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\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline & \textbf{Haemoglobinuria Kinh N = 82} & \textbf{Healthy Kinh N = 266} & \textbf{Healthy S'tieng N = 258} \\ \hline G6PD deficiencya & 48 (58.5) & 23 (8.65) & 36 (13.95) \\ \hline Suspected malariab & 34 (41.5) \\ \hline Confirmed malariac & 21(25.6) \\ \hline Received anti-malarialsd & 14 (17) \\ \hline Harbour G6PD polymorphisme & 34 (41.5) & 14 (0.05) & 23 (0.09) \\ \hline Harbour G6PD non-synonomous mutation & 21(25.6) & 6 (0.02) & 14 (0.05) \\ \hline Harbour G6PD published mutation & 20 (24.4) & 6 (0.02) & 14 (0.05) \\ \hline \end{tabular} \end{table}
PMC2717975_table_3
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline \textbf{Marker} & \textbf{Position on chromosome 13 (bp)} & \textbf{Allele Counts} & & \textbf{Ο‡2 (1 d.f.)} & \textbf{p value} \\ \hline rs3916965 (M12) & 104901361 & C & T \\ \hline Controls & & 391 & 237 \\ \hline Schizophrenia & & 309 & 223 & 2.101 & 0.147 \\ \hline rs3916967 (M14) & 104915349 & A & G \\ \hline Controls & & 397 & 235 \\ \hline Schizophrenia & & 306 & 228 & 3.675 & 0.055 \\ \hline rs1341402 & 104913510 & C & T \\ \hline Controls & & 138 & 488 \\ \hline Bipolar & & 126 & 472 & 0.172 & 0.679 \\ \hline rs2391191 (M15) & 104917447 & A & G \\ \hline Controls & & 326 & 544 \\ \hline Schizophrenia & & 305 & 473 & 0.521 & 0.470 \\ \hline Bipolar & & 246 & 360 & 1.468 & 0.226 \\ \hline rs1935062 & 104926137 & A & C \\ \hline Controls & & 416 & 210 & 0.172 & 0.679 \\ \hline Bipolar & & 401 & 205 & 0.011 & 0.917 \\ \hline rs947267 (M18) & 104937663 & A & C \\ \hline Controls & & 502 & 368 \\ \hline Schizophrenia & & 454 & 348 & 0.203 & 0.652 \\ \hline Bipolar & & 358 & 246 & 0.362 & 0.548 \\ \hline rs778294 (M19) & 104940236 & C & T \\ \hline Controls & & 639 & 237 \\ \hline Schizophrenia & & 593 & 211 & 0.141 & 0.707 \\ \hline Bipolar & & 438 & 166 & 0.033 & 0.856 \\ \hline rs954581 & 104950267 & C & T \\ \hline Controls & & 102 & 518 \\ \hline Bipolar & & 123 & 479 & 3.221 & 0.073 \\ \hline rs778293 (M22) & 104967200 & A & G \\ \hline Controls & & 522 & 499 \\ \hline Schizophrenia & & 338 & 293 & 0.93 & 0.335 \\ \hline rs3918342 (M23) & 104983750 & C & T \\ \hline Controls & & 444 & 412 \\ \hline Schizophrenia & & 358 & 422 & 5.824 & 0.016 \\ \hline Bipolar & & 281 & 325 & 4.293 & 0.038 \\ \hline Combined & & 639 & 747 & 7.044 & 0.008 \\ \hline rs1421292 (M24) & 104996236 & A & T \\ \hline Controls & & 462 & 398 \\ \hline Schizophrenia & & 388 & 402 & 3.499 & 0.062 \\ \hline Bipolar & & 301 & 305 & 2.337 & 0.126 \\ \hline Combined & & 689 & 707 & 4.059 & 0.044 \\ \hline \end{tabular} \end{table}
PMC2717980_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline \textbf{Marker} & \textbf{Position on chromosome 12 (bp)} & \textbf{Allele Counts} & & \textbf{Ο‡2 (1 d.f.)} & \textbf{p value} \\ \hline rs2111902 (MDAO-4) & 107781213 & A & C \\ \hline Controls & & 604 & 266 \\ \hline Schizophrenia & & 522 & 226 & 0.025 & 0.875 \\ \hline rs3918346 (MDAO-5) & 107784350 & C & T \\ \hline Controls & & 655 & 221 \\ \hline Schizophrenia & & 601 & 181 & 0.976 & 0.323 \\ \hline rs3741775 (MDAO-6) & 107786069 & T & G \\ \hline Controls & & 483 & 379 \\ \hline Schizophrenia & & 418 & 354 & 0.587 & 0.444 \\ \hline \end{tabular} \end{table}
PMC2717980_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline \multicolumn{3}{c|}{\textbf{Alleles}} & \multicolumn{2}{c|}{\textbf{Estimated frequencies}} \\ \hline \textbf{M22} & \textbf{M23} & \textbf{M24} & \textbf{Controls} & \textbf{Schizophrenia} \\ \hline A & C & A & 0.145 & 0.122 \\ \hline A & T & T & 0.456 & 0.502 \\ \hline G & C & A & 0.371 & 0.330 \\ \hline G & T & A & 0.018 & 0.036 \\ \hline \end{tabular} \end{table}
PMC2717980_table_2
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|l|} \hline Orthosis & \multicolumn{2}{c|}{Component Mass (g)} & Artificial Muscles & \multicolumn{2}{c|}{Muscle Length (cm)} & \multicolumn{2}{c|}{Moment Arm Length (cm)} \\ \hline & Mean & SD & & Mean & SD & Mean & SD \\ \hline Artificial Muscle & 128 & 7 & Plantarflexor & 47.5 & 2.3 & 10.3 & 1.0 \\ \hline Load Cell & 94 & 0 & Dorsiflexor & 38.5 & 4.4 & 11.3 & 1.6 \\ \hline Blow Valve & 152 & 0 & Medial Knee Extensor & 34.0 & 5.2 & 3.2 & 0.6 \\ \hline Thigh & 1089 & 90 & Lateral Knee Extensor & 34.0 & 1.0 & 2.8 & 0.8 \\ \hline Shank & 1408 & 89 & Medial Knee Flexor & 29.0 & 3.0 & 4.0 & 1.0 \\ \hline Foot & 388 & 34 & Lateral Knee Flexor & 31.0 & 2.0 & 3.2 & 1.0 \\ \hline Total & 2884 & 134 \\ \hline \end{tabular} \end{table}
PMC2717982_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|} \hline & \multicolumn{4}{c|}{\textbf{Pearson r-value}} \\ \hline & \multicolumn{2}{c|}{\textbf{PM}} & \multicolumn{2}{c|}{\textbf{PM}FI} & \textbf{ANOVA p-value; Power} & \textbf{THSD} \\ \hline & \textbf{\textbf{Mean}} & \textbf{\textbf{SE}} & \textbf{\textbf{Mean}} & \textbf{\textbf{SE}} \\ \hline Orthosis Ankle Torque & 0.85 & 0.05 & 0.76 & 0.11 & p = 0.28 P = 0.14 \\ \hline Orthosis Ankle Power & 0.53 & 0.11 & 0.72 & 0.07 & *p = 0.04 P = 0.70 & \textbf{PM}FI > \textbf{PM} \\ \hline Orthosis Knee Torque & -0.01 & 0.21 & 0.55 & 0.04 & p = 0.09 P = 0.42 \\ \hline Orthosis Knee Power & -0.03 & 0.06 & 0.17 & 0.11 & p = 0.33 P = 0.12 \\ \hline Ankle Angle & 0.49 & 0.13 & 0.74 & 0.04 & *p = 0.05 P = 0.80 & \textbf{PM}FI > \textbf{PM} \\ \hline Knee Angle & 0.90 & 0.03 & 0.95 & 0.03 & p = 0.17 P = 0.24 \\ \hline Hip Angle & 0.98 & 0.01 & 0.98 & 0.00 & p = 0.71 P = 0.06 \\ \hline \end{tabular} \end{table}
PMC2717982_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|l|l|l|} \hline & & \multicolumn{6}{c|}{\textbf{Work (J/kg)}} \\ \hline & & \multicolumn{2}{c|}{\textbf{Without}} & \multicolumn{2}{c|}{\textbf{Orthosis PM}} & \multicolumn{2}{c|}{\textbf{Orthosis PM}FI} & \textbf{ANOVA p-value; Power} & \textbf{THSD} \\ \hline & & \textbf{\textbf{\textbf{Mean}}} & \textbf{\textbf{\textbf{SE}}} & \textbf{\textbf{\textbf{Mean}}} & \textbf{\textbf{\textbf{SE}}} & \textbf{\textbf{\textbf{Mean}}} & \textbf{\textbf{\textbf{SE}}} \\ \hline \multirow{2}{*}{ANKLE} & Pos. & 0.21 & 0.03 & 0.18 & 0.03 & 0.21 & 0.02 & p = 0.52 P = 0.11 \\ \hline Neg. & 0.25 & 0.03 & 0.10 & 0.02 & 0.11 & 0.02 & *p = 0.03 P = 0.76 & PM < WO PMFI < WO \\ \hline \multirow{2}{*}{KNEE} & Pos. & 0.05 & 0.02 & 0.06 & 0.02 & 0.09 & 0.03 & p = 0.65 P = 0.09 \\ \hline Neg. & 0.31 & 0.02 & 0.04 & 0.02 & 0.06 & 0.03 & *p = 0.003 P = 0.99 & PM < WO PMFI < WO \\ \hline \end{tabular} \end{table}
PMC2717982_table_2
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline \textbf{Measure} & \multicolumn{3}{c|}{\textbf{Mean $\pm$ standard deviation}} \\ \hline & \textbf{0–2 min} & \textbf{2–4 min} & \textbf{4–6 min} \\ \hline Distance (m)* & 100.5 $\pm$ 46.1 (18 – 198) & 94.1 $\pm$ 45.6 (23 – 195) & 88.7 $\pm$ 49.1 (14 – 192) \\ \hline Rest time** (s) & 5.1 $\pm$ 11.6 (0 – 31) & 8.4 $\pm$ 16.1 (0 – 44) & 31.7 $\pm$ 26.4 (0 – 80) \\ \hline Gait Speed (cm/s)* & 92.2 $\pm$ 39.3 (23.3 – 181.9) & 91.0 $\pm$ 39.1 (25.8 – 175.2) & 88.7 $\pm$ 39.3 (16.6 – 172.4) \\ \hline Gait Symmetry Ratio & 1.48 $\pm$ 0.49 (1.04 – 2.60) & 1.46 $\pm$ 0.46 (1.02 – 2.60) & 1.61 $\pm$ 1.16 (1.03 – 6.67) \\ \hline \end{tabular} \end{table}
PMC2717983_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline & & \multicolumn{2}{c|}{\textbf{HIV-1 IN}} & \multicolumn{2}{c|}{\textbf{ASV IN}} \\ \hline \textbf{Cofactor} & \textbf{Assay} & \textbf{60'} & \textbf{120'} & \textbf{15'} & \textbf{30'} \\ \hline \multirow{3}{*}{Mn++} & a. Fluorescence & 61 & 78 & 126 & 155 \\ \hline b. Gel & 2.5 & 3.4 & 4.2 & 4.5 \\ \hline Fold Difference (a/b) & 24.4 & 23 & 30 & 34 \\ \hline \multirow{3}{*}{Mg++} & c. Fluorescence & 21.4 & 26.5 & 26.3 & 31.3 \\ \hline d. Gel* & -- & 2.6* & -- & 1.3* \\ \hline Fold Difference (c/d) & & 10 & & 24 \\ \hline \end{tabular} \end{table}
PMC2717984_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|l|l|l|} \hline \textbf{Library} & \textbf{Sequence direction} & \textbf{Number of clones sequenced} & \multicolumn{2}{c|}{\textbf{Chromatographs checked (EST number)}} & \multicolumn{2}{c|}{\textbf{Sequence quality checked (EST number)}} & \textbf{Average length (bp)} & \textbf{Number of contigs b} & \textbf{Number of singletons} \\ \hline & & & \textbf{\textbf{Good quality}} & \textbf{\textbf{Poor quality} a} & \textbf{\textbf{Good quality}} & \textbf{Poor quality} \\ \hline Plasmid & 3'-end & 1,152 & 764 & 388 & 722 & 42 & 441 \\ \hline Uni-ZAP RX & 5'-end & 13,848 & 12,302 & 1,546 & 11,797 & 505 & 674 \\ \hline Total & -- & 15,000 & 13,066 & 1,934 & 12,519 & 547 & 656 & 1,157 & 1,738 \\ \hline \end{tabular} \end{table}
PMC2717985_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline \textbf{Contig Identification} & \textbf{Putative identities} & \textbf{Number of ESTs} & \textbf{Length (bp)} & \textbf{\% Total} & \textbf{E-value} \\ \hline Contig [0038] & Trypsin-like protease T25 precursor & 525 & 942 & 4.1 & 3e-148 \\ \hline Contig [0026] & Chymotrypsin-like serine protease & 197 & 1,321 & 1.5 & 1e-149 \\ \hline Contig [0062] & Trypsin-like serine protease & 132 & 1,076 & 1.0 & 1e-131 \\ \hline Contig [0074] & Unknown & 131 & 824 & 1.04 & -- \\ \hline Contig [0059] & Trypsin-like serine protease & 129 & 1,497 & 1.0 & 1e-117 \\ \hline Contig [0076] & Trypsin-like serine protease & 129 & 1,133 & 1.0 & 1e-148 \\ \hline Contig [0077] & Unknown & 97 & 652 & 0.77 & -- \\ \hline Contig [0060] & Unknown & 94 & 1,218 & 0.75 & -- \\ \hline Contig [0125] & Ribosomal protein s13 & 87 & 888 & 0.69 & 1e-79 \\ \hline Contig [0092] & Trypsin-like serine protease & 80 & 1,238 & 0.63 & 1e-149 \\ \hline Contig [0102] & Unknown & 80 & 800 & 0.63 & -- \\ \hline Contig [0040] & Thymosin isoform 1 & 78 & 1,447 & 0.62 & 1e-80 \\ \hline Contig [0243] & Trypsin-like serine protease & 78 & 701 & 0.62 & 1e-120 \\ \hline Contig [0034] & Unkown & 76 & 567 & 0.60 & 1e-60 \\ \hline Contig [0124] & Pancreatic triacylglycerol lipase & 75 & 1,263 & 0.59 & 1e-99 \\ \hline Contig [0426] & Chymotrypsin-like serine protease & 73 & 1,439 & 0.58 & 1e-129 \\ \hline Contig [0146] & Unknown & 71 & 839 & 0.56 & -- \\ \hline Contig [0997] & Unknown & 71 & 574 & 0.56 & -- \\ \hline Contig [0013] & Unknown & 68 & 1,244 & 0.54 & -- \\ \hline Contig [0175] & Phosphate mannosyltransferase & 65 & 1,121 & 0.51 & 1e-20 \\ \hline \end{tabular} \end{table}
PMC2717985_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline \textbf{pPAU1 plasmid CDS} & \textbf{Protein} & \textbf{Organism} & \textbf{Score} & \textbf{E-value} \\ \hline pPA0001 & IS21 family transposase & Yersinia pestis Angola & 357 & 8.00E-097 \\ \hline pPA0002 & hypothetical protein YPMT1.86c – putative transposase & Yersinia pestis CO92 & 101 & 1.00E-019 \\ \hline pPA0003 & putative integrase & Yersinia pestis FV-1 & 331 & 6.00E-089 \\ \hline pPA0004 & hypothetical protein & Pasteurella pneumotropica & 43.5 & 0.035 \\ \hline pPA0005 & hypothetical protein PROPEN_02818 & Proteus penneri ATCC 35198 & 206 & 4.00E-051 \\ \hline pPA0006 & hypothetical protein HCM2.0001c & Salmonella enterica subsp enterica serovar Typhi str. CT18 & 66.2 & 5.00E-009 \\ \hline pPA0007 & replication protein repA & Escherichia coli & 220 & 2.00E-055 \\ \hline pPA0008 & hypothetical protein plu0861 & Photorhabdus luminescens subsp. laumondii TTO1 & 162 & 4.00E-038 \\ \hline pPA0010 & hypothetical protein plu0862 & Photorhabdus luminescens subsp. laumondii TTO1 & 295 & 5.00E-078 \\ \hline pPA0011 & NO HITS & NO HITS \\ \hline pPA0012 & NO HITS & NO HITS \\ \hline pPA0013 & replication protein repA & Escherichia coli & 342 & 5.00E-092 \\ \hline pPA0014 & NO HITS & NO HITS \\ \hline pPA0016 & replication protein repA & Escherichia coli & 342 & 5.00E-092 \\ \hline pPA0017 & hypothetical protein HCM2.0001c & Salmonella enterica subsp. enterica serovar Typhi str. CT18 & 114 & 2.00E-023 \\ \hline pPA0018 & resolvase & Yersinia pestis biovar Orientalis strain IP275 & 236 & 4.00E-060 \\ \hline pPA0019 & hypothetical protein Gura_3302 & Geobacter uraniireducens Rf4 & 370 & 2.00E-100 \\ \hline pPA0020 & transposase & Yersinia pestis Antiqua & 1561 & 0 \\ \hline pPA0021 & putative transposase & Yersinia pestis CO92 & 149 & 5.00E-034 \\ \hline pPA0022 & hypothetical protein pG8786_001 & Yersinia pestis & 340 & 1.00E-091 \\ \hline pPA0023 & transposase & Yersinia pestis Pestoides F & 365 & 5.00E-099 \\ \hline pPA0024 & putative transposase & Yersinia pestis CO92 & 117 & 2.00E-024 \\ \hline pPA0025 & putative transposase & Yersinia pestis CO92 & 860 & 0 \\ \hline pPA0026 & transposase & Yersinia pestis Antiqua & 112 & 8.00E-023 \\ \hline pPA0027 & putative transposase & Yersinia pestis CO92 & 124 & 2.00E-026 \\ \hline pPA0028 & putative transposase & Yersinia pestis CO92 & 233 & 3.00E-059 \\ \hline pPA0029 & putative transposase & Yersinia pestis CO92 & 52.8 & 6.00E-005 \\ \hline \end{tabular} \end{table}
PMC2717986_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|} \hline \textbf{Feature} & \textbf{P. asymbiotica ATC43949} & \textbf{P. luminescens TTO1} \\ \hline Chromosome size (base pairs) & 5,064,808 & 5,688,987 \\ \hline G+C(\%) & 42.2 & 42.80 \\ \hline Average CDS length & 956 & 985 \\ \hline Protein-coding sequences (CDS) & 4403 & 4905 \\ \hline Conserved with assigned function & 2678 (60.82\%) & 2666 (54.35\%) \\ \hline Conserved with unknown function & 1725 (39.18\%) & 2239 (45.63\%) \\ \hline tRNA genes & 81 & 85 \\ \hline \end{tabular} \end{table}
PMC2717986_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|} \hline \textbf{Function} \\ \hline Pathogenicity/adaptation & 325 (7.4\%) \\ \hline Energy metabolism & 64 (1.5\%) \\ \hline DNA replication/transcription/restriction modification & 329 (7.5\%) \\ \hline Transmembrane/outer membrane & 528 (12\%) \\ \hline Stable RNA & 49 (1.1\%) \\ \hline Degradation of large molecules & 73 (1.6\%) \\ \hline Degradation of small molecules & 72 (1.6\%) \\ \hline Central/Intermediary/miscellaneous metabolism & 797 (18.1\%) \\ \hline Hypothetical protein & 1733 (39.28\%) \\ \hline Regulation & 135 (3\%) \\ \hline Pseudogenes & 2 (0.05\%) \\ \hline Transposons and phage & 296 (6.7\%) \\ \hline \end{tabular} \end{table}
PMC2717986_table_2
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline \textbf{Locus} & \textbf{Species} & \textbf{Gene Region} & \textbf{Size (Kb)} & \textbf{Products of interest} \\ \hline 1 & P. luminescens & plu0179-plu0190 & 8.5 & Carbapenem biosynthesis operon \\ \hline 2 & P. luminescens & plu0404-plu0419 & 14.3 & Fimbrial proteins, adhesin \\ \hline 3 & P. luminescens & plu0525-plu0541 & 16 & Hemolysins \\ \hline 4 & P. luminescens & plu0545-plu0549 & 16.6 & Hemolysins \\ \hline 5 & P. luminescens & plu0634-plu0643 & 14.2 & Hemolysins, peptidase \\ \hline 6 & P. luminescens & plu0751-plu0767 & 20 & Proteins involved in antibiotic synthesis \\ \hline 7 & P. luminescens & plu0777-plu0793 & 18 & Fimbrial proteins \\ \hline 8 & P. luminescens & plu0802-plu0808 & 12.8 & Tc Insecticidal toxins \\ \hline 9 & P. luminescens & plu0887-plu0900 & 20.7 & Pyocins, proteins involved in antibiotic synthesis \\ \hline 10 & P. luminescens & plu0917-plu0925 & 8 & Lux-R transcriptional regulators \\ \hline 11 & P. luminescens & plu0961-plu0968 & 29 & Tc Insecticidal toxins \\ \hline 12 & P. luminescens & plu0991-plu0994 & 3.7 & Adhesin \\ \hline 13 & P. luminescens & plu1030-plu1059 & 27.6 & Pili operon \\ \hline 14 & P. luminescens & plu1063-plu1113 & 51 & Peptide synthetase, phage, transposable elements \\ \hline 15 & P. luminescens & plu1204-plu1224 & 29.6 & Proteins involved in antibiotic synthesis, transposable elements \\ \hline 16 & P. luminescens & plu1408-plu1413 & 6.7 & Hemolysins \\ \hline 17 & P. luminescens & plu1514-plu1515 & 2.2 & Proteins involved in tetracycline resistance \\ \hline 18 & P. luminescens & plu1536-plu1537 & 1.3 & Similar to Bt Insecticidal toxin \\ \hline 19 & P. luminescens & plu2188-plu2200 & 14.1 & Proteins involved in antibiotic synthesis \\ \hline 20 & P. luminescens & plu2213-plu2223 & 15.3 & Nematicidal protein \\ \hline 21 & P. luminescens & plu2903-plu2960 & 33.6 & Phage \\ \hline 22 & P. luminescens & plu3124-plu3129 & 6.2 & Proteins involved in toxin secretion \\ \hline 23 & P. luminescens & plu3423-plu3489 & 47.5 & Phage \\ \hline 24 & P. luminescens & plu3520-plu3535 & 46.5 & Proteins involved in antibiotic synthesis \\ \hline 25 & P. luminescens & plu3667-plu3669 & 2.4 & RTX toxins \\ \hline 26 & P. luminescens & plu3915-plu3925 & 13 & Proteins involved in antibiotic synthesis \\ \hline 27 & P. luminescens & plu4165-plu4175 & 15.3 & Tc Insecticidal toxins TccB1, TccA1, pyocins \\ \hline 28 & P. luminescens & plu4182-plu4186 & 9.1 & Tc Insecticidal toxins TccC6 \\ \hline 29 & P. luminescens & plu4187-plu4197 & 11.4 & Anthraquinone biosynthesis \\ \hline 30 & P. luminescens & plu4234-plu4243 & 10.5 & Photopexin A & B \\ \hline 31 & P. luminescens & plu4488 & 2.8 & Insecticidal toxins TccC7 \\ \hline 32 & P. luminescens & plu4621-plu4630 & 14.6 & Siderophore biosynthesis operon \\ \hline 33 & P. luminescens & plu4812-plu4830 & 17.1 & Lipopolysaccharide biosynthesis \\ \hline 34 & P. asymbiotica & pau00446-pau00458 & 21.2 & Hemolysin, Proteins involved in antibiotic synthesis \\ \hline 35 & P. asymbiotica & pau00704-pau00699 & 8.3 & Fucose operon \\ \hline 36 & P. asymbiotica & pau00881-pau00897 & 23.6 & Tc Insecticidal toxin TccC3 \\ \hline 37 & P. asymbiotica & pau00911-pau00921 & 18.7 & Fatty acid biosynthesis operon \\ \hline 38 & P. asymbiotica & pau01194-pau01201 & 16.8 & Proteins involved in antibiotic synthesis \\ \hline 39 & P. asymbiotica & pau01335-pau01351 & 20.1 & RTX toxins \\ \hline 40 & P. asymbiotica & pau02124-pau02142 & 16.3 & Insecticidal toxin TccZ \\ \hline 41 & P. asymbiotica & pau02212-pau02264 & 88.7 & Syringomycin synthetase, insecticidal toxin, lectin \\ \hline 42 & P. asymbiotica & pau02551 & 4.6 & Similar to syringomycin synthetase \\ \hline 43 & P. asymbiotica & pau04327-pau04342 & 18.3 & Lipopolysaccharide biosynthesis \\ \hline \end{tabular} \end{table}
PMC2717986_table_3
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline \textbf{Locus tag} & \textbf{Protein} & \textbf{Organism} & \textbf{Score} & \textbf{E-value} \\ \hline pau03443 & Hypothetical \textbf{Protein} YPK_0252 & Yersinia pseudotuberculosis & 44.3 & 0.004 \\ \hline pau03444 & hypothetical protein A55_B0283 & Vibrio cholerae & 97.1 & 5.00E-019 \\ \hline pau03445 & putative adhesion protein & Vibrio parahaemolyticus & 152 & 1.00E-035 \\ \hline pau03446 & hypothetical protein A55_B0283 & Vibrio cholerae & 263 & 5.00E-069 \\ \hline pau03447 & hypothetical protein A59_1855 & Vibrio cholerae & 77 & 5.00E-013 \\ \hline pau03448 & peptidoglycan-associated lipoprotein & Vibrio cholerae & 251 & 1.00E-065 \\ \hline pau03449 & putative adhesion protein & Vibrio parahaemolyticus & 378 & 9.00E-104 \\ \hline pau03450 & putative type III secretion system apparatus protein VcrD2 & Vibrio parahaemolyticus & 686 & 0 \\ \hline pau03451 & hypothetical protein A55_B0283 & Vibrio cholerae & 157 & 2.00E-037 \\ \hline pau03452 & hypothetical protein A55_B0283 & Vibrio cholerae & 169 & 6.00E-041 \\ \hline pau03453 & putative adhesion protein & Vibrio parahaemolyticus & 87 & 5.00E-016 \\ \hline pau03454 & hypothetical protein VPA1359 & Vibrio parahaemolyticus & 164 & 2.00E-039 \\ \hline pau03455 & hypothetical protein VCB_002823 & Vibrio cholerae & 107 & 5.00E-022 \\ \hline pau03456 & hypothetical protein A55_B0283 & Vibrio cholerae & 169 & 8.00E-041 \\ \hline pau03457 & putative type III secretion system translocon protein VopB2 & Vibrio parahaemolyticus & 278 & 9.00E-074 \\ \hline pau03458 & putative adhesion protein & Vibrio parahaemolyticus & 239 & 8.00E-062 \\ \hline pau03459 & putative adhesion protein & Vibrio parahaemolyticus & 253 & 4.00E-066 \\ \hline pau03460 & putative two-component response regulator & Vibrio parahaemolyticus & 174 & 2.00E-042 \\ \hline pau03461 & peptidoglycan-associated lipoprotein & Vibrio cholerae & 87 & 5.00E-016 \\ \hline pau03462 & peptidoglycan-associated lipoprotein & Vibrio cholerae & 206 & 6.00E-052 \\ \hline pau03463 & putative adhesion protein & Vibrio parahaemolyticus & 88.2 & 2.00E-016 \\ \hline pau03464 & peptidoglycan-associated lipoprotein & Vibrio cholerae & 117 & 3.00E-025 \\ \hline pau03465 & DNA topoisomerase I & Vibrio cholerae & 84 & 4.00E-015 \\ \hline pau03466 & putative type III secretion apparatus protein & Vibrio parahaemolyticus & 101 & 2.00E-020 \\ \hline pau03467 & ATPase, histidine kinase-, DNA gyrase B-, and HSP90-like domain containing protein & Tetrahymena thermophila & 40.8 & 0.043 \\ \hline pau03468 & putative adhesion protein & Vibrio parahaemolyticus & 88.2 & 2.00E-016 \\ \hline pau03469 & Flagellar biosynthesis/type III secretory pathway ATPase & Vibrio cholerae & 696 & 0 \\ \hline pau03470 & putative type III secretion system apparatus protein VscC2 & Vibrio parahaemolyticus & 639 & 0 \\ \hline pau03471 & NO HITS & NO HITS \\ \hline pau03472 & DNA topoisomerase I & Vibrio cholerae & 217 & 3.00E-055 \\ \hline pau03473 & putative type III secretion system apparatus protein VscR2 & Vibrio parahaemolyticus & 226 & 4.00E-058 \\ \hline pau03474 & hypothetical protein A55_2001 & Vibrio cholerae & 89.7 & 8.00E-017 \\ \hline \end{tabular} \end{table}
PMC2717986_table_4
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|l|l|} \hline & & & \multicolumn{2}{c|}{\textbf{GK vs WKY}} & \multicolumn{2}{c|}{\textbf{STZ vs WKY}} & \multicolumn{2}{c|}{\textbf{STZ vs GK}} \\ \hline \textbf{Gene Symbol} & \textbf{Gene description} & \textbf{Genbank} & \textbf{\textbf{\textbf{TR}}} & \textbf{\textbf{\textbf{p-value}}} & \textbf{\textbf{\textbf{TR}}} & \textbf{\textbf{\textbf{p-value}}} & \textbf{\textbf{\textbf{TR}}} & \textbf{\textbf{\textbf{p-value}}} \\ \hline \multicolumn{2}{c|}{Human 3q23-q29} \\ \hline Bdh & 3-hydroxybutyrate dehydrogenase & NM_053995 & +1.3 & Ns & -1.2 & Ns & -1.6 & 0.007 \\ \hline Centb2 & Centaurin beta 2 & BM389190 & -1.4 & Ns & 1.0 & Ns & +1.3 & 0.047 \\ \hline Clcn2 & Chloride channel 2 & NM_017137 & +1.2 & Ns & -1.1 & Ns & -1.4 & 0.038 \\ \hline Cldn16 & Claudin 16 & NM_131905 & -1.1 & Ns & -1.6 & 0.002 & -1.4 & 0.01 \\ \hline Dgkg & Diacylglycerol kinase gamma & NM_013126 & +1.2 & Ns & +1.6 & 0.025 & +1.3 & Ns \\ \hline Dnajb11 & DnaJ (Hsp40) subfamily B11 & BI295873 & 1.0 & Ns & -1.3 & 0.043 & -1.3 & Ns \\ \hline Eif4g1 & Eukaryotic translation initiation factor & BC098868 & +1.1 & Ns & -1.2 & Ns & -1.4 & 0.011 \\ \hline Fad104 & FAD104 (predicted) & AI176320 & +1.3 & Ns & -1.3 & 0.05 & -1.7 & 5 Γ— 10-4 \\ \hline Fam43a & Family with sequence similarity 43A & BE108405 & -1.1 & Ns & -1.7 & 0.017 & -1.5 & Ns \\ \hline Hrg & Histidine-rich glycoprotein & NM_133428 & -1.2 & Ns & +2.0 & 0.034 & +2.5 & 0.007 \\ \hline \multirow{2}{*}{Mfn1} & Mitofusin 1 & AI169627 & 1.0 & Ns & +1.7 & 0.046 & +1.7 & 0.035 \\ \hline & AA943135 & 1.0 & Ns & +1.5 & 0.018 & +1.5 & 0.009 \\ \hline Ncbp2 & Nuclear cap binding protein subunit 2 & BI282103 & +1.3 & Ns & -1.5 & 0.046 & -2 & 0.002 \\ \hline Pld1 & Phospholipase D1 & U69550 & -1.3 & Ns & -1.8 & 0.036 & -1.4 & Ns \\ \hline Pigx & Subunit of GPI-mannosyltransferase & AI172192 & +1.3 & Ns & 1.0 & Ns & -1.3 & 0.043 \\ \hline Rbp1 & Retinol binding protein 1 & NM_012733 & 1.0 & Ns & +2.3 & 3 Γ— 10-4 & +2.2 & 3 Γ— 10-4 \\ \hline Siat1 & Sialyltransferase 1 & M83143 & 1.0 & Ns & -1.6 & 0.002 & -1.6 & 0.001 \\ \hline Slc2a2 & Solute carrier family 2 member 2 (Glut2) & NM_012879 & +3.0 & 5 Γ— 10-4 & +3.6 & 1 Γ— 10-4 & +1.2 & Ns \\ \hline Ssr3 & Signal sequence receptor gamma & NM_031120 & -1.2 & Ns & +1.3 & Ns & +1.6 & 0.003 \\ \hline Zbed4 & Zinc finger, BED domain containing 4 & AI170289 & -1.1 & Ns & -1.3 & 0.046 & -1.2 & Ns \\ \hline --- & Similar to protein NP_079596 & AI412011 & +1.4 & Ns & -1.5 & 0.044 & -2.1 & 0.001 \\ \hline \multicolumn{2}{c|}{Human 7q32.3-q33} \\ \hline Akr1b4 & Aldo-keto reductase family 1B4 & NM_012498 & 1.0 & Ns & +2.2 & Ns & +2.1 & 0.024 \\ \hline Akr1b8 & Aldo-keto reductase family 1B8 & NM_173136 & -6.2 & 6 Γ— 10-5 & +1.4 & Ns & +8.5 & 8 Γ— 10-6 \\ \hline Slc35b4 & Solute carrier family 35 member B4 & XM_216122 & +1.2 & Ns & -1.1 & Ns & -1.4 & 0.010 \\ \hline \multicolumn{2}{c|}{Human 18q12-q23} \\ \hline Acaa2 & Acetyl-Coenzyme A acyltransferase 2 & NM_130433 & -1.6 & 0.041 & -1.3 & Ns & +1.2 & Ns \\ \hline Brunol4 & RNA binding protein bruno-like 4 & AW530502 & +1.1 & Ns & +1.3 & 0.036 & +1.2 & Ns \\ \hline Cndp1 & Carnosinase 1 & AI231438 & 1.0 & Ns & -3.4 & 3 Γ— 10-5 & -3.5 & 8 Γ— 10-6 \\ \hline Cndp2 & Carnosinase 2 & BI279729 & +1.1 & Ns & -1.3 & 0.042 & -1.4 & 0.01 \\ \hline G0S2 & Putative lymphocyte G0/G1 switch gene & AI406939 & +1.3 & Ns & -1.6 & Ns & -2.1 & 0.004 \\ \hline Mapk4 & Mitogen-activated protein kinase 4 & BG378232 & +1.3 & Ns & +1.5 & 0.023 & +1.2 & Ns \\ \hline Mep1b & meprin 1 beta (endopeptidase-2) & NM_013183 & 1.0 & Ns & -1.4 & 0.042 & -1.4 & 0.050 \\ \hline Pqlc1 & PQ loop repeat containing 1 & AI228284 & +1.6 & 0.044 & +1.7 & 0.011 & +1.1 & Ns \\ \hline \multirow{2}{*}{Slc14a2} & Solute carrier family 14, member 2 & NM_019347 & -1.1 & Ns & +1.5 & 0.020 & +1.7 & 0.005 \\ \hline & AF042167 & -1.1 & Ns & +1.4 & Ns & +1.6 & 0.035 \\ \hline \multicolumn{2}{c|}{Human 20p12.3-p13} \\ \hline Cdc25b & Cell division cycle 25 homolog B & NM_133572 & +1.2 & Ns & +1.6 & 0.028 & +1.4 & Ns \\ \hline Prnp & Prion protein & NM_012631 & +1.6 & 0.029 & +1.1 & Ns & -1.5 & 0.030 \\ \hline \end{tabular} \end{table}
PMC2717999_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|l|l|l|} \hline & & & & \multicolumn{2}{c|}{\textbf{GK vs WKY}} & \multicolumn{2}{c|}{\textbf{STZ-WKY vs WKY}} & \multicolumn{2}{c|}{\textbf{STZ-WKY v GK}} \\ \hline \textbf{Human Ensembl} & \textbf{Description} & \textbf{Symbol} & \textbf{Rat Ensembl} & \multirow{2}{*}{\textbf{\textbf{\textbf{TR}}}} & \multirow{2}{*}{\textbf{\textbf{\textbf{p-value}}}} & \multirow{2}{*}{\textbf{\textbf{\textbf{TR}}}} & \multirow{2}{*}{\textbf{\textbf{\textbf{p-value}}}} & \multirow{2}{*}{\textbf{\textbf{\textbf{TR}}}} & \multirow{2}{*}{\textbf{\textbf{\textbf{p-value}}}} \\ \hline \textbf{(ENSG00000)} & & & \textbf{(ENSRNO G000000)} \\ \hline Human 3q23 \\ \hline 175066 & Glycerol kinase 5 & GK5 & 10942 & 1.00 & Ns & 0.66 & 0.026 & 0.67 & 2 Γ— 10-3 \\ \hline 114120 & Solute carrier family 25, member 36 & SLC25A36 & 39085 & 1.28 & Ns & 1.54 & 4 Γ— 10-3 & 1.21 & Ns \\ \hline 175093 & SPRY domain-containing SOCS box protein 4 & SPSB4 & 12862 & 0.78 & Ns & 0.37 & 5 Γ— 10-3 & 0.47 & 0.013 \\ \hline 114126 & Transcription factor Dp-2 (E2F dimerization partner 2) & TFDP2 & 11241 & 0.76 & Ns & 1.56 & Ns & 2.04 & Ns \\ \hline 114127 & 5'-3' exoribonuclease 1 & XRN1 & 10027 & 0.71 & Ns & 0.66 & 0.030 & 0.93 & Ns \\ \hline 177311 & Zinc finger and BTB domain- containing protein 38 & ZBTB38 & 12386 & 1.08 & Ns & 1.27 & 0.026 & 1.17 & Ns \\ \hline 206250 & Protein coding sequence & - & 22555 & 0.81 & Ns & 0.82 & Ns & 1.01 & Ns \\ \hline Human 7q33 \\ \hline 146856 & ATP/GTP binding protein-like 3 & AGBL3 & 10397 & 0.95 & Ns & 0.52 & 1 Γ— 10-4 & 0.55 & 3 Γ— 10-4 \\ \hline 198074 & Aldo-keto reductase 1 member B10 & AKR1B10 & 27433 & 1.94 & 0.035 & 0.77 & Ns & 0.40 & 1 Γ— 10-4 \\ \hline 122783 & Uncharacterized protein C7orf49 & C7orf49 & 26958 & 0.95 & Ns & 0.59 & 0.016 & 0.62 & 5 Γ— 10-3 \\ \hline \multicolumn{2}{c|}{Human 18q22.3-23} \\ \hline 179981 & Teashirt zinc finger homeobox 1 & TSHZ1 & 16246 & 0.91 & Ns & 1.00 & Ns & 1.10 & Ns \\ \hline 141665 & F-box only protein 15 & FBXO15 & 38225 & 0.72 & Ns & 0.69 & Ns & 0.97 & Ns \\ \hline 130856 & Zinc finger protein 236 & ZNF236 & 16303 & 1.45 & 0.025 & 1.48 & 0.011 & 1.02 & Ns \\ \hline 166540 & zinc finger protein 407 & ZNF407 & 16008 & 0.87 & Ns & 0.77 & 0.015 & 0.88 & Ns \\ \hline 101493 & Zinc finger protein 516 & ZNF516 & 16258 & 1.07 & Ns & 1.20 & Ns & 1.12 & Ns \\ \hline \multicolumn{2}{c|}{Human 20p12.3-13} \\ \hline 149451 & Disintegrin and metalloproteinase 33 & ADAM33 & 21242 & 0.85 & Ns & 1.28 & Ns & 1.51 & Ns \\ \hline 101222 & Uncharacterized protein C20orf28 & C20orf28 & 21247 & 1.19 & Ns & 0.80 & Ns & 0.67 & 0.016 \\ \hline 101311 & Unc-112-related protein 1 (Kindlin-1) & C20orf42 & 21274 & 0.70 & 0.050 & 0.53 & 2.2 Γ— 10-3 & 0.75 & Ns \\ \hline 125872 & Uncharacterized protein C20orf75 & C20orf75 & 32989 & 1.65 & Ns & 5.48 & 1 Γ— 10-3 & 3.31 & 1 Γ— 10-3 \\ \hline 171984 & Uncharacterized protein C20orf196 & C20orf196 & 21268 & 1.40 & Ns & 1.22 & Ns & 0.87 & Ns \\ \hline 125885 & Minichromosome maintenance complex component 8 & MCM8 & 21272 & 2.63 & Ns & 2.82 & Ns & 1.08 & Ns \\ \hline 171864 & Prion protein 2 & PRND & 21260 & 0.64 & Ns & 0.53 & Ns & 0.83 & Ns \\ \hline 101236 & RING finger protein 24 & RNF24 & 21250 & 0.81 & Ns & 0.60 & 0.010 & 0.74 & Ns \\ \hline 088827 & Sialic acid-binding Ig-like lectin 1 & SIGLEC1 & 21243 & 0.73 & 0.033 & 0.81 & Ns & 1.11 & Ns \\ \hline 149345 & Putative ubiquitin-conjugating enzyme E2 D3-like & U2D3L & 13741 & 1.27 & Ns & 0.64 & 0.020 & 0.51 & 2 Γ— 10-3 \\ \hline \end{tabular} \end{table}
PMC2717999_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline & \textbf{Low} & \textbf{Medium} & \textbf{High} \\ \hline \textbf{Low} & 1;(Ξ±j 1A;Ξ±j* k = 1D) = = & 2;(Ξ±j 1A;Ξ±j* k = 2D) = = & 3;(Ξ±j 1A;Ξ±j* k = 3D) = = \\ \hline \textbf{Medium} & 4;(Ξ±j 2A;Ξ±j* k = 1D) = = & 5;(Ξ±j 2A;Ξ±j* k = 2D) = = & 6;(Ξ±j 2A;Ξ±j* k = 3D) = = \\ \hline \textbf{High} & 7;(Ξ±j 3A;Ξ±j* k = 1D) = = & 8;(Ξ±j 3A;Ξ±j* k = 2D) = = & 9;(Ξ±j 3A;Ξ±j* k = 3D) = = \\ \hline \end{tabular} \end{table}
PMC2718000_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline & \textbf{Low} & \textbf{Medium} & \textbf{High} \\ \hline \textbf{Low} & 4.3\%; 7.3\% & 3.7\%; 18.6\% & 3.0\%; 34.5\% \\ \hline \textbf{Medium} & 13.6\%; 6.7\% & 12.1\%; 17.0\% & 9.9\%; 32.0\% \\ \hline \textbf{High} & 29.7\%; 5.4\% & 27.0\%; 14.1\% & 22.8\%; 27.4\% \\ \hline \end{tabular} \end{table}
PMC2718000_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline & \textbf{Low} & \textbf{Medium} & \textbf{High} \\ \hline \textbf{Low} & 1,567 (5.3\%) & 9,509 (32.0\%) & 4,481 (15.1\%) \\ \hline \textbf{Medium} & 3,426 (11.5\%) & 4,497 (15.2\%) & 1,283 (4.3\%) \\ \hline \textbf{High} & 4,854 (16.3\%) & 74 (0.2\%) & 0 (0.0\%) \\ \hline \end{tabular} \end{table}
PMC2718000_table_2
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline \textbf{Gene} & \textbf{CNA class} & \textbf{Cytoband} & \textbf{Deletion (\%)} & \textbf{Amplification (\%)} \\ \hline FHIT & k = 3 (D) & 3p14.2 & 52.3 & 1.5 \\ \hline LIMD1 & k = 3 (D) & 3p21.3 & 34.4 & 1.5 \\ \hline hTERT & k = 7 (A) & 5p15.33 & 6.2 & 55.4 \\ \hline SKP2 & k = 7 (A) & 5p13 & 1.5 & 38.5 \\ \hline EGFR-1 & k = 7 (A) & 7p11.2 & 1.5 & 24.6 \\ \hline c-MET & k = 7 (A) & 7q31 & 7.7 & 23.1 \\ \hline c-MYC & k = 7 (A) & 8q24.12-13 & 4.6 & 36.9 \\ \hline CDKN2A & k = 3 (D) & 9p21 & 29.2 & 6.2 \\ \hline PTEN & k = 2 (D) & 10q23.3 & 18.5 & 5.2 \\ \hline CCND1 & k = 7 (A) & 11q13 & 6.2 & 21.5 \\ \hline RB & k = 3 (D) & 13q14.2 & 43.1 & 1.5 \\ \hline NKX2-1 & k = 7 (A) & 14q13.3 & 3.1 & 21.5 \\ \hline WWOX & k = 3 (D) & 16q23.3-24.1 & 33.8 & 6.2 \\ \hline P53 & k = 3 (D) & 17p13.1 & 36.9 & 4.6 \\ \hline E2F & k = 7 (A) & 20q11.2 & 3.1 & 23.1 \\ \hline \end{tabular} \end{table}
PMC2718000_table_3
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline & & & \multicolumn{2}{c|}{\textbf{Significance of difference between slow and fast growers†}} \\ \hline & \textbf{\textbf{Total (N = 113)}} & \textbf{*Non-obligatory symbiont only (N = 77)} & \textbf{\textbf{Total (N = 113)}} & \textbf{Β§Non-obligatory symbionts (N = 77)} \\ \hline \multirow{2}{*}{Genome size (bp)} & -0.30 & -0.04 & 0.001 & 0.4 \\ \hline (0.001) & (0.7) & (S: 2,695,676, F: 3,402,099) & (S: 3,614,838, F: 3,479,053) \\ \hline \multirow{2}{*}{Network size} & -0.38 & -0.13 & 0.002 & 0.3 \\ \hline (3.1e-05) & (0.2) & (S: 326, F: 410) & (S: 408, F: 431) \\ \hline Fraction of & -0.42 & -0.21 & 4e-4 & 0.2 \\ \hline regulatory genes [33] & (0.0004) & (0.13) & (S: 0.03, F: 0.05) & (S: 0.04, F: 0.05) \\ \hline Estimate of & -0.34 & -0.07 & 1e-4 & -‑ \\ \hline environmental complexity [19] & (2-04) & (0.5) & (S: 3, F: 4) \\ \hline \multirow{2}{*}{ESI} & -0.25 & -0.23 & 0.03 & 0.06 \\ \hline (0.008) & (0.04) & (S: 0.006, F: 0.02) & (S: 0.008, F: 0.02) \\ \hline ESI: random & -0.47 & -0.35 & 8e-6 & 0.002 \\ \hline environmentsΒ§ & (1.6e-07) & (0.002) & (S: 0.007, F: 0.03) & (S: 0.01, F: 0.004) \\ \hline \multirow{2}{*}{Maximal-CHS} & -0.27 & -0.28 & 0.03 & 0.02 \\ \hline (0.03) & (0.01) & (S: 14, F: 27) & (S: 20, F: 31) \\ \hline Maximal-CHS: random & -0.34 & -0.23 & 6e-4 & 0.01 \\ \hline environmentsΒ§ & (1e-4) & (0.05) & (S: 39, F: 72) & (S: 50, F: 85) \\ \hline \end{tabular} \end{table}
PMC2718495_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline & \textbf{Number of species*} & \textbf{Mean duplication time} & \textbf{Median duplication time} & \textbf{Mean network size} \\ \hline Aerobic bacteria & 40 & 13 & 3 & 412 \\ \hline Anaerobic bacteria & 18 & 5.3 & 1.6 & 318 \\ \hline Facultative bacteria & 41 & 1.7 & 0.8 & 380 \\ \hline \end{tabular} \end{table}
PMC2718495_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline & \textbf{Total} & \textbf{H3K27me3 target genes} & \textbf{Observed} & Enriched for \textbf{H3K27me3 target genes}?* & Depleted of \textbf{H3K27me3 target genes}?* \\ \hline me1+me2-me3- & 179 & 31 & 17.32\% & No (P = 1) & Yes (P = 1.6 Γ— 10-5) \\ \hline me1-me2+me3- & 445 & 206 & 46.29\% & Yes (P < 10-10) & No (P = 1) \\ \hline me1-me2-me3+ & 675 & 69 & 10.22\% & No (P = 1) & Yes (P < 10-10) \\ \hline me1-me2+me3- & 171 & 33 & 19.30\% & No (P = 1) & Yes (P = 3.0 Γ— 10-4) \\ \hline me1+me2-me3+ & 437 & 14 & 3.20\% & No (P = 1) & Yes (P < 10-10) \\ \hline me1-me2+me3+ & 954 & 173 & 18.13\% & No (P = 1) & Yes (P < 10-10) \\ \hline me1+me2+me3+ & 507 & 16 & 3.16\% & No (P = 1) & Yes (P < 10-10) \\ \hline me1-me2-me3- & 2,441 & 1,266 & 51.86\% & Yes (P < 10-10) & No (P = 1) \\ \hline \end{tabular} \end{table}
PMC2718496_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|} \hline & \textbf{Total regions} & \textbf{Overlap with H3K27me3} & \textbf{\%} & \textbf{Random overlapping*} & \textbf{Enriched for H3K27me3?} & \textbf{Depleted of H3K27me3?} \\ \hline H3K4me1 & 15,475 & 178 & 1.15 & 4.78\textbf{\%} & No (P = 1) & Yes (P < 10-10) \\ \hline H3K4me2 & 12,781 & 881 & 6.89 & 6.09\textbf{\%} & Yes (P = 1.0 Γ— 10-4) & No (P = 1) \\ \hline H3K4me3 & 15,894 & 572 & 3.60 & 7.12\textbf{\%} & No (P = 1) & Yes (P < 10-10) \\ \hline \end{tabular} \end{table}
PMC2718496_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline \textbf{H3K4me} & \textbf{Chromosome} & \textbf{CG} & \textbf{CHG} & \textbf{CHH} \\ \hline \multirow{5}{*}{\textbf{H3K4me}1} & 1 & 41.78\% & 0.41\% & 0.32\% \\ \hline 2 & 41.52\% & 0.42\% & 0.31\% \\ \hline 3 & 40.38\% & 0.45\% & 0.33\% \\ \hline 4 & 42.46\% & 0.42\% & 0.32\% \\ \hline 5 & 42.03\% & 0.40\% & 0.30\% \\ \hline \multirow{5}{*}{\textbf{H3K4me}2} & 1 & 4.22\% & 0.39\% & 0.32\% \\ \hline 2 & 4.11\% & 0.38\% & 0.34\% \\ \hline 3 & 3.89\% & 0.39\% & 0.33\% \\ \hline 4 & 4.78\% & 0.36\% & 0.33\% \\ \hline 5 & 4.32\% & 0.38\% & 0.32\% \\ \hline \multirow{5}{*}{\textbf{H3K4me}3} & 1 & 2.93\% & 0.40\% & 0.32\% \\ \hline 2 & 2.96\% & 0.45\% & 0.35\% \\ \hline 3 & 2.85\% & 0.39\% & 0.32\% \\ \hline 4 & 3.35\% & 0.44\% & 0.34\% \\ \hline 5 & 3.08\% & 0.43\% & 0.33\% \\ \hline \end{tabular} \end{table}
PMC2718496_table_2
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|l|} \hline \textbf{Domain} & \textbf{Taxonomic grouping} & \textbf{Partial genomes} & \textbf{Partial genome sequences} & \textbf{Complete genomes} & \textbf{Complete genome sequences} & \textbf{nr sequences} & \textbf{Total sequences} \\ \hline Archaea & Crenarchaeota & - & - & 4 & 11,120 & 12,339 & 23,459 \\ \hline Archaea & Euryarchaeota & - & - & 14 & 30,396 & 38,863 & 69,259 \\ \hline Archaea & Archaea - Other & - & - & 1 & 563 & 3,180 & 3,743 \\ \hline Archaea & Total & - & - & 19 & 42,079 & 54,382 & 96,461 \\ \hline Bacteria & Actinobacteridae & - & - & 14 & 49,608 & 68,041 & 117,649 \\ \hline Bacteria & Alphaproteobacteria & - & - & 14 & 48,997 & 81,233 & 130,230 \\ \hline Bacteria & Betaproteobacteria & - & - & 9 & 37,184 & 51,947 & 89,131 \\ \hline Bacteria & Gammaproteobacteria & - & - & 27 & 94,933 & 188,458 & 283,391 \\ \hline Bacteria & Deltaproteobacteria & - & - & 4 & 13,778 & 15,449 & 29,227 \\ \hline Bacteria & Epsilonproteobacteria & - & - & 4 & 7,128 & 16,452 & 23,580 \\ \hline Bacteria & Cyanobacteria & - & - & 6 & 20,983 & 32,380 & 53,363 \\ \hline Bacteria & Firmicutes & - & - & 31 & 72,975 & 163,215 & 236,190 \\ \hline Bacteria & Spirochaetes & - & - & 4 & 10,163 & 18,324 & 28,487 \\ \hline Bacteria & Bacteria - Other & - & - & 14 & 36,760 & 61,550 & 98,310 \\ \hline Bacteria & Total & - & - & 127 & 392,509 & 697,049 & 1,089,558 \\ \hline Eukarya & Protist - Alveolata & 10 & 29,707 & 2 & 8,691 & 24,211 & 62,609 \\ \hline Eukarya & Protist - Euglenozoa/ Haptophyceae/ Stramenophiles & 7 & 13,846 & 1* & 11,397* & 9,484 & 34,727 \\ \hline Eukarya & Protist - Other & - & - & - & - & 12,862 & 12,862 \\ \hline Eukarya & Protists - Total & 17 & 43,553 & 3 & 20,088 & 46,557 & 110,198 \\ \hline Eukarya & Fungi - Ascomycota & 17 & 44,358 & 9 & 52,271 & 67,765 & 164,394 \\ \hline Eukarya & Fungi - Basidiomycota & 7 & 14,785 & 1† & 431† & 10,264 & 25,049 \\ \hline Eukarya & Fungi - Glomeromycota/ Zygomycota & 3 & 3,398 & - & - & 734 & 4,132 \\ \hline Eukarya & Fungi - Other & - & - & 1 & 1,996 & 2,558 & 4,554 \\ \hline Eukarya & Fungi - Total & 27 & 62,541 & 10 & 52,271 & 78,763 & 193,575 \\ \hline Eukarya & Metazoa - Lophotrochozoa & 4 & 14,631 & - & - & 12,416 & 27,047 \\ \hline Eukarya & Metazoa - Arthropods/ Tardigrades & 17 & 22,528 & 2 & 33,585 & 95,953 & 152,066 \\ \hline Eukarya & Metazoa - Deuterostomes & 21 & 90,244 & 2 & 57,406 & 276,682 & 424,332 \\ \hline Eukarya & Metazoa - Nematoda & 34 & 95,345 & 2 & 39,464 & 38,657 & 173,466 \\ \hline Eukarya & Metazoa - Other & - & - & - & - & 3,424 & 3,424 \\ \hline Eukarya & Metazoa - Total & 76 & 222,748 & 6 & 130,455 & 427,132 & 780,335 \\ \hline Eukarya & Plantae & 76 & 221,896 & 2 & 30,533 & 190,711 & 443,140 \\ \hline Eukarya & Total & 196 & 550,738 & 21 & 233,347 & 743,163 & 1,527,248 \\ \hline Total & & 196 & 550,738 & 167 & 667,935 & 1,494,594 & 2,713,267 \\ \hline \end{tabular} \end{table}
PMC2718497_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|} \hline Analyzed genomes \\ \hline Number of genomes & 119 \\ \hline Number of ORFs & 351,111 \\ \hline Number of atypical ORFs & 58,487 (16\% of all genes) \\ \hline Number of CAGs & 2,377 \\ \hline Number of ORFs in CAGs & 47,441 (13\% of all genes) \\ \hline Newly identified CAGs \\ \hline Number of CAGs & 2,104 \\ \hline CAGs of likely plasmid origin & 674 (32\%) \\ \hline CAGs of likely virus origin & 164 (8\%) \\ \hline CAGs of likely viruse and plasmid origin & 341 (16\%) \\ \hline CAGs likely from cellular sources & 145 (7\%) \\ \hline CAGs unclassified & 780 (37\%) \\ \hline ORFans \\ \hline Number of ORFans & 8,987 \\ \hline Number of ORFans in CAGs & 3,475 (39\%) \\ \hline ORFans in annotated proviruses and CAGs of likely virus origin & 875 (25.1\% of all ORFans inside CAGs) \\ \hline Number of ORFans in CAGs of likely plasmid origin & 680 (19.5\% of all ORFans inside CAGs) \\ \hline Number of ORFans in CAGs of likely virus and plasmid origin & 224 (6.4\% of all ORFans inside CAGs) \\ \hline Number of ORFans in CAGs likely from cellular sources & 54 (1.5\% of all ORFans inside CAGs) \\ \hline Number of ORFans in unclassified CAGs & 1,642 (47.5\% of all ORFans inside CAGs) \\ \hline \end{tabular} \end{table}
PMC2718499_table_0
\begin{table} \cente\textbf{r}ing \label{tab:tablelabel} \begin{tabula\textbf{r}}{|l|l|l|l|l|} \hline \textbf{ID} & Genome \textbf{ID} & \textbf{Name} & \textbf{r} & \textbf{Function} \\ \hline CL4038Contig1 & [Esi0355_0025] & HSP70 & 0.87 & HSP70 \\ \hline LQ0AAB7YD09FM1.SCF & [Esi0155_0065] & NADH & 0.94 & NADH dehyd\textbf{r}ogenase \\ \hline CL7513Contig1 & [Esi0269_0011] & P\textbf{r}oDH & 0.79 & P\textbf{r}oline dehyd\textbf{r}ogenase \\ \hline CL3741Contig1 & [Esi0024_0066] & TF & 0.90 & Putative t\textbf{r}ansc\textbf{r}iption facto\textbf{r} \\ \hline LQ0AAB12YN05FM1.SCF & [Esi0399_0008] & WD_\textbf{r}ep & 0.66 & WD \textbf{r}epeat gene \\ \hline CL1Contig3 & [Esi0085_0055] & CLB1 & 0.95 & Chlo\textbf{r}ophyll binding p\textbf{r}otein \\ \hline CL43Contig1 & [Esi0199_0054] & CLB2 & 0.98 & Fucoxanthin binding p\textbf{r}otein \\ \hline CL7742Contig1 & [Esi0026_0055] & TagS & 0.69 & TAG synthase \\ \hline CL2765Contig1 & [Esi0526_0006] & NH4-T\textbf{r} & 0.96 & Ammonium t\textbf{r}anspo\textbf{r}te\textbf{r} \\ \hline CL3832Contig1 & [Esi0437_0012] & FOR & 0.67 & Phycoe\textbf{r}yth\textbf{r}obilin:fe\textbf{r}\textbf{r}edoxin oxido\textbf{r}eductase \\ \hline LQ0AAA16YN10FM1.SCF & [Esi0153_0004] & A\textbf{r}g-MetT\textbf{r} & 0.71 & A\textbf{r}ginine N-methylt\textbf{r}ansfe\textbf{r}ase \\ \hline CL7099Contig1 & [Esi0018_0111] & HSD & 0.83 & Homose\textbf{r}ine dehyd\textbf{r}ogenase \\ \hline CL6576Contig1 & [Esi0107_0059] & IGPS & 0.97 & Indole-3-glyce\textbf{r}ol-phosphate synthase \\ \hline CL7231Contig1 & [Esi0686_0001] & CDPK & 0.85 & cAMP-dependent p\textbf{r}otein kinase \\ \hline CL4027Contig1 & [Esi0122_0054] & mGST & -0.48 & Mic\textbf{r}osomal glutathione S-t\textbf{r}ansfe\textbf{r}ase \\ \hline CL4274Contig1 & [Esi0023_0183] & SNR & 0.57 & SNR (vesicula\textbf{r} t\textbf{r}anspo\textbf{r}t) \\ \hline CL5850Contig1 & [Esi0109_0088] & mG & 0.99 & Glycin-\textbf{r}ich p\textbf{r}otein \\ \hline CL455Contig1 & [Esi0159_0021] & G6PD & 0.91 & Glucose-6-phosphate 1-dehyd\textbf{r}ogenase \\ \hline CL6746Contig1 & [Esi0116_0065] & IF4E & 0.91 & Euka\textbf{r}yotic initiation facto\textbf{r} 4E \\ \hline \end{tabula\textbf{r}} \end{table}
PMC2718500_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline \textbf{ID} & Genome \textbf{ID} & \textbf{Name} & \textbf{Maximum change ARRAY} & \textbf{Maximum change QPCR} & \textbf{Function} \\ \hline LQ0AAB30YA12FM1.SCF & [Esi0298_0008] & Dyn & 0.23 & 0.77 & Dynein \\ \hline CL1914Contig1 & [Esi0021_0024] & ARP2.1 & 0.22 & 0.44 & Actin related protein \\ \hline CL3Contig2 & [Esi0387_0021] & EF1A & 0.08 & 0.46 & Elongation factor 1 alpha \\ \hline CL8Contig12 & [Esi0053_0059] & TUA & 0.57 & 0.91 & Alpha tubulin \\ \hline CL1073Contig1 & [Esi0054_0059] & UBCE & 0.22 & 0.38 & Ubiquitin-conjugating enzyme \\ \hline CL29Contig4 & [Esi0302_0019] & UBQ & 0.18 & 0.82 & Ubiquitin \\ \hline CL461Contig1 & [Esi0072_0068] & R26S & 0.22 & n/a & Ribosomal protein S26 \\ \hline \end{tabular} \end{table}
PMC2718500_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|} \hline \textbf{LG_Chr*} & \textbf{Chromosome size (Mb)†} & \textbf{Total markers‑} & \textbf{Mapped markersΒ§} & \textbf{Map length (cM)} & \textbf{Adjusted map length (cM)} & \textbf{Interval spacing (cM/ interval)ΒΆ} \\ \hline LG1_Chr1 & 62.4 & 58 & 51 & 209.15 & 218.95 & 4.18 \\ \hline LG3_Chr2 & 41.2 & 32 & 28 & 192.24 & 204.98 & 7.12 \\ \hline LG4_Chr3 & 40.8 & 28 & 24 & 121.16 & 132.04 & 5.27 \\ \hline LG5_Chr4 & 35.1 & 27 & 24 & 132.65 & 144.03 & 5.77 \\ \hline LG9_Chr5 & 21.7 & 10 & 10 & 71.30 & 84.84 & 7.927 \\ \hline LG6_Chr6 & 21.2 & 18 & 16 & 86.61 & 98.00 & 5.777 \\ \hline LG7_Chr7 & 16.9 & 14 & 13 & 88.08 & 101.04 & 7.34 \\ \hline LG2_ChrZ & 60.7 & 56 & 44 & 233.65 & 244.70 & 5.437 \\ \hline Total & 300 & 243 & 210 & 1134.84 & 1228.59 & 5.62 \\ \hline \end{tabular} \end{table}
PMC2718505_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|l|} \hline \multirow{2}{*}{\textbf{pH}} & \multirow{2}{*}{\textbf{Time (h)}} & \multirow{2}{*}{\textbf{ΞΌmax (h-1)}} & \multirow{2}{*}{\textbf{Biomass (g/L)}} & \multirow{2}{*}{\textbf{Glucose (g/L)}} & \multirow{2}{*}{\textbf{Citrate (g/L)}} & \multirow{2}{*}{\textbf{Oxalate (g/L)}} & \multirow{2}{*}{\textbf{Gluconate (g/L)}} \\ \hline \\ \hline 2.5 & 22.77 $\pm$ 0.40 & 0.21 $\pm$ 0.01 & 4.68 $\pm$ 0.16 & 8.93 $\pm$ 1.84 & 0.01 $\pm$ 0.01 & 0.00 $\pm$ 0.00 & 0.00 $\pm$ 0.00 \\ \hline 4.5 & 22.72 $\pm$ 0.63 & 0.21 $\pm$ 0.01 & 4.40 $\pm$ 0.47 & 7.87 $\pm$ 1.97 & 0.05 $\pm$ 0.05 & 0.02 $\pm$ 0.02 & 2.39 $\pm$ 3.05 \\ \hline 6.0 & 21.47 $\pm$ 0.69 & 0.22 $\pm$ 0.02 & 3.71 $\pm$ 0.42 & 5.24 $\pm$ 1.21 & 0.02 $\pm$ 0.03 & 0.07 $\pm$ 0.05 & 6.36 $\pm$ 1.90 \\ \hline \end{tabular} \end{table}
PMC2718513_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|} \hline \textbf{Gene} & \multicolumn{2}{c|}{\textbf{ORFs}} \\ \hline & \textbf{A. nidulans} & \textbf{A. niger} \\ \hline palA & AN4351 & 119792 \\ \hline palB & AN0256 & 171058 \\ \hline palC & AN7560 & 48740 \\ \hline palF & AN1844 & Not found* \\ \hline palH & AN6886 & 120044 \\ \hline palI & AN4853 & 52449 \\ \hline vps32/snf7 & AN4240 & 136905 \\ \hline pacC & AN2855 & 47049 \\ \hline \end{tabular} \end{table}
PMC2718513_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline & \multicolumn{2}{c|}{\textbf{Major copy type: mean divergence* (maximum)}} & \multicolumn{2}{c|}{\textbf{Atypical sequences: number (divergence)}} \\ \hline & \textbf{5' end} & \textbf{3' end} & \textbf{Variant copies†} & Variant \textbf{5' end}s‑ \\ \hline R1 elements \\ \hline D. simulans R1A & 0.000 (0.000) & 0.002 (0.003) & & 4 (0.01-0.03) \\ \hline D. sechellia R1A & <0.001 (0.003) & <0.001 (0.002) \\ \hline D. melanogaster R1A & 0.001 (0.008) & 0.003 (0.015) & 2 (0.07) \\ \hline D. yakuba R1A & 0.001 (0.005) & 0.000 (0.000) & 1 (0.02) \\ \hline R1A D. erecta & 0.002 (0.005) & 0.001 (0.007) \\ \hline D. ananassae R1A & 0.013 (0.043) & <0.001 (0.003) & & 1 (0.08-0.11) \\ \hline D. ananassae R1B & 0.000 (0.000) & 0.002 (0.005) & & 3 (0.15-0.22) \\ \hline D. pseudoobscura R1A & 0.000 (0.000) & 0.002 (0.010) & & 1 (0.04) \\ \hline D. persimilis R1A & ND & 0.000 (0.000) & 1 (0.02) \\ \hline D. willistoni R1A & 0.002 (0.005) & 0.001 (0.003) \\ \hline D. mojavensis R1A & 0.000 (0.000) & 0.000 (0.000) \\ \hline D. virilis R1B & 0.001 (0.008) & <0.001 (0.003) & 6 (0.01-0.05) \\ \hline D. grimshawi R1B1 & 0.000 (0.000) & 0.001 (0.005) \\ \hline D. grimshawi R1B2 & 0.000 (0.000) & 0.000 (0.000) \\ \hline R2 elements \\ \hline D. simulans R2 & 0.001 (0.008) & 0.000 (0.000) \\ \hline D. sechellia R2 & 0.000 (0.000) & <0.001 (0.003) \\ \hline D. melanogaster R2 & 0.002 (0.005) & 0.001 (0.015) & 6 (0.02-0.05) \\ \hline D. yakuba R2 & 0.002 (0.013) & 0.006 (0.018) \\ \hline D. ananassae R2 & 0.004 (0.008) & 0.001 (0.005) \\ \hline D. persimilis R2 & ND & ND \\ \hline D. pseudoobscura R2 & ND & 0.005 (0.010) \\ \hline D. willistoni R2 sub1 & 0.001 (0.003) & 0.002 (0.008) \\ \hline D. willistoni R2 sub2Β§ & 0.003 (0.006) & 0.015 (0.028) \\ \hline \end{tabular} \end{table}
PMC2718515_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline \textbf{Species} & \textbf{Fraction of rDNA units} & \textbf{Tandem*} & \textbf{Non-28S*} \\ \hline D. simulans & 0.08 & - & + \\ \hline D. sechellia & 0.62 & + & + \\ \hline D. melanogaster & 0.11 & -† & + \\ \hline D. yakuba & 0.11 & - & + \\ \hline D. erecta & 0.36 & + & - \\ \hline D. ananassae R1A & 0.17 & ++‑ & ++ \\ \hline D. ananassae R1B & 0.13 & +++ & +++ \\ \hline D. pseudoobscura & 0.40 & +++ & +++ \\ \hline D. persimilis & 0.26 & +++ & ++ \\ \hline D. willistoni & 0.10 & + & ++ \\ \hline D. mojavensis & 0.68 & + & + \\ \hline D. virilis & 0.75 & ++ & + \\ \hline D. grimshawi & 0.20 & + & + \\ \hline \end{tabular} \end{table}
PMC2718515_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline \textbf{Dataset} & \textbf{Description} & \textbf{Samples} & \textbf{Cel file sample replicates} & \textbf{References} \\ \hline [GEO:GSE1133] & Normal tissues and cell lines & 144 & 72 Γ— 2 & [71] \\ \hline [GEO:GSE2361] & Normal human tissues & 36 & 36 Γ— 1 & [72] \\ \hline \multirow{4}{*}{[GEO:GSE2004]} & Normal spleen & 22 & 3 Γ— 3 (spleen) & - \\ \hline liver and kidney & & 2 Γ— 3 (liver) \\ \hline & & 1 Γ— 3 (liver) \\ \hline & & 1 Γ— 4 (kidney) \\ \hline [GEO:GSE781] & Normal kidney samples & 5 & 1 Γ— 5 & [70] \\ \hline Total & & 207 & 75 \\ \hline \end{tabular} \end{table}
PMC2718516_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline & \textbf{Total*} & \textbf{Unique†} & \textbf{Match‑} & \textbf{PercentageΒ§} \\ \hline Category of disorder \\ \hline Highly disordered & 877 & 827 & 257 & 31.08 \\ \hline Highly ordered & 5,693 & 5,351 & 782 & 14.61 \\ \hline Disordered & 15,095 & 14,282 & 5,056 & 35.40 \\ \hline Ordered & 18,774 & 17,766 & 3,433 & 19.32 \\ \hline All proteins & 33,869 & 32,010 & 8,468 & 26.45 \\ \hline Percentage of disorder \\ \hline Disordered \\ \hline [0,20] & 4,271 & 4,055 & 1,402 & 34.57 \\ \hline (20,40] & 6,957 & 6,603 & 2,300 & 34.83 \\ \hline (40,60] & 3,036 & 2,866 & 1,119 & 39.04 \\ \hline (60,80] & 679 & 644 & 233 & 36.18 \\ \hline (80,100] & 152 & 143 & 20 & 13.99 \\ \hline Total & 15,095 & 14,311 & 5,074 & 35.45 \\ \hline Ordered \\ \hline [0,20] & 16,341 & 15,503 & 3,037 & 19.59 \\ \hline (20,40] & 2,173 & 2,024 & 362 & 17.89 \\ \hline (40,60] & 214 & 207 & 35 & 16.91 \\ \hline (60,80] & 33 & 31 & 4 & 12.9 \\ \hline (80,100] & 13 & 9 & 0 & 0 \\ \hline Total & 18,774 & 17,774 & 3,438 & 19.34 \\ \hline Proteome \\ \hline [0,20] & 20,612 & 19,536 & 4,429 & 22.67 \\ \hline (20,40] & 9,130 & 8,618 & 2,658 & 30.84 \\ \hline (40,60] & 3,250 & 3,073 & 1,154 & 37.55 \\ \hline (60,80] & 712 & 675 & 237 & 35.11 \\ \hline (80,100] & 165 & 152 & 20 & 13.16 \\ \hline Total & 33,869 & 32,010 & 8,468 & 26.45 \\ \hline \end{tabular} \end{table}
PMC2718516_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline \textbf{Expressor type} & \textbf{Total transcripts (frequency value)} & \textbf{Percentage of transcripts with different expression profiles} & \textbf{Transcripts with miRNA (frequency value)} & \textbf{Transcripts with no miRNA (frequency value)} & \textbf{Transcripts with miRNA (\%)} \\ \hline Tissue specific & 50 (47) & 19.31 & 32 & 15 & 68.09 \\ \hline High & 43 (41) & 16.60 & 27 & 14 & 65.85 \\ \hline Medium & 31 (31) & 11.97 & 15 & 16 & 48.39 \\ \hline Constitutive & 4 (1) & 1.54 & 0 & 1 & 0 \\ \hline Transient or low & 131 (129) & 50.58 & 62 & 67 & 48.06 \\ \hline Total & 259 \\ \hline \end{tabular} \end{table}
PMC2718516_table_2
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline \textbf{Term} & \textbf{Description} & \textbf{Disorder (60,80]\%} & \textbf{Disorder (80,100]\%} \\ \hline [GO:0005769] & Early endosome & Down & Down \\ \hline [GO:0005770] & Late endosome & Down & Down \\ \hline [GO:0005838] & Proteasome regulatory particle & Down & Down \\ \hline [GO:0016272] & Prefoldin complex & Down \\ \hline [GO:0031371] & Ubiquitin conjugating enzyme complex & Down \\ \hline [GO:0000145] & Exocyst & Down \\ \hline [GO:0000502] & Proteasome complex & Down \\ \hline [GO:0032991] & Macromolecular complex & & Up \\ \hline [GO:0043234] & Protein complex & & Up \\ \hline [GO:0019872] & Small conjugating protein ligase activity & & Up \\ \hline [GO:0042803] & Protein homodimerization activity & & Up \\ \hline [GO:0051131] & Chaperone-mediated protein complex assembly & & Up \\ \hline [GO:0008639] & Small protein conjugating enzyme activity & & Up \\ \hline [GO:0004842] & Ubiquitin-protein ligase activity & & Up \\ \hline [GO:0016874] & Ligase activity & & Up \\ \hline [GO:0006512] & Ubiquitin cycle & & Up \\ \hline [GO:0004869] & Cysteine protease inhibitor activity & Up & Up \\ \hline [GO:0004866] & Endopeptidase inhibitor activity & Up & Up \\ \hline [GO:0030414] & Protease inhibitor activity & Up & Up \\ \hline [GO:0051082] & Unfolded protein binding & Up & Up \\ \hline [GO:0046983] & Protein dimerization activity & Up & Up \\ \hline [GO:0051291] & Protein hetero-oligomerization & Up \\ \hline [GO:0007032] & Endosome organization and biogenesis & Up \\ \hline [GO:0006983] & ER overload response & Up \\ \hline [GO:0051087] & Chaperone binding & Up \\ \hline [GO:0031579] & Lipid raft organization and biogenesis & Up \\ \hline [GO:0016235] & Aggresome & Up \\ \hline [GO:0016234] & Inclusion body & Up \\ \hline [GO:0016926] & Protein desumoylation & Up \\ \hline [GO:0008581] & Ubiquitin specific protease 5 activity & Up \\ \hline [GO:0006622] & Protein targeting to lysosome & Up \\ \hline [GO:0019783] & Small conjugating protein-specific protease activity & & Down \\ \hline [GO:0008219] & Cell death & & Down \\ \hline [GO:0007049] & Cell death & & Down \\ \hline [GO:0051603] & Proteolysis involved in cellular protein catabolic process & Down & Down \\ \hline [GO:0004221] & Ubiquitin thiolesterase activity & Down & Down \\ \hline [GO:0016197] & Endosome transport & Down & Down \\ \hline [GO:0016874] & Ligase activity & Down & Down \\ \hline [GO:0004843] & Ubiquitin-specific protease activity & Down & Down \\ \hline [GO:0051082] & Unfolded protein binding & Down & Down \\ \hline [GO:0000209] & Protein polyubiquitination & Down & Down \\ \hline [GO:0006511] & Ubiquitin-dependent protein catabolic process & Down \\ \hline [GO:0006512] & Ubiquitin cycle & Down \\ \hline [GO:0051087] & Chaperone binding & Down \\ \hline [GO:0030968] & Unfolded protein response & Down \\ \hline [GO:0030100] & Regulation of endocytosis & Down \\ \hline [GO:0043488] & Regulation of mRNA stability & Down \\ \hline [GO:0031396] & Regulation of protein ubiquitination & Down \\ \hline \end{tabular} \end{table}
PMC2718516_table_3
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline \textbf{P. fluorescens strain} & \textbf{SBW25} & \textbf{Pf0-1} & \textbf{Pf-5*} \\ \hline Number of bases & 6,722,539 bp & 6,438,405 bp & 7,074,893 bp \\ \hline Number of CDSs & 6,009 & 5,741 & 6,144 \\ \hline Pseudogenes & 88 & 9 & NA \\ \hline Coding percentage & 88.3\% & 90\% & 88.7\% \\ \hline \%GC & 60.5 & 60.62 & 63.3 \\ \hline tRNAs & 66 & 73 & 71 \\ \hline rRNA genes (clusters) & 16 (5) & 19 (6) & 15 (5) \\ \hline Intergenic repeat families & 6 (with a total of 1,199 repeats) & 9 (with a total of 231 repeats) & 5 (with a total of 748 repeats) \\ \hline \end{tabular} \end{table}
PMC2718517_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|} \hline \textbf{Strain pairing} & \textbf{AAI} \\ \hline P. fluorescens \\ \hline Pf0-1/Pf-5 & 82.786 \\ \hline SBW25/Pf0-1 & 81.784 \\ \hline SBW25/Pf-5 & 81.589 \\ \hline P. aeruginosa \\ \hline PA7/PA14 & 94.974 \\ \hline PA7/PAO1 & 95.070 \\ \hline PA14/PAO1 & 98.887 \\ \hline P. syringae \\ \hline pv. syringae/pv. phaseolicola & 94.238 \\ \hline pv. syringae/pv. tomato & 92.025 \\ \hline pv. phaseolicola/pv. tomato & 92.597 \\ \hline \end{tabular} \end{table}
PMC2718517_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|} \hline \textbf{Repeat family} & \textbf{Size (bp)} & \textbf{G+C\%} & \textbf{SBW25} & \textbf{Pf0-1} & \textbf{Pf-5} & \textbf{Structure} \\ \hline R0 & 89 & 59.81 & 612 & 36 & - & IRs: 24 bp \\ \hline R1 & 80 & 68.31 & - & 9 & 621 & IRs: 30 bp \\ \hline R2 & 110 & 66.52 & 516 & - & 4 & IRs: 43 bp \\ \hline R5 & 50 & 65.07 & 2 & 52 & - \\ \hline R6 & 177 & 59.09 & - & 50 & - & IRs: 34 bp \\ \hline R6-partial & 120 & 59.61 & - & 9 & - & - \\ \hline R26 & 352 & 60.76 & - & 20 & - & - \\ \hline R30 & 120 & 58.47 & 4 & 15 & - & - \\ \hline R69 & 62 & 64.67 & - & 12 & - & - \\ \hline R87 & 58 & 68.94 & - & - & 106 & - \\ \hline R178 & 101 & 61.86 & 18 & 28 & 9 & IRs: 11 bp (internal) \\ \hline R200 & 320 & 60.25 & 47 & - & 8 & - \\ \hline Total elements & - & - & 1,199 & 231 & 748 & - \\ \hline Inverted repeats* \\ \hline IR1_g & 23-28 & 66.52 & & 125 & & - \\ \hline IR1_g & 21-28 & 64.7 & 922 & & & - \\ \hline IR1_g & 23-27 & 65.2 & & & 36 & - \\ \hline \end{tabular} \end{table}
PMC2718517_table_2
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|l|l|l|l|} \hline \textbf{Number} & \textbf{Chromoso me length (bp)} & \textbf{Number} of reads* & \textbf{Total contig length (bp)} & \textbf{Coverage by contigs} & \textbf{Average reads/kb} & \textbf{Type II SNPs* (Green†)} & \textbf{Type III SNPs‑ (Blue†)} & \textbf{Novel SNPsΒ§ (Orange†)} & \textbf{Major SNPΒΆ density/kb} & \textbf{Minor SNPΒ₯ density/kb} \\ \hline Ia & 1,896,408 & 20,649 & 1,585,140 & 83.59\% & 13.03 & 2 & 128 & 7 & 0.067 & 0.005 \\ \hline Ib & 1,956,324 & 20,583 & 1,639,876 & 83.82\% & 12.55 & 1 & 1,483 & 10 & 0.758 & 0.006 \\ \hline II & 2,302,931 & 24,968 & 1,939,495 & 84.22\% & 12.87 & 4,370 & 73 & 52 & 1.898 & 0.054 \\ \hline III & 2,470,845 & 26,771 & 2,060,909 & 83.41\% & 12.99 & 27 & 4,224 & 73 & 1.710 & 0.040 \\ \hline IV & 2,576,468 & 27,510 & 2,150,897 & 83.48\% & 12.79 & 4,731 & 176 & 60 & 1.836 & 0.092 \\ \hline V & 3,147,601 & 33,619 & 2,582,080 & 82.03\% & 13.02 & 54 & 5,725 & 26 & 1.819 & 0.025 \\ \hline VI & 3,600,655 & 39,723 & 3,042,491 & 84.50\% & 13.06 & 1,985 & 168 & 99 & 0.551 & 0.074 \\ \hline VIIa & 4,502,211 & 48,365 & 3,797,608 & 84.35\% & 12.74 & 8,663 & 79 & 56 & 1.924 & 0.030 \\ \hline VIIb & 5,023,822 & 53,768 & 4,231,651 & 84.23\% & 12.71 & 62 & 5,530 & 41 & 1.101 & 0.021 \\ \hline VIII & 6,923,375 & 75,308 & 5,851,305 & 84.52\% & 12.87 & 123 & 6,775 & 158 & 0.979 & 0.041 \\ \hline IX & 6,384,456 & 72,298 & 5,337,365 & 83.60\% & 13.55 & 8,119 & 325 & 269 & 1.272 & 0.093 \\ \hline X & 7,418,475 & 85,205 & 6,298,377 & 84.90\% & 13.53 & 13,459 & 236 & 209 & 1.814 & 0.060 \\ \hline XI & 6,570,290 & 70,653 & 5,549,592 & 84.46\% & 12.73 & 49 & 60 & 117 & - & 0.034 \\ \hline XII & 6,871,637 & 74,458 & 5,770,139 & 83.97\% & 12.90 & 58 & 4,809 & 75 & 0.700 & 0.019 \\ \hline Total & 61,645,498 & 673,878 & 51,836,925 & 84.09\% & 13.00 & 41,703 & 29,791 & 1,252 & 1.264 & 0.042 \\ \hline \end{tabular} \end{table}
PMC2718519_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|l|l|l|l|l|l|l|l|l|l|} \hline \textbf{Locus} & \multicolumn{16}{c|}{\textbf{IV-8}} \\ \hline \textbf{Me49 (II)} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{C} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{\textbf{G}}}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{\textbf{G}}}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{\textbf{G}}}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{\textbf{G}}}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{\textbf{G}}}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{\textbf{G}}}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} \\ \hline VE\textbf{\textbf{\textbf{\textbf{\textbf{\textbf{G}}}}}} (III) & * & * & * & * & * & * & * & * & * & * & * & * & * & * & * & * \\ \hline \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}}g\textbf{C}kUg6 & * & * & * & * & * & * & * & * & * & * & * & * & * & * & * & * \\ \hline \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}}g\textbf{C}kUg5 & * & * & * & * & * & * & * & * & * & * & * & * & * & * & * & * \\ \hline \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}}g\textbf{C}kUg9 & * & * & * & * & * & * & * & * & * & * & * & * & * & * & * & * \\ \hline \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}}g\textbf{C}kUg7 & * & * & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{C} & \textbf{C} & \textbf{C} & * & * & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & * & * & \textbf{\textbf{\textbf{\textbf{\textbf{\textbf{G}}}}}} & \textbf{C} & \textbf{C} & * \\ \hline \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}}g\textbf{C}kUg1 & \textbf{C} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{C} & \textbf{C} & \textbf{C} & \textbf{C} & \textbf{C} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{\textbf{G}}}}}} & \textbf{C} & \textbf{C} & \textbf{\textbf{\textbf{\textbf{A}}}} \\ \hline \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}}g\textbf{C}kUg2 & \textbf{C} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{C} & \textbf{C} & \textbf{C} & \textbf{C} & \textbf{C} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{\textbf{G}}}}}} & \textbf{C} & \textbf{C} & \textbf{\textbf{\textbf{\textbf{A}}}} \\ \hline \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}}g\textbf{C}kUg3 & \textbf{C} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{C} & \textbf{C} & \textbf{C} & \textbf{C} & \textbf{C} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{\textbf{G}}}}}} & \textbf{C} & \textbf{C} & \textbf{\textbf{\textbf{\textbf{A}}}} \\ \hline \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}}g\textbf{C}kUg8 & \textbf{C} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{C} & \textbf{C} & \textbf{C} & \textbf{C} & \textbf{C} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{\textbf{G}}}}}} & \textbf{C} & \textbf{C} & \textbf{\textbf{\textbf{\textbf{A}}}} \\ \hline \textbf{\textbf{\textbf{\textbf{\textbf{\textbf{G}}}}}}\textbf{\textbf{\textbf{\textbf{\textbf{T}}}}}1 (I) & \textbf{C} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{C} & \textbf{C} & \textbf{C} & \textbf{C} & \textbf{C} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{A}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{\textbf{G}}}}}} & \textbf{C} & \textbf{C} & \textbf{\textbf{\textbf{\textbf{A}}}} \\ \hline \end{tabular} \end{table}
PMC2718519_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|} \hline \textbf{Gene ID (v4.3)*} & & \multicolumn{2}{c|}{\textbf{Novel SNPs in TgCkUg2}} & \multicolumn{2}{c|}{\textbf{SNPs between the three lineages†}} \\ \hline & \textbf{Number} & \textbf{\textbf{Synonymous}} & \textbf{\textbf{Non-synonymous}} & \textbf{\textbf{Synonymous}} & \textbf{\textbf{Non-synonymous}} & \textbf{Protein description} \\ \hline 641.m01562 & IV & 1 & 1 & 12 & 86 & SRS16B \\ \hline 641.m02553 & IV & 1 & 1 & 6 & 1 & WD-40 repeat protein, putative \\ \hline 49.m03276 & VI & 1 & 1 & 0 & 4 & ROP29 \\ \hline 49.m03279 & VI & 2 & 8 & 1 & 13 & Hypothetical \\ \hline 49.m03372 & VI & 1 & 1 & 13 & 3 & Long chain fatty acid CoA ligase \\ \hline 55.m04829 & VIIb & 1 & 3 & 1 & 2 & SRS26A \\ \hline 44.m02583 & VIII & 0 & 2 & 9 & 11 & Hypothetical \\ \hline 44.m05903 & VIII & 0 & 2 & 7 & 8 & Hypothetical \\ \hline 57.m01765 & IX & 0 & 2 & 143 & 231 & Protein kinase domain containing \\ \hline 2.m00067 & IX & 3 & 7 & 0 & 0 & Hypothetical \\ \hline 57.m01732 & IX & 0 & 2 & 7 & 8 & Hypothetical \\ \hline 80.m02252 & IX & 1 & 1 & 4 & 2 & Phosphoenolpyruvate carboxykinase, putative \\ \hline 42.m07434 & X & 0 & 2 & 0 & 0 & Hypothetical \\ \hline 551.m00238 & XII & 3 & 6 & 8 & 44 & ROP5 \\ \hline 65.m00001 & XII & 4 & 0 & 9 & 6 & NTPase I \\ \hline \end{tabular} \end{table}
PMC2718519_table_2
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline \textbf{Chromosome (type*)} & \textbf{Comparator} & \textbf{Gene ID (v4.3)} & \textbf{Protein description} & \textbf{dN/dS ratio†} & \textbf{P-value} \\ \hline Ia (III) & Me49 (II) & 83.m02145 & Rhoptry kinase ROP4/ROP7 & Infinity & 0.025 <P < 0.050 \\ \hline IV (II) & VEG (III) & 641.m01516 & Hypothetical & Infinity & 0.005 <P < 0.010 \\ \hline V (III) & Me49 (II) & 39.m00623 & Proline-rich protein & Infinity & 0.010 <P < 0.025 \\ \hline V (III) & Me49 (II) & 31.m01816 & Iron-sulfur cluster assembly accessory protein, putative & Infinity & 0.010 <P < 0.025 \\ \hline V (III) & Me49 (II) & 76.m01544 & Hypothetical & Infinity & 0.010 <P < 0.025 \\ \hline VI (II) & VEG (III) & 49.m03376 & Hypothetical & Infinity & 0.025 <P < 0.050 \\ \hline VI (II) & VEG (III) & 49.m03382 & Hypothetical & Infinity & 0.010 <P < 0.025 \\ \hline VI (II) & VEG (III) & 49.m03431 & Hypothetical & Infinity & 0.010 <P < 0.025 \\ \hline VIII (III) & Me49 (II) & 59.m07776 & Hypothetical & Infinity & 0.025 <P < 0.050 \\ \hline VIII (III) & Me49 (II) & 59.m03361 & Transporter, major facilitator family domain containing & 4.325 & 0.010 <P < 0.025 \\ \hline X (II) & Me49 (II) & 42.m07434 & Hypothetical & Infinity & 0.010 <P < 0.025 \\ \hline X (II) & VEG (III) & 42.m03570 & LytB domain-containing protein & Infinity & 0.025 <P < 0.050 \\ \hline X (II) & VEG (III) & 42.m00013 & GRA3 & Infinity & 0.010 <P < 0.025 \\ \hline X (II) & VEG (III) & 46.m02909 & Hypothetical & Infinity & 0.025 <P < 0.050 \\ \hline XII (III) & Me49 (II) & 551.m00237 & Hypothetical & Infinity & 0.025 <P < 0.050 \\ \hline XII (III) & Me49 (II) & 145.m00337 & Hypothetical & 6.527 & 0.010 <P < 0.025 \\ \hline \end{tabular} \end{table}
PMC2718519_table_3
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline \textbf{Chromosome} & \textbf{Intron length* (bp)} & \textbf{Minor SNPs in introns} & \textbf{MRCA Me49/UgII (years)} & \textbf{MRCA VEG/UgIII (years)} \\ \hline Type II \\ \hline II & 89,003 & 34 & 19,691 \\ \hline IV & 85,471 & 58 & 34,979 \\ \hline VI & 152,385 & 65 & 21,987 \\ \hline VIIa & 198,902 & 28 & 7,256 \\ \hline IX & 266,876 & 117 & 22,598 \\ \hline X & 334,181 & 79 & 12,186 \\ \hline Total II & 1,126,818 & 381 & 17,429 \\ \hline Type III \\ \hline Ia & 80,522 & 2 & & 1,280 \\ \hline Ib & 85,805 & 8 & & 4,806 \\ \hline III & 82,660 & 9 & & 5,612 \\ \hline V & 119,536 & 15 & & 6,468 \\ \hline VIIb & 220,517 & 39 & & 9,116 \\ \hline VIII & 337,557 & 78 & & 11,911 \\ \hline XII & 352,605 & 78 & & 11,403 \\ \hline Total III & 1,279,202 & 229 & & 9,228 \\ \hline \end{tabular} \end{table}
PMC2718519_table_4
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline \textbf{Chromosome} & \textbf{Length* (bp)} & \textbf{Minor SNPs} & \textbf{Major SNPs} & \textbf{MRCA Me49/UgII (years)} & \textbf{MRCA VEG/UgIII (years)} \\ \hline Type II \\ \hline II & 2,302,931 & 125 & 4,370 & 4,291 \\ \hline IV & 2,576,468 & 236 & 4,731 & 7,483 \\ \hline VI > 2.6 Mb & 1,000,655 & 70 & 1,913 & 5,489 \\ \hline VIIa & 4,502,211 & 135 & 8,663 & 2,338 \\ \hline IX 0.5-4 Mb & 3,500,000 & 205 & 6,349 & 4,843 \\ \hline X & 7,418,475 & 445 & 13,459 & 4,960 \\ \hline Total II & 21,300,740 & 1,216 & 39,845 & 4,578 \\ \hline Type III \\ \hline Ib > 1.2 Mb & 756,324 & 6 & 1,375 & & 655 \\ \hline III < 1.9 Mb & 1,900,000 & 33 & 3,953 & & 1,252 \\ \hline V & 3,147,601 & 80 & 5,725 & & 2,096 \\ \hline VIIb < 2.5 Mb & 2,500,000 & 43 & 5,069 & & 1,272 \\ \hline VIII > 4 Mb & 2,923,375 & 49 & 6,268 & & 1,173 \\ \hline XII < 1.5 Mb & 1,500,000 & 69 & 3,259 & & 3,176 \\ \hline Total III & 12,727,300 & 280 & 25,648 & & 1,638 \\ \hline \end{tabular} \end{table}
PMC2718519_table_5
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|l|l|l|l|l|l|l|l|} \hline \textbf{Locus amino acid position} & \multicolumn{10}{c|}{\textbf{SRS22H (VI-13)}} & \multicolumn{3}{c|}{\textbf{Toxofilin}} & \textbf{SRS16B} \\ \hline & \textbf{111} & \textbf{113} & \textbf{138} & \textbf{139} & \textbf{140} & \textbf{141} & \textbf{143} & \textbf{144} & \textbf{146} & \textbf{150} & \textbf{147} & \textbf{168} & \textbf{176} & \textbf{77} \\ \hline Me49 (II) & E & E & K & P & S & A & H & R & T & D & L & E & K & A \\ \hline TgCkUg5 & * & G & * & G & * & * & * & * & * & * & * & * & R & * \\ \hline TgCkUg9 & * & * & * & * & * & * & * & * & * & V & * & D & R & * \\ \hline TgCkUg7 & * & * & * & * & * & * & * & * & * & * & Q & D & R & E \\ \hline TgCkUg1 & * & * & * & * & * & * & * & * & * & * & Q & * & * & E \\ \hline TgCkUg8 & * & * & * & * & * & * & * & * & * & * & Q & * & * & E \\ \hline TgCkUg3 & * & * & * & * & * & * & * & * & * & V & Q & * & * & E \\ \hline TgCkUg2 & D & G & T & G & T & G & R & * & P & V & Q & * & * & E \\ \hline TgCkUg6 & D & G & N & G & * & G & R & S & P & V & E & * & * & T \\ \hline VEG (III) & * & * & * & * & * & * & * & * & * & * & E & * & * & T \\ \hline GT1 (I) & * & G & S & A & T & E & R & S & D & G & Q & * & R & A \\ \hline \end{tabular} \end{table}
PMC2718519_table_6
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|l|l|l|l|l|l|l|l|} \hline \textbf{Locus position} & \multicolumn{7}{c|}{\textbf{VIII-19 0.9 Mb}} & \multicolumn{4}{c|}{\textbf{VIII-20 2.1 Mb}} & \multicolumn{3}{c|}{\textbf{VIII-21 5.8 Mb}} \\ \hline \textbf{Me49 (II)} & \textbf{\textbf{A}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{\textbf{\textbf{\textbf{G}}}} & \textbf{\textbf{\textbf{C}}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{\textbf{\textbf{C}}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{\textbf{\textbf{\textbf{G}}}} & \textbf{\textbf{A}} & \textbf{\textbf{\textbf{\textbf{G}}}} & \textbf{\textbf{\textbf{C}}} & \textbf{\textbf{\textbf{\textbf{G}}}} \\ \hline \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}}g\textbf{\textbf{\textbf{C}}}kUg5 & * & * & * & * & * & * & * & * & * & * & * & * & * & * \\ \hline \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}}g\textbf{\textbf{\textbf{C}}}kUg8 & * & * & * & * & \textbf{\textbf{A}} & \textbf{\textbf{\textbf{C}}} & * & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & * & \textbf{\textbf{A}} & * & * & * & * \\ \hline \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}}g\textbf{\textbf{\textbf{C}}}kUg2 & * & * & * & * & \textbf{\textbf{A}} & \textbf{\textbf{\textbf{C}}} & * & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & * & \textbf{\textbf{A}} & * & \textbf{\textbf{A}} & \textbf{\textbf{A}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} \\ \hline \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}}g\textbf{\textbf{\textbf{C}}}kUg6 & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & * & \textbf{\textbf{\textbf{C}}} & \textbf{\textbf{\textbf{\textbf{G}}}} & * & * & \textbf{\textbf{\textbf{C}}} & * & \textbf{\textbf{\textbf{C}}} & * & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{\textbf{A}} & \textbf{\textbf{A}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} \\ \hline VE\textbf{\textbf{\textbf{\textbf{G}}}} (III) & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{\textbf{\textbf{C}}} & \textbf{\textbf{\textbf{C}}} & \textbf{\textbf{\textbf{\textbf{G}}}} & * & * & \textbf{\textbf{\textbf{C}}} & * & \textbf{\textbf{\textbf{C}}} & * & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} & \textbf{\textbf{A}} & \textbf{\textbf{A}} & \textbf{\textbf{\textbf{\textbf{\textbf{T}}}}} \\ \hline \end{tabular} \end{table}
PMC2718519_table_7
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline & \multicolumn{5}{c|}{\textbf{Ontology}} \\ \hline \textbf{Entity} & \textbf{At} & \textbf{Hs} & \textbf{Sc} & \textbf{Sp} & \textbf{Total} \\ \hline Proteins & 3,572 & 26,220 & 14,685 & 2,388 & 46,865 \\ \hline Genes & 3,027 & 8,699 & 4,498 & 1,439 & 17,663 \\ \hline Protein protein interactions & 1,524 & 8,707 & 9,903 & 447 & 20,581 \\ \hline \end{tabular} \end{table}
PMC2718524_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline & \multicolumn{5}{c|}{\textbf{Ontology}} \\ \hline \textbf{Type of proteins} & \textbf{At} & \textbf{Hs} & \textbf{Sc} & \textbf{Sp} & \textbf{Total} \\ \hline Core cell cycle & 3,276 & 9,114 & 1,648 & 1,348 & 15,386 \\ \hline Added from IntAct & 166 & 1,671 & 2,777 & 80 & 4,694 \\ \hline Modified proteins added from UniProt & 126 & 15,328 & 10,200 & 926 & 26,580 \\ \hline \textbf{Total} & 3,572 & 26,220 & 14,685 & 2,388 & 46,865 \\ \hline \end{tabular} \end{table}
PMC2718524_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline & \multicolumn{5}{c|}{\textbf{Ontology}} \\ \hline \textbf{Entity} & \textbf{At} & \textbf{Hs} & \textbf{Sc} & \textbf{Sp} & \textbf{Total} \\ \hline Proteins & 14,892 & 54,109 & 18,007 & 3,635 & 90,643 \\ \hline Genes & 4,595 & 10,005 & 4,695 & 1,744 & 21,039 \\ \hline Orthology types & - & - & - & - & 5,772 \\ \hline \end{tabular} \end{table}
PMC2718524_table_2
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|} \hline \textbf{Mutant alias} & \textbf{Mutated residues} \\ \hline CDK-3A & S553A, S697A, S811A \\ \hline CDK-4A & S553A, S697A, T704A, S811A \\ \hline PAK-A & S563A, S729A, TTSSS(737–741)AAAAA \\ \hline CDK-A/PAK-A & S245A, S553A, S563A, S697A, T704A, S729A, TTSSS(737–741)AAAAA, S811A \\ \hline CDK-DE & S553D, S697D, T704E, S811D \\ \hline PAK-DE & S563D, S729D, T738E, S741D \\ \hline \end{tabular} \end{table}
PMC2718613_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|} \hline \textbf{Mutant alias} & \textbf{Mutated residues} \\ \hline PH-A & All mapped residues within the PH domain \\ \hline Linker-A & All mapped residues within the linker region and T704A \\ \hline PH-A/linker-A & All mapped residues within PH and linker regions and T704A \\ \hline 35A & All 35 mapped residues and T134A, S245A, T704A \\ \hline \end{tabular} \end{table}
PMC2718613_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline \textbf{HLA allele} & \textbf{Imputed number of alleles} & \textbf{2/2} & \textbf{2/+} & \textbf{+/+} \\ \hline \multirow{16}{*}{Cw*0602} & 0 & 247 & 0 & 0 \\ \hline 0.805 & 0 & 1 & 0 \\ \hline 0.955 & 0 & 1 & 0 \\ \hline 0.991 & 0 & 2 & 0 \\ \hline 0.992 & 0 & 1 & 0 \\ \hline 0.993 & 0 & 3 & 0 \\ \hline 0.994 & 0 & 1 & 0 \\ \hline 0.995 & 0 & 1 & 0 \\ \hline 0.996 & 0 & 7 & 0 \\ \hline 0.997 & 0 & 6 & 0 \\ \hline 0.998 & 0 & 4 & 0 \\ \hline 0.999 & 0 & 13 & 0 \\ \hline 1 & 0 & 115 & 0 \\ \hline 1.992 & 0 & 0 & 1 \\ \hline 1.998 & 0 & 0 & 3 \\ \hline 2 & 0 & 0 & 3 \\ \hline \multirow{6}{*}{Cw*1203} & 0 & 368 & 1 & 0 \\ \hline 0.991 & 0 & 2 & 0 \\ \hline 0.998 & 0 & 1 & 0 \\ \hline 0.999 & 0 & 7 & 0 \\ \hline 1 & 1 & 28 & 0 \\ \hline 2 & 0 & 0 & 2 \\ \hline \end{tabular} \end{table}
PMC2718700_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|} \hline \textbf{Cw*0602} & \textbf{rs13437088a} & \textbf{rs2073048b} & \textbf{Case (\%)} & \textbf{Control (\%)} & \textbf{O.R. [95\%CI]} & \textbf{p-value} \\ \hline - & - & - & 54 (4) & 146 (10) & 1 & Ref. \\ \hline - & - & + & 306 (23) & 518 (37) & 1.60 [1.13–2.25] & 0.007 \\ \hline - & + & - & 86 (6) & 189 (14) & 1.23 [0.82–1.84] & 0.31 \\ \hline - & + & + & 277 (20) & 308 (22) & 2.43 [1.71–3.46] & 561027 \\ \hline + & - & - & 25 (2) & 19 (1) & 3.56 [1.81–6.97] & 0.0001 \\ \hline + & - & + & 192 (14) & 86 (6) & 6.04 [4.04–9.03] & 1610219 \\ \hline + & + & - & 75 (6) & 28 (2) & 7.24 [4.24–12.4] & 2610214 \\ \hline + & + & + & 342 (25) & 104 (7) & 8.89 [6.07–13.0] & 5610233 \\ \hline \end{tabular} \end{table}
PMC2718700_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline \textbf{HLA-B serotype} & \textbf{[95\%CI]a Adjusted O.R.} & \textbf{p-valuea Adjusted} & \textbf{[95\%CI]b Cw6 -/- O.R.} & \textbf{p-valueb Cw6 -/-} \\ \hline 7 & 0.90 [0.75–1.07] & 0.24 & 0.91 [0.74–1.10] & 0.33 \\ \hline 8 & 1.13 [0.93–1.37] & 0.23 & 1.13 [0.91–1.38] & 0.27 \\ \hline 13 & 1.16 [0.83–1.64] & 0.38 & 1.26 [0.47–3.37] & 0.64 \\ \hline 15 & 1.01 [0.81–1.26] & 0.91 & 1.09 [0.86–1.39] & 0.48 \\ \hline 18 & 0.96 [0.71–1.30] & 0.80 & 0.93 [0.68–1.29] & 0.67 \\ \hline 35 & 0.91 [0.74–1.13] & 0.40 & 0.90 [0.71–1.14] & 0.38 \\ \hline 40 & 0.61 [0.47–0.79] & 0.0002c & 0.65 [0.49–0.87] & 0.003c \\ \hline 44 & 0.85 [0.71–1.03] & 0.09 & 0.77 [0.62–0.95] & 0.01 \\ \hline 57 & 1.66 [1.25–2.19] & 0.0004c & 2.92 [1.36–6.25] & 0.006 \\ \hline 58 & 1.22 [0.54–2.73] & 0.64 & 1.09 [0.44–2.71] & 0.85 \\ \hline \end{tabular} \end{table}
PMC2718700_table_2
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|} \hline \textbf{Isolate} & \textbf{Top Hit (Genbank Number)} & \textbf{Identity\%} \\ \hline 1B & Bacillus sp. RC33 (FJ263036.1) & 100 \\ \hline 1C & Bacillus sp. W1-17 (FJ560473.1) & 100 \\ \hline 1D & Bacillus niacini strain YM1C7 (EU221338.1) & 97.93 \\ \hline 2A# & Enterobacter sp. CTSP29 (EU855207.1) & 99 \\ \hline 2B & Bacillus sp. SX51 (DQ227355.1) \\ \hline 2C, 3B, 4A, 5A, 5B & Bacillus thuringiensis serovar tenebrionis (EU429671.1) & 100 \\ \hline 3A & Bacterium 3A13 (DQ298760.1) & 99 \\ \hline 3C & Arthrobacter sp. FB24 (EU147009.1) & 100 \\ \hline 3E, 3F & Bacillus sp. A1 (2008) (FJ535468.1) & 100 \\ \hline 5C & Bacillus sp. BM1-4 (FJ528077.1) & 100 \\ \hline 6A, 6C* & Pseudomonas putida strain J312 (EF203210.1) & 98.50 \\ \hline 6B*, # & Stenotrophomonas maltophilia strain CMG3098 (EU048328.1) & 98.99 \\ \hline 6E* & Pseudomonas plecoglossicida strain S19 (DQ095907.1) & 98.52 \\ \hline 6F* & Pseudomonas sp. lm10 (EU240462.1) & 98.72 \\ \hline 6G* & Pseudomonas sp. GNE25 (AM397659.1) & 95 \\ \hline 7A*, # & Aeromonas sp. LD151 (AM913921.1) & 97.34 \\ \hline 7Ca* & Shewanella sp. Hac353 (DQ307734.1) & 99 \\ \hline 7Cb & Bacillus pumilus strain TPR18 (EU373436.1) & 99 \\ \hline 8A*, # & Paenibacillus sp. oral clone CA007 (AF385540.1) & 92 \\ \hline 8B*,# & Aeromonas hydrophila strain IB343 (EU770277.1) & 99 \\ \hline \end{tabular} \end{table}
PMC2718701_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|} \hline \textbf{Designation} & \textbf{Genotype or Description} & \textbf{Reference or Source} \\ \hline Plasmids \\ \hline pBME53-YopT & CmR pACYC184 derivative containing HindIII-sycE-yopE53-BamHI-yopT-SalI. & [56] \\ \hline pBME53-Cre & Derivative of pBME53-YopT. BamHI-yopT – SalI fragment was replaced by BamHI –nls-cre–SalI CmR resulting in HindIII- sycE-yopE53-BamHI-nls-cre-SalI. & This study \\ \hline pIV2 & Cloning vector based on a small kryptic plasmid from Y. enterocolitica biogroup 1A strain 29807 KanR modified with a kanamycin resistance marker and a pBluescript MCS. & [57] \\ \hline pIV2-SycE-YopE53-Cre & KanR Derivative of pIV2 with insertion of HindIII sycE-yopE53-BamHI-nls-cre-SalI into MCS. & This study \\ \hline pMK4 & Derivative of pIV2-SycE-YopE53-Cre with insertion of asd under control of its own promoter KanR between the ApaI and XhoI sites. & This study \\ \hline pMK1 & SK(+). AmpR SalI-asd 39UTR-EcoRI-asd 59UTR-XbaI in pBluescript II & This study \\ \hline pMK2 & CmR 39UTR-EcoRI-asd 59UTR-XbaI SalI-asd in pMRS101. & This study \\ \hline pMK3 & CmR asd mutator plasmid, derived from pMK2 by NotI digestion and relegation. & This study \\ \hline pMRS101 & CmR Mutator plasmid. & [59] \\ \hline pBME53-Bla & Derivative of pBME53-YopT. BamHI-yopT – SalI fragment was replaced by BamHI–bla– SalI CmR resulting in HindIII sycE-yopE53-BamHI-bla-SalI. & This study \\ \hline pMK-Bla & HindIII sycE-yopE53-BamHI-NLS-Cre-SalI fragment of pMK4 was replaced by a HindIII KanR sycE-yopE53-BamHI-bla-SalI fragment of pBM53-Bla. & This study \\ \hline pYopE1–138Ova247–355 & pACYC184 derivative containing HindIII- sycE-yopE138-BamHI-ova147–355- SalI & [58] \\ \hline pBME53-Ova & Derivative of pBME53-YopT. BamHI-yopT – SalI fragment was replaced by CmR BamHI– ova147–355- SalI. & This study \\ \hline pMK-Ova & Derivative of pMK-Bla. BamHI-bla-SalI was replaced by BamHI– ova147–355- SalI from KanR pBME53-Ova. & This study \\ \hline pMSL41 & ArsR pYV40 with deletion in the yscN gene (yscND169–177). & [27,59] \\ \hline Y. enterocolitica E40 strains \\ \hline E40 & NalR, ArsR Serotype O:9 patient isolate. & [27] \\ \hline E40 Dasd & E40 strain with asd gene knockout, deficient in L-aspartate-dehydrogenase expression. NalR, ArsR, DAPaux & This study \\ \hline E40-pBla & NalR, ArsR, KanR E40 Dasd strain transformed by pMK-Bla. & This study \\ \hline pYV2 Dasd pBla & NalR, KanR E40 Dasd pMK-Bla strain without pYV40 virulence plasmid. & This study \\ \hline DYscN-pBla & pYV2 NalR, ArsR, KanR Dasd pBla strain transformed by pMSL41. & This study \\ \hline E40-pOva & NalR, ArsR, KanR E40 Dasd strain transformed by pMK-Ova. & This study \\ \hline \end{tabular} \end{table}
PMC2718809_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|} \hline \textbf{Lipid class} & \textbf{Wt Mtb (\%)} & \textbf{MtbDwhiB3 (\%)} \\ \hline DIM A & 10 & 50 \\ \hline DIM B & 5 & 20 \\ \hline SL-1 & 45 & 4 \\ \hline PAT & 29 & 10 \\ \hline DAT & 5 & 1 \\ \hline TAG & 1 & 5 \\ \hline polara Highly & 5 & 10 \\ \hline \end{tabular} \end{table}
PMC2718811_table_0
\begi\textbf{n}{table} \ce\textbf{n}teri\textbf{n}g \label{tab:tablelabel} \begi\textbf{n}{tabular}{|l|l|l|l|l|l|l|l|l|} \hli\textbf{n}e \textbf{Populatio\textbf{n}} & \textbf{n} & \textbf{K(\%)} & \textbf{Sd} & \textbf{SD(SE)} & \textbf{Pi} & \textbf{hk (95\%)} & \textbf{Tajma’SD(P)f} & \textbf{Fu’s Fs (P)f} \\ \hli\textbf{n}e Bhumia & 20 & 15(75) & 32 & 0.9708 (0.0273) & 6.269 (3.112) & 30.88(12.14–83.86) & 21.25(21.109) & 25.74 \\ \hli\textbf{n}e Che\textbf{n}chu & 97 & 57(59) & 62 & 0.9794 (0.0056) & 4.616(2.285) & 57.08(38.05–85.91) & 21.99 & 225.63 \\ \hli\textbf{n}e Dhurva & 15 & 12(80) & 25 & 0.9619 (0.039) & 4.933(2.544) & 25.68(9.10–78.00) & 21.45(20.071) & 24.99 \\ \hli\textbf{n}e Dommari & 80 & 52(65) & 59 & 0.9601(0.015) & 3.708(1.89) & 63.30(40.33–100.24) & 22.26 & 226.06 \\ \hli\textbf{n}e Dusadh & 77 & 33(43) & 43 & 0.9651 (0.007) & 5.147(2.52) & 21.34(13.40–33.70) & 21.33(20.087) & 216.13 \\ \hli\textbf{n}e Gadaba & 16 & 13(81) & 29 & 0.9667 (0.035) & 4.808(2.477) & 30.01(10.75–90.51) & 21.85 & 26 \\ \hli\textbf{n}e Go\textbf{n}d & 60 & 46(76) & 70 & 0.9887 (0.005) & 6.671(3.192) & 88.42(50.67–158.73) & 21.9 & 225.11 \\ \hli\textbf{n}e Ka\textbf{n}war & 32 & 29(90) & 62 & 0.9940 (0.009) & 8.917(4.21) & 144.67(56.00–415.50) & 21.45(20.068) & 219.37 \\ \hli\textbf{n}e Korku & 37 & 28(75) & 43 & 0.9775 (0.013) & 6.366(3.08) & 50.73(25.63–104.23) & 21.36(20.084) & 217.49 \\ \hli\textbf{n}e Koya & 37 & 25(67) & 41 & 0.9715 (0.013) & 5.276(2.60) & 32.62(17.08–63.60) & 21.65 & 214.41 \\ \hli\textbf{n}e Malaya\textbf{n} & 28 & 18(64) & 35 & 0.8995 (0.051) & 3.896(2.01) & 20.69(10.04– 43.44) & 22.09 & 29.66 \\ \hli\textbf{n}e Mudiraj & 79 & 61(77) & 67 & 0.9880 (0.005) & 5.492(2.67) & 120.96(73.75–203.17) & 21.97 & 225.37 \\ \hli\textbf{n}e Mu\textbf{n}da & 29 & 15(52) & 30 & 0.9655 (0.012) & 6.004 (2.94) & 11.79(5.80–23.89) & 20.77(20.235) & 22.57(.146) \\ \hli\textbf{n}e Mutharsui & 38 & 32(84) & 44 & 0.9872 (0.010) & 4.012(2.05) & 92.86(43.64–210.72) & 22.19 & 225.85 \\ \hli\textbf{n}e Padmashal & 52 & 39(75) & 49 & 0.9864 (0.007) & 4.843(2.40) & 69.21(38.60–127.64) & 21.89 & 225.59 \\ \hli\textbf{n}e Pa\textbf{n}ika & 87 & 57(65) & 63 & 0.9821 (0.006) & 5.778(2.79) & 70.71(45.80–110.15) & 21.75 & 225.27 \\ \hli\textbf{n}e Rajkoya & 62 & 42(68) & 47 & 0.9841 (0.006) & 5.276(2.58) & 55.98(33.52–94.84) & 21.58 & 225.46 \\ \hli\textbf{n}e Reddy & 30 & 24(80) & 46 & 0.9793 (0.016) & 5.287(2.62) & 53.53(24.48– 123.85) & 22.02 & 216.77 \\ \hli\textbf{n}e Savara & 21 & 18(86) & 37 & 0.9810 (0.022) & 6.561(3.23) & 56.67(21.08–166.84) & 21.42(20.075) & 29.31 \\ \hli\textbf{n}e So\textbf{n}r & 96 & 40(77) & 52 & 0.9594 (0.009) & 6.558(3.12) & 25.22(16.55–38.16) & 21.12(20.132) & 217.78 \\ \hli\textbf{n}e Thoti & 30 & 12(40) & 34 & 0.9218 (0.025) & 6.287(3.06) & 6.91(3.32–14.06) & 20.97(20.176) & 20.06(.512) \\ \hli\textbf{n}e Bo\textbf{n}da & 29 & 21(72) & 37 & 0.9631(0.023) & 4.837(2.43) & 32.71(15.61–70.95) & 21.79 & 212.3 \\ \hli\textbf{n}e Lambadi & 55 & 49(89) & 61 & 0.9960(0.004) & 5.296(2.59) & 211.85(102.56–470.83) & 22.07 & 225.45 \\ \hli\textbf{n}e Valmiki & 53 & 35(66) & 51 & 0.9819(0.007) & 5.20(2.55) & 43.76(25.33–76.65) & 21.84 & 225.19 \\ \hli\textbf{n}e Tadvi & 35 & 25(71) & 32 & 0.9714(0.016) & 4.349(2.20) & 37.70(19.16–76.36) & 21.55 & 218.28 \\ \hli\textbf{n}e Jua\textbf{n}g & 48 & 24(50) & 34 & 0.9001(0.034) & 5.743(2.8) & 18.43(10.47–32.33) & 20.84(20.225) & 28.28 \\ \hli\textbf{n}e Bharia & 35 & 22(63) & 36 & 0.9323(0.030) & 4.793(2.39) & 24.37(12.69–47.45) & 21.61 & 211.3 \\ \hli\textbf{n}e Sugali & 21 & 11(52) & 24 & 0.9238(0.036) & 4.590(2.34) & 8.61(3.80–19.44) & 21.18(20.126) & 21.83(.2) \\ \hli\textbf{n}e Kotwalia & 91 & 24(26) & 44 & 0.9399(0.009) & 5.69(2.75) & 10.29(6.28–16.53) & 21.08(20.134) & 23.83(.119) \\ \hli\textbf{n}e Pardha\textbf{n} & 42 & 32(76) & 63 & 0.9861(0.008) & 6.55(3.16) & 59.62(31.15–118.21) & 21.97 & 221.96 \\ \hli\textbf{n}e \e\textbf{n}d{tabular} \e\textbf{n}d{table}
PMC2718812_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline \textbf{Prediction method} & \textbf{Data used} & \textbf{Reference gDNA} & \textbf{Correct Positive Rate} & \textbf{Sensitivity} & \textbf{Specificity} \\ \hline Threshold & hybridisation intensity & None & 0.6672 & 0.9592 & 0.1620 \\ \hline Threshold & hybridisation intensity & Pba1043 & 0.7587 & 0.8943 & 0.5239 \\ \hline Threshold & log hybridisation ratio & Pba1043 & 0.7715 & 0.8975 & 0.5534 \\ \hline HMM & hybridisation intensity & None & 0.6952 & 0.9585 & 0.2399 \\ \hline HMM & hybridisation intensity & Pba1043 & 0.7715 & 0.9078 & 0.5355 \\ \hline HMM & log hybridisation ratio & Pba1043 & 0.7796 & 0.9060 & 0.5607 \\ \hline \end{tabular} \end{table}
PMC2718846_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline \textbf{Analysis Method} & \textbf{Correct Prediction Rate} & \textbf{Positive Prediction Rate} & \textbf{Sensitivity} & \textbf{Count} \\ \hline Pba1043:Dda3937 & & & & 1630 \\ \hline HMM (Pba1043:Dda3937) & 0.7796 & 0.7752 & 0.5607 & 1179 \\ \hline GACK (0\% EPP) & 0.6512 & 0.9642 & 0.0497 & 84 \\ \hline GACK (50\% EPP) & 0.7011 & 0.9360 & 0.1975 & 344 \\ \hline GACK (100\%EPP) & 0.7355 & 0.8807 & 0.3214 & 595 \\ \hline MPP (BPP) & 0.6337 & 0.0000 & 0.0000 & 0 \\ \hline MPP (EPP) & 0.6337 & 0.0000 & 0.0000 & 0 \\ \hline Lactococcus lactis & & & & 379 \\ \hline HMM (Lactococcus) & 0.8404 & 0.7253 & 0.1741 & 91 \\ \hline GACK (0\% EPP) & 0.8210 & 0.0000 & 0.0000 & 0 \\ \hline GACK (50\% EPP) & 0.7616 & 0.2418 & 0.1557 & 244 \\ \hline GACK (100\%EPP) & 0.7616 & 0.2418 & 0.1557 & 244 \\ \hline MPP (BPP) & 0.8220 & 1.0000 & 0.0053 & 2 \\ \hline MPP (EPP) & 0.8210 & 0.5000 & 0.0053 & 4 \\ \hline \end{tabular} \end{table}
PMC2718846_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline \textbf{Island} & \textbf{Locus tags} & \textbf{Genomic location} & \textbf{Putative phenotype, and representative genes} \\ \hline PbaI5 & ECA0487-ECA0491 & 563151-567396 & phosphonate metabolism (fom1, fom2, phnG) \\ \hline PbaI7 & ECA0600-ECA0610 & 659712-682903 & coronafacic acid synthesis (cfa1-8B, cfl) \\ \hline PbaI13 & ECA1420-ECA1441 & 1611940-1636204 & polysaccharide and O-antigen synthesis (rfb, nah) \\ \hline PbaI14 & ECA1477-ECA1481 & 1673637-1678411 & transcriptional regulators \\ \hline PbaI22 & ECA2068-ECA2073 & 2355814-2362568 & permease and transporter \\ \hline PbaI27 & ECA2294-ECA2295 & 2599459-2602654 & glycosyl transferase \\ \hline PbaI33 & ECA2693-ECA2705 & 3028797-3040751 & polyketide synthase, phenazine synthesis (ehpA-G, ehpR) \\ \hline PbaI39 & ECA2933-ECA2936 & 3278434-3281122 & nitrogen fixation (nifQ) \\ \hline PbaI41 & ECA2972-ECA2982 & 3322878-3332514 & multidrug efflux (emrE) \\ \hline PbaI44 & ECA3446-ECA3450 & 3865038-3872587 & multidrug efflux (oprJ, mexBC, nfxB) \\ \hline PbaI55 & ECA4452-ECA4455 & 4993334-5000237 & hemin storage (hms) \\ \hline PectoI7 & ECA0149-ECA0163 & 169392-186544 & lipopolysaccharide synthesis (waa) \\ \hline PectoI25-27 & ECA0516-ECA0615 & 590843-689677 & mobile element (SPI7-like) \\ \hline PectoI50 & ECA1089-ECA1107 & 1217226-1255583 & cell wall enzymes (pel3, pehA), Type I secretion \\ \hline PectoI61 & ECA1485-ECA1490 & 1680732-1681461 & syringomycin-like non-ribosomal peptide synthase (syrE) \\ \hline PectoI82 & ECA2111-ECA2118 & 2398202-2426503 & type III effectors (dspE, hrpW), agglutinins (hecAB) \\ \hline PectoI96 & ECA2430-ECA2438 & 2744003-2745227 & virulence regultors (rdgAB) \\ \hline PectoI122 & ECA3116-ECA3122 & 3478243-3490068 & type I restriction \\ \hline PectoI129 & ECA3370-ECA3387 & 3786824-3801913 & pyoverdine biosynthesis (pvc) \\ \hline PectoI151 & ECA4078-ECA4084 & 4546706-4554057 & octopine transport (occQMP) \\ \hline PectoI153 & ECA4109-ECA4119 & 4579773-4594107 & siderophore synthesis / receptor \\ \hline \end{tabular} \end{table}
PMC2718846_table_2
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline \textbf{HAI} & \textbf{Locus tags} & \textbf{Pba1039 Islands} & \textbf{Pcc193 Islands} & \textbf{Dda3937 Islands} & \textbf{Putative Phenotypes} \\ \hline \textbf{HAI}1 & ECA0499-ECA0510 & - & - & - & Capsular polysaccharide biosynthesis \\ \hline \textbf{HAI}2 & ECA0516-ECA0614 & - & PccI6-PccI7 & DdaI24 & Polyketide phytotoxin cfa, SPI7 \\ \hline \textbf{HAI}3 & ECA0665-ECA0678 & - & PccI8 & DdaI27 & Phage genes \\ \hline \textbf{HAI}4 & ECA1054-ECA1067 & Pba1039I2-Pba1039I3 & PccI12 & DdaI44 & Phage genes/integrases \\ \hline \textbf{HAI}5 & ECA1417-ECA1443 & - & PccI14 & DdaI55 & Exopolysaccharide and O-antigen biosynthesis (rfb, nah) \\ \hline \textbf{HAI}6 & ECA1446-ECA1488 & - & PccI15 & DdaI56-DdaI58 & Syringomycin-like NRPS (syrE) \\ \hline \textbf{HAI}7 & ECA1598-ECA1679 & Pba1039I4-Pba1039I6 & PccI18 & DdaI62 & Integrases, type IV secretion, arsenate resistance (ars) \\ \hline \textbf{HAI}8 & ECA2045-ECA2182 & - & PccI24-PccI28 & DdaI76-DdaI84 & Type III secretion (hrp), agglutinins (hecAB) \\ \hline \textbf{HAI}9 & ECA2598-ECA2637 & Pba1039I10-Pba1039I11 & PccI34-PccI35 & DdaI100-DdaI101 & P2 family prophage \\ \hline \textbf{HAI}10 & ECA2694-ECA2705 & - & PccI36 & DdaI103 & Phenazine antibiotic biosynthesis (ehp) \\ \hline \textbf{HAI}11 & ECA2750-ECA2759 & - & PccI37 & DdaI104 & Phage genes \\ \hline \textbf{HAI}12 & ECA2850-ECA2879 & Pba1039I12 & PccI38-PccI40 & DdaI107-DdaI108 & Hypothetical, putative type VI substrate (vgrG) \\ \hline \textbf{HAI}13 & ECA2889-ECA2921 & Pba1039I13 & PccI41 & DdaI109 & Putative integrated plasmid \\ \hline \textbf{HAI}14 & ECA2922-ECA3000 & Pba1039I14 & PccI42-PccI44 & DdaI109-DdaI113 & Nitrogen fixation (nif) \\ \hline \textbf{HAI}15 & ECA3262-ECA3270 & - & - & DdaI122 & Agglutination/adhesion (aggA) \\ \hline \textbf{HAI}16 & ECA3378-ECA3460 & - & PccI45-PccI48 & DdaI124-DdaI128 & Multidrug resistance (mex-opr-nfxB) \\ \hline \textbf{HAI}17 & ECA3695-ECA3742 & Pba1039I15 & PccI49-PccI51 & DdaI137-DdaI140 & Prophage \\ \hline \end{tabular} \end{table}
PMC2718846_table_3
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline \textbf{Component analyzed (unit of activity)} & \textbf{Group I (normal)} & \textbf{Group II (cataract-untreated)} & \textbf{Group III (cataract-treated)} \\ \hline Reduced glutathione (ΞΌmoles/gram tissue) & 8.14$\pm$0.10 & 4.6$\pm$0.73* & 7.36$\pm$0.40* \\ \hline Glutathione reductase (nmoles of NADPH oxidized/min/mg protein) & 0.183$\pm$0.07 & 0.115$\pm$0.06* & 0.168$\pm$0.07* \\ \hline Glutathione-S-transferase (ΞΌmoles of CDNB conjugated with GSH/min) & 5.50$\pm$0.32 & 2.89$\pm$0.38* & 4.5$\pm$0.44* \\ \hline Glutathione peroxidase (ΞΌmoles glutathione oxidized/mg protein/min) & 43.41$\pm$4.9 & 25.41$\pm$1.59* & 34.59$\pm$1.67* \\ \hline \end{tabular} \end{table}
PMC2718851_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline \textbf{Enzyme analyzed (unit of activity)} & \textbf{Group I (normal)} & \textbf{Group 2 (cataract-untreated)} & \textbf{Group 3 (cataract-treated)} \\ \hline 1. Catalase (ΞΌmoles hydrogen peroxide consumed/mg protein/min) & 7.45$\pm$0.33 & 4.5$\pm$0.47* & 6.54$\pm$0.31* \\ \hline 2. Superoxide dismutase (units/mg protein) & 2.35$\pm$0.25 & 0.88$\pm$0.08* & 1.66$\pm$0.11* \\ \hline \end{tabular} \end{table}
PMC2718851_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline & \textbf{Total (n = 176)} & \textbf{Boys (n = 87)} & \textbf{Girls (n = 89)} & \textbf{Younger adolescents (n = 98)} & \textbf{Older adolescents (n = 78)} \\ \hline MVPA minutes/day \\ \hline 25th percentile & 30.5 & 37.6 & 25.5** & 39.2 & 22.6*** \\ \hline 50th percentile & 44.1 & 49.3 & 40.5 & 48.1 & 38.1 \\ \hline 75th percentile & 56.4 & 64.3 & 53.1 & 65.1 & 49.5 \\ \hline Frequency of FV consumption/day \\ \hline 25th percentile & 3.1 & 2.8 & 3.3 & 2.5 & 3.8*** \\ \hline 50th percentile & 4.5 & 4.8 & 4.4 & 3.9 & 5.4 \\ \hline 75th percentile & 6.7 & 6.7 & 6.9 & 6.1 & 7.8 \\ \hline Frequency of breakfast consumption, days/week \\ \hline 25th percentile & 4 & 5 & 2.5** & 4 & 4 \\ \hline 50th percentile & 7 & 7 & 6 & 7 & 7 \\ \hline 75th percentile & 7 & 7 & 7 & 7 & 7 \\ \hline \end{tabular} \end{table}
PMC2718856_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline & \textbf{Total (n = 176)} & \textbf{Boys (n = 87)} & \textbf{Girls (n = 89)} & \textbf{Younger adolescents (n = 98)} & \textbf{Older adolescents (n = 78)} \\ \hline Meet >60 minutes MVPA per day, n (\%) \\ \hline No & 137 (78.8) & 63 (72.4) & 74 (83.1) & 68 (69.4) & 69 (88.5) \\ \hline Yes & 39 (22.2) & 24 (27.6) & 15 (16.8) & 30 (30.6) & 9 (11.5)** \\ \hline Meet >5 portions fruits/ vegetables, n (\%) \\ \hline No & 98 (55.2) & 45 (51.2) & 53 (59.6) & 63 (64.3) & 35 (44.9)** \\ \hline Yes & 78 (44.8) & 42 (48.3) & 36 (40.4) & 35 (35.7) & 43 (55.1) \\ \hline Meet >5 days a week eating breakfast, n (\%) \\ \hline No & 41 (23.3) & 13 (14.9) & 28 (31.5) & 23 (23.5) & 18 (23.1) \\ \hline Yes & 135 (76.7) & 74 (85.1) & 61 (68.5)** & 75 (76.5) & 60 (76.9) \\ \hline Number of risk behaviours, n (\%) \\ \hline 0 & 11 (6.2) & 9 (10.3) & 2 (2.2) & 7 (7.1) & 4 (5.1) \\ \hline 1 & 71 (40.3) & 40 (46.0) & 31 (34.8) & 36 (36.7) & 35 (44.9) \\ \hline 2 & 77 (43.8) & 33 (37.9) & 44 (49.4) & 47 (48.0) & 30 (38.5) \\ \hline 3 & 17 (9.7) & 5 (5.7) & 12 13.5)** & 8 (8.2) & 9 (11.5) \\ \hline \end{tabular} \end{table}
PMC2718856_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline \textbf{Number of risk behaviours} & \textbf{Percent of sample} & \textbf{Boys (n = 87)} & \textbf{Girls (n = 89)} & \textbf{Younger adolescents (n = 98)} & \textbf{Older adolescents (n = 78)} \\ \hline 3: All three risk behaviours & 9.7 & 5.7 & 13.5** & 8.2 & 11.5 \\ \hline 2: MVPA < 60 minutes/day and < 5 fruit/vegetables per day & 33.0 & 31.0 & 34.8 & 36.7 & 28.2 \\ \hline 2: MVPA < 60 minutes/day and < 5 days a week eating breakfast & 6.2 & 1.1 & 11.2** & 5.1 & 7.7 \\ \hline 2: < 5 fruit/vegetables per and day < 5 days a week eating breakfast & 5.7 & 5.7 & 5.6 & 8.2 & 2.6 \\ \hline 1: MVPA < 60 minutes/day & 29.0 & 34.5 & 23.6** & 19.4 & 41.0** \\ \hline 1: < 5 fruit/vegetables per day & 7.4 & 9.2 & 5.6 & 11.2 & 2.6** \\ \hline 1: < 5 days a week eating breakfast & 2.8 & 2.3 & 3.4 & 4.1 & 1.3 \\ \hline 0: No risk behaviours & 6.2 & 10.3 & 2.2** & 7.1 & 5.1 \\ \hline \end{tabular} \end{table}
PMC2718856_table_2
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|} \hline VS & $\leq$ $\leq$ $\leq$ $\leq$ $\leq$ Auditory 2 AND Visual 1 AND Motor 2 AND Oromotor/Verbal 2 AND Communication = 0 AND Arousal 2 \\ \hline MCS & Auditory = 3–4 OR Visual = 2–5 OR Motor = 3–5 OR Oromotor/Verbal = 3 OR Communication = 1 \\ \hline Emergence from MCS & Motor = 6 OR Communication = 2 \\ \hline \end{tabular} \end{table}
PMC2718857_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline \textbf{Behavior} & \textbf{VS} & \textbf{MCS} & \textbf{Unsure of diagnosis} \\ \hline 1 – response to verbal order & 4 & * & 4 \\ \hline 2 – purposeful eye movements & 8 & * & 6 \\ \hline 3 – automatic motor response & 1 & * & 1 \\ \hline 4 – pain localization & 1 & * & 1 \\ \hline 5 – several criteria for \textbf{MCS} & 4 & * & 4 \\ \hline 6 – communication & * & 1 & * \\ \hline 7 – functional object use & * & 1 & * \\ \hline 8 – several criteria for E\textbf{MCS} & * & 2 & * \\ \hline Total & 18 & 4 & 16 \\ \hline \end{tabular} \end{table}
PMC2718857_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline & \multicolumn{2}{c|}{\textbf{Full final model $\geq$ (cTnT 0.04, n = 344)}} & \multicolumn{2}{c|}{\textbf{Restricted final model (cTnT 0.04 – 0.09, n = 263)}} \\ \hline \textbf{Characteristic} & \textbf{\textbf{OR}} & \textbf{\textbf{95\% CI}} & \textbf{\textbf{OR}} & \textbf{\textbf{95\% CI}} \\ \hline (ΞΌmol/l) Creatinine + 10 & 1.21 & 1.12 – 1.32 & 1.11 & 0.99 – 1.94 \\ \hline Hemoglobin +1 (mg/dl) & 0.80 & 0.69 – 0.92 & 0.84 & 0.71 – 1.00 \\ \hline Neutrophil count + 5 (106/ml) & 1.52 & 1.20 – 1.94 & 1.48 & 1.13 – 1.94 \\ \hline Heart rate + 10 (beats/minute) & 1.24 & 1.09 – 1.42 & 1.17 & 1.00 – 1.36 \\ \hline CIIS +10 (points) & 1.45 & 1.15 – 1.82 & 1.25 & 0.95 – 1.64 \\ \hline \end{tabular} \end{table}
PMC2718858_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|l|l|l|l|} \hline \textbf{Variable} & \textbf{year} & \multicolumn{2}{c|}{\textbf{Sample size}} & \multicolumn{3}{c|}{\textbf{Population}} & \multicolumn{2}{c|}{\textbf{GDP per capita}} & \multicolumn{2}{c|}{\textbf{Adult literacy rate}} \\ \hline & & \textbf{\textbf{Men}} & \textbf{\textbf{Women}} & \textbf{Total (millions 2005)} & \textbf{Growth rate (1975 – 2005)} & \textbf{\%urban (2005)} & \textbf{Value (US$ 2005)} & \textbf{Growth rate (1990 – 2005)} & \textbf{\textbf{Men}} & \textbf{\textbf{Women}} \\ \hline Benin & 2006 & 6000 & 18000 & 8.5 & 3.2 & 40.1 & 508 & 1.4 & 47.9 & 23.3 \\ \hline Burkina Faso & 2003 & 3605 & 12477 & 13.9 & 2.8 & 18.3 & 391 & 1.3 & 31.4 & 16.6 \\ \hline Ethiopia & 2005 & 6033 & 14070 & 79 & 2.8 & 16 & 157 & 1.5 & 50.0 & 22.8 \\ \hline Ghana & 2003 & 5015 & 5691 & 22.5 & 2.6 & 47.8 & 485 & 2.0 & 66.4 & 49.8 \\ \hline Kenya & 2003 & 3578 & 8195 & 35.6 & 3.2 & 20.7 & 547 & -.1 & 77.7 & 70.2 \\ \hline Lesotho & 2004 & 2797 & 7095 & 2.0 & 1.8 & 18.7 & 808 & 2.3 & 73.7 & 90.3 \\ \hline Liberia & 2007 & 6009 & 7092 & 3.4 & 2.5 & 58.1 & 167 & 2.3 & 58.3 & 45.7 \\ \hline Madagascar & 2004* & 2432 & 7949 & 18.6 & 2.9 & 26.8 & 271 & -.7 & 76.5 & 65.3 \\ \hline Malawi & 2004 & 3261 & 11698 & 13.2 & 3.1 & 17.2 & 161 & 1.0 & 74.9 & 54.0 \\ \hline Mozambique & 2003 & 2900 & 12418 & 20.5 & 2.2 & 34.5 & 335 & 4.3 & 54.8 & 25.0 \\ \hline Namibia & 2007 & 3915 & 9804 & 2.0 & 2.7 & 35.1 & 3016 & 1.4 & 86.8 & 83.5 \\ \hline Nigeria & 2003 & 2346 & 7620 & 141.4 & 2.8 & 48.2 & 752 & 0.8 & 78.2 & 60.1 \\ \hline Rwanda & 2005 & 4820 & 11321 & 9.2 & 2.5 & 19.3 & 238 & 0.1 & 71.4 & 59.8 \\ \hline Swaziland & 2006 & 4156 & 4987 & 1.1 & 2.5 & 24.1 & 2414 & 0.2 & 80.9 & 78.3 \\ \hline Tanzania & 2004 & 2635 & 10329 & 38.5 & 2.9 & 24.2 & 316 & 1.7 & 77.5 & 62.2 \\ \hline Uganda & 2006 & 2503 & 8531 & 28.9 & 3.3 & 12.6 & 303 & 3.2 & 76.8 & 57.7 \\ \hline Zimbabwe & 2006* & 7175 & 8907 & 13.1 & 2.5 & 35.9 & 259 & -2.1 & 92.7 & 86.2 \\ \hline \end{tabular} \end{table}
PMC2718859_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|} \hline \textbf{Age at delivery(yrs)} & \textbf{Number} & \textbf{Percent} \\ \hline 12–19 & 16573 & 18 \\ \hline 20–29 & 52385 & 57 \\ \hline 30–34 & 14345 & 16 \\ \hline 35–50 & 8396 & 9 \\ \hline Status of referral \\ \hline Non official & 80705 & 88 \\ \hline Official & 10994 & 12 \\ \hline Parity \\ \hline 1 & 40187 & 44 \\ \hline 2 & 23141 & 25 \\ \hline 3–5 & 24006 & 26 \\ \hline 6+ & 4365 & 5 \\ \hline Mode of delivery \\ \hline Vaginal & 72431 & 79 \\ \hline CS & 19268 & 21 \\ \hline Birth Weight \\ \hline 2500 g or above & 76889 & 84 \\ \hline 1500 g–2499.9 g & 11962 & 13 \\ \hline <1500 g & 2848 & 3 \\ \hline Use of Oxytocin \\ \hline Not used & 85198 & 93 \\ \hline Used & 6501 & 7 \\ \hline APGAR Score at five minutes \\ \hline 8–10 & 75095 & 82 \\ \hline $\leq$ 7 & 16604 & 18 \\ \hline \end{tabular} \end{table}
PMC2718860_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline & \textbf{All (n = 50)} & \textbf{Males (n = 23)} & \textbf{Females (n = 27)} \\ \hline Age (years) & 11 (0.7 – 18) & 11 (0.7 – 16) & 10 (0.7 – 18) & n.s \\ \hline Weight (kg) & 35 (7–69) & 36 (7 – 69) & 33 (8 – 60) & n.s \\ \hline Height (cm) & 146 (66 – 181) & 147 (67 – 181) & 144 (66 – 170) & n.s \\ \hline BSA (m2) & 1.18 (0.37 – 1.85) & 1.21 (0.37 – 1.85) & 1.18 (0.38 – 1.67) & n.s \\ \hline Heart rate & 84 (55–127) & 78 (55–99) & 88 (58–127) & n.s \\ \hline \end{tabular} \end{table}
PMC2718870_table_0
\\textbf{b}egin{ta\textbf{b}le} \centering \la\textbf{b}el{ta\textbf{b}:ta\textbf{b}lela\textbf{b}el} \\textbf{b}egin{ta\textbf{b}ular}{|l|l|l|l|l|l|l|} \hline & \text\textbf{b}f{a males} & \text\textbf{b}f{a females} & \textbf{b} & \textbf{SD} & \textbf{r2} & \textbf{p-value} \\ \hline LVEDV (ml) & 77.5 & 67.8 & 1.380 & 0.0426 & 0.98 & <0.00005 \\ \hline LVESV (ml) & 29.7 & 26.1 & 1.370 & 0.0647 & 0.95 & <0.005 \\ \hline LVSV (ml) & 47.4 & 41.7 & 1.394 & 0.0500 & 0.97 & <0.0005 \\ \hline LVCO (ml/min) & 3890 & 3622 & 1.062 & 0.0727 & 0.89 & ns \\ \hline LVM (g) & 53 & 45.2 & 1.304 & 0.0475 & 0.97 & <0.00005 \\ \hline Papillary muscle (g) & 1.9 & 1.6 & 1.451 & 0.0976 & 0.85 & <0.05 \\ \hline RVEDV (ml) & 83.8 & 72.7 & 1.469 & 0.0499 & 0.97 & <0.0001 \\ \hline RVESV (ml) & 35.3 & 30.2 & 1.559 & 0.0737 & 0.95 & <0.005 \\ \hline RVSV (ml) & 48.2 & 42.1 & 1.407 & 0.0524 & 0.97 & <0.0005 \\ \hline RVCO (ml/min) & 3947.3 & 3658.3 & 1.076 & 0.0783 & 0.88 & ns \\ \hline RVM (g) & 16.7 & 14.9 & 1.331 & 0.0605 & 0.95 & <0.01 \\ \hline \end{ta\textbf{b}ular} \end{ta\textbf{b}le}
PMC2718870_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|} \hline & \multicolumn{3}{c|}{\textbf{Interobsverser variability}} & \multicolumn{3}{c|}{\textbf{Intraobserver variability}} \\ \hline & \textbf{\textbf{mean difference}} & \textbf{\textbf{limits of agreement}} & \textbf{\textbf{coefficient of variability \%}} & \textbf{\textbf{mean difference}} & \textbf{\textbf{limits of agreement}} & \textbf{\textbf{coefficient of variability \%}} \\ \hline LVEDV (ml) & 1.8 & -1.7/5.2 & 2.3 & -0.1 & -2.3/2.0 & 1.4 \\ \hline LVESV (ml) & 2.5 & -1.8/6.8 & 7.1 & 0.0 & -1.6/1.6 & 2.8 \\ \hline LVM (g) & -5.6 & -11.4/0.3 & 6.3 & -0.5 & -3.2/2.2 & 2.8 \\ \hline LVEF (\%) & -2.6 & -7.9/2.6 & 4.5 & -0.2 & -1.7/1.3 & 1.3 \\ \hline RVEDV (ml) & 0.7 & -6.2/7.5 & 4.2 & -2.3 & -6.5/1.9 & 2.6 \\ \hline RVESV (ml) & 0.2 & -3.4/3.9 & 5.4 & -0.5 & -3.1/2.0 & 3.8 \\ \hline RVM (g) & -3.2 & -5.8/-0.5 & 10.1 & 1.0 & -2.0/3.9 & 9.4 \\ \hline RVEF (\%) & 0.0 & -5.0/5.1 & 4.4 & -0.5 & -4.6/3.5 & 3.5 \\ \hline \end{tabular} \end{table}
PMC2718870_table_2
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline & & \textbf{Mean} & \textbf{Standard deviation} \\ \hline \multirow{2}{*}{Lowest} & Pre-assessment & 67.88 & 17.88 \\ \hline Post-assessment & 69.63 & 16.19 \\ \hline \multirow{2}{*}{Highest} & Pre-assessment & 69.50 & 11.45 \\ \hline Post-assessment & 76.36 & 11.04 \\ \hline \end{tabular} \end{table}
PMC2718872_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline & \multicolumn{2}{c|}{\textbf{Study 1 (The first administration) (n = 166)}} & \multicolumn{2}{c|}{\textbf{Study 2 (n = 2095)}} \\ \hline \textbf{Items} & \textbf{\textbf{Mean}} & \textbf{\textbf{SD}} & \textbf{\textbf{Mean}} & \textbf{\textbf{SD}} \\ \hline Avoidance \\ \hline 1. Put off making appointment & 1.4 & 0.8 & 1.5 & 0.9 \\ \hline 2. Cancelled or failed to appear & 1.1 & 0.4 & 1.2 & 0.6 \\ \hline 8. Making an appointment & 1.4 & 0.8 & 1.4 & 0.7 \\ \hline 9. Approaching dental office & 1.9 & 1.0 & 1.7 & 0.9 \\ \hline 10. Sitting in the waiting room & 1.8 & 1.0 & 1.7 & 0.9 \\ \hline 11. Sitting in dental chair & 2.1 & 1.0 & 2.0 & 1.0 \\ \hline 12. Smell of dental office & 1.8 & 1.0 & 1.6 & 0.9 \\ \hline 13. Seeing the dentist & 1.8 & 1.0 & 1.7 & 0.9 \\ \hline Physiological arousal \\ \hline 3. Muscle tenseness & 2.2 & 0.9 & 2.3 & 1.0 \\ \hline 4. Increase breathing rate & 1.5 & 0.7 & 1.8 & 0.9 \\ \hline 5. Perspiration & 1.6 & 0.8 & 1.6 & 0.8 \\ \hline 6. Nausea & 1.3 & 0.7 & 1.3 & 0.6 \\ \hline 7. Heart beat faster & 2.0 & 0.9 & 1.8 & 0.9 \\ \hline Fears of specific stimuli/situations \\ \hline 14. Seeing anesthetic needle & 2.7 & 1.3 & 2.5 & 1.2 \\ \hline 15. Feeling anesthetic needle & 2.6 & 1.3 & 2.5 & 1.2 \\ \hline 16. Seeing drill & 2.5 & 1.3 & 2.3 & 1.2 \\ \hline 17. Hearing drill & 2.6 & 1.4 & 2.5 & 1.3 \\ \hline 18. Feeling drill & 2.6 & 1.3 & 2.5 & 1.2 \\ \hline 19. Having teeth cleaned & 1.3 & 0.7 & 1.4 & 0.8 \\ \hline 20. Overall fear of dentistry & 2.1 & 1.0 & 2.1 & 1.0 \\ \hline Total & 38.3 & 13.9 & 37.4 & 14.1 \\ \hline \end{tabular} \end{table}
PMC2718877_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|} \hline \textbf{0} & \textbf{No complaints. No objective physical signs} \\ \hline I & Pain. No objective physical signs. \\ \hline II & Pain. Objective musculoskeletal signs, e.g. stiffness. \\ \hline III & Pain. Objective neurological signs, e.g. weakness, numbness, absent tendon reflexes. \\ \hline IV & Pain. Radiological evidence of skeletal injury or dislocation. \\ \hline \end{tabular} \end{table}
PMC2718879_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|} \hline & \multicolumn{2}{c|}{\textbf{ICC Value}} \\ \hline \textbf{C-Spine Motion Variables} & \textbf{Pre-Session Measure} & \textbf{Post-Session Measure} \\ \hline Extension & 0.979 & 0.987 \\ \hline Flexion & 0.912 & 0.956 \\ \hline Left Lateral Flexion & 0.983 & 0.963 \\ \hline Right Lateral Flexion & 0.952 & 0.972 \\ \hline Right Rotation & 0.973 & 0.986 \\ \hline Left Rotation & 0.971 & 0.986 \\ \hline \end{tabular} \end{table}
PMC2718879_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|} \hline & \textbf{Pre-op} & \textbf{Post-op} & \multicolumn{2}{c|}{\textbf{Mean change}} & \multicolumn{2}{c|}{\textbf{Paired t-test}} \\ \hline & \textbf{\textbf{Mean $\pm$ SD}} & \textbf{\textbf{Mean $\pm$ SD}} & \textbf{Degrees} & \textbf{Percent} & \textbf{t statistic} & \textbf{p-value} \\ \hline Flexion & 25.2 $\pm$ 11.9 & 39.6 $\pm$ 12.9 & 14.4 & 57 & -3.61 & 0.002 \\ \hline Extension & 29.3 $\pm$ 13.8 & 44.4 $\pm$ 20.2 & 15.1 & 52 & -4.16 & 0.0008 \\ \hline L Rotation & 36.1 $\pm$ 21.0 & 54.1 $\pm$ 18.2 & 18.0 & 50 & -4.21 & 0.0007 \\ \hline R Rotation & 37.3 $\pm$ 16.3 & 59.1 $\pm$ 16.1 & 21.8 & 58 & -5.78 & 0.00006 \\ \hline L Lat Flexion & 19.4 $\pm$ 14.1 & 25.9 $\pm$ 16.2 & 6.5 & 34 & -3.07 & 0.005 \\ \hline R Lat Flexion & 22.9 $\pm$ 1201 & 32.7 $\pm$ 10.2 & 9.8 & 42 & -4.97 & 0.0002 \\ \hline \end{tabular} \end{table}
PMC2718879_table_2
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|} \hline & \textbf{Pre-op} & \textbf{Post-op} & \multicolumn{2}{c|}{\textbf{Mean Difference}} & \multicolumn{2}{c|}{\textbf{Paired t-test}} \\ \hline & \textbf{\textbf{Mean $\pm$ SD}} & \textbf{\textbf{Mean $\pm$ SD}} & \textbf{Degrees} & \textbf{Percent} & \textbf{t statistic} & \textbf{p-value} \\ \hline Walking speed (cm/sec) & 98.5 $\pm$ 29.1 & 112.4 $\pm$ 17.4 & 13.9 & 14 & -2.94 & 0.007 \\ \hline Cadence (steps/min) & 105.9 $\pm$ 13.8 & 112.1 $\pm$ 7.6 & 6.2 & 6 & -2.32 & 0.02 \\ \hline Step length (cm) & 54.5 $\pm$ 11.1 & 59.7 $\pm$ 7.9 & 5.2 & 10 & -2.79 & 0.009 \\ \hline \end{tabular} \end{table}
PMC2718879_table_3
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|} \hline & \textbf{Pre-op} & \textbf{Post-op} & \multicolumn{2}{c|}{\textbf{Mean change}} & \multicolumn{2}{c|}{\textbf{Paired t-test}} \\ \hline & \textbf{\textbf{Mean $\pm$ SD}} & \textbf{\textbf{Mean $\pm$ SD}} & \textbf{VAS} & \textbf{Percent} & \textbf{t statistic} & \textbf{p-value} \\ \hline Typical day average & 6.2 $\pm$ 2.0 & 2.5 $\pm$ 1.8 & 3.7 & -60 & 3.75 & 0.002 \\ \hline Increase during test & 1.6 $\pm$ 2.4 & 0 $\pm$ 1.9 & 1.6 & -100 & 1.82 & 0.05 \\ \hline \end{tabular} \end{table}
PMC2718879_table_4
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline \textbf{Location of Injury in Surgical Group} & \multicolumn{3}{c|}{\textbf{Number of Elements Evaluated Operatively}} \\ \hline & \textbf{Missile Injury} & \textbf{Shrapnel Injury} & \textbf{Total} \\ \hline Spinal nerve to trunk or trunk (supraclavicular)(n = 22) \\ \hline C5–C6 to upper trunk or upper trunk & 7 & 6 & 13 \\ \hline C7 to middle trunk or middle trunk & 11 & 12 & 23 \\ \hline C8 to T1 to lower trunk or lower trunk & 4 & 3 & 7 \\ \hline Divisions to cord or cord (n = 141)(infraclavicular) \\ \hline Lateral & 24 & 43 & 67 \\ \hline Medial & 82 & 87 & 169 \\ \hline Posterior & 19 & 38 & 57 \\ \hline Cord to nerve or nerve (n = 102) (infraclavicular) \\ \hline Lateral to musculocutaneous & 13 & 18 & 31 \\ \hline Lateral to median & 17 & 13 & 30 \\ \hline Medial to median & 15 & 29 & 44 \\ \hline Medial to ulnar & 12 & 11 & 23 \\ \hline Posterior to radial & 21 & 37 & 58 \\ \hline Posterior to axillary & 10 & 9 & 19 \\ \hline \textbf{Total} (265) & 235 & 306 & 541 \\ \hline \end{tabular} \end{table}
PMC2718880_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|} \hline \multicolumn{3}{c|}{\textbf{Motor recovery}} \\ \hline \textbf{Poor} & \textbf{M0} & \textbf{No contraction} \\ \hline & M1 & Return of perceptible contraction in the proximal muscles \\ \hline \multirow{2}{*}{Fair} & M2 & Return of perceptible contraction in both proximal and distal muscles \\ \hline M3 & Return of perceptible contraction in both proximal and distal muscles of such of degree that all important muscles are sufficiently powerful to act against resistance \\ \hline \multirow{2}{*}{Good} & M4 & Return of function as in stage 3 with the addition that all synergic and independent movements are possible \\ \hline M5 & Complete recovery \\ \hline Sensory & \multicolumn{2}{c|}{recovery} \\ \hline \multirow{2}{*}{\textbf{Poor}} & S0 & No sensation \\ \hline S1 & Deep pain re-established \\ \hline \multirow{2}{*}{Fair} & S2 & Some response to touch and pin, with over-response \\ \hline S3 & Good response to touch and pin, without over-response \\ \hline \multirow{2}{*}{Good} & S4 & Location and some tactile discrimination \\ \hline S5 & Complete recovery \\ \hline \end{tabular} \end{table}
PMC2718880_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline \multicolumn{4}{c|}{\textbf{Final Outcome for Repair Level (\%)}} \\ \hline \textbf{Location of Injury in Surgical Group} & \textbf{Good} & \textbf{Fair} & \textbf{Poor} \\ \hline Spinal nerve to trunk or trunk \\ \hline C5–C6 to upper trunk or upper trunk & 53,85 & 38,46 & 7,69 \\ \hline C7 to middle trunk or middle trunk & 30,43 & 60,87 & 8,7 \\ \hline C8 to T1 to lower trunk or lower trunk & 14,29 & 57,14 & 28,57 \\ \hline Divisions to cord or cord \\ \hline Lateral & 40,3 & 50,75 & 8,96 \\ \hline Medial & 26,63 & 51,48 & 21,89 \\ \hline Posterior & 38,6 & 49,12 & 12,28 \\ \hline Cord to nerve or nerve \\ \hline Lateral to musculocutaneous & 29,03 & 58,06 & 12,9 \\ \hline Lateral to median & 36,67 & 56,67 & 6,67 \\ \hline Medial to median & 31,82 & 59,09 & 9,09 \\ \hline Medial to ulnar & 21,74 & 56,52 & 21,74 \\ \hline Posterior to radial & 32,76 & 58,62 & 8,62 \\ \hline Posterior to axillary & 21,05 & 63,16 & 15,79 \\ \hline \end{tabular} \end{table}
PMC2718880_table_2
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline \multicolumn{5}{c|}{\textbf{The final outcome for preopertaive interval (\%)}} \\ \hline & \textbf{0–4 months (n = 149)} & \textbf{4–6 months (n = 60)} & \textbf{6–8 months (n = 35)} & \textbf{8–10 months (n = 21)} \\ \hline Poor & 8,72 & 11,67 & 14,29 & 19,05 \\ \hline Fair & 46,31 & 50 & 57,14 & 66,67 \\ \hline Good & 44,97 & 38,33 & 28,57 & 14,29 \\ \hline \end{tabular} \end{table}
PMC2718880_table_3
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline \multicolumn{6}{c|}{\textbf{The final outcome for intraoperative findings (\%)}} \\ \hline & \textbf{Complete rupture (n = 14)} & \textbf{Interrupted by a neuromaor/ and fibrosis at the stump (n = 39)} & \textbf{Partial rupture (n = 25)} & \textbf{Neuroma or/andfibrosis is continuity (n = 110)} & \textbf{Nerve is intact, only compressed by fibrosis (n = 353)} \\ \hline Poor & 21,43 & 20,51 & 16 & 5,45 & 3,68 \\ \hline Fair & 71,43 & 71,79 & 64 & 43,64 & 24,65 \\ \hline Good & 7,14 & 7,69 & 20 & 50,91 & 71,67 \\ \hline \end{tabular} \end{table}
PMC2718880_table_4
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|l|l|} \hline \multicolumn{9}{c|}{\textbf{The final outcome for type of surgery (\%)}} \\ \hline & \textbf{EEIA-SG (n = 24)} & \textbf{EEEA (n = 43)} & \textbf{EEIA (n = 49)} & \textbf{PNE+ EEIA-SG (n = 12)} & \textbf{PNE+ EEEA (n = 19)} & \textbf{PNE+ EEIA (n = 24)} & \textbf{IN (n = 157)} & \textbf{SD+EN (n = 213)} \\ \hline Poor & 29,17 & 18,6 & 12,24 & 25 & 10,53 & 4,17 & 2,55 & 2,35 \\ \hline Fair & 54,17 & 55,81 & 57,14 & 58,33 & 63,16 & 65,5 & 47,77 & 42,72 \\ \hline Good & 16,67 & 25,58 & 30,61 & 16,67 & 26,32 & 30,33 & 49,68 & 54,93 \\ \hline \end{tabular} \end{table}
PMC2718880_table_5
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline \multicolumn{4}{c|}{\textbf{The final outcome for the length of the graft (\%)}} \\ \hline & \textbf{0–3 cm (n = 11)} & \textbf{3,1–5 cm (n = 14)} & \textbf{>5,1 cm (n = 11)} \\ \hline Poor & 0 & 35,71 & 45,45 \\ \hline Fair & 63,64 & 50 & 54,55 \\ \hline Good & 36,36 & 14,29 & 0 \\ \hline \end{tabular} \end{table}
PMC2718880_table_6
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|} \hline \textbf{Performance objective for temporary agency worker or unemployed worker} & \multicolumn{5}{c|}{\textbf{Learning objectives}} \\ \hline & \textbf{Attitude} & \textbf{Skills} & \textbf{Self-efficacy} & \textbf{Assertiveness} & \textbf{Outcome expectations} \\ \hline \multirow{3}{*}{To discuss about RTW implementation plan with RTW coordinator and labour expert} & Positive attitude towards the consensus based RTW implementation plan & Participate in discussion with RTW coordinator and labour expert & Confidence in own ability to discuss with RTW coordinator and labour expert & Dare to participate in discussion with RTW coordinator and labour expert & Having appropriate expectations of (therapeutic) RTW \\ \hline Own initiative/ motivation for (therapeutic) RTW & Making of realizable appointments regarding persons involved and time scheme for RTW & Confidence in own ability to comply with appointments in RTW implementation plan \\ \hline Belief in positive outcome of PE program \\ \hline \end{tabular} \end{table}
PMC2718881_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|} \hline \textbf{Performance objective for temporary agency worker or unemployed worker} & \multicolumn{2}{c|}{\textbf{Change objectives}} \\ \hline & \textbf{Safety and equality} & \textbf{Support} \\ \hline \multirow{2}{*}{To be able to identify and prioritise (physical and mental workload) obstacles for early RTW} & RTW coordinator provides clearness about PE process and his/her role & RTW coordinator provides tools to identify and prioritise obstacles (work related and personal factors) for early RTW \\ \hline RTW coordinator provides clearness about how to identify and prioritise obstacles for RTW \\ \hline \end{tabular} \end{table}
PMC2718881_table_1
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline \textbf{Determinant} & \textbf{Methods from theory} & \textbf{Strategy} & \textbf{Tools/materials} \\ \hline \multirow{6}{*}{Risk perception and knowledge} & Passive learning/providing information & Providing written and verbal information & Letter sent to W about research \\ \hline & & IP explains about personal risk of occupational disability and ending in long term sickness benefit scheme \\ \hline & & Researcher explains participatory RTW program in phone call and sends invitation with folder, IP also explains in first consult. \\ \hline & & RC explains participatory RTW process to W and guides the RTW program \\ \hline Active processing of information & Evaluating understanding & IP instructs inventory of RTW obstacles to W as home assignment \\ \hline & & Inventory of RTW obstacles in RTW intervention program \\ \hline \multirow{3}{*}{Skills} & Guided practise & Guided practise & W practises explanation of obstacles to LE with RC \\ \hline & & Practise thinking in broad outline during brainstorm session with RC RC provides post-it notes to stimulate thinking of multiple solutions \\ \hline & Evaluation & RC checks at the end of the brainstorm session with W if the appointments in the RTW implementation plan are realizable \\ \hline \multirow{2}{*}{Self-efficacy} & Positive reinforcement & Providing feedback & SIP and RC focus on personal abilities and capacities of W regarding RTW \\ \hline & Evaluation & RC performs an evaluation with W by phone \\ \hline \end{tabular} \end{table}
PMC2718881_table_2
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|} \hline \textbf{Step} & & \textbf{Content} & \textbf{Who are involved?} \\ \hline \multirow{4}{*}{1.} & Organisation and preparation & Check if insurance physician and labour expert have been informed about program and agree with it & RTW coordinator \\ \hline & Check if combined consult with insurance physician and labour expert is planned & RTW coordinator \\ \hline & Check who is case manager of vocational rehabilitation agency for placement in temporary (therapeutic) work & RTW coordinator \\ \hline & Plan appointments for conversations & RTW coordinator, worker and labour expert \\ \hline \multirow{2}{*}{2.} & Inventory of obstacles and experienced limitations regarding RTW & Interviews about work tasks, obstacles and experienced limitations for RTW & RTW coordinator has separate interviews with worker and labour expert \\ \hline & Prioritize obstacles and limitations for return-to- work & RTW coordinator, worker and labour expert \\ \hline \multirow{2}{*}{3.} & Inventory of (therapeutic) work possibilities (thinking of and choosing solutions & Thinking of and collecting solutions for suitable (therapeutic) work (places) & RTW coordinator, worker and labour expert \\ \hline & Prioritizing solutions & RTW coordinator, worker and labour expert \\ \hline \multirow{4}{*}{4.} & Preparation of matching (temporary) work(place) and reporting & Make plan for implementation of solutions i.e. placement in matching (therapeutic) work & RTW coordinator, worker and labour expert \\ \hline & Stimulate own initiative of worker. While waiting on placement by agency, worker can also search for a suitable workplace & RTW coordinator, worker and labour expert \\ \hline & Contact with vocational rehabilitation agency for intake & RTW coordinator, worker and case-manager of vocational rehabilitation agency \\ \hline & Intake with vocational rehabilitation agency & Case-manager of vocational rehabilitation agency and worker If desired also RTW coordinator \\ \hline \multirow{2}{*}{5.} & Placement in matching (therapeutic) work and support & Placement in matching (therapeutic) workplace & Case-manager of vocational rehabilitation agency, worker and employer \\ \hline & If necessary, information and instruction at new workplace & Case-manager of agency, worker and employer \\ \hline \multirow{2}{*}{6.} & Evaluation/control & Evaluation by phone: has placement in matching (therapeutic) work been realised? Satisfaction with placement in (therapeutic) work? Are adjustments necessary? & RTW coordinator has separate evaluations with worker and labour expert \\ \hline & If placement has not yet been realised: stimulate own initiative of worker to find a suitable work(place) & Case-manager of rehabilitation agency also evaluates separate with worker and provides feedback to RTW coordinator \\ \hline \end{tabular} \end{table}
PMC2718881_table_3
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|l|l|} \hline \textbf{Reason for Consultation} & \textbf{New or Recurring Symptoms} & \multicolumn{5}{c|}{\textbf{GP's opinion on likelihood of symptoms being pesticide-related}} \\ \hline & & \textbf{Likely} & \textbf{Possible} & \textbf{Unlikely} & \textbf{Definitely not} & \textbf{Total} \\ \hline \multirow{5}{*}{Because of concern about pesticide exposure} & Asymptomatic & 0 & 0 & 0 & 0 & 1 \\ \hline Recurring & 2 & 4 & 6 & 1 & 13 \\ \hline Newly occurring & 10 & 11 & 3 & 0 & 24 \\ \hline Not known & 1 & 3 & 0 & 0 & 4 \\ \hline \textbf{Total} & 13 & 18 & 9 & 1 & 42 \\ \hline \multirow{5}{*}{Pesticide exposure not mentioned by patient} & Asymptomatic & 0 & 0 & 0 & 0 & 14490 \\ \hline Recurring & 5 & 528 & 13451 & 20207 & 34191 \\ \hline Newly occurring & 2 & 972 & 4165 & 4020 & 9159 \\ \hline Not known & 0 & 81 & 932 & 425 & 1438 \\ \hline \textbf{Total} & 7 & 1581 & 18548 & 24652 & 59278 \\ \hline Overall total & & 20 & 1599 & 18557 & 24653 & 59320 \\ \hline \end{tabular} \end{table}
PMC2718882_table_0
\begin{table} \centering \label{tab:tablelabel} \begin{tabular}{|l|l|l|l|l|} \hline \textbf{Pest-control chemical} & \textbf{\textbf{Number} of Patients} & \textbf{Percentage of Pesticide Users} & \multicolumn{2}{c|}{\textbf{Reported more use than usual}} \\ \hline & & & \textbf{Number} & \textbf{\%} \\ \hline Weed killer & 131 & 23.9 & 74 & 56.5 \\ \hline Kill root/nettles etc & 60 & 11.0 & 32 & 53.3 \\ \hline Kill aphids/greenfly etc & 89 & 16.3 & 47 & 52.8 \\ \hline Kill wasp/fly & 78 & 14.3 & 43 & 55.1 \\ \hline Kill ant/cockroach etc & 80 & 14.6 & 57 & 71.3 \\ \hline Fungicidal paint & 7 & 1.3 & 5 & 71.4 \\ \hline Mould/mildew treatment & 48 & 8.8 & 30 & 62.5 \\ \hline Tick/flea control & 98 & 17.9 & 44 & 44.9 \\ \hline Head lice treatment & 17 & 3.1 & 11 & 64.7 \\ \hline Insect repellent & 35 & 6.4 & 20 & 57.1 \\ \hline Other animal repellent & 12 & 2.2 & 9 & 75.0 \\ \hline Rat/mouse poison & 30 & 5.5 & 16 & 53.3 \\ \hline Slug/snail pellets & 149 & 27.2 & 81 & 54.4 \\ \hline Creosol/cuprinol & 57 & 10.4 & 42 & 73.7 \\ \hline Dry rot treatment & 2 & 0.4 & 2 & 100.0 \\ \hline Kill algae/lichen/moss & 15 & 2.7 & 7 & 46.7 \\ \hline Intestinal worm treatment & 55 & 10.1 & 22 & 40.0 \\ \hline Other & 22 & 4.0 & 15 & 68.2 \\ \hline \end{tabular} \end{table}
PMC2718882_table_1