Improved variance estimation of classification performance via reduction of bias caused by small sample size-0

<p><b>Copyright information:</b></p><p>Taken from "Improved variance estimation of classification performance via reduction of bias caused by small sample size"</p><p>BMC Bioinformatics 2006;7():127-127.</p><p>Published online 13 Mar 2006</p><p>PMCID:PMC1435937.</p><p>Copyright © 2006 Wickenberg-Bolin et al; licensee BioMed Central Ltd.</p>ze and the size of the test set was varied from 5% to 70%. For each test set size the data was divided randomly into design and test sets 1,000 times, with the class proportions kept constant. The endpoints (dotted) of a two-sided 95% CIs, based on a histogram of 1,000 estimates, is displayed for the different values of the test set size, . Apparently the widths of the empirical CIs decrease as Nincreases. Also displayed are the estimated averages as a function of the test set size (solid). Since each CI is based on the histograms instead of estimates of the average and variance, note that the CIs are asymmetric with respect to the estimated average

Improved variance estimation of classification performance via reduction of bias caused by small sample size-2

<p><b>Copyright information:</b></p><p>Taken from "Improved variance estimation of classification performance via reduction of bias caused by small sample size"</p><p>BMC Bioinformatics 2006;7():127-127.</p><p>Published online 13 Mar 2006</p><p>PMCID:PMC1435937.</p><p>Copyright © 2006 Wickenberg-Bolin et al; licensee BioMed Central Ltd.</p>ast squares fittings of the simulated average values for 1/. The dashed lines are produced by means of the analytical result in Eq. (2)

Improved variance estimation of classification performance via reduction of bias caused by small sample size-1

<p><b>Copyright information:</b></p><p>Taken from "Improved variance estimation of classification performance via reduction of bias caused by small sample size"</p><p>BMC Bioinformatics 2006;7():127-127.</p><p>Published online 13 Mar 2006</p><p>PMCID:PMC1435937.</p><p>Copyright © 2006 Wickenberg-Bolin et al; licensee BioMed Central Ltd.</p> for the 2-dimensional normal distributions used where = 100. Also displayed are two-sided 95% CIs, based on histograms of the 5000 estimates for different values of the test bag size . The true and were obtained by testing 10,000 independently designed classifiers using 100,000 new, independently generated, test samples from the two normal distributions used. The estimates of are unbiased and the estimates of are unbiased for ≥ 100

Thaspine induces wide-spread activation of caspase-3 in spheroids.

<p>HCT116 spheroids with homogeneous diameters were formed using the hanging drop technique as described <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007238#pone.0007238-Herrmann1" target="_blank">[40]</a>. Five days after formation spheroids were compact and contained proliferating cells only in the surface layers (Ki67 staining, top left). Spheroids were treated with drugs for the times indicated, fixed, sectioned and stained for active caspase-3. Thaspine was used at 20 µM, doxorubicin at 20 µM, and cisplatin at 40 µM.</p

<i>In vivo</i> induction of tumor apoptosis by thaspine.

<p>(A) Induction of apoptosis in HCT116 tumors <i>in vivo</i>. SCID mice were injected with 10 mg/kg thaspine. Mice were sacrificed after 48 hours and tumors stained for active caspase-3 (upper panel: thaspine treated mice; lower panel: PBS injected mice). (B, C) SCID mice carrying HCT116 tumors (B) or FaDu head-neck carcinoma tumors (C) were injected with 10 mg/kg of thaspine or with PBS and the levels of human caspase-cleaved CK18 (CK18-Asp396) were determined in mouse plasma 48 hours after treatment using ELISA. The antibodies used to detect CK18-Asp396 do not bind mouse CK18. Four mice in each group; bars represent S.D. (D) SCID mice carrying FaDu tumors were treated with 10 mg/kg of thaspine (day 1, arrow) and tumor volume was calculated; black circles: untreated mice, red squares: treated mice (4 mice in each group). Error bars are presented as unidirectional for figure clarity. Animals were sacrificed when tumors were approximately 1 cm³ according to local animal welfare regulations. Statistical significance was calculated using Student's t-test.</p

Thaspine is a topoisomerase inhibitor.

<p>(A) Connectivity Map (CMAP) results after treatment with thaspine. The bar view is constructed from 6100 horizontal lines, each representing a single treatment and ordered according to their corresponding enrichment to the query signatures generated after thaspine treatment. Black horizontal lines in the barview represent the individual instances for ellipticine and camptothecin when the thaspine expression signature was used as query signature. Score according to the CMAP database; (B) inhibition of topoisomerase I activity: 1: plasmid +5U topoisomerase I; 2: plasmid; 3: plasmid +5U topoisomerase I+DMSO (1 µm); 4. Marker for nicked plasmid; 5: plasmid +5U topoisomerase I +50 µM thaspine; 6: plasmid +5U topoisomerase I +25 µM thaspine; 7: plasmid +5U topoisomerase I +10 µM thaspine; 8: plasmid + DMSO (1 µm). Topoisomerase I primarily induced nicked plasmid DNA, note the inhibition by thaspine. (C) inhibition of topoisomerase II activity: 1: plasmid +15U topoisomerase II; 2: plasmid; 3: plasmid +15U topoisomerase II + DMSO (1 µm); 4. Marker for nicked plasmid; 5: plasmid +15U topoisomerase II +50 µM thaspine; 6: plasmid +15U topoisomerase II +25 µM thaspine; 7: plasmid +15U topoisomerase II +10 µM thaspine; 8: plasmid + DMSO (1 µm). Topoisomerase II primarily induced nicked plasmid DNA, note the inhibition by thaspine.</p

Induction of apoptosis by thaspine.

<p>(A) chemical structure of thaspine (NSC76022); (B) induction of caspase-cleaved CK18 by thaspine, cisplatin, doxorubicin and mechlorethamine in HCT116 colon carcinoma cells. Treatment was for 24 hours with the indicated concentrations of compounds. Cells were lysed and CK18-Asp396 was determined using the M30 CytoDeath ELISA. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007238#s2" target="_blank">Results</a> are shown with S.D. from triplicate determinations. Similar results (including the biphasic response to doxorubicin) were observed in independent experiments.</p

Induction of the mitochondrial apoptosis pathway by thaspine.

<p>(A) loss of mitochondrial membrane potential in thaspine-treated HCT116 cells. Control and thaspine-treated cells (10 µM, 18 hours) were stained with tetramethyl-rhodamine ethyl ester (TMRE) and fluorescence was measured by flow cytometry; (B) Release of cytochrome c to the cytosol of thaspine-treated cells. Cells were treated with 10 µM thaspine for 7 or 16 hours. Cytochrome c was quantified in mitochondrial and cytosolic fractions by Western blotting. (C) thaspine induces the active conformation of Bak and Bax. Cells were treated with 10 µM thaspine, fixed and stained with conformation-specific antibodies to Bak and Bax. Note induction of the active conformation of both molecules by thaspine (<i>red arrows</i>: immunofluorescent signal in untreated cells; <i>green arrows</i>: immunofluorescent signal in drug-treated cells). (D) Inhibition of thaspine-induced apoptosis by siRNA to Bik and Bid. Cells were transfected with siRNAs in triplicate 96 well plates and treated with thaspine or solvent (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0007238#s4" target="_blank">Material and Methods</a>). After 24 hours the levels of caspase-cleaved CK18 were determined using the M30 CytoDeath ELISA.</p

Compounds in the NCI Natural Product Set that induce caspase cleavage of CK18 in HCT116 cells.

<p>Compounds in the NCI Natural Product Set that induce caspase cleavage of CK18 in HCT116 cells.</p

Effects of thaspine and reference compounds on the HCT116 cell cycle.

<p>Effects of thaspine and reference compounds on the HCT116 cell cycle.</p