Morphological Analysis - Science topic

You can also find potential reviewers from the literature or throw yourself on the mercy of the Editor

The above may be helpful to start with. Good luck.

Dear Alexis Gkantiragas ,

Look the link, maybe useful.

Regards,

Shafagat

Fynn Sebastien Vasco Francesco Comerford Zebrafish are a unique model animal for biomedical research, including studies of biological processes and human disorders, due to their fully sequenced genome, simplicity of genetic modification, high fecundity, external fertilization, quick development, and virtually transparent embryo.

Yes you can

Dear Bante Haile

You can use R software

A simple way would be to obtain two matrices, one for the genetic distances and another for the morphological distances, and then you do a correlation between the two matrices (Mantel test). If you have only one morphological variable, just go ahead and calculate the distance matrix with those values. If you have multiple traits, then you would need to do a PCA of your morphological variables, and then obtain your morphological distance matrix from the PC1 scores.

I hope it helps!

Yes, you might find Zoophycos ichnofacies in shallow to marginal marine (e.g., estuarine) mud-dominated dysoxic setting. However, if the Zoophycos isp. itself can be found can be debated, especially for the Cenozoic.

The best reference I can recommend is Christopher Alexander's The Nature of Order, a four-volume book that was made during a 27 years period. The reason why it is the best is that it deals with not only understanding buildings and cities as living structures, but also making or remaking buildings and cities towards living or more living structures. Herewith a special issue on the four-volume book:

The study of urban morphology must target to the making of living structures, which include architecture, and urban design and planning. However, the mainstream urban morphology is no more than applications of major sciences such as fractal geometry and various mathematics.

found the Boyd paper on JSTOR, details see below.

kind regards

---

Homeostasis, Higher Taxa, and Monophyly

Author(s): Richard Boyd

Source: Philosophy of Science , Vol. 77, No. 5 (December 2010), pp. 686-701

Published by: The University of Chicago Press on behalf of the Philosophy of Science

Association

Stable URL: https://www.jstor.org/stable/10.1086/656551

There are commercial software applications apart from r in common use. In my own work I avoid having to hassle with my own programming mistakes and cut right to the chase. PCA is useful if you limit your analysis to the 3 or four dominant axes.

Dear Fizzah,

If you are planning to get thin sections of the callus you must process with some plant anatomical techniques in order to fix and embed your samples. You can do it with paraffin or historesin.

Have a look on this manuscript:

On the other hand, it seems easy to get the access to the callus cells and also do different staining methods after you just press the callus between the glass slide and coverslip.

Please let me know if I can help you in a more specific way.

Best regards,

João

LAL ( Limulas Ameobocyte Lysate ) is an extrat from horse shoe crab is used the

pyrogen testing for QC study of pareterals or injectable . If this impormation helps

the procedural test of your question I shall be very happy .

Best Wishes !

Usha and Gitte:

Not much can be seen in the central area of the brittle Star. However, in Ophiocomella the spines on the 6-rayed arms are curved away from the central area, whereas in Amphioplus, spines are curved towards the central area as illustrated in your specimen. Better preserved specimens could hold the key for proper identification up to species level..

Best

Syed

Hi,

Thank you very much!

Read this link :

Nidheesh, I've never personally used CD163, but it might work. CD68 is more classical, so you may have to check the literature.

Neoplastic astrocytes in diffuse low grade gliomas frequently express IDH1. 

R package missMDA

Have you looked at the image processing toolbox in Matlab? Regionprops may be helpful.

Dear Rabbul and Michael  thanks for your kind reply. do you have pdf file of the books you recommended?

Great!  Thanks so much Arvind!

Thank You for Your answers! I have dug through litearture and currently there is practically no way to deal with compund morphological data. Albeit polymorphisms can be simply encoded as dummy variables, there are completely different models for continuous and categorical data. I have decided to use Gower's dissimilarity index - just a simple phenetic but there is no other option if You are unwilling to categorize Your data. 

Dear Colleague,

I suggest that you contact Dr. Paula Mabee (in RG).  She has worked intensively on this subject, especially on ontologies. See her list of publications.

Best wishes,

I think RAPD markers are inefficient for determining such a complex processes like Sex determination

If the change in phenotype is only happening with your particular cells and not in the rest of the lab, it could be your culturing technique and how well you maintain your cells. I've noticed that if you let the BEAS-2B cells get too confluent before passaging them, then they start to look like you described, elongated/spindly. I try to passage the cells when they are at about 80% confluent on a flask.

Ok. I will keep then. I think it is important to show if there is "morphological long branch". Even in parsimony it is interesting if there is a branch full of "autapomorphies", because it highlights that the taxon is very different from the others, and taxa such as these are usually "wildcards" too;

Hi Jonathan, yes the modification was recognized during the sp. description in 1822 by Say (in C. pilorides), later Owen wrote about this rare modification. It is not a pathology .I dont know any studies about histology. The modification is like to those changes in structures that  looking for more superficy. However I dont know or remember if the cell in liver border are different function than cell from depper part. I need to check. the case is that this kind of liver could have a more superficy that the normal liver. I connect with the mistery every some time.

A hitological study could be important but functional and metabolism of blood and comparative studies with the othes spp. could be very important too.

I have been very interested in this problems for year, thinking that it could be important for liver anatomy studies, blood metabolism, etc.

There are not anything in literature and I have been looking for any other papers about liver and it are no helping me so much.

It occurs to me that it is possible to quantify changes color for each spot or group of spots on the back and undersides of the wings of butterflies.

You can analyse color photographs from analysis of the three (RGB) components that make up the color. The scale is from 0 to 255 for each color.

Grace ,

i think that the following link can help a bit.

Regards

Google scholar indeed provides ample references, but I would like to make an aside: the most important part of any such system would in fact be POS tagging since when you know for sure which POS you are dealing with, it is relatively easy to infer any relevant info — just strip the prefixes/suffixes one by one and do look-ups. In the context of known POS rule-based models would surely blow HMMs out of the water because they know what they are doing.

Firstly..You needed to assay the anti-biogram of the microbe(s) you are assaying ;then to distinguish through application of transfer of the antibiotic resistance to check whether its chromosomally located or plasmid-born located genes.You could distinguish that through  the frequency of transfer of the antibiotic(s) under study.

Have a look at the Stanford Parser (http://nlp.stanford.edu/software/lex-parser.shtml) and Stanford CoreNLP (http://stanfordnlp.github.io/CoreNLP/index.html).

You might also have come across the Moses MT toolkit (http://www.statmt.org/moses/) ? 

It would be fairly simple to do this using a trained Convolutional Neural Network.

Someone has already done this...

Dear Jason,

The following publications cover the answer to your question:

1-Synthesis and biological evaluation of 6H-1-benzopyrano[4,3-b]

quinolin-6-one derivatives as inhibitors of colon cancer cell growth

Tie-Ling Li1

, Hai-Feng Guo2, Fu-Juan Li3, Zhi-Guo Sun2 and Heng-Chun Zhang2

Abstract:

A convenient synthesis of 6H-1-benzopyrano[4,3-b]quinolin-6-one derivatives

was reported using 4-chloro-2-oxo-2H-chromene-3-carbaldehyde with different

aromatic amines using silica sulfuric acid. The compounds were tested for

their anticancer activity against colon (HCT-116 and S1-MI-80), prostate (PC3

and DU-145), breast (MCF-7 and MDAMB-231) cancer cells. These compounds

showed more selectivity and potent cytotoxic activity against colon

cancer cells. 3c was tested against five other colon cancer cell lines (HT-29,

HCT-15, LS-180, LS-174, and LoVo), which had similar cytotoxicity and

selectivity. 3c did not induce PXR-regulated ABCB1 or ABCG2 transporters.

In fact, 3c induced cytotoxicity in HEK293 cells over expressing ABCB1 or

ABCG2 to the same extent as in normal HEK293 cells. It was cytotoxic

approximately 3- and 5-fold to resistant colon carcinoma S1-MI-80 cells. 3c

also produced concentration-dependent changes in HCT-116 colon cancer

cells, in mitochondrial membrane potential, leading to apoptosis, and submicromolar concentrations caused chromosomal DNA fragmentation.

Cell culture

Colon carcinoma cell lines [HCT-116, HCT-15, HT-29, Lovo, LS-180, LS-174, S1 (a clone of LS174T cells)] and prostatic cancer cell lines [DU-145 and PC -3] and breast carcinoma cells [MDA-MB-231 and MCF-7] were grown as adherent monolayers in flasks with Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) in a humidified incubator containing 5% CO2 at 37ºC. A G482 mutant ABCG2-overexpressing, drug-resistant colon cancer cell line, S1-M1-80, was maintained in medium with 80 µM mitoxantrone (Miri et al., 2011; Robey et al., 2001). The assay media for PXR transactivation assays included phenol red-free DMEM (Lonza) supplemented with

5% charcoal/dextran-treated FBS (HyClone) and the other additives.

PXR transactivation assay HepG2 cells were transfected with pcDNA3-hPXR

and CYP3A4-luc plasmids using FuGENE 6 (Promega). After 24 hours of transfection in growth media, 10,000 cells were plated into wells of 96-well

culture plates (PerkinElmer), and treated with DMSO, RIF, or 3c for an additional 24 hours. At 48 hours of transfection, a luciferase assay was performed to measure luminescence using the Neolite Reporter Gene Assay System (PerkinElmer) and a

FLUOstar Optima microplate reader (BMG Labtech). Normalized CYP3A4 promoter activity was expressed as fold induction over the DMSO control. Cell viability was measured in parallel by CellTiter-Glo luminescent assays (Promega), which determine the number of metabolically active cells by quantifying the ATP present. Luminescence was measured with a FLUOstar Optima plate reader (BMG Labtech).

Cell cytotoxicity as determined by MTT assays and morphological analysis

The MTT assay (Carmichael et al., 1987) was used to determine cytotoxicity of the compounds to the following cells: HCT-116, HCT-15, HT-29, LS-180, LS-174,

Lovo, S1, DU-145, PC-3, MDA-MB-231 and MCF-7. Briefly, the cells were harvested with trypsin and suspended at a final concentration of 5 X 103 cells/well. Cells were seeded (180 µL/well) into 96-well multiplates. Different concentrations of 6H-1-benzopyrano [4,3-b]quinolin-6-one derivatives (20 µL/well) were added. After 72 hours of incubation, 20 µL of MTT solution (4 mg/mL) was added in each well, and the plates were incubated further 4 hours, allowing the viable cells to convert the yellow-colored MTT into dark -blue formazan crystals. Subsequently, the medium was removed, and DMSO (100 µL) was added in each well to dissolve the formazan crystals. The absorbance was determined at 570 nm with an OPSYS microplate Reader (DYNEX Technologies, Inc., Chantilly, VA, USA). The means ± SD concentrations were calculated from at least three experiments performed in triplicate. The IC50 values were calculated from survival curves using the Bliss method. At 68 hours, cells with or without treatment were photographed by use of an inverted microscope (Olympus, BX53F) with fluorescent lamps and digital cameras. The data were acquired and analyzed by CellSens software.

For more details, please see attached file.

2-Bioorg Med Chem. 2015 May 1;23(9):2148-58. doi: 10.1016/j.bmc.2015.03.002. Epub 2015 Mar 21.

Design, synthesis and in vitro cell-based evaluation of the anti-cancer activities of hispolon analogs.

Balaji NV1, Ramani MV1, Viana AG2, Sanglard LP2, White J2, Mulabagal V3, Lee C2, Gana TJ4, Egiebor NO5, Subbaraju GV1, Tiwari AK6.

Author information

 

Abstract

Phytochemicals play an important role in cancer therapy. Hispolon and 26 of its analogs (9 known and 17 new) were synthesized and evaluated for their antiproliferative activities in a panel of six independent human cancer cell lines using the in vitro cell-based MTT assay. Among the hispolon analogs tested, compound VA-2, the most potent overall, produced its most significant effect in the colon cancer cell lines HCT-116 (IC₅₀ 1.4 ± 1.3 μM) and S1 (IC₅₀ 1.8 ± 0.9 μM) compared to its activity in the normal HEK293/pcDNA3.1 cell line (IC₅₀ 15.8±3.7 μM; p<0.01 for each comparison). Based on our results, VA-2 was about 9- to 11-times more potent in colon cancer cells and 2- to 3-times more potent in prostate cancer cells compared to HEK293/pcDNA3.1 cells. Morphological analysis of VA-2 showed significant reduction of cell number, while the cells' sizes were also markedly increased and were obvious at 68 h of treatment with 1 μM in HCT-116 (colon) and PC-3 (prostate) cancer cells. A known analog, compound VA-4, prepared by simple modifications on the aromatic functional groups of hispolon, inhibited prostate and colon cancer cell lines with IC₅₀ values <10 μM. In addition, hispolon isoxazole and pyrazole analogs, VA-7 and VA-15 (known), respectively, have shown significant activity with the mean ICv values in the range 3.3-10.7 μM in all the cancer cell lines tested. Activity varied among the analogs in which aromatic functional groups and β-diketone functional groups are modified. But the activity of analogs VA-16 to VA-27 was completely lost when the side chain double-bond was hydrogenated indicating the crucial role of this functionality for anticancer activity. Furthermore, many of the compounds synthesized were not substrates for the ABCB1-transporter, the most common cause of multidrug resistance in anti-cancer drugs, suggesting they may be more effective anticancer agents.

Hoping this will be helpful,

Rafik

Dear Marjan. Trichromes, either Papanicolaou's trichrome (rather green for conjonctive tissues), or Masson's blue (rather blue for conjonctive tissues) are the best to stain ovarian tissues. More important, for granulosa cells, is the fixation. Formalin does not give good results. The best fixative are Bouin's fluid and AFA (ethanol 80, 100 ml; formaldehyde 38%: 10 ml, glacial acetic acid: 5 ml; Saccharose or NaCl: 10g, distilled water: 20 ml)

Morphology is used in two ways: (1) as an analytical tool to investigate the composition of an existing product, and (2) as a creative and synthesizing tool for designing a new product. Designing has two major divisions: (a) for artistic designing, with emphasis on appearance and ergonomics, and (b) for engineering designing, with emphasis on the (internal and cross-boundary) workings of a technical product, ref Eder W.E. US-China Educational Review A, April 2013, Vol. 3, No. 4, p. 259-280. Prescriptive design methods are mainly applicable to synthesizing engineering products (2b), often include use of a morphological matrix, and are most useful for novel products, or when an intuitive approach does not yield a good solution, refs Eder, W.E. and Hosnedl, S., Design Engineering: A Manual for Enhanced Creativity, Boca Raton: CRC-Press, 2007, and Eder, W.E. and Hosnedl, S., Introduction to Design Engineering: Systematic Creativity and Management, Leiden, NL: CRC Press/Balkema, 2010. The working group around Vladimir Hubka has published 23 case examples of worked conceptual designing, each including an application of a morphological matrix for synthesizing an engineering product (2b), see ref Eder, W.E., ‘Case Example of Systematic Design Engineering – Linear Friction Test Equipment’, paper 1002, in Proc 3rd International Conference on Design Engineering and Science – ICDES 2014, Japan Society for Design Engineering, 31 Aug - 3 Sept 2014, Pilsen, Czech Republic.

Yes, Norris and Zwicky did pioneering work on this subject. Many others have contributed, but I think that our approach is the one based on scientific logic, and a (complete as possible) Theory of Technical Systems, ref Hubka and Eder, Theory of Technical Systems, Berlin/Heidelberg and New York: Springer-Verlag, 1988. Hope my comments help.

You can see this journal

Digital curves can be detected using the so-called Generalized Hough Transform. Regarding chain code, each curve pixel is represented by a number (0,1,...8) indicating its orientation with respect to its preceding pixel. Differential chain code is invariant to image rotation.

Comparison of an authentic

isolate of S. platensis from Chad and of S.

maxima from Mexico, grown in the laboratory

under identical conditions, showed that S. maxima

is characterized by a diameter of the helix of

50 to 60 p.m and pitch of 80 pm; values >35 to 50

p.m and 60 pm, respectively, were observed for

S. platensis. On the other hand, cell dimensions

were greater in S. platensis than in S. maxima

(diameter, 6 to 8 p.m in the former and 4 to 6 p.m

in the latter) (97). The cytoplasm of the smaller

species appears homogeneous, with no gas vacuoles

or inclusions and scarcely visible septa.

On the contrary, the larger species such as S.

platensis and S. maxima have a granular cytoplasm

containing gas vacuoles and easily visible

septa. (Ciferri 1983 Spirulina, the Edible Microorganism)

After you characterize based on the result, try to identify the best sesame cultivar for climate change adaptation.

Hi Nancy

The freezing temperature was applied in the night and I visually scored the symptoms of frost (loss of leaf turgidity and loss of leaf color) during the day and before the next night. As I described above. So I give one score for leaves in each treatment.

This may sound like a very obscure publication, but it is good, still quite recent, and has excellent illustrations.  Contact Dr. Schrock at Emporia State University in Kansas; he can probably send a hard-copy.

Fauquest, C.M., J. R. Schrock. 2006. Classification of Viruses. Kansas School Naturalist. Vol. 53 (1): 3 - 15.

Dear Mr. Kacem,

Thank you. I would appreciate that. However, I wish to know what kind of statistics you are planing to use, Just for my knowledge. I know you can answer better after seeing the Raw data. let me know your ID. I shall send the data. I have many sets of such data. If you can send me some information i can continue later. however, your analysis will be properly acknowledge in the manuscript.

Regards

tapas

This can be easily done if running a RAxML phylogeny, especially if this is done on the CIPRES web portal.  You need to create a constraint file.  I usually do this in a good text editor such as TextWrangler (Mac) or Notepad++ (PC).  Upload this file when setting your parameters.  Here is an example of what your constraint file should look like:

((Taxa1, Taxa2),(Taxa3, Taxa4, Taxa5, Taxa6, Taxa7, Taxa8, Taxa9, Taxa10));

This would result in a tree were Taxa 1 and 2 are always sister, but the relationships of taxa 3-10 would be inferred by the analysis.

Dear Aher

Thank you so much for your email and useful suggested paper.

Saleh

To build a matrix, you just have to compare the characters shown by the terminals. For example, if one character would be the number of pairs of legs presented by some animals (the terminals you are comparing), you should compare this character in each of them: terminal A – 2 (pairs), terminal B – 1, terminal C – 3, terminal D – 2, and so on.

At the lines of the matrix, you have the character state of each terminal, at the columns, you have this information displayed by each character.

After that step, you can code your characters using different possible methods. You may begin using the outgroup method. You choose a group that you know that is outside (but not too far away) from the group of the terminals you are comparing. If the outgroup would have two pairs of legs, in comparing it with each one of the terminals in the above example, you would have tA – 0, tB -1, tC – 1, tD -0 (for if the character state equals that of the outgroup, you code as 0, if not, 1).

Doig this for all characters, you will have your matrix.

Hi, I have written a Matlab package for computing Minkwoski measures from binary 2D or 3D images. Just follow the link at the bottom of the answer. It does not manage Minkwoski tensors.

Some other software also implement Minkowski Measures, you can search for MAVI (Modular Algorithms for Volume Images) for example.

Do you have access to Merck chemicals and reagens? 1.09204 Giemsa’s Azure Eosin Methylene Blue Solution. The datasheet also provides a staining protocol. I've attached a publication from 1975. But nowadays it is unusual to prepare the stock solution by oneself.

We use this reagens for staining paraffin slides and our working solution is a 1:5 dilution of the stock in dest. water. It has always to be prepared freshly.

Combining morphological characters and molecular characters into the same phylogenetic analysis can be done in MrBayes (if you are ok with a Bayesian approach), regardless of missing taxa or characters.

You make one matrix including both types of data. I make a nexus file in a text editor like Text Wrangler. The matrix is then partitioned to assign the different rate models to the different kinds of data (the same way you would for a multigene dataset). Here is an example of a MrBayes block I wrote for my matrix of 7 genes and a set of morphological characters:

begin mrbayes;

    charset 12S = 1-376;

    charset 16S = 377-987;

    charset cytb = 988-1701;

    charset RAG1 = 1702-3221;

    charset NCX1 = 3222-4532;

    charset SLC8A3 = 4533-5693;

    charset CXCR4 = 5694-6332;

    charset morphology = 6333-6444;

    partition favored = 8: 12S, 16S, cytb, RAG1, NCX1, SLC8A3, CXCR4, morphology;

    set partition = favored;

    outgroup AscaphusT;

    lset applyto=(1,2,3,4,6,7) nst=6 rates=invgamma;

    lset applyto=(5) nst=2 rates=invgamma;

    lset applyto=(8) rates=gamma;

    unlink statefreq=(all) revmat=(all) shape=(all) pinvar=(all);

    prset applyto=(all) ratepr=variable;

    mcmcp ngen=5000000 samplefreq=1000 printfreq=1000 savebrlens=yes;

end;

The MrBayes wiki page describes this in detail as well and will explain some of the lines of code if these are unfamiliar to you. Hope this helps! 

 

As a palaeontologist, the answer to this one is rather obvious.... it's hard to get DNA out of a 500-million-year-old sponge in a completely extinct lineage. When describing the evolutionary past, we use whatever tools are at our disposal; genetics is one of them, morphology another. There are even some other approaches, such as stratophenetics, which have been developed in order to make use of the data available, whatever they may be. We would do well to remember that all of these tools are just that; the truth is an abstract that we try to approach by using them.

There is many solutions :

--> Hough apply to circle :

for rapid testing :

--> USING A WEIGHTED MSE ESTIMATOR

--> Active contour might be a good solution too

A last this work give examples :

work well!

I use fluorescence deconvolution microscopy

SamiVarjo Thank u for sharing the link.....

The attributes (features) are designed to have multiple values

I would also follow Peters's discourse. Asymmetry is rather the rule, beginning with the unicellular organisms. Maybe symmetric structures - like the skeleton of the diatoms - are a consequence of crystalin disposition of ions and molecules at that level, or, for multicellular ones, the effect of the natural selection for more efficient functioning in the environment, gravity considered (balance, speed). This may be the reason for the symmetry being one criterion for beauty, although seldom reached in fact. The symmetric structures themselves are not identical. Our ears, eyes, brain hemisferes, hands, muscles, blood vessels etc, all are different between themselves in some degree.

This i will suggest if u r interested to preserve the slide / for SEM image (Morphology studies) ... http://homepage.ntu.edu.tw/~jmhu/hulab/protocols/SEM%20sample%20preparation.pdf

What organisms that you are looking for?