Thursday, March 31, 2011

Word of the day: centroid

The word of the day is centroid:
< centre n. and adj. (or its source) + -oid suffix.

1. = centrode n.  [In this sense introduced by Prof. A. B. W. Kennedy, 1876, on the analogy of cycloid and other names of curves, but subsequently abandoned for centrode.]
2. Centre of mass, or of gravity.

"The main features of this algorithm are isotope cluster identification, automated charge determination, generation of a theoretical isotopic abundance distribution, matching the theoretical and experimental isotopic abundance distributions, identification of other overlapping isotopic peak clusters, determination of improved accuracy of averaged centroid mass values, matching of assigned mass values to proteolytic or MS/MS fragment ions, and baseline plus S/N calculations using data between the isotopic peaks."

 - Bogdanov and Smith, "Proteomics by FTICR mass spectrometry: top down and bottom up", Mass Spectrometry Reviews 24:168 (2005)

I think what they mean here is the averaged mass of all the isotopes, as opposed to the monoisotopic mass.

Monday, March 28, 2011

Word of the day: abscissa

The word of the day is abscissa:

< post-classical Latin abscissa portion of the axis of symmetry of a conic section lying between its vertex and a given chord (1673 (in Leibniz) or earlier), (in Cartesian coordinates) distance of a point from the y-axis, measured parallel to the x-axis (1692 (in Leibniz) or earlier), use as noun (short for abscissa linea a cut-off line) of feminine past participle of classical Latin abscindereabscind v. With sense 1 compare slightly earlier absciss n. Compare also earlier ordinate n.
In plural form abscissae after the Latin plural form.

 1. The portion of a conic section lying between its points of intersection with two parallel chords; (also) the portion of the axis of symmetry of a conic section lying between its vertex and a given chord. Cf. ordinate n. 1. Obs.    
2. In Cartesian coordinates: the distance of a point from the y-axis, measured parallel to the x-axis; the x-coordinate of a point. Formerly also: a straight line drawn from a given point parallel to the x-axis and meeting the y-axis. Cf. ordinate n. 2. (OED)

"FTICR mass spectra (the abscissa represents a convolution of the deuterium incorporation after 1 hr and the initial natural-abundance isotopic distribution of the fully protonated ion) following gas-phase H/D exchange for 1 hr at 2 x 10^-7 Torr D2O for the 11 - 13+ charge states of bovine ubiquitin."

 - Bogdanov and Smith, "Proteomics by FTICR mass spectrometry: top down and bottom up", Mass Spectrometry Reviews 24:168 (2005)

As far as I can tell, this word has been replaced by "x-axis" and "x-coordinate" (depending on its use).  I guess Dr. Bogdanov didn't get the memo.

Tuesday, March 22, 2011

Word of the day: flange

The word of the day is flange:

Etymology:  See flanch n.2
 1. A widening or branching out; the part that widens out:
a. in a pan.  
b. in a metallic vein.   
2. A projecting flat rim, collar, or rib, used to strengthen an object, to guide it, to keep it in place, to facilitate its attachment to another object, or for other purposes.
3.a. Any rim or projecting surface.
b. A flattened-out disc. Also, blank-flange 
c. transf. Of natural objects: a rim or fan which stands out from the main part of the object. Also fig. (OED)

"An open, cylindrical Penning trap was constructed from OFHC copper stock and assembled with ceramic spacers, aluminum support rods, and titanium machine screws.  The cell assembly was secured on a 4.625-in.-diameter conflat-type flange at the far end of the high vacuum region.  Note that the vacuum manifold is pumped from only one end; in addition, the second quadrupole terminates ~20 cm from the cell flange.  As a result, we chose somewhat atypical dimensions for the cell electrodes (trap plates, 1.125-in. length; excite/detect plates, 3.5-in. length), in an attempt to obtain an acceptable compromise between trapping field quadrupolarity, excitation field linearity, and overall ion storage capacity."

 - Martin et al., "Subfemtomole MS and MS/MS peptide sequence analysis using nano-HPLC micro-ESI Fourier transform ion cyclotron resonance mass spectrometry", Analytical Chemistry 72: 4266 (2000).

Tuesday, March 08, 2011

Word of the day: vide infra

The word of the day is vide infra:

Latin .
see below (used especially to refer a reader to parts of a text). (
"3-beta-Cholestanol and 3-alpha-coprostanol (AB cis) were also examined, but did not undergo remote oxidation (vide infra)."
 - R. Breslow et al., "Remote oxidation of steroids by photolysis of attached benzophenone groups", Journal of the American Chemical Society 95:10 (May 16, 2973) 

Wednesday, March 02, 2011

Molecule of the day: cystine

The molecule of the day is cystine:

Not to be confused with cysteine:

Quote of the day

"Anyone who can tell you what they had for lunch three weeks ago last Tuesday is too weird to be in a cohort study."

 - heard in a seminar on the molecular pathogenesis of prostate cancer

The incidence of prostate cancer depends enormously on geography.  Asians (who live in Asia) have a much, much lower incidence than Americans do.  But: the incidence among Asian-Americans (born in the U.S.) is just as high as for caucasians.

Whence the difference?  Environmental exposure to carcinogens, presumably.

Another fact: all male mammals have prostates, but only ones that seem to get prostate cancer spontaneously are humans and dogs.  That suggests the carcinogen in question is in the diet.  (The subsequent discussion on how you would go about studying that prompted today's quote.)

Note to self: eat less beef.  Especially pan-fried beef.

Word of the day: disproportionation

The word of the day is disproportionation:

Any chemical reaction of the type D01799-0, where A, A' and A'' are different chemical species. For example:

"The neutral radicals lead to the final photolysis products via dimerization and disproptionatation reactions."

 - D. N. Nikogosyan and H. Gorner, "Photolysis of aromatic amino acids in aqueous solution by nanosecond 248 and 193 nm laser light", Journal of Photochemistry and Photobiology B: Biology 13:219 (1992)

Tuesday, March 01, 2011

Word of the day: geminate

The word of the day is geminate:

< Latin gemināt-us, past participle of gemināre to double, < geminus twin.
 A. adj.
Duplicated, combined in pairs, twin, binate.
geminate leaves, leaves springing in pairs from the same node, one leaf beside the other.  
B. n.
A doubled consonant. (OED)

But the meaning I was going for was geminate recombination: "This expression refers to the reaction, with each other, of two transient species produced from a common precursor in solution." (IUPAC)

"The calculations show that probability of formation of a photoproduct for absorption in the T1 state exceeds that for the S1 state about 40 times.  This may be due to a much higher probability of geminate recombination of cation-electron pairs Tyr+-(e- aq) produced in a singlet SN state as compared with pairs Tyr+-(e- aq) produced in a triplet TN state and to the difference between the absorption cross sections from S1 and T1 levels."

 - D.N. Nikogosyan et al., "Asymmetric photolysis of biomolecules under high-intensity UV laser irradiation", Chemical Physics 147:437 (1990).