Datasets:

TomTBT

/

pmc_open_access_figure_comm

like 1

PMC1112585

15826304

1471-2407-5-38-3

Figure 3 Relationship of surface and cytoplasmic expression of CD66c. Percentage of surface expression of CD66c in ALL blasts is plotted against cytoplasmic expression (after cell membrane permeabilization). Samples of 20 patients at ALL diagnosis are shown, 12 CD66c negative and 8 CD66c positive. Regression coefficient R 2 = 0.927

CC BY

no

2022-01-12 14:24:31

BMC Cancer. 2005 Apr 12; 5:38

PMC1112585

15826304

1471-2407-5-38-4

Figure 4 Transcription of CEACAM6 versus surface CD66c expression on sorted cells. FACSsorted CD66c surface negative (CD66c neg ) or positive (CD66c pos ) ALL lymphoblasts, five patients with heterogeneous CD66c expression were sorted into both CD66c negative and CD66c positive fraction (lines connect sorted fractions from the same specimen). Mann-Whitney test was used to compare groups (n = 32). CEACAM6n value is normalized to beta-2-microglobulin (see Methods).

CC BY

no

2022-01-12 14:24:31

BMC Cancer. 2005 Apr 12; 5:38

PMC1112585

15826304

1471-2407-5-38-5

Figure 5 Western blot of granulocytes, ALL samples of CD66c positive cases and surface CD66c neg cell lines with TEL/AML1pos (REH), MLL/AF4pos (RS4;11) translocation and with no fusion (NALM-6).

CC BY

no

2022-01-12 14:24:31

BMC Cancer. 2005 Apr 12; 5:38

PMC1112585

15826304

1471-2407-5-38-6

Figure 6 Stability of CD66c from diagnosis to relapse. Each circle represents one patient (n = 39). Percentage of CD66c pos blasts at diagnosis is plotted against percentage of CD66c pos blasts at relapse. Regression line with 95% confidence R 2 = 0.755

CC BY

no

2022-01-12 14:24:31

BMC Cancer. 2005 Apr 12; 5:38

PMC1112585

15826304

1471-2407-5-38-7

Figure 7 Relapse free survival of cases with CD66c pos (blue line) or CD66c neg (red line) B-precursor ALL. Unselected consecutive patients treated on ALL BFM95 protocol (median follow up 3.64 years). Since surface CD66c associates with genotype, separate analyses for distinct genotype subgroups are shown.

CC BY

no

2022-01-12 14:24:31

BMC Cancer. 2005 Apr 12; 5:38

PMC1112586

15860134

1471-2407-5-43-1

Figure 1 Sequence of FANCA promoter allele in the polymorphic region. Allele 1 has a single copy of a 13 base pair sequence. This has been defined as GGCCACGACGCAA in accordance with current nomenclature for mutations [21] although it could theoretically be GCCACGACGCAAG or CCACGACGCAAGG. Allele 2 has two tandemly arranged copies of this sequence. The 13 base pair sequence is located at -98 to -110 bases upstream of the beginning of transcription as defined by the NCBI reference sequence NM_000135.1. Exon 1 is in bold and the coding sequence in capitals.

CC BY

no

2022-01-12 14:24:31

BMC Cancer. 2005 Apr 29; 5:43

PMC1112586

15860134

1471-2407-5-43-2

Figure 2 Genotyping the FANCA promoter polymorphism by PCR. Allele 1 amplifies as a band of 151 base pair, allele 2 as a band of 164 base pair. The 3 genotypes are readily distinguishable on a 3 % agarose gel run at 100 V for 1 hour. Homozygous samples for both allele 1 and allele 2 are shown as are heterozygous samples which have both bands.

CC BY

no

2022-01-12 14:24:31

BMC Cancer. 2005 Apr 29; 5:43

PMC1112590

15836779

1471-2164-6-55-1

Figure 1 Gene ontology of custom chip probes . The ontological classification of 3531 cell surface or secreted genes was extracted from the Gene Ontology at the third level. Genes lacking GO annotations at this level were derived from level 2.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 Apr 18; 6:55

PMC1112590

15836779

1471-2164-6-55-2

Figure 2 Principal components analysis of array data . The mean expression values of all samples from all arrays were analyzed by principal components analysis. The first 3 principal components of the analysis are shown from the best vantage point to show separation of the three classes. Open circles represent the parental cell lines, "X" denotes the various xenograft tumors, and the small solid dots are the reference cDNA sample (derived from the Universal RNA) co-hybridized with all experimental samples. The cell lines corresponding to the various tissue sources of the parental cell lines were: Ovary, SKOV3; Prostate, PC3; Breast, MDA MB-231; Colon, HCT116; and Lung, A549.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 Apr 18; 6:55

PMC1112590

15836779

1471-2164-6-55-3

Figure 3 Genes identified by linear discriminant analysis . The top 70 PCA coefficients along the third principal component were selected. Panel A : Plot of linear discriminant profile of 70 probes that distinguish xenograft tumors from parental cell lines. Positive values in orange indicate "Xenograft tumor" while negative values in blue indicate "Parental Cell line". The y-axis shows either numbered tumor (left) or parental cell (right) samples and the x-axis is an arbitrarily scaled output reflecting the accuracy in assigning a sample as a xenograft tumor or parental cell line. The numbered tumors were grouped according to tissue type as indicated by C for colon (HCT116), B for breast (MDA MB-231), L for lung (A549), P for prostate (PC3) and O for ovary (SKOV-3). Panel B : Graphical representation of the LD-p54 genes expression profiles. For genes with multiple probes, the highest value is shown. Classified by a non-redundant filtering of the Gene Ontology biological process terms, the genes are shown with a color scale representing relative fold induction to all parental cell line data. The left-most color column designated by 'X' is the average ratio, while the remaining five columns correspond to Colon (HCT116), Breast (MDA MB-231), Lung (A549), Prostate (PC3) and Ovarian (SKOV-3) carcinoma xenografts respectively.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 Apr 18; 6:55

PMC1112590

15836779

1471-2164-6-55-5

Figure 5 Quantitative PCR analysis of selected genes . Two tumors of each tumor type were analyzed by quantitative PCR. The measured fold change relative to cell line was determined. RNA amounts per well being normalized by betaactin signal. In general <2-fold changes are not significant. Hence a call of 1.5 fold down may not actually differ from 1.5 up. Specific tumor types are indicated by the first initial followed by the tumor number: i.e. C1 = colon tumor #1, O1 = ovary tumor #1, L1 = lung tumor #1, B1 = breast tumor #1, P1 = prostate tumor #1.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 Apr 18; 6:55

PMC1112590

15836779

1471-2164-6-55-6

Figure 6 Overlap of differentially expressed genes identified by three analyses: ANOVA-p149 = 149 genes derived from the ANOVA analysis of all data, LD-p54 = linear discriminant list of 54 genes from all data, and ANOVA-i12 = twelve genes resulting from a comparison of differentially expressed genes from the ANOVA analysis of individual tumors compared to parental cell lines. An estimate for the statistical significance for the overlap of differentially expressed genes by the 3 analytical methods was estimated by calculating the product of individual probabilities for the results of each analytical method applied to 3531 genes. The null hypothesis in this case is that each method's "call" as to a given gene's differential expression is independent of the call made by the other two methods. Thus if p1, p2, and p3 represent the chance that each method calls a given gene as differentially expressed (easily estimated as number of genes called/ number of total genes), the chance that all three methods do so is simply pAll = p1*p2*p3 = (54/3531)*(149/3531)*(12/3531) = 2.193e-5. Under our null hypothesis, the total number of genes called by all three methods k will follow a binomial distribution with parameters p = pAll, n = 3531 where P(k = L) ~ Bin(pAll, N). Standard calculation techniques allow us to calculate a p-value for this; i.e. p = P(k > = K) – the chance under the null hypothesis we see as much or more overlap than was actually observed. For our data, we thus have p = P(k> = 7) < 1E-6. Thus, if the methods identified random noise as differential expression, they would be very unlikely to produce the overlap observed, thus supporting the statistical significance of the results. The heat maps indicate relative fold-induction or suppression in a linear color-encoded scale shown at the bottom. Mean ratios are indicated by X, C = colon, B = breast, L = lung, P = prostate, O = ovary.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 Apr 18; 6:55

PMC1112590

15836779

1471-2164-6-55-4

Figure 4 Comparison of differential expression of genes in parental cells versus reference cDNA synthesized from universal RNA (left) and all tumors versus parental cell lines (right) . Genes differentially expressed in the parental cells relative to the reference cDNA were analyzed by a 2-way ANOVA (Pcorr < .001). A subset of the differentially expressed genes is shown. The corresponding cognate tumors with differential expression at a 99.9% confidence level by ANOVA analysis of tumors vs parental cell line data are shown. The heat maps indicate relative fold-induction or suppression in a linear color-encoded scale shown at the bottom. Mean ratios are indicated by X, C = colon, B = breast, L = lung, P = prostate, O = ovary.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 Apr 18; 6:55

PMC1112591

15854223

1471-2164-6-58-1

Figure 1 Ancylostoma NemaGene v2.0 clustering showing the distribution of ESTs by cluster size. For example, there are three A. caninum cluster of size 22 containing a sum of 66 ESTs and there were eight A. ceylanicum clusters of size 22 containing a sum of 176 ESTs. Cluster size (x-axis) is shown to scale for 1–75 members, with the size of larger clusters indicated.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 Apr 26; 6:58

PMC1112591

15854223

1471-2164-6-58-2

Figure 2 Venn diagram of A. caninum (A) and A. ceylanicum (B) clusters, based on stage of origin of each cluster's EST members. The majority of clusters are represented by only one stage in this investigation, though greater depth of sampling would likely increase representation by multiple stages.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 Apr 26; 6:58

PMC1112591

15854223

1471-2164-6-58-3

Figure 3 Venn diagram showing distribution of A. caninum (A) and A. ceylanicum (B) cluster BLAST matches by database. Amino acid level homologies (≥ e-05) were identified to non- Ancylostoma sequences for 65.8% (2,646/4,020) of A. caninum and 83.1% (2,801/3,369) of A. ceylanicum clusters. Databases used are: for C. elegans , Wormpep v.97 and mitochondrial protein sequences; for other nematodes, all GenBank nucleotide data for nematodes except C. elegans and Ancylostoma ; for non-nematodes, nrGenBank (3/20/2003) with all nematode sequences removed.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 Apr 26; 6:58

PMC1112591

15854223

1471-2164-6-58-4

Figure 4 Distribution of A. caninum and A. ceylanicum contigs with and without database amino acid level homology by size of the longest predicted open reading frame (ORF).

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 Apr 26; 6:58

PMC1112591

15854223

1471-2164-6-58-5

Figure 5 Distribution of dN/dS ratios among Ancylostoma ortholog pairs. dN and dS are the rates of nonsynonymous and synonymous amino acid substitutions, respectively.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 Apr 26; 6:58

PMC1112591

15854223

1471-2164-6-58-6

Figure 6 Relative distance based upon protein maximum likelihood. A. ceylanicum to A. cananum distance is similar to C. elegans to C. briggsae distance. Ancylostoma to Caenorhabditis distance for any species is 4.3X the Ancylostoma to Ancylostoma distance and 4.1X the Caenorhabditis to Caenorhabditis distance. The length of each line segment is proportional to the calculated branch length between the species.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 Apr 26; 6:58

PMC1112592

15869710

1471-2164-6-60-1

Figure 1 Pathway Voyager mapping procedure . The analysis and mapping procedure of PathwayVoyager is shown in a flowchart diagram. Manual selection of organisms and pathways present in the KEGG database, at the time of analysis, results in the retrieval of a specific set of protein sequences that are subsequently reformatted into a BlastP database. Protein query sequences are then used as templates for local BlastP analyses. Results are subjected to a user-defined threshold and subsequently parsed to retrieve tagged KEGG pathway maps. Pathway graphs and parsed BlastP results are stored as a flatfile database and can be displayed using the graphical browser. Opposite double arrows represent Internet-access using the KEGG API. Symbols used are according to general flowchart conventions.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 May 3; 6:60

PMC1112592

15869710

1471-2164-6-60-2

Figure 2 PathwayVoyager main window . Screenshot of the graphical user interface. (A) and (B) indicate listboxes showing the organisms that can be individually selected and pathways represented in KEGG at the time of analysis. Button for exiting the software, redo the analysis, and accessing the setup are located beneath both boxes. Section (C) resembles the step-by-step design to start the analysis, retrieve the selected organisms and pathways, and subsequently obtain the respective protein sequences. In manual mode, the KEGG analysis and pathway retrieval can be activated by the user. Existing KEGG analyses can be reviewed by accessing the lowest button. On-the-fly options, for re-using previous organism-pathway selections and respective BlastP results, are located in the top region of section (C).

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 May 3; 6:60

PMC1112592

15869710

1471-2164-6-60-3

Figure 3 Interactive KEGG Pathway display . The screenshot illustrates KEGG pathway mapping for the glycolysis/gluconeogenesis pathway using the predicted ORFeome of the GAMOLA annotated L. acidophilus NCFM genome as query template. The e-value threshold was set to 1e-10. Section (A) shows all pathways used for this analysis. Section (B) lists the marked entries. Section (C) represents the graphical representation of a selected pathway. Elements exhibiting BlastP hits below the selected threshold e-value are marked as red boxes. Section (D) shows the corresponding BlastP results, comprising the respective query protein designation, the corresponding KEGG hit, its amino-acid length, the BlastP-score, and e-value. Entries are sorted by ascending e-values.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 May 3; 6:60

PMC1112593

15877817

1471-2164-6-65-1

Figure 1 Maximum parsimony and Neighbor joining trees for F41D9.1 (A, B) and C13F10.4 genes (C,D) . Illustration of the criteria that has been applied in order to select the genes. Only genes able to produce trees as shown in A and B (F41D9.1) were subjected to experimental work.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 May 6; 6:65

PMC1112593

15877817

1471-2164-6-65-2

Figure 2 F41D9.1::GFP expression. Widespread through the neural system. Panel A shows the general expression pattern in an L1 stage animal. Many cells in the nerve ring, the ventral nerve cord (vnc) and the tail region express GFP. Panel B presents the tail region in greater detail, scanning through the animal at three focal planes from right (Bi) to left (Biii), with the ventral side facing down. A cluster of laterally symmetrical cells is visible in panels Bi and Biii, whereas in Bii cells of the vnc are visible. Magnification is 100×. Fig C presents 3 focal planes from dorsal (Panel Ci) to ventral (Panel Ciii) through the worm head, with the posterior pharyngeal bulb to the left. The GFP images have undergone deconvolution to increase resolution. Cells of the dorsal ganglion are visible in Ci, the retrovesicular ganglion is marked in Cii, and processes leading to it are indicated in Ciii. Scale bar represents10 μm.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 May 6; 6:65

PMC1112593

15877817

1471-2164-6-65-3

Figure 3 C17E4.3::GFP reporter expression. Present in the head and tail regions of larval stages. Panel Ai shows an overview of an L1 animal, with distinct cells near the anterior pharyngeal bulb as well as in the tail. Close up of the head reveals GFP expressing cells (Panel Bii), including muscle cells located in the posterior pharyngeal bulb (Panel Biv, labeled 'p'). Sheath/socket cells located at the anterior pharyngeal bulb are indicated in panels Biv, Dii and Diii. Dye-filling tests (see Materials and Methods) to stain sensory amphid (head) and phasmid (tail) neurons are shown in panels C and D. The amphids are specifically visualized in panel Civ (red fluorescence), and under an FITC filter in Ciii (yellow fluorescence, not in nucleus) and green with an EGFP filter, and are not the same as the cells expressing the C17E4.3::GFP reporter (arrow in panels Cii and Ciii). In the tail, phasmids (labeled 'ph') are clearly seen in panel Div just below the anus (cl), but are not expressing GFP, which is instead present in several hypodermal cells (arrow panel Diii). Scale bar represent 10 μm.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 May 6; 6:65

PMC1112593

15877817

1471-2164-6-65-4

Figure 4 ZK795.3::GFP reporter expression . Evident in the excretory cell system (panel A) in about 20% of animals, but was always present in the excretory cell (labeled 'ex', panels A and Bi). The anal sphincter and/or depressor cell around the anus ('cl') also expressed GFP (panel Bii), as did the juvenile vulva ('v', panel Biii) and the spermathecae (panel C). Scale bar represents 10 μm.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 May 6; 6:65

PMC1112593

15877817

1471-2164-6-65-5

Figure 5 C09D4.1::GFP expression. Limited to the nuclei of intestinal cells. The top figure is an overlay of the DIC and GFP images. Scale bar represents 10 μm.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 May 6; 6:65

PMC1112593

15877817

1471-2164-6-65-6

Figure 6 Subcellular localization of recombinant fusion proteins in human cell lines. Human protein NP_219484 ( C. elegans protein ZK795.3) was detected in transfected HeLa cells with goat anti-V5 conjugated with FITC and co-localized with human anti-fibrillarin subsequently detected by donkey anti-rabbit Cy3 (A). Nuclei were stained with DAPI. This protein displays both a nucleolar (top row) and nuclear speckle (bottom row) pattern (A). NP_848545 (C. elegans protein C17E4.3) was detected in HEK293 cells with mouse anti-V5 and goat anti-mouse Alexa 488 (B). Cells were costained with rabbit anti-Lamin and donkey anti-rabbit Cy3 illustrating a colocalization with the nuclear envelope (B). Partial ER and nuclear distributions were observed for NP_115683 by co-detection with rabbit anti-calreticulin in HeLa cells (C). AAP34400.1 was detected in HeLa cells at the plasma membrane by co-staining with Annexin II (left panel, D) and a partial colocalization with beta-actin was also detected (right panel, D). Scale bars represent 10 μm.

CC BY

no

2022-01-12 14:36:30

BMC Genomics. 2005 May 6; 6:65

PMC1112594

15847683

1472-6963-5-30-1

Figure 1 Flowchart of recruitment process

CC BY

no

2022-01-12 14:33:58

BMC Health Serv Res. 2005 Apr 22; 5:30

PMC1112595

15871735

1471-2334-5-30-1

Figure 1 Chest X-ray (PA view) at initial presentation showing early right lower lobe consolidation.

CC BY

no

2022-01-12 14:32:36

BMC Infect Dis. 2005 May 4; 5:30

PMC1112595

15871735

1471-2334-5-30-2

Figure 2 Chest X-ray (PA view), 5 days later, showing progression of disease with infiltrates in right and left lower lobes.

CC BY

no

2022-01-12 14:32:36

BMC Infect Dis. 2005 May 4; 5:30

PMC1112595

15871735

1471-2334-5-30-3

Figure 3 A section of CT scan of chest performed 8 days after hospitalization showing bilateral consolidation of lungs, mainly of lower lung fields.

CC BY

no

2022-01-12 14:32:36

BMC Infect Dis. 2005 May 4; 5:30

PMC1112595

15871735

1471-2334-5-30-4

Figure 4 Chest X-ray (PA view) – after 8 days of intravenous antibiotic therapy, showing further worsening of bilateral lower lung disease with nodular pattern – raising suspicion of metastatic disease.

CC BY

no

2022-01-12 14:32:36

BMC Infect Dis. 2005 May 4; 5:30

PMC1112595

15871735

1471-2334-5-30-5

Figure 5 Wet preparation of sputum [25% NaOH with 5% Glycerol as the mounting medium, 40× magnification] showing budding yeast [blastocyst]

CC BY

no

2022-01-12 14:32:36

BMC Infect Dis. 2005 May 4; 5:30

PMC1112595

15871735

1471-2334-5-30-6

Figure 6 Chest X-ray (PA view) at initial presentation showing consolidation within the right mid and both lower lobes.

CC BY

no

2022-01-12 14:32:36

BMC Infect Dis. 2005 May 4; 5:30

PMC1112595

15871735

1471-2334-5-30-7

Figure 7 Map of Northeastern Ontario, showing the location of exposure [adapted from , accessed April 2, 2005].© Queens Printer for Ontario, 2002. Adapted and reproduced with permission

CC BY

no

2022-01-12 14:32:36

BMC Infect Dis. 2005 May 4; 5:30

PMC1112596

15850480

1472-698X-5-4-1

Figure 1 A scatter graph of Mean Governance Ranking and HIV prevalence for 149 countries.

CC BY

no

2022-01-12 14:33:17

BMC Int Health Hum Rights. 2005 Apr 25; 5:4

PMC1112599

15833137

1471-2202-6-28-1

Figure 1 Experimental approach; A) Schematic overview of the utilised amplification protocol. For details see text. B) Experimental design. NSCs were isolated from the lateral ventricular region of brains from three pools of mice (three isolations) and grown as neurospheres. Sample G was induced to differentiate by withdrawing the growth factors from the culture medium, plating on solid support and adding serum. RNA was isolated from different passages as indicated and used for subsequent microarray hybridisations. Blue arrows represent duplicate hybridisations, arrowhead represents labelling with Cy5 and arrow tail represents labelling with Cy3.

CC BY

no

2022-01-12 14:36:19

BMC Neurosci. 2005 Apr 15; 6:28

PMC1112599

15833137

1471-2202-6-28-2

Figure 2 B-value distribution for each of the comparisons; The B-value is calculated through empirical Bayes statistics and scores the genes according to their probability of differential expression. Higher B-value means higher probability of differential expression. NS = neurosphere, DC = differentiated cells.

CC BY

no

2022-01-12 14:36:19

BMC Neurosci. 2005 Apr 15; 6:28

PMC1112599

15833137

1471-2202-6-28-3

Figure 3 Graphs displaying the variability of the data at different levels of replication; In all graphs one dot represents one gene. Panel A) shows MA-plots for each comparison. The x-axis represents the intensity of the feature (A = 1/2log 2 (Cy5*Cy3)). The y-axis represents the magnitude of differential expression of the gene (M = log 2 (Cy5/Cy3)), calculated after filtration and normalisation of the data. Dotted lines are drawn at M-values 1 and -1, i.e. at a 2-fold difference in signal intensity between the compared samples. Panel B) shows volcano plots for each sample. The x-axis shows the M-value for each gene and the y-axis the corresponding B-value (calculated by empirical Bayes moderated t-test) for that gene. Panel C) shows scatter plots for each comparison. The x-axis displays the average signal intensity for one sample and the y-axis the average signal intensity for the other sample. Also shown are the values of the Pearson correlation coefficient (r) and the coefficient of determination (R 2 ).

CC BY

no

2022-01-12 14:36:19

BMC Neurosci. 2005 Apr 15; 6:28

PMC1112599

15833137

1471-2202-6-28-4

Figure 4 The number of differentially expressed genes in each comparison; Genes with p < 0.001, calculated by empirical Bayes moderated t-test and false discovery rate adjustment, are included. NS = neurosphere, DC = differentiated cells.

CC BY

no

2022-01-12 14:36:19

BMC Neurosci. 2005 Apr 15; 6:28

PMC1112599

15833137

1471-2202-6-28-5

Figure 5 Overlap of differentially expressed genes; Compared are the results from the parallel cultures (CI-CII and CII-CIII) and the neurosphere vs. differentiated cells comparison (F-G). Genes with p < 0.001, calculated by empirical Bayes moderated t-test and false discovery rate adjustment, are included.

CC BY

no

2022-01-12 14:36:19

BMC Neurosci. 2005 Apr 15; 6:28

PMC1112601

15840173

1471-2458-5-40-4

Figure 4 Incidents of homicide in NSW, 1997–2002

CC BY

no

2022-01-12 14:32:51

BMC Public Health. 2005 Apr 19; 5:40

PMC1112601

15840173

1471-2458-5-40-1

Figure 1 Proportion of IDU reporting cocaine use in the past six months, daily use, and use on the day preceding interview, 1996–2003

CC BY

no

2022-01-12 14:32:51

BMC Public Health. 2005 Apr 19; 5:40

PMC1112601

15840173

1471-2458-5-40-2

Figure 2 Incidents of cocaine possession/use in NSW, 1997–2002

CC BY

no

2022-01-12 14:32:51

BMC Public Health. 2005 Apr 19; 5:40

PMC1112601

15840173

1471-2458-5-40-3

Figure 3 Incidents of robbery offences in NSW 1997–2002

CC BY

no

2022-01-12 14:32:51

BMC Public Health. 2005 Apr 19; 5:40

PMC1112601

15840173

1471-2458-5-40-5

Figure 5 Incidents of assault in NSW, 1997–2002

CC BY

no

2022-01-12 14:32:51

BMC Public Health. 2005 Apr 19; 5:40

PMC1112601

15840173

1471-2458-5-40-6

Figure 6 Incidents of weapons offences, NSW 1997–2002

CC BY

no

2022-01-12 14:32:51

BMC Public Health. 2005 Apr 19; 5:40

PMC1112602

15836788

1471-2229-5-6-1

Figure 1 Alignment of the predicted amino acid sequences from selected Adh gene representatives. The lines indicate the groups that correspond to those in Figure 2.

CC BY

no

2022-01-12 14:24:46

BMC Plant Biol. 2005 Apr 18; 5:6

PMC1112602

15836788

1471-2229-5-6-2

Figure 2 The phylogenetic tree based on Adh gene sequences obtained by the maximum-likelihood method. The log-likelihood of the best ML tree is -3981.05. The numbers below the branches are the bootstrap values of 50% or more support. The Adh genes from legumes roughly fall into two monophyletic clades that we denoted as Clade I and Clade II.

CC BY

no

2022-01-12 14:24:46

BMC Plant Biol. 2005 Apr 18; 5:6

PMC1112602

15836788

1471-2229-5-6-3

Figure 3 Part of the simplest reconciled tree that has the lowest number of duplication and deletion events. The reconciled tree involves 24 gene duplications and 44 gene losses for a total cost of 68, and requires 40 deep coalescenses. The solid boxes indicate gene duplications that were inferred on the basis of mismatches between the gene tree and the species tree. The open boxes indicate those duplications that required multiple copies of Adh genes within the same species. The gray lines indicate the lineages that are presumed to be lost after the duplications or were not found in our analysis.

CC BY

no

2022-01-12 14:24:46

BMC Plant Biol. 2005 Apr 18; 5:6

PMC1112603

15831104

1471-2482-5-8-1

Figure 1 Correlation between age of the patients, POSSUM Physiological Score (PPS) and the postoperative course of 137 patients with gastrectomy and D2-lymphadenectomy: M = case with postoperative mortality, size of circles shows the number of cases with the same PPS.

CC BY

no

2022-01-12 14:32:32

BMC Surg. 2005 Apr 15; 5:8

PMC1112604

15865627

1472-6874-5-5-1

Figure 1 Comparison of the menstrual irregularities type of case and control groups

CC BY

no

2022-01-12 14:33:31

BMC Womens Health. 2005 May 2; 5:5

PMC1112605

15862131

1475-925X-4-29-1

Figure 1 Propagation of photons between source and detector and parameters for Modified Beer Lambert Law

CC BY

no

2022-01-12 14:35:49

Biomed Eng Online. 2005 Apr 29; 4:29

PMC1112605

15862131

1475-925X-4-29-2

Figure 2 System containing computer, control box and probe

CC BY

no

2022-01-12 14:35:49

Biomed Eng Online. 2005 Apr 29; 4:29

PMC1112605

15862131

1475-925X-4-29-3

Figure 3 Block diagram of the cwNIRS system

CC BY

no

2022-01-12 14:35:49

Biomed Eng Online. 2005 Apr 29; 4:29

PMC1112605

15862131

1475-925X-4-29-4

Figure 4 The first prototype of the "flexible" probe holding low power LED and detectors

CC BY

no

2022-01-12 14:35:49

Biomed Eng Online. 2005 Apr 29; 4:29

PMC1112605

15862131

1475-925X-4-29-5

Figure 5 Baby hat method used for optode-scalp coupling (see "Acknowledgment")

CC BY

no

2022-01-12 14:35:49

Biomed Eng Online. 2005 Apr 29; 4:29

PMC1112605

15862131

1475-925X-4-29-6

Figure 6 Summary of the filtering operation

CC BY

no

2022-01-12 14:35:49

Biomed Eng Online. 2005 Apr 29; 4:29

PMC1112605

15862131

1475-925X-4-29-7

Figure 7 Temperature increase & SNR vs. pulse repetition rate (duty ratio = 12.5%)

CC BY

no

2022-01-12 14:35:49

Biomed Eng Online. 2005 Apr 29; 4:29

PMC1112605

15862131

1475-925X-4-29-8

Figure 8 Temperature increase & SNR vs. duty ratio (pulse repetition rate = 10 Hz)

CC BY

no

2022-01-12 14:35:49

Biomed Eng Online. 2005 Apr 29; 4:29

PMC1112605

15862131

1475-925X-4-29-9

Figure 9 Changes in hemoglobin concentration during red blood cell addition

CC BY

no

2022-01-12 14:35:49

Biomed Eng Online. 2005 Apr 29; 4:29

PMC1112605

15862131

1475-925X-4-29-10

Figure 10 Changes in hemoglobin concentration (1), OXY and BV values (2) during the yeast test

CC BY

no

2022-01-12 14:35:49

Biomed Eng Online. 2005 Apr 29; 4:29

PMC1112605

15862131

1475-925X-4-29-11

Figure 11 Average changes in hemodynamic parameters in response to hearing screening test

CC BY

no

2022-01-12 14:35:49

Biomed Eng Online. 2005 Apr 29; 4:29

PMC1112609

15831093

1477-7525-3-25-1

Figure 1 MacDQoL present QoL and MD-specific overview items with scores shown.

CC BY

no

2022-01-12 14:36:01

Health Qual Life Outcomes. 2005 Apr 14; 3:25

PMC1112609

15831093

1477-7525-3-25-2

Figure 2 MacDQoL domain-specific item with scores shown.

CC BY

no

2022-01-12 14:36:01

Health Qual Life Outcomes. 2005 Apr 14; 3:25

PMC1112609

15831093

1477-7525-3-25-3

Figure 3 Mean weighted impact scores of MacDQoL domains.

CC BY

no

2022-01-12 14:36:01

Health Qual Life Outcomes. 2005 Apr 14; 3:25

PMC1112610

15860131

1740-3391-3-6-1

Figure 1 Daily rhythm of tryptophan blood level in the horse . Each time point represents the mean value ± SD. Φ represents the acrophase. Black and white stripes at the bottom of the graphic represent dark and light duration of the natural photoperiod.

CC BY

no

2022-01-12 14:36:21

J Circadian Rhythms. 2005 Apr 28; 3:6

PMC1112610

15860131

1740-3391-3-6-2

Figure 2 Daily rhythm of serotonin blood level in the horse . Each time point represents the mean value ± SD. Φ represents the acrophase. Black and white stripes at the bottom of the graphic represent dark and light duration of the natural photoperiod.

CC BY

no

2022-01-12 14:36:21

J Circadian Rhythms. 2005 Apr 28; 3:6

PMC1112611

15840176

1476-9255-2-3-1

Figure 1 IL-9 RT-PCR. A. Time course. PBMC were incubated for various times with OKT3, RNA was extracted, IL-9 real time RT-PCR was performed, and the mean threshold cycle (Ct) was determined. The data shown are from an experiment on one representative individual. The values are means of duplicate determinations. B. Gel electrophoresis. PBMC were incubated for 24 h with or without OKT3 and with or without Dex (10-6 M). RNA was extracted and IL-9 RT-PCR performed for 40 cycles. For each condition, duplicate PCRs were performed on cDNA from one representative individual. Products were analysed in a 2% agarose gel. The left lane contains HaeIII cut ΦX174 molecular size markers (Roche); the arrow indicates the position of the 281/271 bp markers.

CC BY

no

2022-01-12 14:35:23

J Inflamm (Lond). 2005 Apr 20; 2:3

PMC1112611

15840176

1476-9255-2-3-2

Figure 2 Concentration-response effect of Dex on IL-9 mRNA in activated PBMC. Cells were incubated with OKT3 and the stated concentration of Dex. 24 hours later, RNA was extracted and real time RT-PCR for IL-9 was performed. Data were corrected for amplification efficiency as described in Methods. Each sample was measured in duplicate. The results are expressed as the % of the response in cells not treated with Dex. The data are the mean ± SEM of four different individuals.

CC BY

no

2022-01-12 14:35:23

J Inflamm (Lond). 2005 Apr 20; 2:3

PMC1112611

15840176

1476-9255-2-3-3

Figure 3 Effect of Dex on IL-9 secretion by PBMC. Cells from 11 different individuals were treated with OKT3 and with or without 10 -6 M Dex. Culture supernatants were harvested 48 hours later and measured for IL-9 by sandwich ELISA. Data represent the mean ± SD of triplicate determinations.

CC BY

no

2022-01-12 14:35:23

J Inflamm (Lond). 2005 Apr 20; 2:3

PMC1112611

15840176

1476-9255-2-3-4

Figure 4 Effect of Dex on IL-9 secretion by CD4+ T cells. Cells from 7 different individuals were treated with OKT3 and with or without 10 -6 M Dex. Culture supernatants were harvested 48 hours later and measured for IL-9 by sandwich ELISA. Data represent the mean ± SD of triplicate determinations.

CC BY

no

2022-01-12 14:35:23

J Inflamm (Lond). 2005 Apr 20; 2:3

PMC1112612

15813970

1742-2094-2-10-1

Figure 1 TNFα and its receptors increased as demyelination proceeded. A-B: Quantification of mRNA for TNFα (A) and its receptors (B). The copies of mRNA for TNFα have increased in twi/twi (■) after PND 30, especially in the cerebellum, when compared with those in +/+ (▴). Those for TNFR1 in the cerebellum have increased in twi/twi after PND 30. The copies of mRNA for TNFR2 have increased in twi/twi only after PND 40, when compared with those for +/+, but the difference was not significant (B). Bar represents mean ± SE. * p < 0.01. C-F: TNFα immunostaining in the cerebellum. There are no TNFα-positive cells in the cerebellum of twi/twi mice at PND 20 (C). Immunoreactive cells for TNFα are progressively increased in number in the twi/twi cerebellar white matter between PND 30 (D) and PND 40 (E). In contrast, there are no TNFα positive cells in +/+ brains at any ages examined (F). Tw and W represent twi/twi and wild-type mice, respectively. The data represent mean ± SE. IG: internal granular layer, CWM: cerebellar white matter. Scale bar = 50 μm.

CC BY

no

2022-01-12 14:36:04

J Neuroinflammation. 2005 Apr 6; 2:10

PMC1112612

15813970

1742-2094-2-10-2

Figure 2 TNFα is expressed in activated microglia/macrophages in the regions where many apoptotic OLs are recognized with severe demyelination. A: Double labeling of TNFα and RCA-1 of the twi/twi cerebrum at PND 40. Arrows indicate microglia/macrophages, which are double positive for TNFα and RCA-1. B-J : In twi/twi at PND 40, there are many TNFα-positive cells (B, E) as well as many TUNEL-positive cells (C, F) in the CWM and sp5, where severe demyelination was present as judged from the results of MBP immunostaining (D, G). These apoptotic cells are immunostained with pi-GST, identified to be OLs (inset in C). In the corpus callosum (cc), there are only a few TNFα-positive cells (H) and TUNEL-positive cells (I), where demyelination was milder than in the cerebellum (J). Asterisks and double asterisks represent the same region in the serial sections. Scale bars = 50 μm (B-J), 10 μm (inset in "C").

CC BY

no

2022-01-12 14:36:04

J Neuroinflammation. 2005 Apr 6; 2:10

PMC1112612

15813970

1742-2094-2-10-3

Figure 3 A : Two twi/twi at PND 44, one ibudilast-treated and other vehicle-treated from PND 30. The ibudilast-treated twi/twi is much bigger and can walk faster and reach the feedbox, in spite of mild paralysis and spasticity in lower limbs. In contrast, the vehicle-treated twi/twi can no longer walk nor feed itself. In addition, the ibudilast-treated twi/twi has much milder tremor than the vehicle-treated twi/twi . B : The change of body weight (g) of ibudilast- and vehicle-treated twi/twi . Both twi/twi treated with ibudilast or vehicle from PND 15 (●: ibudilast-treated twi/twi , ○: vehicle-treated twi/twi ) showed less weight gain compared with those treated from PND 30 (■: ibudilast-treated twi/twi , □: vehicle-treated twi/twi ), and no prolongation of the life span. However, ibudilast-treated twi/twi showed less body weight loss than vehicle-treated twi/twi . N = 3 and 2 in ibudilast- and vehicle-treated twi/twi from PND 15. The ibudilast-treated twi/twi from PND 30 were bigger and showed milder clinical detrerioration. N = 5 and 4 in ibudilast- and vehicle-treated twi/twi from PND 30. The data represent mean ± SE.

CC BY

no

2022-01-12 14:36:04

J Neuroinflammation. 2005 Apr 6; 2:10

PMC1112612

15813970

1742-2094-2-10-4

Figure 4 Suppression of TNF mRNA expression is accompanied by inhibition of apoptosis and subsequent milder demyelination in ibudilast-treated twi/twi at PND45. A, B, E, F, I, J: CWM, C, D, G, H, K, L: sp5. A-D: In situ hybridization of TNFα mRNA in vehicle-treated twi/twi (A, C) and ibudilast-treated twi/twi (B, D). Whereas vehicle-treated twi/twi show abundant signals in CWM (A) and sp5 (C), TNFα mRNA signals are remarkably reduced in the ibudilast-treated twi/twi (B, D). Inset in "A" shows TNF-α mRNA-positive microglia. E-H: TUNEL staining of vehicle-treated twi/twi (E, G) and ibudilast-treated twi/twi (F, H). Ibudilast-treated twi/twi shows fewer TUNEL-positive cells than are seen in vehicle-treated twi/twi . Arrowheads indicate TUNEL-positive cells. I-L: LFB-PAS staining of vehicle-treated twi/twi (I, K) and ibudilast-treated twi/twi (J, L). In the ibudilast-treated twi/twi , CWM and sp5 show much milder demyelination than in vehicle-treated twi/twi . Scale bar = 100 μm (I-L), 50 μm (A-H), 10 μm (inset in "A").

CC BY

no

2022-01-12 14:36:04

J Neuroinflammation. 2005 Apr 6; 2:10

PMC1112612

15813970

1742-2094-2-10-5

Figure 5 Ibudilast-treated twi/twi show pathological improvement. Population of TUNEL-positive cells and neuropathological scores of LFB-PAS in ibudilast- (closed-boxed; N = 4) or vehicle-treated (hatched; N = 3) twi/twi . In CWM, 8 n, and sp5 of the ibudilast-treated twi/twi , the number of TUNEL-positive cells is decreased to half of those in the vehicle-treated twi/twi . They also recognized significantly milder demyelination in LFB-PAS stain. 8 n: the 8 th nerve. *p < 0.01, **p < 0.05. The error bars represented standard deviations.

CC BY

no

2022-01-12 14:36:04

J Neuroinflammation. 2005 Apr 6; 2:10

PMC1112612

15813970

1742-2094-2-10-6

Figure 6 Ibudilast surpresses proliferation of NG2-positive OL progenitors. A: Vehicle-treated twi/twi shows many NG2-positive OL progenitors. B: Ibudilast-treated twi/twi shows decreased number of NG2-positive OL progenitors. Allows: NG2-positive OL progenitors labeled with Alexa 488. Scale bar = 50 μm

CC BY

no

2022-01-12 14:36:04

J Neuroinflammation. 2005 Apr 6; 2:10

PMC1112614

15857512

1475-2875-4-21-1

Figure 1 A: Parasite densities in the six volunteers from whom parasite isolates were established. Note that parasitaemia scales are different. Closed circles indicate time points where parasite density was determined by PCR. Time points where blood samples were cultured successfully are underlined. A cross indicates time of chloroquine treatment. B: Representation of parasite generation and stage composition of a P. falciparum infection after liver release. Parasites were first detected on day 6,33. Estimates of parasite release from the liver (~24 hours, over all volunteers), duration of circulating stages (1,18 days) and adhesive stages (0,64 days) were taken from reference 24. Time of blood sampling is framed. When sampling blood the early circulating stages are isolated, i.e. blood drawn on day 8 predominantly contains first-generation parasites after liver release.

CC BY

no

2022-01-12 14:35:48

Malar J. 2005 Apr 27; 4:21

PMC1112614

15857512

1475-2875-4-21-2

Figure 2 Var gene transcription profile of NF54 ring-stage parasite cultures established on day 8 from six volunteers. The mean transcription levels ± 1 SD of primer bias-corrected and normalized values of the six cultures are shown relative to the overall mean var transcription level. Var gene name and group are indicated.

CC BY

no

2022-01-12 14:35:48

Malar J. 2005 Apr 27; 4:21

PMC1112614

15857512

1475-2875-4-21-3

Figure 3 Fold difference in var gene transcription between NF54 ring-stage parasites isolated from the same volunteer on different days. Genes are sorted by gene groups as defined in [13]. Note that the fold-change scale for volunteer 1 is different from the other panels. Vertical dashed lines mark an arbitrarily defined two-fold cut off value for biologically significant changes in var gene transcription. Experiments with volunteer 1 were repeated three times and results are shown as means ± SD.

CC BY

no

2022-01-12 14:35:48

Malar J. 2005 Apr 27; 4:21

PMC1112614

15857512

1475-2875-4-21-4

Figure 4 PfEMP1 expression in trophozoite-stage cultures of unselected 3D7 (3D7 UM ), 3D7 selected for expression of VSA SM -type IE surface antigens (3D7 SM ) and of NF54 established from six volunteers on different days after infection. A: Western blot using antibodies (αATS) targeting the acidic terminal segment (ATS), which is conserved between most PfEMP1 types. Black arrows indicate changes in protein expression between isolates of the same volunteer. B: Western blot identifying the αATS-detected 400 kDa band in the day 10 culture of volunteer 1 as PFD1235w/VAR4 using an αDBL5δ antibody. VAR4 is expressed on the surface of the 3D7 SM line selected for high immune serum recognition [17].

CC BY

no

2022-01-12 14:35:48

Malar J. 2005 Apr 27; 4:21

PMC1112614

15857512

1475-2875-4-21-5

Figure 5 Plasma recognition profiles of trophozoite-stage cultures of NF54 established from six volunteers on different days after infection. Profiles of unselected 3D7 (UM) and 3D7 selected in vitro for expression of VSA SM -type IE surface antigens (SM) are shown for comparison. Recognition was measured by flow cytometry using IgG from Ghanaian adults and children (see Materials and Methods). Filled boxes indicate mean FITC-fluorescenceindex (MFI)abovea cut-off defined by the mean + 2 standard deviations of 8 Danish control plasma.

CC BY

no

2022-01-12 14:35:48

Malar J. 2005 Apr 27; 4:21

PMC1112615

15819978

1465-9921-6-30-1

Figure 1 Histological appearance of murine lung 24 hours following final ovalbumin challenge. H&E staining of (A) saline sensitised/challenged and (B) ovalbumin sensitised/challenged airways at 24 hours after final challenge. Control airways did not show any inflammatory cell infiltration. A mixed inflammatory cell infiltrate can be seen around ovalbumin sensitised/challenged airways, particularly in those adjacent to blood vessels where margination and diapedesis of cells are seen. H&E staining of typical areas of parenchyma from (C) saline sensitised/challenged and (D) ovalbumin sensitised/challenged mice are similar, demonstrating the lack of interstitial inflammation produced by this model. PAS/Alcian Blue staining of (E) saline sensitised/challenged and (F) ovalbumin sensitised/challenged airways at 24 hours after final challenge. Most of the epithelial cells are replaced by blue/purple staining goblet cells in ovalbumin sensitised/challenged airways. Scale bar represents 50 μm.

CC BY

no

2022-01-12 14:35:25

Respir Res. 2005 Apr 8; 6(1):30

PMC1112615

15819978

1465-9921-6-30-2

Figure 2 Increased sub-epithelial collagen deposition in the airways of ovalbumin sensitised and challenged mice. MSB staining of representative airways from each treatment group at 12 days after final challenge. (A) saline sensitisation/saline challenge (B) saline sensitisation/ovalbumin challenge (C) ovalbumin sensitisation/saline challenge (D) ovalbumin sensitisation/ovalbumin challenge. Increased blue-staining sub-epithelial collagen is seen in the ovalbumin sensitised/challenged airway compared with the three controls, which have similar appearances. Scale bar represents 50 μm.

CC BY

no

2022-01-12 14:35:25

Respir Res. 2005 Apr 8; 6(1):30

PMC1112615

15819978

1465-9921-6-30-3

Figure 3 The effect of different sensitisation/challenge combinations on sub-epithelial collagen deposition. The area of sub-epithelial collagen/unit lumen perimeter was quantitated in mouse airways using image analysis of MSB stained sections. (A) Mean values for all suitable airways in each experimental group were compared. The numbers of mice/total airways analysed per group were: saline sensitised/saline challenged (NS/NS) 8/89, saline sensitised/ovalbumin challenged (NS/Ova) 9/95, ovalbumin sensitised/saline challenged (Ova/NS) 7/88 and ovalbumin sensitised/ovalbumin challenged (Ova/Ova) 11/147. (B) Mean values for all suitable larger (perimeter>1000 μm) airways in the same mice were also compared. The numbers of airways analysed were NS/NS 48, NS/Ova 30, Ova/NS 22 and Ova/Ova 39. * p < 0.01 compared with the mean of the controls.

CC BY

no

2022-01-12 14:35:25

Respir Res. 2005 Apr 8; 6(1):30

PMC1112615

15819978

1465-9921-6-30-4

Figure 4 The effect of ovalbumin sensitisation and challenge on airway sub-epithelial deposition of type III collagen. Immunostaining of representative saline sensitised/challenged (A) and ovalbumin sensitised/challenged (B) airways for type III collagen 12 days after final challenge. In control lungs staining was localised to the alveolar septa, airway and vessel walls. Airway sub-epithelial staining was increased following ovalbumin sensitisation/ challenge. Scale bar represents 50 μm.

CC BY

no

2022-01-12 14:35:25

Respir Res. 2005 Apr 8; 6(1):30

PMC1112615

15819978

1465-9921-6-30-5

Figure 5 The effect of ovalbumin sensitisation and challenge on airway sub-epithelial proteoglycan and decorin deposition. Cupromeronic Blue staining of representative airways from (A) control and (B) ovalbumin sensitised/challenged airways 12 days after final challenge. The reticular pattern of staining is seen particularly around the airway circumference in a distribution corresponding to the sub-epithelial layer. Staining is greater in ovalbumin sensitised/challenged airways. Decorin immunostaining of representative airways from (C) control and (D) ovalbumin sensitised/challenged airways at the same time point. Immunostaining is concentrated in the walls of airways and vessels and is not seen in the lung parenchyma. Immunostaining is greater in ovalbumin sensitised/challenged airways and vessels. Scale bars represent 50 μm.

CC BY

no

2022-01-12 14:35:25

Respir Res. 2005 Apr 8; 6(1):30

PMC1112615

15819978

1465-9921-6-30-6

Figure 6 The effect of ovalbumin sensitisation/challenge on sub-epithelial total proteoglycans and decorin. (A) The area of sub-epithelial proteoglycan/unit lumen perimeter was quantitated using image analysis of Cupromeronic Blue stained sections. The numbers of mice/total airways analysed per group were: Control 9/32 and Ova/Ova 10/52. (B) The area of sub-epithelial decorin/unit lumen perimeter was quantitated using decorin immunostaining. The numbers of mice/total airways analysed per group were: Control 7/40 and Ova/Ova 10/70. * p < 0.05, ** p < 0.01.

CC BY

no

2022-01-12 14:35:25

Respir Res. 2005 Apr 8; 6(1):30

PMC1127019

15833142

1471-2105-6-100-1

Figure 1 Likelihood ratios for genomic features.

CC BY

no

2022-01-12 14:24:23

BMC Bioinformatics. 2005 Apr 18; 6:100

PMC1127019

15833142

1471-2105-6-100-2

Figure 2 ROC curve for the combination of genomic features using 10-fold cross validations. The dotted line shows the empirical ROC curve, while the solid line shows the fitted ROC curve (obtained using JROCFIT). Each point on the ROC curve corresponds to sensitivity and specificity for one or a combination of more than one genomic features. d: interacting Pfam domains; g: similar GO annotations; h: homologous interactions; none: no genomic features. More than one genomic features are indicated by listing the features separated by a '+' sign.

CC BY

no

2022-01-12 14:24:23

BMC Bioinformatics. 2005 Apr 18; 6:100

PMC1127019

15833142

1471-2105-6-100-3

Figure 3 Percentage of interactions predicted true across different high-throughput data sets.

CC BY

no

2022-01-12 14:24:23

BMC Bioinformatics. 2005 Apr 18; 6:100

PMC1127019

15833142

1471-2105-6-100-4

Figure 4 Percentage of interactions predicted true in high and low confidence interactions across different high-throughput data sets.

CC BY

no

2022-01-12 14:24:23

BMC Bioinformatics. 2005 Apr 18; 6:100

PMC1127019

15833142

1471-2105-6-100-5

Figure 5 Some low confidence interactions predicted to be true by our method and confirmed by other publications. The Likelihood ratio for each interaction is indicated. Interactions with a Likelihood ratio greater than 100 are shown with a solid line, while those with a Likelihood ratio less than 10 are shown with a dashed line. (A) Interactions between proteins co-regulating the alternative splicing of Dscam exon 4 in D. menalogaster . (B) Interactions between proteins in the Lsm1-7 complex in S. cerevisiae confirmed by similar interactions found in H. sapiens .

CC BY

no

2022-01-12 14:24:23

BMC Bioinformatics. 2005 Apr 18; 6:100

PMC1127068

15850479

1471-2105-6-106-1

Figure 1 Flow chart of the quadratic regression method . The gene selection and pattern classification procedure of our quadratic regression method. y ij is the expression level; x is time; β 0 j , β 1 j , and β 2 j are the parameters of intercept, linear effect, and quadratic effect, respectively; ε ij is the random error. Among the 9 regression patterns, FLAT stands for no statistically significant differential expression over time; LU stands for linear up; LD stands for linear down; QC stands for quadratic concave; QV stands for quadratic convex; QLCU stands for quadratic linear concave up; QLCD stands for quadratic linear concave down; QLVU stands for quadratic linear convex up; QLVD stands for quadratic linear convex down.

CC BY

no

2022-01-12 14:35:10

BMC Bioinformatics. 2005 Apr 25; 6:106

PMC1127068

15850479

1471-2105-6-106-2

Figure 2 Histogram of the Shapiro-Wilk p-values for normality test . The Shapiro-Wilk statistic was applied to the olfactory receptor neuron data for normality test. The horizontal axis is the Shapiro-Wilk p-values, and the vertical axis is the corresponding percentages. This histogram indicates that most of the 3834 present genes do not have a significant departure from the normality.

CC BY

no

2022-01-12 14:35:10

BMC Bioinformatics. 2005 Apr 25; 6:106

PMC1127068

15850479

1471-2105-6-106-3

Figure 3 Flow chart of the filtering steps and quadratic regression analysis on the olfactory receptor neuron data . Our regression method is applied to the olfactory receptor neuron data. At first, Affymetrix quality controls, expressed sequence tags, and genes which have "A" calls across all chips were removed from the analysis. Nine regression patterns were identified among 3834 remaining genes (colored in red). FLAT stands for no statistically significant differential expression over time detected by the regression method; LU stands for linear up regulated regression pattern; LD stands for linear down regulated regression pattern; QC stands for quadratic concave regulated regression pattern; QV stands for quadratic convex regulated regression pattern; QLCU stands for quadratic linear concave up regulated regression pattern; QLCD stands for quadratic linear concave down regulated regression pattern; QLVU stands for quadratic linear convex up regulated regression pattern; QLVD stands for quadratic linear convex down regulated regression pattern.

CC BY

no

2022-01-12 14:35:10

BMC Bioinformatics. 2005 Apr 25; 6:106

PMC1127068

15850479

1471-2105-6-106-4

Figure 4 An illustration of the nine temporal expression patterns identified by the quadratic regression method . The horizontal axis is the log transformation of time. The vertical axis is the hybridization signals obtained from the microarrays. The blue dots are the hybridization signals. The red line or curve is the fitted regression pattern. FLAT stands for no statistically significant differential expression over time detected by the regression method; LU stands for linear up regulated regression pattern; LD stands for linear down regulated regression pattern; QC stands for quadratic concave regulated regression pattern; QV stands for quadratic convex regulated regression pattern; QLCU stands for quadratic linear concave up regulated regression pattern; QLCD stands for quadratic linear concave down regulated regression pattern; QLVU stands for quadratic linear convex up regulated regression pattern; QLVD stands for quadratic linear convex down regulated regression pattern. The corresponding gene symbols are: FLAT. Cldn11 ; LU. Gba ; LD. Col6a3 ; QC. Rab18 ; QV. unknown ; QLCU. Psmb6 ; QLCD. Hnrpa2b1 ; QLVU. Tyrobp ; QLVD. Acvr2b .

CC BY

no

2022-01-12 14:35:10

BMC Bioinformatics. 2005 Apr 25; 6:106

PMC1127068

15850479

1471-2105-6-106-5

Figure 5 Examples of genes in the comparison among regression patterns and Peddada et al.'s profiles . a. Gdp2 ; b. Ccl2 ; c. Prom1 ; d. Oazin ; e. Grik5 ; f. Ubl1 ; g. Bub3 ; h. Fut9 ; i. Phgdh . The genes in a, b, and c all have Peddada et al.'s MI profile, but are in 3 different regression patterns LU, QLCU and QLVU, the difference among the temporal profiles of these genes is the rate of increase. The genes in d, e, and f all have Peddada et al.'s UD2 profile, but are in 3 different regression patterns QLCD, LD, and QC. The genes in g, h, and i all have Peddada et al.'s UD3 profile, but are in 3 different regression patterns QC, QLCU, and QLCD. The differences among d, e, f and among g, h, i are due to the relationship among all time points and with the maximum. The horizontal axis is the log transformation of time. The blue dots are the signals. The red line or curve is the fitted regression pattern.

CC BY

no

2022-01-12 14:35:10

BMC Bioinformatics. 2005 Apr 25; 6:106