Bicluster – MTB EGRIN 2.0

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Call Stack
#	Time	Memory	Function	Location
1	0.0000	398256	{main}( )	.../index.php:0
2	0.0001	398536	require( '/local/apache-stuff/mtb_egrin2/wp-blog-header.php' )	.../index.php:17
3	0.1308	7193168	require_once( '/local/apache-stuff/mtb_egrin2/wp-includes/template-loader.php' )	.../wp-blog-header.php:19
4	0.1336	7196912	include( '/local/apache-stuff/mtb_egrin2/wp-content/themes/twentyseventeen/page.php' )	.../template-loader.php:106
5	0.1985	7717672	get_template_part( )	.../page.php:28
6	0.1985	7718248	locate_template( )	.../general-template.php:206
7	0.1985	7718376	load_template( )	.../template.php:720
8	0.1986	7718688	require( '/local/apache-stuff/mtb_egrin2/wp-content/themes/twentyseventeen/template-parts/page/content-page.php' )	.../template.php:787
9	0.1993	7735864	the_content( )	.../content-page.php:22
10	0.1995	7736112	apply_filters( )	.../post-template.php:256
11	0.1995	7736512	WP_Hook->apply_filters( )	.../plugin.php:205
12	0.2005	7742040	do_shortcode( )	.../class-wp-hook.php:310
13	0.2007	7748096	preg_replace_callback ( )	.../shortcodes.php:273
14	0.2007	7748720	do_shortcode_tag( )	.../shortcodes.php:273
15	0.2007	7748720	bicluster_info_shortcode( )	.../shortcodes.php:433
16	0.2007	7748920	file_get_contents ( )	.../short_codes.php:666

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Call Stack
#	Time	Memory	Function	Location
1	0.0000	398256	{main}( )	.../index.php:0
2	0.0001	398536	require( '/local/apache-stuff/mtb_egrin2/wp-blog-header.php' )	.../index.php:17
3	0.1308	7193168	require_once( '/local/apache-stuff/mtb_egrin2/wp-includes/template-loader.php' )	.../wp-blog-header.php:19
4	0.1336	7196912	include( '/local/apache-stuff/mtb_egrin2/wp-content/themes/twentyseventeen/page.php' )	.../template-loader.php:106
5	0.1985	7717672	get_template_part( )	.../page.php:28
6	0.1985	7718248	locate_template( )	.../general-template.php:206
7	0.1985	7718376	load_template( )	.../template.php:720
8	0.1986	7718688	require( '/local/apache-stuff/mtb_egrin2/wp-content/themes/twentyseventeen/template-parts/page/content-page.php' )	.../template.php:787
9	0.1993	7735864	the_content( )	.../content-page.php:22
10	0.1995	7736112	apply_filters( )	.../post-template.php:256
11	0.1995	7736512	WP_Hook->apply_filters( )	.../plugin.php:205
12	0.2005	7742040	do_shortcode( )	.../class-wp-hook.php:310
13	0.2007	7748096	preg_replace_callback ( )	.../shortcodes.php:273
14	0.2007	7748720	do_shortcode_tag( )	.../shortcodes.php:273
15	0.2007	7748720	bicluster_info_shortcode( )	.../shortcodes.php:433

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Call Stack
#	Time	Memory	Function	Location
1	0.0000	398256	{main}( )	.../index.php:0
2	0.0001	398536	require( '/local/apache-stuff/mtb_egrin2/wp-blog-header.php' )	.../index.php:17
3	0.1308	7193168	require_once( '/local/apache-stuff/mtb_egrin2/wp-includes/template-loader.php' )	.../wp-blog-header.php:19
4	0.1336	7196912	include( '/local/apache-stuff/mtb_egrin2/wp-content/themes/twentyseventeen/page.php' )	.../template-loader.php:106
5	0.1985	7717672	get_template_part( )	.../page.php:28
6	0.1985	7718248	locate_template( )	.../general-template.php:206
7	0.1985	7718376	load_template( )	.../template.php:720
8	0.1986	7718688	require( '/local/apache-stuff/mtb_egrin2/wp-content/themes/twentyseventeen/template-parts/page/content-page.php' )	.../template.php:787
9	0.1993	7735864	the_content( )	.../content-page.php:22
10	0.1995	7736112	apply_filters( )	.../post-template.php:256
11	0.1995	7736512	WP_Hook->apply_filters( )	.../plugin.php:205
12	0.2005	7742040	do_shortcode( )	.../class-wp-hook.php:310
13	0.2007	7748096	preg_replace_callback ( )	.../shortcodes.php:273
14	0.2007	7748720	do_shortcode_tag( )	.../shortcodes.php:273
15	0.2007	7748720	bicluster_info_shortcode( )	.../shortcodes.php:433

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Call Stack
#	Time	Memory	Function	Location
1	0.0000	398256	{main}( )	.../index.php:0
2	0.0001	398536	require( '/local/apache-stuff/mtb_egrin2/wp-blog-header.php' )	.../index.php:17
3	0.1308	7193168	require_once( '/local/apache-stuff/mtb_egrin2/wp-includes/template-loader.php' )	.../wp-blog-header.php:19
4	0.1336	7196912	include( '/local/apache-stuff/mtb_egrin2/wp-content/themes/twentyseventeen/page.php' )	.../template-loader.php:106
5	0.1985	7717672	get_template_part( )	.../page.php:28
6	0.1985	7718248	locate_template( )	.../general-template.php:206
7	0.1985	7718376	load_template( )	.../template.php:720
8	0.1986	7718688	require( '/local/apache-stuff/mtb_egrin2/wp-content/themes/twentyseventeen/template-parts/page/content-page.php' )	.../template.php:787
9	0.1993	7735864	the_content( )	.../content-page.php:22
10	0.1995	7736112	apply_filters( )	.../post-template.php:256
11	0.1995	7736512	WP_Hook->apply_filters( )	.../plugin.php:205
12	0.2005	7742040	do_shortcode( )	.../class-wp-hook.php:310
13	0.2007	7748096	preg_replace_callback ( )	.../shortcodes.php:273
14	0.2007	7748720	do_shortcode_tag( )	.../shortcodes.php:273
15	0.2007	7748720	bicluster_info_shortcode( )	.../shortcodes.php:433

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Call Stack
#	Time	Memory	Function	Location
1	0.0000	398256	{main}( )	.../index.php:0
2	0.0001	398536	require( '/local/apache-stuff/mtb_egrin2/wp-blog-header.php' )	.../index.php:17
3	0.1308	7193168	require_once( '/local/apache-stuff/mtb_egrin2/wp-includes/template-loader.php' )	.../wp-blog-header.php:19
4	0.1336	7196912	include( '/local/apache-stuff/mtb_egrin2/wp-content/themes/twentyseventeen/page.php' )	.../template-loader.php:106
5	0.1985	7717672	get_template_part( )	.../page.php:28
6	0.1985	7718248	locate_template( )	.../general-template.php:206
7	0.1985	7718376	load_template( )	.../template.php:720
8	0.1986	7718688	require( '/local/apache-stuff/mtb_egrin2/wp-content/themes/twentyseventeen/template-parts/page/content-page.php' )	.../template.php:787
9	0.1993	7735864	the_content( )	.../content-page.php:22
10	0.1995	7736112	apply_filters( )	.../post-template.php:256
11	0.1995	7736512	WP_Hook->apply_filters( )	.../plugin.php:205
12	0.2005	7742040	do_shortcode( )	.../class-wp-hook.php:310
13	0.2007	7748096	preg_replace_callback ( )	.../shortcodes.php:273
14	0.2007	7748720	do_shortcode_tag( )	.../shortcodes.php:273
15	0.2007	7748720	bicluster_info_shortcode( )	.../shortcodes.php:433

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Call Stack
#	Time	Memory	Function	Location
1	0.0000	398256	{main}( )	.../index.php:0
2	0.0001	398536	require( '/local/apache-stuff/mtb_egrin2/wp-blog-header.php' )	.../index.php:17
3	0.1308	7193168	require_once( '/local/apache-stuff/mtb_egrin2/wp-includes/template-loader.php' )	.../wp-blog-header.php:19
4	0.1336	7196912	include( '/local/apache-stuff/mtb_egrin2/wp-content/themes/twentyseventeen/page.php' )	.../template-loader.php:106
5	0.1985	7717672	get_template_part( )	.../page.php:28
6	0.1985	7718248	locate_template( )	.../general-template.php:206
7	0.1985	7718376	load_template( )	.../template.php:720
8	0.1986	7718688	require( '/local/apache-stuff/mtb_egrin2/wp-content/themes/twentyseventeen/template-parts/page/content-page.php' )	.../template.php:787
9	0.1993	7735864	the_content( )	.../content-page.php:22
10	0.1995	7736112	apply_filters( )	.../post-template.php:256
11	0.1995	7736512	WP_Hook->apply_filters( )	.../plugin.php:205
12	0.2005	7742040	do_shortcode( )	.../class-wp-hook.php:310
13	0.2007	7748096	preg_replace_callback ( )	.../shortcodes.php:273
14	0.2007	7748720	do_shortcode_tag( )	.../shortcodes.php:273
15	0.2007	7748720	bicluster_info_shortcode( )	.../shortcodes.php:433

ID:
# Conditions:
# Genes:
Residual:

Bicluster Motifs

Bicluster Genes

Rv0866
Rv0869c
Rv1090
Rv1340
Rv1648
Rv1678
Rv1704c
Rv1822
Rv1901
Rv1919c
Rv2456c
Rv2612c
Rv2772c
Rv2778c
Rv2992c
Rv2994
Rv3014c
Rv3492c
Rv3554
Rv3579c

Bicluster Conditions

H37Rv.0.05..SDS.exposure.for.1h.rep.1
H37Rv.0.05..SDS.exposure.for.1h.rep.3
H37Rv.0.05..SDS.exposure.for.1h.rep.4
H37Rv.0.05..SDS.exposure.for.1h.rep.5
H37Rv.0.05..SDS.exposure.for.1h.rep.6
MTB.strain.1254.Ctrl.vs.low.aeration..0.2..oxygen..2hr.rep.2
H37Rv.vs..H37Rv.SDS.treated.rep.5
H37Rv.0.2..Oxygen..2h..1
H37Rv.0.2..Oxygen..2h..4
pH4.8vspH6.8..2h.
pH4.8vspH6.8..2h.A
pH4.8vspH6.8..2h.B
pH4.8vspH6.8..4h.
pH4.8vspH6.8..4h.A
pH4.8vspH6.8..4h.B
pH4.8vspH6.8..4h.C
pH4.8vspH6.8..5h.
pH4.8vspH6.8..5.5h.
pH4.8vspH6.8..7h.
pH4.8vspH6.8..11h.
pH5.2vspH6.8..10.5h.
pH5.2vspH6.8..11h.
pH5.2vspH6.8..16h.
pH5.6vspH6.8..2h.
pH5.6vspH6.8..2h.A
pH5.6vspH6.8..4h.
pH5.6vspH6.8..4h.B
pH5.6vspH6.8..11h.
H37Rv.wild.type.control.vs.0.05..SDS.for.60.min.rep.1
H37Rv.wild.type.control.vs.0.05..SDS.for.60.min.rep.2
H37Rv.wild.type.control.vs.0.05..SDS.for.60.min.rep.3
H37Rv.wild.type.control.vs.0.05..SDS.for.60.min.rep.6
Whole.Lung.Surfactant.2hrs.rep.1
Whole.Lung.Surfactant.30min.rep.1
Whole.Lung.Surfactant.30min.rep.2
Whole.Lung.Surfactant.30min.rep.4
Extracted.Lung.Surfactant.2hrs.rep.2
Extracted.Lung.Surfactant.30min.rep.2
Extracted.Lung.Surfactant.30min.rep.4
Purified.Surfactant.Lipids.30min.rep.1
Purified.Surfactant.Lipids.30min.rep.2
Purified.Human.SP.A.Coated.2hrs.rep2
Purified.Human.SP.A.Uncoated.2hrs.rep3
MTB1254_SDS_90MIN_01
MTB1254_SDS_90MIN_02
MTB1254_SDS_90MIN_03
MTB1254_SDS_90MIN_04
SDS_3h_01
Clinical.isolate.12954.03_Beijing.extra.vs.intracellular.in.activated.macrophages.rep.1
Clinical.isolate.1500.03_Beijing.extra.vs.intracellular.in.activated.macrophages.rep.2
Clinical.isolate.1934.03_Beijing.extra.vs.intracellular.in.activated.macrophages.rep.1
Clinical.isolate.1934.03_Beijing.extra.vs.intracellular.in.activated.macrophages.rep.2
Clinical.isolate.2169.99_Uganda.extra.vs.intracellular.in.activated.macrophages.rep.1
Clinical.isolate.2191.99_Uganda.extra.vs.intracellular.in.activated.macrophages.rep.1
Clinical.isolate.2336.02_Haarlem.extra.vs.intracellular.in.activated.macrophages.rep.2
Clinical.isolate.4130.02_Haarlem.extra.vs.intracellular.in.activated.macrophages.rep.1
Clinical.isolate.4130.02_Haarlem.extra.vs.intracellular.in.activated.macrophages.rep.2
Clinical.isolate.4850.03_EAI.extra.vs.intracellular.in.activated.macrophages.rep.1
Clinical.isolate.947.01_EAI.extra.vs.intracellular.in.activated.macrophages.rep.1
Clinical.isolate.9532.03_Haarlem.extra.vs.intracellular.in.activated.macrophages.rep.2
H37Rv.extra.vs.intracellular.in.activated.macrophages.rep.2
CDC1551.extra.vs.intracellular.in.activated.macrophages.rep.1
Mtb.response.to.pH.5.5..6.replicates.
BCG.2hr.phagosomal.profile
BCG.24hr.phagosomal.profile
M..tuberculosis.CDC1551.2hr.phagosome.expression.profile
M..tuberculosis.CDC1551.24hr.phagosome.expression.profile
Russell_Lab_Spotted_Oligos_1.2..14.day.resting.macrophage.infection.2hr..rep.2..Russell_Lab_Spotted_Oligos_1.2..
Russell_Lab_Spotted_Oligos_1.5..14.day.resting.macrophage.infection.Day.4..rep.1..Russell_Lab_Spotted_Oligos_1.5..
Russell_Lab_Spotted_Oligos_1.7..14.day.resting.macrophage.infection.Day.6..rep.1..Russell_Lab_Spotted_Oligos_1.7..
Russell_Lab_Spotted_Oligos_1.10.14.day.resting.macrophage.infection.Day.8..rep.2..Russell_Lab_Spotted_Oligos_1.10.
Russell_Lab_Spotted_Oligos_1.11.14.day.resting.macrophage.infection.Day.10..rep.1..Russell_Lab_Spotted_Oligos_1.11.
Russell_Lab_Spotted_Oligos_1.13.14.day.resting.macrophage.infection.Day.12..rep.1..Russell_Lab_Spotted_Oligos_1.13.
Russell_Lab_Spotted_Oligos_1.14.14.day.resting.macrophage.infection.Day.12..rep.2..Russell_Lab_Spotted_Oligos_1.14.
Russell_Lab_Spotted_Oligos_1.15.14.day.resting.macrophage.infection.Day.14..rep.1..Russell_Lab_Spotted_Oligos_1.15.
Russell_Lab_Spotted_Oligos_1.16.14.day.resting.macrophage.infection.Day.14..rep.2..Russell_Lab_Spotted_Oligos_1.16.
WT_140mM_NaCl_Rep1
WT_140mM_NaCl_Rep4
X40ug.mL.5CL.pH5.6..2h..2
X40ug.mL.5CL.pH5.6..4h..1
X40ug.mL.5CL.pH5.6..4h..2
X40ug.mL.5CL.pH5.6..4h..3
X80ug.mL.5CL.pH5.6..2h.
X0.12mg.mL.BZA.pH5.6..4h..1
X0.12mg.mL.BZA.pH5.6..4h..2
X0.12mg.mL.BZAvspH5.6..11h.
X0.12mg.mL.Nam.pH5.6..2h..1
X0.12mg.mL.Nam.pH5.6..2h..2
X0.12mg.mL.Nam.pH5.6..4h..1
X0.12mg.mL.Nam.pH5.6..4h..2
X0.12mg.mL.NamvspH5.6..4h.
X0.12mg.mL.NamvspH5.6..5.5h.
X0.12mg.mL.NamvspH5.6..7h.
X1.2mg.mL.NamvspH5.6..5h.
X1.2mg.mL.NamvspH5.6..10.5h.
X0.12mg.mL.PZA.pH5.6..2h.
X0.12mg.mL.PZA.pH5.6..2.5h.
X0.12mg.mL.PZA.pH5.6..4h..2
X0.12mg.mL.PZAvspH5.6..4h.
X0.12mg.mL.PZAvspH5.6..4h.A
X0.12mg.mL.PZAvspH5.6..6h.A
X1.2mg.mL.PZA.pH5.6..2h..
X1.2mg.mL.PZAvspH5.6..4h.
X1.2mg.mL.PZAvspH5.6..4h.A
X1.2mg.mL.PZAvspH5.6..4h.B
X1.2mg.mL.PZAvspH5.6..7h.A
X1.2mg.mL.PZAvspH5.6..10.5h.

Column members cluster 552f2cfab744335b89d54852 Species (TODO)

H37Rv.0.05..SDS.exposure.for.1h.rep.1
H37Rv.0.05..SDS.exposure.for.1h.rep.3
H37Rv.0.05..SDS.exposure.for.1h.rep.4
H37Rv.0.05..SDS.exposure.for.1h.rep.5
H37Rv.0.05..SDS.exposure.for.1h.rep.6
MTB.strain.1254.Ctrl.vs.low.aeration..0.2..oxygen..2hr.rep.2
H37Rv.vs..H37Rv.SDS.treated.rep.5
H37Rv.0.2..Oxygen..2h..1
H37Rv.0.2..Oxygen..2h..4
pH4.8vspH6.8..2h.
pH4.8vspH6.8..2h.A
pH4.8vspH6.8..2h.B
pH4.8vspH6.8..4h.
pH4.8vspH6.8..4h.A
pH4.8vspH6.8..4h.B
pH4.8vspH6.8..4h.C
pH4.8vspH6.8..5h.
pH4.8vspH6.8..5.5h.
pH4.8vspH6.8..7h.
pH4.8vspH6.8..11h.
pH5.2vspH6.8..10.5h.
pH5.2vspH6.8..11h.
pH5.2vspH6.8..16h.
pH5.6vspH6.8..2h.
pH5.6vspH6.8..2h.A
pH5.6vspH6.8..4h.
pH5.6vspH6.8..4h.B
pH5.6vspH6.8..11h.
H37Rv.wild.type.control.vs.0.05..SDS.for.60.min.rep.1
H37Rv.wild.type.control.vs.0.05..SDS.for.60.min.rep.2
H37Rv.wild.type.control.vs.0.05..SDS.for.60.min.rep.3
H37Rv.wild.type.control.vs.0.05..SDS.for.60.min.rep.6
Whole.Lung.Surfactant.2hrs.rep.1
Whole.Lung.Surfactant.30min.rep.1
Whole.Lung.Surfactant.30min.rep.2
Whole.Lung.Surfactant.30min.rep.4
Extracted.Lung.Surfactant.2hrs.rep.2
Extracted.Lung.Surfactant.30min.rep.2
Extracted.Lung.Surfactant.30min.rep.4
Purified.Surfactant.Lipids.30min.rep.1
Purified.Surfactant.Lipids.30min.rep.2
Purified.Human.SP.A.Coated.2hrs.rep2
Purified.Human.SP.A.Uncoated.2hrs.rep3
MTB1254_SDS_90MIN_01
MTB1254_SDS_90MIN_02
MTB1254_SDS_90MIN_03
MTB1254_SDS_90MIN_04
SDS_3h_01
Clinical.isolate.12954.03_Beijing.extra.vs.intracellular.in.activated.macrophages.rep.1
Clinical.isolate.1500.03_Beijing.extra.vs.intracellular.in.activated.macrophages.rep.2
Clinical.isolate.1934.03_Beijing.extra.vs.intracellular.in.activated.macrophages.rep.1
Clinical.isolate.1934.03_Beijing.extra.vs.intracellular.in.activated.macrophages.rep.2
Clinical.isolate.2169.99_Uganda.extra.vs.intracellular.in.activated.macrophages.rep.1
Clinical.isolate.2191.99_Uganda.extra.vs.intracellular.in.activated.macrophages.rep.1
Clinical.isolate.2336.02_Haarlem.extra.vs.intracellular.in.activated.macrophages.rep.2
Clinical.isolate.4130.02_Haarlem.extra.vs.intracellular.in.activated.macrophages.rep.1
Clinical.isolate.4130.02_Haarlem.extra.vs.intracellular.in.activated.macrophages.rep.2
Clinical.isolate.4850.03_EAI.extra.vs.intracellular.in.activated.macrophages.rep.1
Clinical.isolate.947.01_EAI.extra.vs.intracellular.in.activated.macrophages.rep.1
Clinical.isolate.9532.03_Haarlem.extra.vs.intracellular.in.activated.macrophages.rep.2
H37Rv.extra.vs.intracellular.in.activated.macrophages.rep.2
CDC1551.extra.vs.intracellular.in.activated.macrophages.rep.1
Mtb.response.to.pH.5.5..6.replicates.
BCG.2hr.phagosomal.profile
BCG.24hr.phagosomal.profile
M..tuberculosis.CDC1551.2hr.phagosome.expression.profile
M..tuberculosis.CDC1551.24hr.phagosome.expression.profile
Russell_Lab_Spotted_Oligos_1.2..14.day.resting.macrophage.infection.2hr..rep.2..Russell_Lab_Spotted_Oligos_1.2..
Russell_Lab_Spotted_Oligos_1.5..14.day.resting.macrophage.infection.Day.4..rep.1..Russell_Lab_Spotted_Oligos_1.5..
Russell_Lab_Spotted_Oligos_1.7..14.day.resting.macrophage.infection.Day.6..rep.1..Russell_Lab_Spotted_Oligos_1.7..
Russell_Lab_Spotted_Oligos_1.10.14.day.resting.macrophage.infection.Day.8..rep.2..Russell_Lab_Spotted_Oligos_1.10.
Russell_Lab_Spotted_Oligos_1.11.14.day.resting.macrophage.infection.Day.10..rep.1..Russell_Lab_Spotted_Oligos_1.11.
Russell_Lab_Spotted_Oligos_1.13.14.day.resting.macrophage.infection.Day.12..rep.1..Russell_Lab_Spotted_Oligos_1.13.
Russell_Lab_Spotted_Oligos_1.14.14.day.resting.macrophage.infection.Day.12..rep.2..Russell_Lab_Spotted_Oligos_1.14.
Russell_Lab_Spotted_Oligos_1.15.14.day.resting.macrophage.infection.Day.14..rep.1..Russell_Lab_Spotted_Oligos_1.15.
Russell_Lab_Spotted_Oligos_1.16.14.day.resting.macrophage.infection.Day.14..rep.2..Russell_Lab_Spotted_Oligos_1.16.
WT_140mM_NaCl_Rep1
WT_140mM_NaCl_Rep4
X40ug.mL.5CL.pH5.6..2h..2
X40ug.mL.5CL.pH5.6..4h..1
X40ug.mL.5CL.pH5.6..4h..2
X40ug.mL.5CL.pH5.6..4h..3
X80ug.mL.5CL.pH5.6..2h.
X0.12mg.mL.BZA.pH5.6..4h..1
X0.12mg.mL.BZA.pH5.6..4h..2
X0.12mg.mL.BZAvspH5.6..11h.
X0.12mg.mL.Nam.pH5.6..2h..1
X0.12mg.mL.Nam.pH5.6..2h..2
X0.12mg.mL.Nam.pH5.6..4h..1
X0.12mg.mL.Nam.pH5.6..4h..2
X0.12mg.mL.NamvspH5.6..4h.
X0.12mg.mL.NamvspH5.6..5.5h.
X0.12mg.mL.NamvspH5.6..7h.
X1.2mg.mL.NamvspH5.6..5h.
X1.2mg.mL.NamvspH5.6..10.5h.
X0.12mg.mL.PZA.pH5.6..2h.
X0.12mg.mL.PZA.pH5.6..2.5h.
X0.12mg.mL.PZA.pH5.6..4h..2
X0.12mg.mL.PZAvspH5.6..4h.
X0.12mg.mL.PZAvspH5.6..4h.A
X0.12mg.mL.PZAvspH5.6..6h.A
X1.2mg.mL.PZA.pH5.6..2h..
X1.2mg.mL.PZAvspH5.6..4h.
X1.2mg.mL.PZAvspH5.6..4h.A
X1.2mg.mL.PZAvspH5.6..4h.B
X1.2mg.mL.PZAvspH5.6..7h.A
X1.2mg.mL.PZAvspH5.6..10.5h.