The Feminists Go Swimming.

The Feminists Go Swimming

Appendix C. Observed and expected range overlap of exclusive congeneric and within-guild pairs.

Observed and expected range overlap of exclusive congeneric and within-guild pairs

Appendix E. Congeneric and within-guild pairs of species identified as true complete checkerboards (TCC) or true partial checkerboards.

Congeneric and within-guild pairs of species identified as true complete checkerboards (TCC) or true partial checkerboards

Appendix D. Observed numbers of TCC, TPC, and significance tests.

Observed numbers of TCC, TPC, and significance tests

Supplement 2. MATLAB function files to perform MCMC analysis and the analysis of covariance.

<h2>File List</h2><div> <p><a href="Supplement2/Road_map_to_programs.pdf">Road_map_to_programs.pdf</a> (MD5: 6cabea12cc599775aadafa59fa0c87d2)</p> <p><a href="Supplement2/readdata.m">readdata.m</a> (MD5: 3bdfbc7154cb9aac0aa62d280824a911)</p> <p><a href="Supplement2/nantest.m">nantest.m</a> (MD5: 1053c9d8b0bb9605d7e5dd848d7c8555)</p> <p><a href="Supplement2/matrixmcmcgr.m">matrixmcmcgr.m</a> (MD5: 2ef6a1d52b626d669abcad0630dc2fdb)</p> <p><a href="Supplement2/polyover.m">polyover.m</a> (MD5: f00007a67b901771ff1ec5853a73861b)</p> <p><a href="Supplement2/conpoly.m">conpoly.m</a> (MD5: 634b9340a0f7870e69b5f0a65967ae09)</p> <p><a href="Supplement2/overlap.m">overlap.m</a> (MD5: bc4038bbd510126a527ccfd4843087a3)</p> <p><a href="Supplement2/permissible.m">permissible.m</a> (MD5: 33ee427066e5ae51c3975d24a04362f6)</p> <p><a href="Supplement2/actual_count.m">actual_count.m</a> (MD5: 7061c1d5e10b7c540c4c0fb0bc839a8a)</p> <p><a href="Supplement2/actual_count_numshar.m">actual_count_numshar.m</a> (MD5: e9a93094a093c39e9a23bca65518fed0)</p> <p><a href="Supplement2/pvals.m">pvals.m</a> (MD5: 0dc6f6c67cbdfc69328ffb93f2ccfa97)</p> <p><a href="Supplement2/pvals_numshar.m">pvals_numshar.m</a> (MD5: 2aa826aa93072c4171ed06015331af01)</p> <p><a href="Supplement2/polyover2.m">polyover2.m</a> (MD5: 406c9c9bb45c08d7b1f51fda35fe0a0f)</p> <p><a href="Supplement2/fixpartial.m">fixpartial.m</a> (MD5: a5ac36ba552b19151576c2b022b10d9b)</p> <p><a href="Supplement2/simulated_count.m">simulated_count.m</a> (MD5: f804cd8ab2638d8669de5a0f14006bd9)</p> <p><a href="Supplement2/simulated_count_numshar.m">simulated_count_numshar.m</a> (MD5: b131ba01d7ef613644e6082d144ad57d)</p> <p><a href="Supplement2/ancova_prog.m">ancova_prog.m</a> (MD5: d3b1b7232d2f02a7bada58ade3d78911)</p> </div><h2>Description</h2><div> <p>PDF file Road_map_to_programs.pdf provides an overview of how the programs work together.</p> <p>MATLAB script file readdata.m reads in the data on species incidences, island group membership, and island coordinates.</p> <p>MATLAB script file nantest.m is called by readdata.m to convert not-a-number and uncertain status entries in the species occurrence matrix into absences.</p> <p>MATLAB script file matrixmcmcgr.m is the main program function for the MCMC analysis. </p> <p>MATLAB script file polyover.m uses the observed data to calculate overlap between each pair, and also creates index variables to code each pair as congeneric, within-guild, sharing island groups or not.</p> <p>MATLAB script file conpoly.m is called by polyover.m repeatedly to generate the coordinates on the convex hull for each species.</p> <p>MATLAB script file overlap.m uses the convexhulls to calculate the overlaps between pairs.</p> <p>MATLAB script file permissible.m creates a binary permissibility matrix. </p> <p>MATLAB script file actual_count.m generates the actual number of true complete checkerboards.</p> <p>MATLAB script file actual_count_numshar.m generates the actual number of true partial checkerbaords.</p> <p>MATLAB script file pvals.m generates the expected values, sd’s, and <i>p</i> values associated with tests based on defining a true complete checkerboard as observed overlap > expected overlap.</p> <p>MATLAB script file pvals_numshar.m generates the expected values, sd’s, and <i>p</i> values associated with tests based on defining a true partial checkerboard as observed overlap > expected overlap.</p> <p>MATLAB script file polyover2.m calculates the pair-wise overlap for each pair in a simulated matrix.</p> <p>MATLAB script file fixpartial.m determines which pairs are true partial checkerboards (TPC) at a variety of α levels.</p> <p>MATLAB script file simulated_count.m is used to determine in each simulated matrix which pairs are true complete checkerboards.</p> <p>MATLAB script file simulated_count_numshar.m is used to determine in each simulated matrix which pairs are true partial checkerboards.</p> <p>MATLAB script file ancova_prog.m performs the analysis of covariance using the observed and expected values generated by the simulation. </p> </div

Appendix A. Demonstration that the conditional trial-swap algorithm is unbiased.

Demonstration that the conditional trial-swap algorithm is unbiased

Appendix B. Detailed description of analytical algorithms.

Detailed description of analytical algorithms

Appendix F. Color versions of manuscript Figs. 2–4.

Color versions of manuscript Figs. 2–4

Supplement 1. Data on species incidences, island group membership, and coordinates of island perimeters.

<h2>File List</h2><div> <p><a href="Supplement1/bismarcks-islands.csv">bismarcks-islands.csv</a> (MD5: 85146e9d4760445ca261e985f44d75c7)</p> <p><a href="Supplement1/bismarcks-species-matrix.csv">bismarcks-species-matrix.csv</a> (MD5: 68d0b38c7c352c5575cbbc12ae80088f)</p> <p><a href="Supplement1/nhbirds-islands.csv">nhbirds-islands.csv</a> (MD5: adfeffb8b2367698c71a79df58a7e282)</p> <p><a href="Supplement1/nhbirds-species-matrix.csv">nhbirds-species-matrix.csv</a> (MD5: cbc955403bb8d17d81c123a3c7a59c6a)</p> <p><a href="Supplement1/solomons-islands.csv">solomons-islands.csv</a> (MD5: dc09dfb69d2674dd790c6947944921c8)</p> <p><a href="Supplement1/solomons-species-matrix.csv">solomons-species-matrix.csv</a> (MD5: 5605bc6505efabdd98c4b77816723e6d)</p> </div><h2>Description</h2><div> <p>bismarcks-islands.csv - A data file for the Bismarck islands with island names and associations in columns B–G, coordinates of island perimeters in columns Y–BV, and coordinates of approximate island mid-points in column CA–CB. Column pairs give latitude and longitude in decimal degrees.</p> <p>bismarcks-species-matrix.csv - A data file for the Bismarck islands with species names in column A, species and genus codes in columns E–F, guild membership in column G–H, and guild codes in columns H–I. The species incidence matrix is in columns J–AX (rows 2–151). Island abbreviations in row 1 (columns J–AX), and the island group code for each island in row 153 (columns J–AX). The island group memberships for each species are found in columns AZ–BC (rows 2–151). </p> <p>nhbirds-islands.csv - A data file for Vanuatu with island names in column A, the coordinates of the approximate mid-points of each island in columns B–C, and the coordinates of the island perimeters in columns E–AN. Each pair of columns gives the latitude and longitude of a coordinate in decimal degrees.</p> <p>nhbirds-species-matrix.csv - A data file for Vanuatu with species, genus, and family names in columns A–C. Columns D–G contain the family code, genus code, multi-species genus code, and guild codes of each species. Columns H–AI gives the species incidence matrix. </p> <p>solomons-islands.csv - A data file for the Solomon Islands with island number in column A, island abbreviation in column B, island name in column C, the coordinates of the approximate mid-points of each island in columns AU–AV, and the coordinates of the island perimeters in columns D–AS. Each pair of columns gives the latitude and longitude of a coordinate in decimal degrees.</p> <p>solomons-species-matrix.csv - A data file for the Solomon Islands with species, genus, family names, and codes in columns A–J, and guild codes in columns K–M. Columns The species incidence matrix is in columns O–EZ (rows 2–142). Island abbreviations in row 1 (columns O–EZ), and the island group code for each island in row 144 (columns O–EZ). The island group memberships for each species are found in columns FB-FG (rows 2–142). </p> </div

4-Hydroxybenzyl Modification of the Highly Teratogenic Retinoid, 4-[(1<i>E</i>)-2-(5,5,8,8-Tetramethyl-5,6,7,8-tetrahydro-2-naphthalenyl)-1-propen-1-yl]benzoic Acid (TTNPB), Yields a Compound That Induces Apoptosis in Breast Cancer Cells and Shows Reduced Teratogenicity

Retinoids are a class of compounds with structural similarity to vitamin A. These compounds inhibit the proliferation of many cancer cell lines but have had limited medical application as they are often toxic at therapeutic levels. Efforts to synthesize retinoids with a greater therapeutic index have met with limited success. 4-[(1<i>E</i>)-2-(5,5,8,8-tetramethyl-5,6,7,8-tetrahydro-2-naphthalenyl)-1-propen-1-yl]benzoic acid (TTNPB) is one of the most biologically active all-<i>trans</i>-retinoic acid (atRA) analogues and is highly teratogenic. In this study, we show that modification of the TTNPB carboxyl group with an <i>N</i>-(4-hydroxyphenyl)amido (4HPTTNPB) or a 4-hydroxybenzyl (4HBTTNPB) group changes the activity of the compound in cell culture and <i>in vivo</i>. Unlike TTNPB, both compounds induce apoptosis in cancer cells and bind poorly to the retinoic acid receptors (RARs). Like the similarly modified all-<i>trans</i>-retinoic acid (atRA) analogues <i>N</i>-(4-hydroxyphenyl)retinamide (4-HPR/fenretinide) and 4-hydroxybenzylretinone (4-HBR), 4HBTTNPB is a potent activator of components of the ER stress pathway. The amide-linked analogue, 4HPTTNPB, is less toxic to developing embryos than the parent TTNPB, and most significantly, the 4-hydroxybenzyl-modified compound (4HBTTNPB) that cannot be hydrolyzed <i>in vivo</i> to the parent TTNPB compound is nearly devoid of teratogenic liability