PartsList: a web-based system for dynamically ranking protein folds based on disparate attributes, including whole-genome expression and interaction information

As the number of protein folds is quite limited, a mode of analysis that will be increasingly common in the future, especially with the advent of structural genomics, is to survey and re-survey the finite parts list of folds from an expanding number of perspectives. We have developed a new resource, called PartsList, that lets one dynamically perform these comparative fold surveys. It is available on the web at http://bioinfo.mbb.yale.edu/partslist and http://www.partslist.org. The system is based on the existing fold classifications and functions as a form of companion annotation for them, providing ‘global views’ of many already completed fold surveys. The central idea in the system is that of comparison through ranking; PartsList will rank the approximately 420 folds based on more than 180 attributes. These include: (i) occurrence in a number of completely sequenced genomes (e.g. it will show the most common folds in the worm versus yeast); (ii) occurrence in the structure databank (e.g. most common folds in the PDB); (iii) both absolute and relative gene expression information (e.g. most changing folds in expression over the cell cycle); (iv) protein–protein interactions, based on experimental data in yeast and comprehensive PDB surveys (e.g. most interacting fold); (v) sensitivity to inserted transposons; (vi) the number of functions associated with the fold (e.g. most multi-functional folds); (vii) amino acid composition (e.g. most Cys-rich folds); (viii) protein motions (e.g. most mobile folds); and (ix) the level of similarity based on a comprehensive set of structural alignments (e.g. most structurally variable folds). The integration of whole-genome expression and protein–protein interaction data with structural information is a particularly novel feature of our system. We provide three ways of visualizing the rankings: a profiler emphasizing the progression of high and low ranks across many pre-selected attributes, a dynamic comparer for custom comparisons and a numerical rankings correlator. These allow one to directly compare very different attributes of a fold (e.g. expression level, genome occurrence and maximum motion) in the uniform numerical format of ranks. This uniform framework, in turn, highlights the way that the frequency of many of the attributes falls off with approximate power-law behavior (i.e. according to V–b, for attribute value V and constant exponent b), with a few folds having large values and most having small values.

Consequences of Kondo exchange on quantum spins

When individual quantum spins are placed in close proximity to conducting substrates, the localized spin is coupled to the nearby itinerant conduction electrons via Kondo exchange. In the strong coupling limit this can result in the Kondo effect — the formation of a correlated, many body singlet state — and a resulting renormalization of the density of states near the Fermi energy. However, even when Kondo screening does not occur, Kondo exchange can give rise to a wide variety of other phenomena. In addition to the well known renormalization of the g factor and the finite spin decoherence and relaxation times, Kondo exchange has recently been found to give rise to a newly discovered effect: the renormalization of the single ion magnetic anisotropy. Here we put these apparently different phenomena on equal footing by treating the effect of Kondo exchange perturbatively. In this formalism, the central quantity is ρJ, the product of the density of states at the Fermi energy ρ and the Kondo exchange constant J. We show that perturbation theory correctly describes the experimentally observed exchange induced shifts of the single spin excitation energies, demonstrating that Kondo exchange can be used to tune the effective magnetic anisotropy of a single spin.

Catharine Waugh McCullouch papers in the Mary Earhart Dillon collection, 1869-1945

Collection primarily documents McCulloch's research on women's legal status, and her work with the Illinois Equal Suffrage Association, the National American Woman Suffrage Association, and the League of Women Voters. There is also documentation of women in the legal profession, of McCulloch's friendships with the other women suffragists and lawyers, and some biographical material. The papers contain little information about her family or social life.

Statement of trips, 1795

Thirteen statements of trips of the Cyrus between April 23, 1795 and December 9, 1795 signed by Steward Caleb Gannett. The statements list the cords of wood added to the College's supply and the cords sold. The statements are on thirteen slips of paper of various sizes bound with thread.

Letter from Samuel P. Russell to Ebenezer Storer, 1798 March 7

Half-page letter from Samuel Russell to Treasurer Ebenezer Storer informing him that the sloop Cyrus has been sold and requesting a bill of sale.

Mathematical notebook, and commonplace book, circa 1689-1769

Manuscript notebook, possibly kept by Harvard students, containing 17th century English transcriptions of arithmetic and geometry texts, one of which is dated 1689-1690; 18th century transcriptions from John Ward’s “The Young Mathematician’s Guide”; and notes on physics lectures delivered by John Winthrop, the Hollis Professor of Mathematics and Natural Philosophy at Harvard from 1738 to 1779. The notebook also contains 18th century reading notes on Henry VIII, Tudor succession, and English history from Daniel Neal’s “The History of the Puritans” and David Hume’s “History of England,” and notes on Ancient history, taken mainly from Charles Rollin’s “The Ancient History of the Egyptians, Carthaginians, Assyrians, Babylonians, Medes and Persians, Macedonians and Grecians.” Additionally included are an excerpt from Plutarch’s “Lives” and transcriptions of three articles from “The Gentleman’s Magazine, and Historical Chronicle,” published in 1769: “A Critique on the Works of Ovid”; a book review of “A New Voyage to the West-Indies”; and “Genuine Anecdotes of Celebrated Writers, &.” The flyleaf contains the inscription “Semper boni aliquid operis facito ut diabolus te semper inveniat occupatum,” a variation on a quote of Saint Jerome that translates approximately as “Always good to do some work so that the devil may always find you occupied.” In the seventeenth and eighteenth centuries, Harvard College undergraduates often copied academic texts and lecture notes into personal notebooks in place of printed textbooks. Winthrop used Ward’s textbook in his class, while the books of Hume, Neal, and Rollin were used in history courses taught at Harvard in the 18th century.

Map of Lyndon Township. Town 1 South. Range 3 east [plat]

Drawn and Compiled by Cyrus Wheelock. Publication information: Chicago, Ill. : Everts & Stewart, 1874.

Sylvan Township and Chelsea (Mich.) residences, ca. 1874

Left to right: Res. of Henry Warren, Sec. 33, Webster Tp. Mich.; Res. of Skidmore, Sec. 17, Lyndon Tp. Mich.; Res. of J.H. Collins, Sec. 4, Lyndon Tp. Mich.; Res. of Wm. A. Jones, Sec. 32, Dexter Tp. Mich.; Res. of Hanson Sesions, Sec.2, Northfield Tp. Mich.; Res. of A.E. Collins, Sec. 4, Lyndon Tp. Mich. Drawn and Compiled by Cyrus Wheelock. Publication information: Chicago, Ill. : Everts & Stewart, 1874.

Map of Scio Township. Town 2. south. Range 5 east [plat]

Drawn and Compiled by Cyrus Wheelock. Publication information: Chicago, Ill. : Everts & Stewart, 1874.

Map of Superior Township. Town 2 south. Range 7 east [plat]

Drawn & compiled by Cyrus Wheelock. Publication information: Chicago, Ill. : Everts & Stewart, 1874.

Map of Manchester Township. Town four south. Range four east [plat]

Drawn & Compiled by Cyrus Wheelock. Publication information: Chicago, Ill. : Everts & Stewart, 1874.

Map of Dexter Village [plat]

Drawn & Compiled by Cyrus Wheelock. Publication information: Chicago, Ill. : Everts & Stewart, 1874.

Julius Cæsar,

Mode of access: Internet.