diff --git a/src/main/java/org/contentmine/cproject/metadata/CMDOI.java b/src/main/java/org/contentmine/cproject/metadata/CMDOI.java index efd4cc5cd..e19768b07 100644 --- a/src/main/java/org/contentmine/cproject/metadata/CMDOI.java +++ b/src/main/java/org/contentmine/cproject/metadata/CMDOI.java @@ -17,19 +17,19 @@ public class CMDOI extends AbstractCM { /** * -http://dx.doi.org/10.5539/cis.v9n2p126 -http://dx.doi.org/10.1530/edm-16-0003 -http://dx.doi.org/10.12968/bjsn.2016.11.4.166 -http://dx.doi.org/10.14358/pers.82.5.320 -http://dx.doi.org/10.3109/10715762.2016.1162299 -http://dx.doi.org/10.1127/ejm/2015/0027-2502 -http://dx.doi.org/10.7467/ksae.2016.24.3.285 -http://dx.doi.org/10.20488/austd.22645 -http://dx.doi.org/10.1177/2150135116645604 -http://dx.doi.org/10.1525/irqr.2016.9.1.29 +https://doi.org/10.5539/cis.v9n2p126 +https://doi.org/10.1530/edm-16-0003 +https://doi.org/10.12968/bjsn.2016.11.4.166 +https://doi.org/10.14358/pers.82.5.320 +https://doi.org/10.3109/10715762.2016.1162299 +https://doi.org/10.1127/ejm/2015/0027-2502 +https://doi.org/10.7467/ksae.2016.24.3.285 +https://doi.org/10.20488/austd.22645 +https://doi.org/10.1177/2150135116645604 +https://doi.org/10.1525/irqr.2016.9.1.29 */ - static Pattern PATTERN = Pattern.compile("https?://dx\\.doi\\.org/(10\\.\\d{3,8})/(.*)"); + static Pattern PATTERN = Pattern.compile("https?://(dx\\.)?doi\\.org/10.\d{4,9}/[-._;()/:A-Za-z0-9]+"); public static CMDOI DUMMY = new CMDOI(null, null); public CMDOI(String prefix, String suffix) { diff --git a/src/main/java/org/contentmine/cproject/metadata/DOIResolver.java b/src/main/java/org/contentmine/cproject/metadata/DOIResolver.java index d0682eff3..b374f7057 100644 --- a/src/main/java/org/contentmine/cproject/metadata/DOIResolver.java +++ b/src/main/java/org/contentmine/cproject/metadata/DOIResolver.java @@ -29,8 +29,8 @@ public class DOIResolver { LOG.setLevel(Level.DEBUG); } - private static final String HTTP_DOI_ORG_API_HANDLES = "http://doi.org/api/handles/"; - private static final String HTTP_DX_DOI_ORG = "http://dx.doi.org/"; + private static final String HTTP_DOI_ORG_API_HANDLES = "https://doi.org/api/handles/"; + private static final String HTTP_DX_DOI_ORG = "https://doi.org/"; private static final String VALUE = "value"; private static final String DATA = "data"; private static final String VALUES = "values"; diff --git a/src/main/java/org/contentmine/cproject/metadata/quickscrape/QSRecord.java b/src/main/java/org/contentmine/cproject/metadata/quickscrape/QSRecord.java index 0c00907c9..bec071a00 100644 --- a/src/main/java/org/contentmine/cproject/metadata/quickscrape/QSRecord.java +++ b/src/main/java/org/contentmine/cproject/metadata/quickscrape/QSRecord.java @@ -19,7 +19,7 @@ */ public class QSRecord { - private static final String HTTP_DX_DOI_ORG = "http://dx.doi.org/"; + private static final String HTTP_DX_DOI_ORG = "https://doi.org/"; private static final Logger LOG = Logger.getLogger(QSRecord.class); static { LOG.setLevel(Level.DEBUG); diff --git a/src/main/java/org/contentmine/cproject/metadata/quickscrape/QuickscrapeLog.java b/src/main/java/org/contentmine/cproject/metadata/quickscrape/QuickscrapeLog.java index 203e3a975..96606a859 100644 --- a/src/main/java/org/contentmine/cproject/metadata/quickscrape/QuickscrapeLog.java +++ b/src/main/java/org/contentmine/cproject/metadata/quickscrape/QuickscrapeLog.java @@ -39,7 +39,7 @@ public class QuickscrapeLog { // info: URL processed private final static Pattern OUTER = Pattern.compile("(trace|debug|info|warn|error)\\:\\s(.*)"); - // [debug] [phantom] opening url: http://dx.doi.org/10.1093/mnras/stw468, HTTP GET + // [debug] [phantom] opening url: https://doi.org/10.1093/mnras/stw468, HTTP GET private final static Pattern INNER1 = Pattern.compile("\\s*\\[(trace|debug|info|warn|error)\\]\\s+\\[(phantom)\\]\\s+(.*)"); // private final static Pattern INNER2 = Pattern.compile("\\[(^\\])+\\]\\s+(.*)"); diff --git a/src/main/java/org/contentmine/cproject/util/CMineUtil.java b/src/main/java/org/contentmine/cproject/util/CMineUtil.java index a55891ecf..a3ddafa96 100644 --- a/src/main/java/org/contentmine/cproject/util/CMineUtil.java +++ b/src/main/java/org/contentmine/cproject/util/CMineUtil.java @@ -43,7 +43,7 @@ public class CMineUtil { LOG.setLevel(Level.DEBUG); } - private static final String HTTP_DX_DOI_ORG2 = "http://dx.doi.org/"; + private static final String HTTP_DX_DOI_ORG2 = "https://doi.org/"; private static final String HTML_START = "<"; private static final String PDF_START = "%PDF"; private static final String URL_PUNCT = "[\\/\\$\\%\\*\\(\\)\\[\\]]"; @@ -310,7 +310,7 @@ public static String stripChars(String s, String regex, String replace) { return s == null ? null : s.replaceAll(regex, replace); } - /** removes "http://dx.doi.org/" from start of string. + /** removes "https://doi.org/" from start of string. * * @param string * @return diff --git a/src/main/java/org/contentmine/norma/biblio/EPMCResultsJsonEntry.java b/src/main/java/org/contentmine/norma/biblio/EPMCResultsJsonEntry.java index f01a737e0..a4064b380 100644 --- a/src/main/java/org/contentmine/norma/biblio/EPMCResultsJsonEntry.java +++ b/src/main/java/org/contentmine/norma/biblio/EPMCResultsJsonEntry.java @@ -87,7 +87,7 @@ public class EPMCResultsJsonEntry extends AbstractMetadata { new CellRenderer(SOURCE).setVisible(false), new CellRenderer(AUTHOR_STRING).setBrief(20), new CellRenderer(ABSTRACT_TEXT).setBrief(20), - new CellRenderer(DOI).setHref0("http://doi.org/"), + new CellRenderer(DOI).setHref0("https://doi.org/"), new CellRenderer(ID).setVisible(false), new CellRenderer(PMID).setVisible(false), new CellRenderer(PMCID).setHref0("foo/").setHref1("/bar").setVisible(false), diff --git a/src/main/resources/org/contentmine/ami/plugins/dictionary/funders.xml b/src/main/resources/org/contentmine/ami/plugins/dictionary/funders.xml index dbb9302d7..3b960cee4 100644 --- a/src/main/resources/org/contentmine/ami/plugins/dictionary/funders.xml +++ b/src/main/resources/org/contentmine/ami/plugins/dictionary/funders.xml @@ -1,11600 +1,11600 @@ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - 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newline at end of file diff --git a/src/main/resources/org/contentmine/ami/tagger/hindawi/documentTagger.xml b/src/main/resources/org/contentmine/ami/tagger/hindawi/documentTagger.xml index 93682c909..05e5827b6 100644 --- a/src/main/resources/org/contentmine/ami/tagger/hindawi/documentTagger.xml +++ b/src/main/resources/org/contentmine/ami/tagger/hindawi/documentTagger.xml @@ -8,7 +8,7 @@ Volume 2014 (2014), Article ID 801626, 8 pages

// doi - http://dx.doi.org/10.1155/2014/801626 + https://doi.org/10.1155/2014/801626 // articleType
Research Article
diff --git a/src/main/resources/org/contentmine/graphics/html/badhtml1.html b/src/main/resources/org/contentmine/graphics/html/badhtml1.html index 75de52859..69f63da5b 100755 --- a/src/main/resources/org/contentmine/graphics/html/badhtml1.html +++ b/src/main/resources/org/contentmine/graphics/html/badhtml1.html @@ -441,7 +441,7 @@

Search Results

Article: Archaeological Investigations at a Wisconsin Petroglyph Site
by
-
Arts 2014, 3(1), 27-45; doi:10.3390/arts3010027
+
Arts 2014, 3(1), 27-45; doi:10.3390/arts3010027
Received: 30 September 2013; in revised form: 28 October 2013 / Accepted: 1 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (3378 KB) @@ -476,7 +476,7 @@

Search Results

Article: Symmetry-Breaking in a Rate Model for a Biped Locomotion Central Pattern Generator
by
-
Symmetry 2014, 6(1), 23-66; doi:10.3390/sym6010023
+
Symmetry 2014, 6(1), 23-66; doi:10.3390/sym6010023
Received: 28 October 2013; in revised form: 13 December 2013 / Accepted: 13 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (4654 KB) @@ -523,7 +523,7 @@

Search Results

Optimization of Scaffold Geometry and Operating Conditions of Radial Flow Packed-Bed Bioreactors for Therapeutic Applications
by ,  and
-
Processes 2014, 2(1), 34-57; doi:10.3390/pr2010034
+
Processes 2014, 2(1), 34-57; doi:10.3390/pr2010034
Received: 18 September 2013; in revised form: 5 December 2013 / Accepted: 19 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (1625 KB) | Download XML Full-text @@ -564,7 +564,7 @@

Search Results

Article: Increasing Phosphatidylinositol (4,5)-Bisphosphate Biosynthesis Affects Basal Signaling and Chloroplast Metabolism in Arabidopsis thaliana
by , , , , ,  and
-
Plants 2014, 3(1), 27-57; doi:10.3390/plants3010027
+
Plants 2014, 3(1), 27-57; doi:10.3390/plants3010027
Received: 4 November 2013; in revised form: 18 December 2013 / Accepted: 20 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (1315 KB) | Download XML Full-text @@ -606,7 +606,7 @@

Search Results

Review: Spruce Beetle Biology, Ecology and Management in the Rocky Mountains: An Addendum to Spruce Beetle in the Rockies
by ,  and
-
Forests 2014, 5(1), 21-71; doi:10.3390/f5010021
+
Forests 2014, 5(1), 21-71; doi:10.3390/f5010021
Received: 4 November 2013; in revised form: 15 December 2013 / Accepted: 18 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (1647 KB) @@ -641,7 +641,7 @@

Search Results

Article: Relationships of the Trade Unions with the Media: The Lithuanian Case
by ,  and
-
Adm. Sci. 2014, 4(1), 1-14; doi:10.3390/admsci4010001
+
Adm. Sci. 2014, 4(1), 1-14; doi:10.3390/admsci4010001
Received: 8 October 2013; in revised form: 16 December 2013 / Accepted: 19 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (415 KB) | Download XML Full-text @@ -680,7 +680,7 @@

Search Results

Article: Toward an A Priori Sustainable Architecture
by
-
Arts 2014, 3(1), 15-26; doi:10.3390/arts3010015
+
Arts 2014, 3(1), 15-26; doi:10.3390/arts3010015
Received: 27 October 2013; in revised form: 2 December 2013 / Accepted: 17 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (1261 KB) @@ -723,7 +723,7 @@

Search Results

Review: The Effects of Uniquely-Processed Titanium on Biological Systems: Implications for Human Health and Performance
by , , ,  and
-
J. Funct. Biomater. 2014, 5(1), 1-14; doi:10.3390/jfb5010001
+
J. Funct. Biomater. 2014, 5(1), 1-14; doi:10.3390/jfb5010001
Received: 27 August 2013; in revised form: 26 November 2013 / Accepted: 27 November 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (1285 KB) | Download XML Full-text @@ -770,7 +770,7 @@

Search Results

Article: Analysis of the Spatial Variation of Hospitalization Admissions for Hypertension Disease in Shenzhen, China
by , , , , ,  and
-
Int. J. Environ. Res. Public Health 2014, 11(1), 713-733; doi:10.3390/ijerph110100713
+
Int. J. Environ. Res. Public Health 2014, 11(1), 713-733; doi:10.3390/ijerph110100713
Received: 14 October 2013; in revised form: 16 December 2013 / Accepted: 18 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (1017 KB) | Download XML Full-text @@ -815,7 +815,7 @@

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Article: Novel Microsatellite Loci Variation and Population Genetics within Leafy Seadragons, Phycodurus eques
by , ,  and
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Diversity 2014, 6(1), 33-42; doi:10.3390/d6010033
+
Diversity 2014, 6(1), 33-42; doi:10.3390/d6010033
Received: 2 October 2013; in revised form: 20 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (285 KB) | Download XML Full-text @@ -860,7 +860,7 @@

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Article: Seasonal Changes in Microbial Community Structure in Freshwater Stream Sediment in a North Carolina River Basin
by , , ,  and
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Diversity 2014, 6(1), 18-32; doi:10.3390/d6010018
+
Diversity 2014, 6(1), 18-32; doi:10.3390/d6010018
Received: 27 October 2013; in revised form: 3 December 2013 / Accepted: 24 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (872 KB) | Download XML Full-text @@ -907,7 +907,7 @@

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Article: Strengthening the Competitiveness and Sustainability of a Semiconductor Manufacturer with Cloud Manufacturing
by
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Sustainability 2014, 6(1), 251-266; doi:10.3390/su6010251
+
Sustainability 2014, 6(1), 251-266; doi:10.3390/su6010251
Received: 11 November 2013; in revised form: 13 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (996 KB) | Download XML Full-text @@ -946,7 +946,7 @@

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Article: Carbon Nanotube- and Carbon Fiber-Reinforcement of Ethylene-Octene Copolymer Membranes for Gas and Vapor Separation
by , , , , , , ,  and
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Membranes 2014, 4(1), 20-39; doi:10.3390/membranes4010020
+
Membranes 2014, 4(1), 20-39; doi:10.3390/membranes4010020
Received: 6 November 2013; in revised form: 26 November 2013 / Accepted: 21 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (1152 KB) | Download XML Full-text @@ -990,7 +990,7 @@

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Article: Optimal Sizing of Battery Storage Systems for Industrial Applications when Uncertainties Exist
by , ,  and
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Energies 2014, 7(1), 130-149; doi:10.3390/en7010130
+
Energies 2014, 7(1), 130-149; doi:10.3390/en7010130
Received: 21 October 2013; in revised form: 11 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (331 KB) @@ -1034,7 +1034,7 @@

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Article: Eurydice at Euston?: Walter Benjamin and Marc Augé Go Underground
by
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Societies 2014, 4(1), 16-29; doi:10.3390/soc4010016
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Societies 2014, 4(1), 16-29; doi:10.3390/soc4010016
Received: 31 October 2013; in revised form: 24 December 2013 / Accepted: 24 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (98 KB) | Download XML Full-text @@ -1078,7 +1078,7 @@

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Article: A Novel Map-Based Dead-Reckoning Algorithm for Indoor Localization
by  and
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J. Sens. Actuator Netw. 2014, 3(1), 44-63; doi:10.3390/jsan3010044
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J. Sens. Actuator Netw. 2014, 3(1), 44-63; doi:10.3390/jsan3010044
Received: 26 November 2013; in revised form: 15 December 2013 / Accepted: 23 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (1638 KB) | Download XML Full-text @@ -1123,7 +1123,7 @@

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Article: Anti-Chikungunya Viral Activities of Aplysiatoxin-Related Compounds from the Marine Cyanobacterium Trichodesmium erythraeum
by , , , ,  and
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Mar. Drugs 2014, 12(1), 115-127; doi:10.3390/md12010115
+
Mar. Drugs 2014, 12(1), 115-127; doi:10.3390/md12010115
Received: 14 October 2013; in revised form: 25 November 2013 / Accepted: 12 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (738 KB) | Download XML Full-text @@ -1161,7 +1161,7 @@

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Article: A Load Fluctuation Characteristic Index and Its Application to Pilot Node Selection
by , , , ,  and
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Energies 2014, 7(1), 115-129; doi:10.3390/en7010115
+
Energies 2014, 7(1), 115-129; doi:10.3390/en7010115
Received: 22 October 2013; in revised form: 17 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (957 KB) @@ -1204,7 +1204,7 @@

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Article: Study on the Carbonation Behavior of Cement Mortar by Electrochemical Impedance Spectroscopy
by , , , ,  and
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Materials 2014, 7(1), 218-231; doi:10.3390/ma7010218
+
Materials 2014, 7(1), 218-231; doi:10.3390/ma7010218
Received: 28 November 2013; in revised form: 17 December 2013 / Accepted: 23 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (636 KB) @@ -1242,7 +1242,7 @@

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Antitumor Effects of Adenoviral-Mediated siRNA against GRP78 Gene on Adenosine-Induced Apoptosis in Human Hepatoma HepG2 Cells
by , , , , , , ,  and
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Int. J. Mol. Sci. 2014, 15(1), 525-544; doi:10.3390/ijms15010525
+
Int. J. Mol. Sci. 2014, 15(1), 525-544; doi:10.3390/ijms15010525
Received: 13 November 2013; in revised form: 19 December 2013 / Accepted: 23 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (2973 KB) @@ -1289,7 +1289,7 @@

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Article: Fabrication of CIS Absorber Layers with Different Thicknesses Using A Non-Vacuum Spray Coating Method
by , , ,  and
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Materials 2014, 7(1), 206-217; doi:10.3390/ma7010206
+
Materials 2014, 7(1), 206-217; doi:10.3390/ma7010206
Received: 8 October 2013; in revised form: 14 December 2013 / Accepted: 19 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (1180 KB) @@ -1325,7 +1325,7 @@

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Article: Molecular Cloning, Bioinformatics Analysis and Expression of Insulin-Like Growth Factor 2 from Tianzhu White Yak, Bos grunniens
by , , , , , ,  and
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Int. J. Mol. Sci. 2014, 15(1), 504-524; doi:10.3390/ijms15010504
+
Int. J. Mol. Sci. 2014, 15(1), 504-524; doi:10.3390/ijms15010504
Received: 30 October 2013; in revised form: 16 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (1353 KB) @@ -1367,7 +1367,7 @@

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Article: Modeling Fire Danger in Galicia and Asturias (Spain) from MODIS Images
by ,  and
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Remote Sens. 2014, 6(1), 540-554; doi:10.3390/rs6010540
+
Remote Sens. 2014, 6(1), 540-554; doi:10.3390/rs6010540
Received: 30 October 2013; in revised form: 25 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (587 KB) @@ -1411,7 +1411,7 @@

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Article: Peat Mapping Associations of Airborne Radiometric Survey Data
by
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Remote Sens. 2014, 6(1), 521-539; doi:10.3390/rs6010521
+
Remote Sens. 2014, 6(1), 521-539; doi:10.3390/rs6010521
Received: 27 September 2013; in revised form: 13 December 2013 / Accepted: 23 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (3862 KB) @@ -1456,7 +1456,7 @@

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Article: Simultaneous Effect of Temperature and Irradiance on Growth and Okadaic Acid Production from the Marine Dinoflagellate Prorocentrum belizeanum
by , , , , ,  and
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Toxins 2014, 6(1), 229-253; doi:10.3390/toxins6010229
+
Toxins 2014, 6(1), 229-253; doi:10.3390/toxins6010229
Received: 11 November 2013; in revised form: 24 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014
Show/Hide Abstract | Download PDF Full-text (795 KB) | Download XML Full-text diff --git a/src/main/resources/org/contentmine/graphics/html/badhtml1a.html b/src/main/resources/org/contentmine/graphics/html/badhtml1a.html index 0d779970a..da237de0f 100755 --- a/src/main/resources/org/contentmine/graphics/html/badhtml1a.html +++ b/src/main/resources/org/contentmine/graphics/html/badhtml1a.html @@ -182,7 +182,7 @@ Arts 2014, 3(1), 27-45; doi: - 10.3390/arts3010027 + 10.3390/arts3010027
Received: 30 September 2013; in revised form: 28 October 2013 / Accepted: 1 December 2013 / Published: 3 January 2014 @@ -221,7 +221,7 @@ Symmetry 2014, 6(1), 23-66; doi: - 10.3390/sym6010023 + 10.3390/sym6010023
Received: 28 October 2013; in revised form: 13 December 2013 / Accepted: 13 December 2013 / Published: 3 January 2014 @@ -263,7 +263,7 @@ Processes 2014, 2(1), 34-57; doi: - 10.3390/pr2010034 + 10.3390/pr2010034
Received: 18 September 2013; in revised form: 5 December 2013 / Accepted: 19 December 2013 / Published: 3 January 2014 @@ -310,7 +310,7 @@ Plants 2014, 3(1), 27-57; doi: - 10.3390/plants3010027 + 10.3390/plants3010027
Received: 4 November 2013; in revised form: 18 December 2013 / Accepted: 20 December 2013 / Published: 3 January 2014 @@ -362,7 +362,7 @@ Forests 2014, 5(1), 21-71; doi: - 10.3390/f5010021 + 10.3390/f5010021
Received: 4 November 2013; in revised form: 15 December 2013 / Accepted: 18 December 2013 / Published: 3 January 2014 @@ -404,7 +404,7 @@ Adm. Sci. 2014, 4(1), 1-14; doi: - 10.3390/admsci4010001 + 10.3390/admsci4010001
Received: 8 October 2013; in revised form: 16 December 2013 / Accepted: 19 December 2013 / Published: 3 January 2014 @@ -442,7 +442,7 @@ Arts 2014, 3(1), 15-26; doi: - 10.3390/arts3010015 + 10.3390/arts3010015
Received: 27 October 2013; in revised form: 2 December 2013 / Accepted: 17 December 2013 / Published: 3 January 2014 @@ -485,7 +485,7 @@ J. Funct. Biomater. 2014, 5(1), 1-14; doi: - 10.3390/jfb5010001 + 10.3390/jfb5010001
Received: 27 August 2013; in revised form: 26 November 2013 / Accepted: 27 November 2013 / Published: 3 January 2014 @@ -526,7 +526,7 @@ Int. J. Environ. Res. Public Health 2014, 11(1), 713-733; doi: - 10.3390/ijerph110100713 + 10.3390/ijerph110100713
Received: 14 October 2013; in revised form: 16 December 2013 / Accepted: 18 December 2013 / Published: 3 January 2014 @@ -567,7 +567,7 @@ Diversity 2014, 6(1), 33-42; doi: - 10.3390/d6010033 + 10.3390/d6010033
Received: 2 October 2013; in revised form: 20 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014 @@ -618,7 +618,7 @@ Diversity 2014, 6(1), 18-32; doi: - 10.3390/d6010018 + 10.3390/d6010018
Received: 27 October 2013; in revised form: 3 December 2013 / Accepted: 24 December 2013 / Published: 3 January 2014 @@ -652,7 +652,7 @@ Sustainability 2014, 6(1), 251-266; doi: - 10.3390/su6010251 + 10.3390/su6010251
Received: 11 November 2013; in revised form: 13 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014 @@ -698,7 +698,7 @@ Membranes 2014, 4(1), 20-39; doi: - 10.3390/membranes4010020 + 10.3390/membranes4010020
Received: 6 November 2013; in revised form: 26 November 2013 / Accepted: 21 December 2013 / Published: 3 January 2014 @@ -743,7 +743,7 @@ Energies 2014, 7(1), 130-149; doi: - 10.3390/en7010130 + 10.3390/en7010130
Received: 21 October 2013; in revised form: 11 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014 @@ -781,7 +781,7 @@ Societies 2014, 4(1), 16-29; doi: - 10.3390/soc4010016 + 10.3390/soc4010016
Received: 31 October 2013; in revised form: 24 December 2013 / Accepted: 24 December 2013 / Published: 3 January 2014 @@ -820,7 +820,7 @@ J. Sens. Actuator Netw. 2014, 3(1), 44-63; doi: - 10.3390/jsan3010044 + 10.3390/jsan3010044
Received: 26 November 2013; in revised form: 15 December 2013 / Accepted: 23 December 2013 / Published: 3 January 2014 @@ -859,7 +859,7 @@ Mar. Drugs 2014, 12(1), 115-127; doi: - 10.3390/md12010115 + 10.3390/md12010115
Received: 14 October 2013; in revised form: 25 November 2013 / Accepted: 12 December 2013 / Published: 3 January 2014 @@ -914,7 +914,7 @@ Energies 2014, 7(1), 115-129; doi: - 10.3390/en7010115 + 10.3390/en7010115
Received: 22 October 2013; in revised form: 17 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014 @@ -961,7 +961,7 @@ Materials 2014, 7(1), 218-231; doi: - 10.3390/ma7010218 + 10.3390/ma7010218
Received: 28 November 2013; in revised form: 17 December 2013 / Accepted: 23 December 2013 / Published: 3 January 2014 @@ -1007,7 +1007,7 @@ Int. J. Mol. Sci. 2014, 15(1), 525-544; doi: - 10.3390/ijms15010525 + 10.3390/ijms15010525
Received: 13 November 2013; in revised form: 19 December 2013 / Accepted: 23 December 2013 / Published: 3 January 2014 @@ -1051,7 +1051,7 @@ Materials 2014, 7(1), 206-217; doi: - 10.3390/ma7010206 + 10.3390/ma7010206
Received: 8 October 2013; in revised form: 14 December 2013 / Accepted: 19 December 2013 / Published: 3 January 2014 @@ -1107,7 +1107,7 @@ Int. J. Mol. Sci. 2014, 15(1), 504-524; doi: - 10.3390/ijms15010504 + 10.3390/ijms15010504
Received: 30 October 2013; in revised form: 16 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014 @@ -1152,7 +1152,7 @@ Remote Sens. 2014, 6(1), 540-554; doi: - 10.3390/rs6010540 + 10.3390/rs6010540
Received: 30 October 2013; in revised form: 25 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014 @@ -1193,7 +1193,7 @@ Remote Sens. 2014, 6(1), 521-539; doi: - 10.3390/rs6010521 + 10.3390/rs6010521
Received: 27 September 2013; in revised form: 13 December 2013 / Accepted: 23 December 2013 / Published: 3 January 2014 @@ -1238,7 +1238,7 @@ Toxins 2014, 6(1), 229-253; doi: - 10.3390/toxins6010229 + 10.3390/toxins6010229
Received: 11 November 2013; in revised form: 24 December 2013 / Accepted: 27 December 2013 / Published: 3 January 2014 diff --git a/src/main/resources/org/contentmine/norma/pubstyle/hindawi/metadata.txt b/src/main/resources/org/contentmine/norma/pubstyle/hindawi/metadata.txt index 3539542d1..2f3651fce 100644 --- a/src/main/resources/org/contentmine/norma/pubstyle/hindawi/metadata.txt +++ b/src/main/resources/org/contentmine/norma/pubstyle/hindawi/metadata.txt @@ -106,7 +106,7 @@ Volume 2014 (2014), Article ID 801626, 8 pages

// doi - http://dx.doi.org/10.1155/2014/801626 + https://doi.org/10.1155/2014/801626 // article type
Research Article
diff --git a/src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml copy.xsl b/src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml copy.xsl index f0754f41e..565d94241 100644 --- a/src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml copy.xsl +++ b/src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml copy.xsl @@ -6,7 +6,7 @@ - https://dx.doi.org/ + https://doi.org/ http://www.ncbi.nlm.nih.gov/pubmed/ @@ -817,7 +817,7 @@
- +
diff --git a/src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml.xsl b/src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml.xsl index d58c8b270..78cb908fd 100644 --- a/src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml.xsl +++ b/src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml.xsl @@ -9,7 +9,7 @@ Generic NLM 10.0000 - https://dx.doi.org/ + https://doi.org/ http://www.ncbi.nlm.nih.gov/pubmed/ @@ -885,7 +885,7 @@ UNKNOWN nlm: alt-text:
- +
diff --git a/src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml.xsl-old b/src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml.xsl-old index eab0cbf3b..76b8ff09d 100644 --- a/src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml.xsl-old +++ b/src/main/resources/org/contentmine/norma/pubstyle/nlm/toHtml.xsl-old @@ -6,7 +6,7 @@ - https://dx.doi.org/ + https://doi.org/ http://www.ncbi.nlm.nih.gov/pubmed/ @@ -796,7 +796,7 @@
- +
diff --git a/src/test/java/org/contentmine/cproject/CProjectCommandIT.java b/src/test/java/org/contentmine/cproject/CProjectCommandIT.java index ff72fd587..e12c2ca6d 100644 --- a/src/test/java/org/contentmine/cproject/CProjectCommandIT.java +++ b/src/test/java/org/contentmine/cproject/CProjectCommandIT.java @@ -39,7 +39,7 @@ public void testInputOutputUrls1() throws IOException { List lines = FileUtils.readLines(outUrls); Collections.sort(lines); Assert.assertEquals("out urls ", 15, lines.size()); - Assert.assertEquals("url ", "http://dx.doi.org/10.1063/1.4943235", lines.get(0)); + Assert.assertEquals("url ", "https://doi.org/10.1063/1.4943235", lines.get(0)); } diff --git a/src/test/java/org/contentmine/cproject/CProjectCommandTest.java b/src/test/java/org/contentmine/cproject/CProjectCommandTest.java index 15c2dc3aa..23ffd261a 100644 --- a/src/test/java/org/contentmine/cproject/CProjectCommandTest.java +++ b/src/test/java/org/contentmine/cproject/CProjectCommandTest.java @@ -50,18 +50,18 @@ public void testCrossrefUnshuffledURLS() throws IOException { List lines = FileUtils.readLines(urls); Assert.assertEquals(30, lines.size()); Assert.assertEquals("[" - + "http://dx.doi.org/10.1002/adaw.30456," - + " http://dx.doi.org/10.1007/s00332-016-9284-y," - + " http://dx.doi.org/10.1007/s00300-016-1897-y," - + " http://dx.doi.org/10.1007/s00294-016-0568-4," - + " http://dx.doi.org/10.1002/acs.2674," - + " http://dx.doi.org/10.1016/j.ijpe.2016.01.022," - + " http://dx.doi.org/10.1007/s00294-016-0564-8," - + " http://dx.doi.org/10.1515/tjj-2015-0056," - + " http://dx.doi.org/10.1002/acs.2662," - + " http://dx.doi.org/10.1007/s00291-015-0429-4," - + " http://dx.doi.org/10.1016/j.ijpe.2016.01.021," - + " http://dx.doi.org/10.1007/s0028", + + "https://doi.org/10.1002/adaw.30456," + + " https://doi.org/10.1007/s00332-016-9284-y," + + " https://doi.org/10.1007/s00300-016-1897-y," + + " https://doi.org/10.1007/s00294-016-0568-4," + + " https://doi.org/10.1002/acs.2674," + + " https://doi.org/10.1016/j.ijpe.2016.01.022," + + " https://doi.org/10.1007/s00294-016-0564-8," + + " https://doi.org/10.1515/tjj-2015-0056," + + " https://doi.org/10.1002/acs.2662," + + " https://doi.org/10.1007/s00291-015-0429-4," + + " https://doi.org/10.1016/j.ijpe.2016.01.021," + + " https://doi.org/10.1007/s0028", lines.toString().substring(0, 500)); } @@ -82,18 +82,18 @@ public void testCrossrefShuffledURLS() throws IOException { List lines = FileUtils.readLines(urls); Assert.assertEquals(30, lines.size()); Assert.assertEquals("[" - + "http://dx.doi.org/10.1002/adaw.30456," - + " http://dx.doi.org/10.1007/s00332-016-9284-y," - + " http://dx.doi.org/10.1007/s00300-016-1897-y," - + " http://dx.doi.org/10.1007/s00294-016-0568-4," - + " http://dx.doi.org/10.1002/acs.2674," - + " http://dx.doi.org/10.1016/j.ijpe.2016.01.022," - + " http://dx.doi.org/10.1007/s00294-016-0564-8," - + " http://dx.doi.org/10.1515/tjj-2015-0056," - + " http://dx.doi.org/10.1002/acs.2662," - + " http://dx.doi.org/10.1007/s00291-015-0429-4," - + " http://dx.doi.org/10.1016/j.ijpe.2016.01.021," - + " http://dx.doi.org/10.1007/s0028", + + "https://doi.org/10.1002/adaw.30456," + + " https://doi.org/10.1007/s00332-016-9284-y," + + " https://doi.org/10.1007/s00300-016-1897-y," + + " https://doi.org/10.1007/s00294-016-0568-4," + + " https://doi.org/10.1002/acs.2674," + + " https://doi.org/10.1016/j.ijpe.2016.01.022," + + " https://doi.org/10.1007/s00294-016-0564-8," + + " https://doi.org/10.1515/tjj-2015-0056," + + " https://doi.org/10.1002/acs.2662," + + " https://doi.org/10.1007/s00291-015-0429-4," + + " https://doi.org/10.1016/j.ijpe.2016.01.021," + + " https://doi.org/10.1007/s0028", lines.toString().substring(0, 500)); } @@ -138,10 +138,10 @@ public void testCreateCrossrefAllHeadersCSV() throws IOException { Assert.assertEquals(132, lines.size()); Assert.assertEquals("[" + "URL,Title,Date,PDFURL,PDFFile,HTMLURL,HTMLFile,XMLURL,XMLFile,DOI,Publisher,Volume,AuthorList,Type,Issue,FirstPage,Description,Abstract,Journal,License,Links,Copyright,ISSN,Keywords,QuickscrapeMD,CrossrefMD,PublisherMD,Prefix," - + " http://dx.doi.org/10.1001/jama.2016.7992,Sodium Reduction—Saving Lives by Putting Choice Into Consumers’ Hands,2016-06-01T23:24:00Z,,N,,N,,N,10.1001/jama.2016.7992,American Medical Association (AMA),,\"[Frieden Thomas R. [{\"\"name\"\":\"\"Centers for Disease Control and Prevention, Atlanta, Georgia\"\"}], ]\",journal-article,,,,,JAMA,0: [],0: [],,0098-7484,\"[[\"\"Medicine(all)\"\"]]\",N,N,N,http://id.crossref.org/prefix/10.1001," - + " http://dx.doi.org/10.1002/ab.21660,\"The relationship between physical aggression, foreign policy and moral choices: Phenotypic and genetic findings\",2016-06-01T04:27:39Z,,N,,N,,N,10.1002/ab.21660,Wiley-Blackwell,,\"[McDermott Rose [{\"\"name\"\":\"\"Brown University; Providence Rhode Island\"\"}], , Hatemi Peter K. [{\"\"name\"\":\"\"Pennsylvania State University; State College Pennsylvania\"\"}], ]\",journal-article,,,,,Aggr. Behav.," - + "\"2: [http://doi.wiley.com/10.1002/tdm_license_1, http://onlinelibrary.wiley.com/termsAndConditions]\",1: [application/pdf http://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fab.21660],,0096-140X,\"[[\"\"Psychology(all)\"\"]]\",N,N,N,http://id.crossref.org/prefix/10.1002, http://dx.doi.org/10.1002/acp.3238,Die Hard in Notting Hill: Gender Differences in Recalling Contents from Action and Romantic Movies,2016-06-01T08:12:49Z,,N,,N,,N,10.1002/acp.3238,Wiley-Blackwell,,\"[Wühr Peter [{\"\"name\"\":\"\"Institut für Psychologie; Technische Universität Dortmund; Dortmund Germany\"\"}], , Schwarz Sascha [{\"\"name\"\":\"\"Institut für Psychologie; Bergische Universität Wuppertal; Wuppertal Germany\"\"}], ]\",journal-article,,,,,Applied Cognitive Psychology," - + "\"2: [http://doi.wiley.com/10.1002/tdm_license_1, http://onlinelibrary.wiley.com/termsAndConditions]\",1: [application/pdf http://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Facp.3238],,0888-4080,\"[[\"\"Experimental and Cognitive Psychology\"\"]]\",N,N,N,http://id.crossref.org/prefix/10.1002, http://dx.doi.org/10.1002/acp.3239,Improving Unfamiliar Face Matching by Masking the External Facial Features,2016-06-01T08:13:03Z,,N,,N,,N,10.1002/acp.3239,Wiley-Blackwell,,\"[Kemp Richard I. [{\"\"name\"\":\"\"School of Psychology; University of New South Wales; Sydney Australia\"\"}], , Caon Alita [{\"\"name\"\":\"\"School of Psychology; University of New South Wales; Sydney Australia\"\"}], , Howard Mark [{\"\"name\"\":\"\"School of Psychology; University of New South Wales; Sydney Australia\"\"}], , Brooks Kevin R. [{\"\"name\"\":\"\"Department of Psychology; Macquarie University; Sydney Australia\"\"},{\"\"name\"\":\"\"Perception in Action Research Centre (PARC), Faculty of Human Sciences; Macquarie University; Sydney Australia\"\"}], ]\",journal-article,,,,,Applied Cognitive Psychology," + + " https://doi.org/10.1001/jama.2016.7992,Sodium Reduction—Saving Lives by Putting Choice Into Consumers’ Hands,2016-06-01T23:24:00Z,,N,,N,,N,10.1001/jama.2016.7992,American Medical Association (AMA),,\"[Frieden Thomas R. [{\"\"name\"\":\"\"Centers for Disease Control and Prevention, Atlanta, Georgia\"\"}], ]\",journal-article,,,,,JAMA,0: [],0: [],,0098-7484,\"[[\"\"Medicine(all)\"\"]]\",N,N,N,http://id.crossref.org/prefix/10.1001," + + " https://doi.org/10.1002/ab.21660,\"The relationship between physical aggression, foreign policy and moral choices: Phenotypic and genetic findings\",2016-06-01T04:27:39Z,,N,,N,,N,10.1002/ab.21660,Wiley-Blackwell,,\"[McDermott Rose [{\"\"name\"\":\"\"Brown University; Providence Rhode Island\"\"}], , Hatemi Peter K. [{\"\"name\"\":\"\"Pennsylvania State University; State College Pennsylvania\"\"}], ]\",journal-article,,,,,Aggr. Behav.," + + "\"2: [http://doi.wiley.com/10.1002/tdm_license_1, http://onlinelibrary.wiley.com/termsAndConditions]\",1: [application/pdf http://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Fab.21660],,0096-140X,\"[[\"\"Psychology(all)\"\"]]\",N,N,N,http://id.crossref.org/prefix/10.1002, https://doi.org/10.1002/acp.3238,Die Hard in Notting Hill: Gender Differences in Recalling Contents from Action and Romantic Movies,2016-06-01T08:12:49Z,,N,,N,,N,10.1002/acp.3238,Wiley-Blackwell,,\"[Wühr Peter [{\"\"name\"\":\"\"Institut für Psychologie; Technische Universität Dortmund; Dortmund Germany\"\"}], , Schwarz Sascha [{\"\"name\"\":\"\"Institut für Psychologie; Bergische Universität Wuppertal; Wuppertal Germany\"\"}], ]\",journal-article,,,,,Applied Cognitive Psychology," + + "\"2: [http://doi.wiley.com/10.1002/tdm_license_1, http://onlinelibrary.wiley.com/termsAndConditions]\",1: [application/pdf http://api.wiley.com/onlinelibrary/tdm/v1/articles/10.1002%2Facp.3238],,0888-4080,\"[[\"\"Experimental and Cognitive Psychology\"\"]]\",N,N,N,http://id.crossref.org/prefix/10.1002, https://doi.org/10.1002/acp.3239,Improving Unfamiliar Face Matching by Masking the External Facial Features,2016-06-01T08:13:03Z,,N,,N,,N,10.1002/acp.3239,Wiley-Blackwell,,\"[Kemp Richard I. [{\"\"name\"\":\"\"School of Psychology; University of New South Wales; Sydney Australia\"\"}], , Caon Alita [{\"\"name\"\":\"\"School of Psychology; University of New South Wales; Sydney Australia\"\"}], , Howard Mark [{\"\"name\"\":\"\"School of Psychology; University of New South Wales; Sydney Australia\"\"}], , Brooks Kevin R. [{\"\"name\"\":\"\"Department of Psychology; Macquarie University; Sydney Australia\"\"},{\"\"name\"\":\"\"Perception in Action Research Centre (PARC), Faculty of Human Sciences; Macquarie University; Sydney Australia\"\"}], ]\",journal-article,,,,,Applied Cognitive Psychology," + "\"2: [http://doi.wiley.com/10.1002/tdm_license_1, http://onlinelibrary.wiley.com/termsAndConditions]\",1: [application/pdf http://api.", lines.toString().substring(0, Math.min(lines.toString().length(), 3000))); } diff --git a/src/test/java/org/contentmine/cproject/metadata/MetadataLongTest.java b/src/test/java/org/contentmine/cproject/metadata/MetadataLongTest.java index c821e5b48..51fbb1df8 100644 --- a/src/test/java/org/contentmine/cproject/metadata/MetadataLongTest.java +++ b/src/test/java/org/contentmine/cproject/metadata/MetadataLongTest.java @@ -48,16 +48,16 @@ public void testGetShuffledDOIURLs() throws IOException { List lines = FileUtils.readLines(shuffledUrlsOutFilename); Assert.assertEquals("lines "+lines.size(), 12141, lines.size()); lines = lines.subList(0, 10); - Assert.assertEquals("lines "+lines.size(), "[http://dx.doi.org/10.1002/zoo.21264," - + " http://dx.doi.org/10.1007/s41105-016-0048-8," - + " http://dx.doi.org/10.1016/s2225-4110(16)00008-0," - + " http://dx.doi.org/10.1017/s2045796016000044," - + " http://dx.doi.org/10.1021/mpv013i002_797621," - + " http://dx.doi.org/10.1016/s2225-4110(16)00007-9," - + " http://dx.doi.org/10.1037/tra0000087.supp," - + " http://dx.doi.org/10.1038/srep20371," - + " http://dx.doi.org/10.1039/c6tc00170j," - + " http://dx.doi.org/10.1049/iet-wss.2014.0090]" + Assert.assertEquals("lines "+lines.size(), "[https://doi.org/10.1002/zoo.21264," + + " https://doi.org/10.1007/s41105-016-0048-8," + + " https://doi.org/10.1016/s2225-4110(16)00008-0," + + " https://doi.org/10.1017/s2045796016000044," + + " https://doi.org/10.1021/mpv013i002_797621," + + " https://doi.org/10.1016/s2225-4110(16)00007-9," + + " https://doi.org/10.1037/tra0000087.supp," + + " https://doi.org/10.1038/srep20371," + + " https://doi.org/10.1039/c6tc00170j," + + " https://doi.org/10.1049/iet-wss.2014.0090]" + "", lines.toString()); } diff --git a/src/test/java/org/contentmine/cproject/metadata/ProjectMetadataAnalyzerTest.java b/src/test/java/org/contentmine/cproject/metadata/ProjectMetadataAnalyzerTest.java index 986d9e566..356baef62 100644 --- a/src/test/java/org/contentmine/cproject/metadata/ProjectMetadataAnalyzerTest.java +++ b/src/test/java/org/contentmine/cproject/metadata/ProjectMetadataAnalyzerTest.java @@ -84,26 +84,26 @@ public void testExtractURLs() throws IOException { projectAnalyzer.setPseudoHost(true); List urls = cProject.extractShuffledCrossrefUrls(); Assert.assertEquals("urls ", "[" - + "http://dx.doi.org/10.1001/jama.2016.7992," - + " http://dx.doi.org/10.1002/adhm.201600266," - + " http://dx.doi.org/10.1002/adhm.201600181," - + " http://dx.doi.org/10.1002/adhm.201600160," - + " http://dx.doi.org/10.1002/adhm.201600126," - + " http://dx.doi.org/10.1002/adhm.201600114," - + " http://dx.doi.org/10.1002/adhm.201600045," - + " http://dx.doi.org/10.1002/adfm.201601550," - + " http://dx.doi.org/10.1002/adfm.201601123," - + " http://dx.doi.org/10.1002/adfm.201601037," - + " http://dx.doi.org/10.1002/adfm.201600909," - + " http://dx.doi.org/10.1002/adfm.201600856," - + " http://dx.doi.org/10.1002/adfm.201600813," - + " http://dx.doi.org/10.1002/adfm.201504999," - + " http://dx.doi.org/10.1002/adem.201600096," - + " http://dx.doi.org/10.1002/acp.3240," - + " http://dx.doi.org/10.1002/acp.3239," - + " http://dx.doi.org/10.1002/acp.3238," - + " http://dx.doi.org/10.1002/ab.21660," - + " http://dx.doi.org/10.1002/adma.201601115" + + "https://doi.org/10.1001/jama.2016.7992," + + " https://doi.org/10.1002/adhm.201600266," + + " https://doi.org/10.1002/adhm.201600181," + + " https://doi.org/10.1002/adhm.201600160," + + " https://doi.org/10.1002/adhm.201600126," + + " https://doi.org/10.1002/adhm.201600114," + + " https://doi.org/10.1002/adhm.201600045," + + " https://doi.org/10.1002/adfm.201601550," + + " https://doi.org/10.1002/adfm.201601123," + + " https://doi.org/10.1002/adfm.201601037," + + " https://doi.org/10.1002/adfm.201600909," + + " https://doi.org/10.1002/adfm.201600856," + + " https://doi.org/10.1002/adfm.201600813," + + " https://doi.org/10.1002/adfm.201504999," + + " https://doi.org/10.1002/adem.201600096," + + " https://doi.org/10.1002/acp.3240," + + " https://doi.org/10.1002/acp.3239," + + " https://doi.org/10.1002/acp.3238," + + " https://doi.org/10.1002/ab.21660," + + " https://doi.org/10.1002/adma.201601115" + "]", urls.toString()); LOG.trace(urls); } diff --git a/src/test/java/org/contentmine/cproject/metadata/crossref/CrossrefTest.java b/src/test/java/org/contentmine/cproject/metadata/crossref/CrossrefTest.java index fa19dc7a4..f6f0a1f1e 100644 --- a/src/test/java/org/contentmine/cproject/metadata/crossref/CrossrefTest.java +++ b/src/test/java/org/contentmine/cproject/metadata/crossref/CrossrefTest.java @@ -128,7 +128,7 @@ public void testLs() throws IOException { @Test @Ignore // requires net public void testResolveDOI() throws Exception { - String crossRefDOI = "http://dx.doi.org/10.3389/fpsyg.2016.00565"; + String crossRefDOI = "https://doi.org/10.3389/fpsyg.2016.00565"; String s = new DOIResolver().resolveDOI(crossRefDOI); // LOG.debug("DOI "+s); } diff --git a/src/test/java/org/contentmine/norma/json/ManifestTest.java b/src/test/java/org/contentmine/norma/json/ManifestTest.java index 6af97dd28..764e112eb 100644 --- a/src/test/java/org/contentmine/norma/json/ManifestTest.java +++ b/src/test/java/org/contentmine/norma/json/ManifestTest.java @@ -89,7 +89,7 @@ public void testReadFirstManifestFromFile() throws IOException { 2 [main] DEBUG org.contentmine.norma.json.ManifestTest - pubModel = "Electronic-eCollection" 2 [main] DEBUG org.contentmine.norma.json.ManifestTest - pubTypeList = {"pubType":["Journal Article"]} 2 [main] DEBUG org.contentmine.norma.json.ManifestTest - subsetList = {"subset":[{"code":["IM"],"name":["Index Medicus"]}]} -2 [main] DEBUG org.contentmine.norma.json.ManifestTest - fullTextUrlList = {"fullTextUrl":[{"availability":["Open access"],"availabilityCode":["OA"],"documentStyle":["pdf"],"site":["Europe_PMC"],"url":["http://europepmc.org/articles/PMC4441471?pdf=render"]},{"availability":["Open access"],"availabilityCode":["OA"],"documentStyle":["html"],"site":["Europe_PMC"],"url":["http://europepmc.org/articles/PMC4441471"]},{"availability":["Subscription required"],"availabilityCode":["S"],"documentStyle":["doi"],"site":["DOI"],"url":["http://dx.doi.org/10.1371/journal.pone.0127339"]}]} +2 [main] DEBUG org.contentmine.norma.json.ManifestTest - fullTextUrlList = {"fullTextUrl":[{"availability":["Open access"],"availabilityCode":["OA"],"documentStyle":["pdf"],"site":["Europe_PMC"],"url":["http://europepmc.org/articles/PMC4441471?pdf=render"]},{"availability":["Open access"],"availabilityCode":["OA"],"documentStyle":["html"],"site":["Europe_PMC"],"url":["http://europepmc.org/articles/PMC4441471"]},{"availability":["Subscription required"],"availabilityCode":["S"],"documentStyle":["doi"],"site":["DOI"],"url":["https://doi.org/10.1371/journal.pone.0127339"]}]} 2 [main] DEBUG org.contentmine.norma.json.ManifestTest - isOpenAccess = "Y" 2 [main] DEBUG org.contentmine.norma.json.ManifestTest - inEPMC = "Y" 2 [main] DEBUG org.contentmine.norma.json.ManifestTest - inPMC = "N" diff --git a/src/test/java/org/contentmine/norma/pubstyle/rs/RSDownloadTest.java b/src/test/java/org/contentmine/norma/pubstyle/rs/RSDownloadTest.java index bb9883439..0897904ca 100644 --- a/src/test/java/org/contentmine/norma/pubstyle/rs/RSDownloadTest.java +++ b/src/test/java/org/contentmine/norma/pubstyle/rs/RSDownloadTest.java @@ -177,7 +177,7 @@ public void testDownloadJsonTidy() throws IOException { }, "page": "20151498", -"update-policy": "http://dx.doi.org/10.1098/crossmarkpolicy", +"update-policy": "https://doi.org/10.1098/crossmarkpolicy", "source": "CrossRef", "title": [ @@ -261,7 +261,7 @@ public void testDownloadJsonTidy() throws IOException { "10.1098/rspb.2015.1498" ], -"URL": "http://dx.doi.org/10.1098/rspb.2015.1498", +"URL": "https://doi.org/10.1098/rspb.2015.1498", "ISSN": [ diff --git a/src/test/resources/org/contentmine/ami/oil5/PMC4391421/scholarly.html b/src/test/resources/org/contentmine/ami/oil5/PMC4391421/scholarly.html index 033efcc2c..1d13f36c0 100644 --- a/src/test/resources/org/contentmine/ami/oil5/PMC4391421/scholarly.html +++ b/src/test/resources/org/contentmine/ami/oil5/PMC4391421/scholarly.html @@ -104,6 +104,6 @@ antimicrobial activity
Introduction

The genus Thymus, member of the Lamiaceae family, contains about 400 species of perennial aromatic, evergreen or semi-evergreen herbaceous plants with many subspecies, varieties, subvarieties and forms [ 1 ]. In Romania, the Thymus genus contains one species cultivated as aromatic plant (Thymus vulgaris) and other 18 wild species [ 2 ]. T. vulgaris (thyme), locally known as "cimbru", is widely used in the Romanian folk medicine for its expectorant, antitussive, antibroncholitic, antispasmodic, anthelmintic, carminative and diuretic properties.

Various studies have aimed to investigate the chemical composition and biological properties of the T. vulgaris essential oil (EO). According to European Pharmacopoeia 5.0 (Ph. Eur. 5.0) [ 3 ], the minimum content of EO in T. vulgaris is 12 mL/kg, but the chemical composition shows variations, six chemotypes being mainly reported, namely geraniol, linalool, gamma-terpineol, carvacrol, thymol and trans-thujan-4-ol/terpinen-4-ol [ 4 , 5 ]. Both the isolation yield and the chemical composition of the EOs are dependent on a number of factors, such as the environment, growth region and cultivation practices [ 6 ]. In addition to the flavoring properties determined by the constitutive active ingredients, the thyme EO exhibits significant antimicrobial activity [ 4 , 7 - 9 ] as well as strong antioxidant properties [ 2 , 8 ].

The aim of this study is to determine the chemical composition together with the antimicrobial properties of the EO of T. vulgaris cultivated in Romania, in order to identify new sources of natural antiseptics with applications in the pharmaceutical and food industry.

Materials and methods

Raw material. Thyme was harvested during the flowering season (July 2012) from the area around the Broşteni commune – Mehedinţi County, Romania. The plant material was dried in well-ventilated areas, sheltered from direct sunlight and then stored in double-layered paper bags at temperatures of 3-5°C until processing. A voucher specimen (V.FPT-451) was deposited in the Herbarium of the Faculty of Pharmacy, "Victor Babeș" University of Medicine and Pharmacy, Timișoara, Romania.

Isolation of essential oils. The EO was obtained by hydrodistillation, according to Ph. Eur. 5.0 [ 3 ], by using a modified Clevenger apparatus (with the EO collection area cooled to prevent the emergence of artifacts). The EO was dried on anhydrous sodium sulfate (Sigma-Aldrich Chemie GmbH) and stored in a tightly sealed brown glass bottle at 0-4°C for testing.

Gas chromatography-mass spectrometry. Samples were analyzed by gas chromatography using a HP6890 instrument coupled with a HP 5973 mass spectrometer. The gas chromatograph is equipped with a split-splitless injector and a Factor FourTM VF-35ms 5% fenil-methylpolysiloxane, 30 m, 0.25 mm, 0.25 μm film thickness capillary column. Gas chromatography conditions include a temperature range of 50 to 250°C at 40°C/min, with a solvent delay of 5 min. The injector was maintained at a temperature of 250°C. The inert gas was helium at a flow of 1.0 mL/min, and the injected volume in the splitless mode was 1 μL. The MS conditions were the following: ionization energy, 70 eV; quadrupole temperature, 100°C; scanning velocity, 1.6 scan/s; weight range, 40-500 amu.

The percent composition of the volatile compounds was calculated. The qualitative analysis was based on the percent area of each peak of the sample compounds. The mass spectrum of each compound was compared with the mass spectrum from the NIST 98 spectrum library (USA National Institute of Science and Technology software).

Determination of antimicrobial activity. Thyme EO was tested on 7 common food-related bacteria and fungus: Staphylococcus aureus (ATCC 25923), Pseudomonas aeruginosa (ATCC 27853), Salmonella typhimurium (ATCC 14028), Escherichia coli (ATCC 25922), Klebsiella pneumoniae (ATCC 13882), Enterococcus faecalis (ATCC 29212) and Candida albicans (ATCC 10231), using the disk diffusion method as previously described [ 10 ]. Briefly, a suspension of the tested microorganism (10^6 cells/mL-1) was spread on the solid media plates (Mueller-Hinton agar for bacteria and Sabouraud cloramphenicol agar for fungi). The paper discs (Whatman No 1 filter paper - 6 mm diameter) were impregnated with 5, 10, 15 and 20µL EO and placed on the inoculated agar. The plates inoculated with bacterial strains were incubated for 24 h at 37°C and 48 h at 30°C for fungi, respectively. As positive controls, ciprofloxacin (30 µg/disk) and cephalexin (10 µg/disk) were used for bacterial strains and fluconazole (10 µg/disk) for fungi. After incubation, the diameter of the zone of inhibition was measured in millimeters. Each test was performed in triplicate on at least three separate experiments.

Statistical analysis. The statistical analysis was performed by using SPSS Version 21 (IBM Corp., NY). The mean inhibition zone for each group of nine observations was compared with the value of the disc diameter (6 mm) using the t-test. The GLM procedure was used to conduct a two-way analysis of variance (ANOVA) on the inhibition zones. The type of microorganism and amount of essential oil were used as factors in the full factorial model. Post-hoc tests for each amount of essential oil were conducted by using Tukey’s HSD method, in order to compare the effect on different types of microorganisms.

-Results and Discussion

The isolation yield was 1.25% (v/w), based on dry plant material and confirmed that the plant analyzed meets the requirements of pharmaceutical quality for thyme as EO source [ 3 ]. The chemical composition determined by GC/ MS is presented in Table 1 . Fifteen components representing 99.91% of the total detected constituents were identified. The major components were p-cymene (8.41%), γ-terpinene (30.90%) and thymol (47.59%), which suggests that the EO analyzed belongs to the thymol chemotype in agreement with those previously reported in Romania [ 2 ]. The other components were present in a total amount of less than 13.01%. The chemical composition of the EO analyzed by us is very different from that previously reported in Morocco and Spain for the same species of thyme [ 11 , 12 ]. Similar studies in Poland, Iran, Spain and Italy, respectively, reported as major compounds in the T. vulgaris EO p-cymene, γ-terpinene and thymol [ 4 , 13 - 15 ]. These differences can be attributed to a large extent to the different chemotypes mentioned above [ 4 , 5 , 13 ].

The antimicrobial activity of thyme oil against 7 common food-related bacteria and fungus tested is presented in Table 2 . The null hypothesis that the inhibition zone is equal to the disc diameter (6 mm) was rejected for each microorganism at every amount of essential oil with a high significance level (p = 0.00). The main finding of the ANOVA analysis is a strong interaction effect between the type of microorganism and the amount of essential oil (p = 0.00). The highly significant interaction effect adds difficulty in drawing general conclusions on the main effects, even if the two factors are also highly significant (p = 0.00). For example, K. pneumoniae has the highest inhibition zone overall but for the amount of 20 [μL], where E. coli and S. typhimurium have higher values. In order to compare more thoroughly the effect of T. vulgaris on each microorganism ( Fig. 1 ), the results of multiple comparisons, at each oil amount, has to be considered. Tukey’s HSD test reveals that the only microorganisms with non-significant differences in the antimicrobial effect are S. typhimurium and E. coli at all oil amounts, and S. typhimurium, E. coli and C. albicans at 10 [μL]. The observed p-value for the pairwise differences in the above-mentioned cases does not pass acceptable significance levels, being larger than 0.4. All the other pairwise differences are highly significant (p = 0.00).

Table 1

Chemical composition of thyme EO

No. RT (min) Area % of total Constituents*
1 5.39 1.06 alpha-Thujene
2 5.63 1.07 alpha-Pinene
3 6.89 0.37 beta-Pinene
4 6.97 1.53 beta-Myrcene
5 7.53 0.33 alpha-Phellandrene
6 7.77 3.76 Carene
7 8.04 0.29 D-Limonene
8 8.26 0.21 beta-Phellandrene
9 8.46 8.41 para-Cymene
10 8.96 30.90 gamma-Terpinene
11 9.48 0.47 Terpineol
12 12.55 0.46 Terpinen-4-ol
13 16.17 47.59 Thymol
14 17.32 2.68 Caryophyllene
15 19.03 0.78 Cyclohexene, 1-methyl-4-(5-methyl-1-methylene-4-hexenyl)
Total 99.91%
*Constituents presented in the order of elution from the VF 35 MS column.

The inhibition of the growth of E. coli, K. pneumoniae, S. aureus, P. aeruginosa and E. faecalis was previously reported [ 4 , 7 , 9 ] along with the efficacy against C. albicans [ 9 , 16 , 17 ] and S. typhimurium [ 4 , 9 ], respectively. In contrast, some studies report the inefficiency of thyme EO against E. coli [ 16 , 17 ], S. aureus [ 16 ] and K. pneumoniae [ 16 ].

The antimicrobial activity of thyme oil, at different amounts, expressed as a mean inhibition zone for each of the nine repeated measurements

Table 2

Effects of thyme oil against bacteria expressed by the mean sizes of the inhibitory zones

Test microorganism Amount of essential oil [μL]
5 10 15 20
Staphylococcus aureus ATCC 25923 23.93 ± 0.33 29.2 ± 0.6 29.9 ± 0.35 31.4 ± 0.47
Salmonella typhimurium ATCC 14028 14.49 ± 0.34 19.71 ± 0.39 30.68 ± 0.33 34.94 ± 0.22
Pseudomonas aeruginosa ATCC27853 11.82 ± 0.27 13.34 ± 0.33 14 ± 0.22 14.13 ± 0.19
E. coli ATCC 25922 14.63 ± 0.36 19.82 ± 0.41 30.67 ± 0.31 34.99 ± 0.19
Klebsiella pneumoniae ATCC 13882 30.21 ± 0.12 31.02 ± 0.31 32.79 ± 0.24 33.93 ± 0.14
Enterococcus faecalis ATCC 29212 8.99 ± 0.15 15.06 ± 0.15 15.99 ± 0.18 24.06 ± 0.15
Candida albicans ATCC 10231 15.14 ± 0.38 19.43 ± 0.55 25.74 ± 0.24 30.2 ± 0.17

The inhibitions are expressed in mm and include the diameter of the paper disc (6 mm). Data distributions were expressed as mean values and standard deviations (SD) (n = 9). Ciprofloxacine and cephalexine (for bacterial strains) and fluconazole (for fungi), respectively, were used as positive controls.

The antimicrobial activity of EOs depends on their chemical constituents. Apparently, the antimicrobial activity of the EO analyzed is related to the presence of phenolic compounds (thymol) and terpene hydrocarbons (γ-terpinene), respectively [ 4 , 7 , 18 ]. p-Cymene, the third major element according to percentage, does not show antibacterial efficacy when used alone [ 7 ], synergistic effects being however attributed to it in relation to thymol and γ-terpinene, respectively [ 19 , 20 ], which might represent another cause of the antimicrobial activity recorded. On the other hand, a number of studies have shown that EOS exhibit stronger antimicrobial activity than that of their major constituents or their mixtures, respectively [ 21 , 22 ], which suggests synergistic effects of the minor components, but also the importance of all components in relation to the biological activity of EOs.

+Results and Discussion

The isolation yield was 1.25% (v/w), based on dry plant material and confirmed that the plant analyzed meets the requirements of pharmaceutical quality for thyme as EO source [ 3 ]. The chemical composition determined by GC/ MS is presented in Table 1 . Fifteen components representing 99.91% of the total detected constituents were identified. The major components were p-cymene (8.41%), γ-terpinene (30.90%) and thymol (47.59%), which suggests that the EO analyzed belongs to the thymol chemotype in agreement with those previously reported in Romania [ 2 ]. The other components were present in a total amount of less than 13.01%. The chemical composition of the EO analyzed by us is very different from that previously reported in Morocco and Spain for the same species of thyme [ 11 , 12 ]. Similar studies in Poland, Iran, Spain and Italy, respectively, reported as major compounds in the T. vulgaris EO p-cymene, γ-terpinene and thymol [ 4 , 13 - 15 ]. These differences can be attributed to a large extent to the different chemotypes mentioned above [ 4 , 5 , 13 ].

The antimicrobial activity of thyme oil against 7 common food-related bacteria and fungus tested is presented in Table 2 . The null hypothesis that the inhibition zone is equal to the disc diameter (6 mm) was rejected for each microorganism at every amount of essential oil with a high significance level (p = 0.00). The main finding of the ANOVA analysis is a strong interaction effect between the type of microorganism and the amount of essential oil (p = 0.00). The highly significant interaction effect adds difficulty in drawing general conclusions on the main effects, even if the two factors are also highly significant (p = 0.00). For example, K. pneumoniae has the highest inhibition zone overall but for the amount of 20 [μL], where E. coli and S. typhimurium have higher values. In order to compare more thoroughly the effect of T. vulgaris on each microorganism ( Fig. 1 ), the results of multiple comparisons, at each oil amount, has to be considered. Tukey’s HSD test reveals that the only microorganisms with non-significant differences in the antimicrobial effect are S. typhimurium and E. coli at all oil amounts, and S. typhimurium, E. coli and C. albicans at 10 [μL]. The observed p-value for the pairwise differences in the above-mentioned cases does not pass acceptable significance levels, being larger than 0.4. All the other pairwise differences are highly significant (p = 0.00).

Table 1

Chemical composition of thyme EO

No. RT (min) Area % of total Constituents*
1 5.39 1.06 alpha-Thujene
2 5.63 1.07 alpha-Pinene
3 6.89 0.37 beta-Pinene
4 6.97 1.53 beta-Myrcene
5 7.53 0.33 alpha-Phellandrene
6 7.77 3.76 Carene
7 8.04 0.29 D-Limonene
8 8.26 0.21 beta-Phellandrene
9 8.46 8.41 para-Cymene
10 8.96 30.90 gamma-Terpinene
11 9.48 0.47 Terpineol
12 12.55 0.46 Terpinen-4-ol
13 16.17 47.59 Thymol
14 17.32 2.68 Caryophyllene
15 19.03 0.78 Cyclohexene, 1-methyl-4-(5-methyl-1-methylene-4-hexenyl)
Total 99.91%
*Constituents presented in the order of elution from the VF 35 MS column.

The inhibition of the growth of E. coli, K. pneumoniae, S. aureus, P. aeruginosa and E. faecalis was previously reported [ 4 , 7 , 9 ] along with the efficacy against C. albicans [ 9 , 16 , 17 ] and S. typhimurium [ 4 , 9 ], respectively. In contrast, some studies report the inefficiency of thyme EO against E. coli [ 16 , 17 ], S. aureus [ 16 ] and K. pneumoniae [ 16 ].

The antimicrobial activity of thyme oil, at different amounts, expressed as a mean inhibition zone for each of the nine repeated measurements

Table 2

Effects of thyme oil against bacteria expressed by the mean sizes of the inhibitory zones

Test microorganism Amount of essential oil [μL]
5 10 15 20
Staphylococcus aureus ATCC 25923 23.93 ± 0.33 29.2 ± 0.6 29.9 ± 0.35 31.4 ± 0.47
Salmonella typhimurium ATCC 14028 14.49 ± 0.34 19.71 ± 0.39 30.68 ± 0.33 34.94 ± 0.22
Pseudomonas aeruginosa ATCC27853 11.82 ± 0.27 13.34 ± 0.33 14 ± 0.22 14.13 ± 0.19
E. coli ATCC 25922 14.63 ± 0.36 19.82 ± 0.41 30.67 ± 0.31 34.99 ± 0.19
Klebsiella pneumoniae ATCC 13882 30.21 ± 0.12 31.02 ± 0.31 32.79 ± 0.24 33.93 ± 0.14
Enterococcus faecalis ATCC 29212 8.99 ± 0.15 15.06 ± 0.15 15.99 ± 0.18 24.06 ± 0.15
Candida albicans ATCC 10231 15.14 ± 0.38 19.43 ± 0.55 25.74 ± 0.24 30.2 ± 0.17

The inhibitions are expressed in mm and include the diameter of the paper disc (6 mm). Data distributions were expressed as mean values and standard deviations (SD) (n = 9). Ciprofloxacine and cephalexine (for bacterial strains) and fluconazole (for fungi), respectively, were used as positive controls.

The antimicrobial activity of EOs depends on their chemical constituents. Apparently, the antimicrobial activity of the EO analyzed is related to the presence of phenolic compounds (thymol) and terpene hydrocarbons (γ-terpinene), respectively [ 4 , 7 , 18 ]. p-Cymene, the third major element according to percentage, does not show antibacterial efficacy when used alone [ 7 ], synergistic effects being however attributed to it in relation to thymol and γ-terpinene, respectively [ 19 , 20 ], which might represent another cause of the antimicrobial activity recorded. On the other hand, a number of studies have shown that EOS exhibit stronger antimicrobial activity than that of their major constituents or their mixtures, respectively [ 21 , 22 ], which suggests synergistic effects of the minor components, but also the importance of all components in relation to the biological activity of EOs.

Conclusions

The results demonstrate the effectiveness of thyme EO against the food-related bacteria and fungus tested. The synergism, antagonism and additive effects, respectively, of the EOs components require further research to elucidate the mechanisms underlying their biological activity, for the purpose of accessing new natural antiseptics applicable in the pharmaceutical and food industry.

References
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BMC Complement Altern Med BMC Complement Altern Med
BMC Complementary and Alternative Medicine
1472-6882
BioMed Central London
pmcid: 5080681 1408 doi: 10.1186/s12906-016-1408-2
+
BMC Complement Altern Med BMC Complement Altern Med
BMC Complementary and Alternative Medicine
1472-6882
BioMed Central London
\ No newline at end of file +References
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    PLoS One PLoS ONE plos plosone
    PLoS ONE
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