"... In PAGE 5: ... Since each analysis comprises a fraction of the motifs included in the previous one, we expect a concomitant reduction in the power of the test due to the smaller sam- pling size. As shown in Table2 , the 27 bp motif is significantly asso- ciated with genes whose molecular function is related to signal transduction and/or transcriptional regulation. In regard to the biological process, there is a significant overrepresentation of genes involved in development, and a significant underrepresentation of genes related to cell growth and/or maintenance.... In PAGE 7: ... Here, we describe a 27 bp long repeti- tive DNA sequence within the Drosophila genome that, based on its characteristics, may be considered one of these cis-acting elements. Mainly, there is a significant association of the 27 bp long motif to genes involved in development, whose molecular function is related to signal transduction and/or transcrip- tional regulation ( Table2 ). This association may be indeed stronger than shown in Table 2, taking into account that any given gene is usually classified under sev- eral different categories of the Gene Ontology classifica- tion.... In PAGE 7: ... Mainly, there is a significant association of the 27 bp long motif to genes involved in development, whose molecular function is related to signal transduction and/or transcrip- tional regulation (Table 2). This association may be indeed stronger than shown in Table2 , taking into account that any given gene is usually classified under sev- eral different categories of the Gene Ontology classifica- tion. For instance, although only 41.... In PAGE 7: ... For instance, although only 41.3% of the biological process classifications of the 22 genes with the motif present within an intron are annotated as involved in development ( Table2 ), 19 of them (~86%) are indeed known to be involved in development. Table 2: Gene Ontology classification of genes associated with the motifs... In PAGE 8: ... There are also several selector or selector-like genes [35], conserved transcription factors that act controlling the development of morphogenetic fields giving rise to specific adult structures, such as twist (twi) in mesoderm tissues, Distal-less (Dll) in the ventral appendages, pannier (pnr) in dorso-medial domains of trunk and head, brachy- enteron (byn) in posterior terminal structures, engrailed these genes apos; function, plus references therein). Thus, this motif may define an important regulatory network, linking together several fundamental genes active during Drosophila development ( Table2 and Additional file 1). Second, our strategy to search for the conservation of the motif in D.... ..."

"... In PAGE 9: ... For each separating cluster of genes (G5, G12, node N505, and node N566) and their combination, we generated a k-nearest neighbor classifier (k H11005 3) and tested its ability to perform class partitions. In all cases, the separation power was found to be significant ( Table5 ). In addition, we tested whether a three-way separation of the tumor types can be performed based on the combination of the four gene clusters.... ..."

"... In PAGE 8: ... Patterns GTACATT, AACATCCG, TACATCC, ACATCC, ACATCCG and ACCCA, ACCCAT, ACCCATA were left out from these clusters respectively as the alignment was done by simple heuristics based on one conserved block. profile for the cluster that produced the 15a0a2a1 highest scor- ing pattern GGTGGCAA is shown in Table2 (we refer to this cluster as GGTGGCAA-cluster). This pattern occurs in 20 out of 40 upstream sequences of the cluster, and only in 96 out of all 6221 upstreams.... ..."

"... In PAGE 8: ... Patterns GTACATT, AACATCCG, TACATCC, ACATCC, ACATCCG and ACCCA, ACCCAT, ACCCATA were left out from these clusters respectively as the alignment was done by simple heuristics based on one conserved block. profile for the cluster that produced the 15D8CW highest scor- ing pattern GGTGGCAA isshownin Table2 (werefertothis cluster as GGTGGCAA-cluster). This pattern occurs in 20 out of 40 upstream sequences of the cluster, and only in 96 out of all 6221 upstreams.... ..."

"... In PAGE 17: ... For this end, we computed the correlations between the probability of agreement with the base inflection and the number of regular and irregular tokens in its mishkal7. Our find- ings are provided in Table7 . The selection of irregular inflection for irregularly sounding nouns correlated positively with the number of irregular friends.... ..."

"... In PAGE 5: ... Of the ten probes listed in Table 1, only probe-6 has an alternative tar- get in the genome with a free energy difference within 10 kcal/mole of the true target free energy. Based on the data in Table2 one could pick the optimum probe (or small set of probes) for the CDC28 gene. This algorithm has been compared with the standard dy- namic programming algorithm with free energy rules to fill the matrix.... ..."

"... In PAGE 19: ...6 kbp. The correlation between G1C content and gene density was also examined in 50-kbp windows along the assembled sequence ( Table9 and Figs. 10 and 11).... ..."

"... In PAGE 9: ...dependencies between the average stability time and the group size or the mean update interarrival time are similar to those observed in the failure free case. Finally, the maximum bu er size needed for the simulation runs is shown in Table1 in the absence of failures, and in Table 2 in the presence of one communication failure per broadcast. The maximum bu er size is shown for the sequencer and the non-sequencers separately.... In PAGE 28: ...1= = 15:0 1= = 50:0 1= = 100:0 1= = 400:0 Amoeba sequencer 151 151 152 152 non-sequencer 152 152 152 152 PositiveACK sequencer 12 8 6 4 non-sequencer 18 9 8 5 Train trainmaster 44 23 16 8 non-trainmaster 25 12 10 5 Isis ABCAST sequencer 410 417 412 412 non-sequencer 285 283 278 278 Table1 0: Maximum bu er size: group size 5; no failures absence and in the presence of communication failures. The explanation for this is the same as that given earlier for the low stability times of these protocols compared to Isis or Amoeba.... In PAGE 28: ... The e ect of a message loss on bu er size requirement is quite signi cant in the Isis and Amoeba protocols, while its e ect on the train and the PA protocols is minimal. Group Size: 3 1= = 15:0 1= = 50:0 1= = 100:0 1= = 400:0 Amoeba sequencer 46 62 62 63 non-sequencer 1090 63 63 63 PositiveACK sequencer 14 8 6 4 non-sequencer 17 9 7 5 Train trainmaster 31 16 14 8 non-trainmaster 18 9 8 4 Isis ABCAST sequencer 190 135 131 144 non-sequencer 192 187 189 208 Table1 1: Maximum bu er size: group size 3; one failure Group Size: 5 1= = 15:0 1= = 50:0 1= = 100:0 1= = 400:0 Amoeba sequencer 152 152 154 152 non-sequencer 165 152 154 152 PositiveACK sequencer 18 9 7 4 non-sequencer 20 11 8 6 Train trainmaster 69 29 19 11 non-trainmaster 42 17 12 6 Isis ABCAST sequencer 412 434 416 420 non-sequencer 292 385 279 278 Table 12: Maximum bu er size: group size 5; one failure 5.3 Average Number of Messages per Broadcast The average number of messages per broadcast in the absence of failures are plotted in gures 58 and 59 as a function of mean interarrival time.... In PAGE 28: ... The e ect of a message loss on bu er size requirement is quite signi cant in the Isis and Amoeba protocols, while its e ect on the train and the PA protocols is minimal. Group Size: 3 1= = 15:0 1= = 50:0 1= = 100:0 1= = 400:0 Amoeba sequencer 46 62 62 63 non-sequencer 1090 63 63 63 PositiveACK sequencer 14 8 6 4 non-sequencer 17 9 7 5 Train trainmaster 31 16 14 8 non-trainmaster 18 9 8 4 Isis ABCAST sequencer 190 135 131 144 non-sequencer 192 187 189 208 Table 11: Maximum bu er size: group size 3; one failure Group Size: 5 1= = 15:0 1= = 50:0 1= = 100:0 1= = 400:0 Amoeba sequencer 152 152 154 152 non-sequencer 165 152 154 152 PositiveACK sequencer 18 9 7 4 non-sequencer 20 11 8 6 Train trainmaster 69 29 19 11 non-trainmaster 42 17 12 6 Isis ABCAST sequencer 412 434 416 420 non-sequencer 292 385 279 278 Table1 2: Maximum bu er size: group size 5; one failure 5.3 Average Number of Messages per Broadcast The average number of messages per broadcast in the absence of failures are plotted in gures 58 and 59 as a function of mean interarrival time.... ..."

"... In PAGE 9: ...90 37.08 + The results of these experiments with bagging show that the accuracy advantages of clustered partial linear models that were observed in Table2 , can only be caused by the effects of clustering the training data. In effect, the results of Table 3, indicate that there is nothing to gain with averaging over several partial linear models.... In PAGE 10: ...ersions obtain similar results (c.f. Tables 2 and 3). However, the results obtained on the two Computer domains and in the Telecomm application are a bit disappointing. A possible cause of these results is the complete inadequacy of linear polynomials to these domains, which can be confirmed by the results of Table2 . Although partial linear models include a smoothing component that could overcome this mismatch, there are situations were this is not possible.... In PAGE 10: ...f. Table2 ). Thus, we claim that these poor results are caused by the lack of adequacy of the base regression models to the domains and not by any difficulty of our proposed methodology.... ..."

"... In PAGE 12: ...cheme of gene classification of MIPS Yeast Genome Database (Mewes et al., 2000). We found that genes of similar function were grouped into the same cluster. Table2 shows 8 main clusters including 16 functional categories of genes. The results are comparable to the data of Tavazoie.... ..."