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Figure 1 in Determination of the ursolic and oleanolic acids content with the antioxidant capacity in apple peel extract of various cultivars
Figure 1. Location of the apple collection (indicated in black dot) in Western Cape, South-Western coast part of South Africa.
M-POPP datasets: Datasets for full page text recognition and information extraction from French handwritten and printed marriage records
<h1><strong>M-POPP datasets</strong></h1> <p>This repository contains 2 datasets created within the <strong>EXO-POPP project</strong> (<a href="https://exopopp.hypotheses.org/">Optical EXtraction of handwritten named entities for marriage records of the POPulation of Paris</a>) for the task of text recognition and information extraction. These datasets have been published in <a href="https://arxiv.org/abs/2404.19329"><code>End-to-end information extraction in handwritten documents: Understanding Paris marriage records from 1880 to 1940</code></a> <code>[1]</code>at ICDAR 2024.</p> <p><strong>This version contains the labels for Handwritten Text Recognition and Handwritten Text Recognition + Information Extraction as used in our new paper "<a href="https://hal.science/hal-04555188">DANIEL: A fast Document Attention Network for Information Extraction and Labelling of handwritten documents</a>" [3].</strong></p> <p><strong>This version makes corrections to the handwritten dataset. </strong>More precisely, it corrects a few errors in transcription annotations and named entities.</p> <p><strong>The printed dataset is unchanged compared to version 2.</strong></p> <p><strong>The performances of the models described in [1] and [3] are detailled in the Leaderboard section.</strong></p> <h2><strong>General information</strong></h2> <p>The <strong>EXO-POPP project</strong> aims to establish a comprehensive database comprising 300,000 marriage records from Paris and its suburbs, spanning the years 1880 to 1940, which are preserved in over 130,000 scans of double pages. Each marriage record may encompass up to 118 distinct types of information that require extraction from plain text. The M-POPP corpus (which stands for Marriage records of the POPulation of Paris) is the corpus on which the EXO-POPP project focuses. This corpus was built by gathering the marriage records of Paris and its suburb regions (Hauts- de-Seine, Seine-Saint-Denis, Val-de-Marne).</p> <p>The M-POPP corpus are a subset of the M-POPP database with annotations for full-page text recognition and named entity recognition/information extraction from both handwritten and printed documents. The first dataset comprises handwritten marriage records, while the second dataset consists of typewritten marriage records. It should be noted that even in typewritten marriage records, some handwritten information occurs, especially concerning the names of the spouses, and notes in the margin.<br>The dataset contains single-page images obtained from the original scans of double pages via page segmentation.</p> <p>The structure of the files is the following:</p> <ul> <li>handwritten: <em>the handwritten dataset</em><br> <ul> <li>images: <em>images of the dataset divided following the split used in [1]</em><br> <ul> <li>train</li> <li>valid</li> <li>test</li> </ul> </li> <li>labels: <em>labels for joint handwritten text recognition and information extraction for each encoding tested in [1]</em></li> </ul> </li> <li>printed: <em>the printed dataset</em><br> <ul> <li>images: <em>images of the dataset divided following the split used in [1]</em><br> <ul> <li>train</li> <li>valid</li> <li>test</li> </ul> </li> <li>labels: <em>labels for joint handwritten text recognition and information extraction for each encoding tested in [1]</em></li> </ul> </li> <li>encoding-2-to-encoding-5.json: <em>a JSON file giving the correspondence between the symbols of encoding 2 and encoding 5.</em></li> </ul> <p> </p> <p>Table 1: Details on the split of the handwritten dataset.</p> <table> <tbody> <tr> <td> </td> <td>Train</td> <td>Validation</td> <td>Test</td> </tr> <tr> <td>Pages</td> <td>250</td> <td>32</td> <td>32</td> </tr> <tr> <td>Acts</td> <td>344</td> <td>51</td> <td>53</td> </tr> <tr> <td>Named entities</td> <td>16727</td> <td>2223</td> <td>2517</td> </tr> </tbody> </table> <p> </p> <p>Table 2: Details on the split of the printed dataset.</p> <table> <tbody> <tr> <td> </td> <td>Train</td> <td>Validation</td> <td>Test</td> </tr> <tr> <td>Pages</td> <td>116</td> <td>14</td> <td>13</td> </tr> <tr> <td>Acts</td> <td>363</td> <td>43</td> <td>30</td> </tr> <tr> <td>Named entities</td> <td>22036</td> <td>2559</td> <td>2405</td> </tr> </tbody> </table> <p> </p> <p>Table 3: Average annotation statistics per act for the two M-POPP datasets.</p> <table> <tbody> <tr> <td>Dataset</td> <td># of characters</td> <td># of words</td> <td># of named entities</td> </tr> <tr> <td>Handwritten</td> <td>1519</td> <td>231</td> <td>48</td> </tr> <tr> <td>Printed</td> <td>1328</td> <td>200</td> <td>60</td> </tr> </tbody> </table> <p> </p> <h3><strong>Document structure Annotation</strong></h3> <p>We employ the procedure applied in [2], which involves adding opening and closing tags to the character set for each text block we want to recognize.<br>In total, we define four types of text blocks.</p> <ul> <li>Block A is located in the margin and contains the last names of the married couple, possibly with their first names and the date of the marriage.</li> <li>Block B is the body of the text. Block B is the one that contains most of the information to be extracted.</li> <li>Block C is optional and corresponds to marginal notes used in various cases, such as the mention of a divorce or a correction made to the act.</li> <li>Block D corresponds to a set containing a block A and a block B, optionally with one or more blocks C.</li> </ul> <p> </p> <h3><strong>Information Extraction annotation</strong></h3> <p>The dataset contains 118 information categories. As explained in the paper, we broke down the named entities into sub-elements pertaining to 4 hierarchical levels, which reduces the total number of categories to 23 instead of 118. Notice that level 1, 2, and 3 categories do not encode named entities but rather the relations that may occur between some lower level categories for example: (day, birth, husband) encodes the fact that the annotated piece of text is the date of birth of the husband. </p> <p>For these datasets, we chose to represent these hierarchical elements with emojis. For instance, the information <em>first name</em> is represented by the emoji 💬.<br>The meaning of each emoji can be found in Table 4. To determine the best way to encode named entities in the ground truth, we compared in [1] 5 types of encoding. To illustrate these encodings, let’s take for instance <em>Louis Alexandre MOUDEL</em> that we define as the father of the bride, where <em>Louis Alexandre</em> are his two first names, and <em>Moudel</em> is his last name. </p> <p>1) Single separate tags before each word: In this approach, each level of information is indicated by a dedicated tag, and the tags are placed before the word they encode information for. With this encoding, the ground truth for the example would be:</p> <p>💬👴👰Louis 💬👴👰Alexandre 🗨️👴👰MOUDEL</p> <p>2) Single separate tags after each word: Similar to the previous approach, except here the tags are placed after the word. With this encoding the previous example becomes:</p> <p>Louis👰👴💬 Alexandre👰👴💬 MOUDEL👰👴🗨️</p> <p>3) Open & close separate tags: Here, each word presenting information to be extracted is surrounded by one or more opening and closing tags, where each tag encodes a level of information. So the example would be as:</p> <p><👰> <👴> <💬> Louis <\💬> <\👴> <\👰><br><👰> <👴> <💬> Alexandre <\💬> <\👴> <\👰><br><👰> <👴> <🗨️> MOUDEL <\🗨️> <\👴> <\👰></p> <p>4) Nested open & close separate tags: Similar to the previous approach, but this time a tag is closed only when the encoded information is no longer the same for that level of information. We can see in the example below that the tags for wife and father are only used twice.</p> <p><👰> <👴> <💬> Louis Alexandre <\💬> <🗨️> MOUDEL <\🗨️></p> <p>5) Single combined tags after each word: In the last approach, one tag encodes all the hierarchical levels constituting information. The tags are located after the word they encode information for. </p> <p>Louis<wife_father_first_name> Alexandre<wife_father_first_name> MOUDEL<wife_father_family_name></p> <p>NB: In the labels file of encoding 5, the information are still encoded with emojis but the chosen emojis do not have a semantic meaning due to the number of information categories to be represented. The correspondence between the symbols of encoding 2 and encoding 5 can be found in the file <em>encoding-2-to-encoding-5.json</em>.<em><br></em></p> <p> </p> <p>Table 4: Details of the hierarchical breakdown of named entities. Each tag is placed in the corresponding hierarchical level and associated with the emoji representing it.</p> <table> <tbody> <tr> <td>Level</td> <td>Tags</td> <td> </td> <td> </td> <td> </td> </tr> <tr> <td>1</td> <td>Administrative 📖</td> <td> <pre>Husband<code> 👨</code></pre> </td> <td>Wife 👰</td> <td>Witness 🥸</td> </tr> <tr> <td>2</td> <td>Father 👴</td> <td>Mother 👵</td> <td>Ex-husband 💔</td> <td> </td> </tr> <tr> <td>3</td> <td>Birth 🏥</td> <td>Residence 🏠</td> <td> </td> <td> </td> </tr> <tr> <td>4</td> <td>First name 💬</td> <td>Family name 🗨️</td> <td>Age ⌛</td> <td>Occupation 🔧</td> </tr> <tr> <td>5</td> <td>Street number 🔟</td> <td>Street type 🛣</td> <td>Street name 🔠</td> <td>City 🌆</td> </tr> <tr> <td> </td> <td>Department 🗺</td> <td>Country 🗺</td> <td>Day 🌞</td> <td>Month 📅</td> </tr> <tr> <td> </td> <td>Year 🗓</td> <td>Hour ⏰</td> <td>Minute ⏱</td> <td> </td> </tr> </tbody> </table> <p> </p> <h2><strong>Leaderboard</strong></h2> <h3><strong>Results on M-POPP handwritten</strong></h3> <p><strong>HTR<br></strong></p> <p>The following table contains the current leaderboard of M-POPP v3 for HTR on the handwritten dataset.</p> <p>In this configuration, layout block C is not considered.</p> <p>These results for DAN NER are given using the named entity encoding format 5 described above.</p> <p>HTR stands for Handwritten Text Recognition and HTR+IE for combined Handwritten Text Recognition and Information Extraction.</p> <p>Metrics are expressed in percentages.</p> <table> <tbody> <tr> <td>Method</td> <td>CER</td> <td>WER</td> <td>LOER</td> <td>mAP CER</td> </tr> <tr> <td>DAN - HTR [1]</td> <td>7.21</td> <td>16.42</td> <td>5.35</td> <td>83.03</td> </tr> <tr> <td>DAN NER - HTR + IE [1]</td> <td>6.52</td> <td>14.80</td> <td>3.79</td> <td>86.29</td> </tr> <tr> <td>DANIEL - HTR [3]</td> <td>5.72</td> <td>14.08</td> <td>1.34</td> <td>89.28</td> </tr> </tbody> </table> <p> </p> <p><strong>NER</strong></p> <p>The following table contains the current leaderboard of M-POPP v3 for NER on the handwritten dataset.</p> <p>In this configuration, layout block C is not considered.</p> <p>These results are given using the named entity encoding format 5 described above.</p> <p>Metrics are expressed in percentages.</p> <table> <tbody> <tr> <td>Method</td> <td>F1</td> </tr> <tr> <td>DAN NER [1]</td> <td>76.37</td> </tr> <tr> <td>DANIEL [3]</td> <td>76.37</td> </tr> </tbody> </table> <h3> </h3> <h3><strong>Results on M-POPP printed</strong></h3> <p><strong>HTR</strong></p> <p>The following table contains the current leaderboard of this version for TR on the printed dataset.</p> <p>The labels, and therefore the results, are the same as in version 2.</p> <p>In this configuration, only layout block B is considered.</p> <p>These results for DAN NER are given using the named entity encoding format 5 described above.</p> <p>TR stands for Text Recognition and TR+IE for combined Text Recognition and Information Extraction.</p> <p>Metrics are expressed in percentages.</p> <p><strong>NB:</strong> The model DANIEL from [3] was not evaluated on the printed dataset.</p> <table> <tbody> <tr> <td>Method</td> <td>CER</td> <td>WER</td> </tr> <tr> <td>DAN - TR [1]</td> <td>0.88</td> <td>3.17</td> </tr> <tr> <td>DAN NER - TR + IE [1]</td> <td>1.54</td> <td>3.55</td> </tr> </tbody> </table> <p> </p> <p><strong>NER</strong></p> <p>The following table contains the current leaderboard of this version for NER on the printed dataset.</p> <p>The labels, and therefore the results, are the same as in version 2.</p> <p>In this configuration, only layout block B is considered.</p> <p>These results are given using the named entity encoding format 5 described above.</p> <p>Metrics are expressed in percentages.</p> <p><strong>NB:</strong> The model DANIEL from [3] was not evaluated on the printed dataset.</p> <table> <tbody> <tr> <td>Method</td> <td>F1</td> </tr> <tr> <td>DAN NER [1]</td> <td>93.04</td> </tr> </tbody> </table> <h2> </h2> <h2><strong>Citation Request</strong></h2> <p>If you publish material based on this database, we request you to include a reference to the paper <code><a href="https://arxiv.org/abs/2404.19329">T. Constum, L. Preel, T. Paquet, P. Tranouez, S. Brée, End-to-end information extraction in handwritten documents: Understanding Paris marriage records from 1880 to 1940, International Conference on Document Analysis and Recognition (ICDAR), Athens, Greece, 2024</a>.</code></p> <p> </p> <h2><strong>Bibliography</strong></h2> <p><a href="https://arxiv.org/abs/2404.19329">1: T. Constum, L. Preel, T. Paquet, P. Tranouez, S. Brée: End-to-end information extraction in handwritten documents: Understanding Paris marriage records from 1880 to 1940, International Conference on Document Analysis and Recognition (ICDAR), Athens, Greece, 2024.</a></p> <p>2: D.Coquenet, C. Chatelain, T. Paquet: DAN: a Segmentation-free Document Attention Network for Handwritten Document Recognition. IEEE Transactions on Pattern Analysis and Machine Intelligence pp. 1–17 (2023).</p> <p><a href="https://hal.science/hal-04555188/">3: T. Constum, T. Paquet, P. Tranouez: DANIEL: A fast Document Attention Network for Information Extraction and Labelling of handwritten documents, preprint, 2024 </a></p>
In-vitro Fungicidal potential of Vitis mustangensis stems and seeds extracts against pathogenic fungi
Open the record for dataset details and reuse information.
◂Fig. 1 Live photos and dissection of parasitized Aphrodita longipalpa and Veneriserva pygoclava. A Ventral view of A. longipalpa. B Dorsal view of A. longipalpa with removed feltage chaetae, revealing the parasite visible through the body wall. C Ventrally dissected A. longipalpa, exposing the sizable female parasite. Veneriserva pygoclava individuals within the host are indicated by arrowheads. D Juvenile female V. pygoclava, with developing oocytes visible through the body wall along the mid-dorsal orange line. E Female V. pygoclava showing the mid-dorsal orange pigmentation and the white mark at the base of the prostomium. F Male V. pygoclava. G A large female and smaller male V. pygoclava, extracted from the same host. The pygidium is club-shaped in both males and females and juveniles. H Juvenile V. pygoclava shown from multiple angles, characterized by a complete white coloration; black jaws are magnified in panel in Hardly Venus's servant-morphological adaptations of Veneriserva to an endoparasitic lifestyle and its phylogenetic position within Dorvilleidae (Annelida)
◂Fig. 1 Live photos and dissection of parasitized Aphrodita longipalpa and Veneriserva pygoclava. A Ventral view of A. longipalpa. B Dorsal view of A. longipalpa with removed feltage chaetae, revealing the parasite visible through the body wall. C Ventrally dissected A. longipalpa, exposing the sizable female parasite. Veneriserva pygoclava individuals within the host are indicated by arrowheads. D Juvenile female V. pygoclava, with developing oocytes visible through the body wall along the mid-dorsal orange line. E Female V. pygoclava showing the mid-dorsal orange pigmentation and the white mark at the base of the prostomium. F Male V. pygoclava. G A large female and smaller male V. pygoclava, extracted from the same host. The pygidium is club-shaped in both males and females and juveniles. H Juvenile V. pygoclava shown from multiple angles, characterized by a complete white coloration; black jaws are magnified in panel
Fig. 2 in Chemical constituents and toxic, repellent, and oviposition-deterrent effects of ethanol-extracted Myristica fragrans (Myristicaceae) oil on Bemisia tabaci (Hemiptera: Aleyrodidae)
Fig. 2. Contact toxicity of nutmeg essential oil to whitefly nymphs in laboratory experiments at concentrations of 10, 5, and 2.5 mg/mL. Values are the means of 8 replications. The mean numbers of nymphs were analyzed by 1-way ANOVA, with a Tukey HSD post-hoc test at a significance level of P <0.05; means topped by the same letter are not significantly different.
Fig. 1 in Chemical constituents and toxic, repellent, and oviposition-deterrent effects of ethanol-extracted Myristica fragrans (Myristicaceae) oil on Bemisia tabaci (Hemiptera: Aleyrodidae)
Fig. 1. Fumigant toxicity of nutmeg essential oil to whitefly adults in laboratory experiments at concentrations of 10, 5, and 2.5 mg/mL. Values are the means of 8 replications. The mean numbers of adults were analyzed by 1-way ANOVA, with a Tukey HSD post-hoc test at a significance level of P <0.05; means topped by the same letter are not significantly different.
Fig. 5 in Chemical constituents and toxic, repellent, and oviposition-deterrent effects of ethanol-extracted Myristica fragrans (Myristicaceae) oil on Bemisia tabaci (Hemiptera: Aleyrodidae)
Fig. 5. Greenhouse experiments with whitefly adults, testing nutmeg essential oil at concentrations of 10, 5, and 2.5 mg/mL. A. Repellency at 24 h, B. repellency at 48 h, C. oviposition at 24 h, D. oviposition at 48 h of exposure. Values are means of 8 replications. The mean numbers of adults and eggs were analyzed by 1-way ANOVA, with a Tukey HSD post-hoc test at a significance level of P <0.05; means topped by the same letter are not significantly different.
Fig. 4 in Chemical constituents and toxic, repellent, and oviposition-deterrent effects of ethanol-extracted Myristica fragrans (Myristicaceae) oil on Bemisia tabaci (Hemiptera: Aleyrodidae)
Fig. 4. Repellency of nutmeg essential oil to whitefly adults in laboratory experiments at A. 24 h, B. 48 h, and C. 72 h of exposure to concentrations of 10, 5, and 2.5 mg/mL. Values are means of 8 replications. The mean numbers of adults were compared by paired t-tests at a significance level of P ≤ 0.05. Asterisk indicates a significant difference between control and treatment.
Supplementary material 2 from: Majaneva M, Diserud OH, Eagle SHC, Hajibabaei M, Ekrem T (2018) Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples. Metabarcoding and Metagenomics 2: e26664. https://doi.org/10.3897/mbmg.2.26664
Final species table. :
Supplementary material 5 from: Majaneva M, Diserud OH, Eagle SHC, Hajibabaei M, Ekrem T (2018) Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples. Metabarcoding and Metagenomics 2: e26664. https://doi.org/10.3897/mbmg.2.26664
Methods (Scripts) :
Supplementary material 3 from: Majaneva M, Diserud OH, Eagle SHC, Hajibabaei M, Ekrem T (2018) Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples. Metabarcoding and Metagenomics 2: e26664. https://doi.org/10.3897/mbmg.2.26664
Number of reads per sample. :
Supplementary material 4 from: Majaneva M, Diserud OH, Eagle SHC, Hajibabaei M, Ekrem T (2018) Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples. Metabarcoding and Metagenomics 2: e26664. https://doi.org/10.3897/mbmg.2.26664
Diversity analyses. :
Supplementary material 1 from: Majaneva M, Diserud OH, Eagle SHC, Hajibabaei M, Ekrem T (2018) Choice of DNA extraction method affects DNA metabarcoding of unsorted invertebrate bulk samples. Metabarcoding and Metagenomics 2: e26664. https://doi.org/10.3897/mbmg.2.26664
Fragment and working PCR conditions. :
Supplementary material 5 from: Deiner K, Lopez J, Bourne S, Holman LE, Seymour M, Grey EK, Lacoursière-Roussel A, Li Y, Renshaw MA, Pfrender ME, Rius M, Bernatchez L, Lodge DM (2018) Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method. Metabarcoding and Metagenomics 2: e28963. https://doi.org/10.3897/mbmg.2.28963
Alternative statistical model :
Supplementary material 4 from: Deiner K, Lopez J, Bourne S, Holman LE, Seymour M, Grey EK, Lacoursière-Roussel A, Li Y, Renshaw MA, Pfrender ME, Rius M, Bernatchez L, Lodge DM (2018) Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method. Metabarcoding and Metagenomics 2: e28963. https://doi.org/10.3897/mbmg.2.28963
4_NTC :
Supplementary material 2 from: Deiner K, Lopez J, Bourne S, Holman LE, Seymour M, Grey EK, Lacoursière-Roussel A, Li Y, Renshaw MA, Pfrender ME, Rius M, Bernatchez L, Lodge DM (2018) Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method. Metabarcoding and Metagenomics 2: e28963. https://doi.org/10.3897/mbmg.2.28963
Bioinformatic pipeline and thresholds :
Supplementary material 3 from: Deiner K, Lopez J, Bourne S, Holman LE, Seymour M, Grey EK, Lacoursière-Roussel A, Li Y, Renshaw MA, Pfrender ME, Rius M, Bernatchez L, Lodge DM (2018) Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method. Metabarcoding and Metagenomics 2: e28963. https://doi.org/10.3897/mbmg.2.28963
Profiling tables for all libraries :
Supplementary material 1 from: Deiner K, Lopez J, Bourne S, Holman LE, Seymour M, Grey EK, Lacoursière-Roussel A, Li Y, Renshaw MA, Pfrender ME, Rius M, Bernatchez L, Lodge DM (2018) Optimising the detection of marine taxonomic richness using environmental DNA metabarcoding: the effects of filter material, pore size and extraction method. Metabarcoding and Metagenomics 2: e28963. https://doi.org/10.3897/mbmg.2.28963
Extraction protocols :
Ultrasonic Assisted Extraction of Artemisinin from Artemisia Annua L. Using Poly(Ethylene Glycol): Toward a Greener Process
<p>Supplementary Materials</p>
DMSA Extracted Features
<p>Pre-computed features for DMSA (https://github.com/stefan-balke/dmsa).</p>
ScienceDex guides
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
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DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.