives hope”, not in science

There has been something on my mind for a couple years, i would like to get UC to change its sineage. …it is a sign that i see when driving north on I75 on a medical building that is an extension of the university. This seems trivial, yet it is a deep moral dilemma. The sign says “In science lives hope.” After 50+ years in research, I know this is not a fair statement.

If i knew a contact person at UC with whom i could speak…. I would suggest that they change this “also somewhat simplistic, often erroneous, misplaced egotistical” claim…. and maybe change it to “In truth lives hope”

We would all be better off if we recognized there are no institutions, organizations, businesses that can claim to be any sort of “hope”…particularly not big institutions, whether religious or academic or for-profit. If the sineage gets changed to “truth” then we are not inclined to whitewash, praise, or criticize academia for mistakes,  amorality, and fallen hypotheses, but perhaps, move on to being hopeful for “truth” after lots of work, and discovering something that has merit beyond and greater than the scientific profession as it currently exists, not always, but often, in a ragged state self-serving state. The “truth” is actually the same in science, politics, religion, culture.

Hexamer and individual peak widths (nm) for four dodecamers of SP-D

As separate trimers, and as hexamers peak width summaries, regardless of how they are sorted seem to be consistent for these first four image and signal processed dodecamers of SP-D.  A model for further peak counting using these parameters for an intelligent signal processing approach might be interesting. The 8 peaks per trimer (15 peaks per hexamer as N is counted as one peak in each trimer and becomes the odd center peak in hexamers) widths are given below.

N, tiny peak, and glycosylation peak(s) proximity in some SP-D dodecamers

AFM images (from rhSP-D at pH 7.4 Arroyo et al) of SP-D are informative and numerous and during a careful analysis of them it seems pretty obvious that there are a significant number of occasions where there is a close “sticking” together of the strands of the trimer from the N termini junction, through the tiny peak on either side of the N peak and up to the glycosylation (often including it) peak(s)(plural here because there are a significant number of imaging and signal processing applications that count more than one peak in the area considered the glycosylation peak).
Here are two images (labels on each show the number of nm diameter, the length in nm of each of the hexamers, and arrows that show where the trimers from two hexamers are in close association. I scanned 83 images from the images of Arroyo et al, and found that such an association (which in order to be visualized with any confidence requires that the dodecamer to be lying such that the rest of the trimer-arms are separated, thus not just overlapping — overlapping trimer arms were not included in the count of closely associated N, tiny peak, and glycosylation peak associations.
I have also given a number (my reference number for the set of thumbnail images, and the set of dodecamers to which some measurements have been applied.
Any reason for such a close association between trimers in that specific location is not known by me, comments welcome. 100 nm bar is given for your “enjoyment”,  green nm measurements correspond to green segmented tracing through the center of the hexamer to which it refers, same for red segmented line and nm values.  Diameter values (orange) are made in ImageJ, and requires that three of the four carbohydrate recognition domains be touched.  It is easy to see that once past the glycosylation peaks, the arms of each trimer are separate. On the bottom image, the trimers are close on the top half of the micrograph, but not the bottom half, as the glycosylation peaks are separate. (42 dodecamers, of 86 total, show N, tiny peak, glycosylation peak closeness on one or both sides of the dodecamer.)