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Codes to replicate statistical analysis in UPLIFT project Deliverable 2.4 Synthesis report, Chapter 6
<p>Policies attempting to mitigate the effects of urban inequality, often disregard affected citizens’ experiences, and thus fail to achieve maximum impact. By incorporating these perspectives into the policy design process, the project "Urban PoLicy Innovation to address inequality with and for Future generaTions" (UPLIFT), funded under the EU Horizon 2020 program aims to find innovative interventions in a bottom-up approach. The aims of UPLIFT project are to understand patterns and trends of inequality across Europe and to understand how individuals experience and adapt to inequality through participatory research. Moreover the project will together with the communities in four locations, co-design a policy tool aimed at addressing and reducing inequality and socio-economic divisions. The activity and results of the project can be followed at <a href="https://www.uplift-youth.eu/">https://www.uplift-youth.eu/</a>.</p> <p>Deliverable 2.4 (Synthesis report: socioeconomic inequalities in different urban contexts) is the final deliverable of work package 2 of the UPLIFT project, which aims to synthetize the main outcomes of the urban reports that described the policy environment around vulnerable individuals in the fields of education, employment and housing in 16 functional urban areas of the EU. In addition section 6.2 "Statistical analysis of linkages between economic development of cities, their public policy performance and inequality outcomes" of the report provides a statistical analysis of how local economic competitiveness and the local policy context affect urban deprivation and inequality among the young in European cities. The analysis is based on data from 2006, 2009, 2012, 2015 and 2019 of the Quality of Life in European Cities survey.</p>
M. Kelly PhD thesis; Chapter 4 - Supplemental Table S1
<p>Supplemental Table for my PhD thesis (Chapter 4). Supplemental Table S1 contains all data relevant to the predator choice tests.</p>
The e-NDP project : collaborative digital edition of the Chapter registers of Notre-Dame of Paris (1326-1504). Ground-truth for handwriting text recognition (HTR) on late medieval manuscripts.
<p>The <a href="https://endp.hypotheses.org/">e-NDP project</a>, funded by the ANR, is led by the <a href="https://lamop.hypotheses.org/6870">LaMOP</a> (Julie Claustre and Darwin Smith).</p> <p>The project's partners are the Archives nationales, the Bibliothèque nationale de France (Department of Manuscripts, Bibliothèque de l'Arsenal), the École nationale des chartes and the Bibliothèque Mazarine.</p> <p>The e-NDP project aims at renewing our knowledge on <strong>Notre-Dame de Paris cathedral</strong> through the creation of a collaborative digital edition of the registers of its Chapter (1326-1504, <em>AN LL 105-128</em>), the community of 51 canons meeting three times a week on set days to take all administrative, financial and practical decisions pertaining to the cathedral, its estate and the society living in its cloister. This corpus has never been the object of a comprehensive study to understand the workings and history of this urban enclave and powerful community. The collaborative digital edition is based on a process of<strong> handwriting text recognition (HTR)</strong>, tested and supervised by scholars, researchers and engineers combining expertise in Medieval history, paleography, philology and digital humanities. The edition shall allow a better insight into the Chapter’s administration, into its economical and political power within Paris, and the relationships it maintained with other institutions in the city.</p> <p> </p> <p><strong>Section 1 : The e-NDP ground-truth dataset for Handwriting text recognition.</strong></p> <p>The full e-NDP corpus kept today in the French National Archives and was entirely digitized and described in its <a href="https://www.siv.archives-nationales.culture.gouv.fr/siv/rechercheconsultation/consultation/ir/consultationIR.action?formCaller=GENERALISTE&irId=FRAN_IR_059635">catalog</a> in 2022.</p> <p>The first major goal of the e-NDP projet is to propose a first automatic transcription of the 14k pages composing the 26 chapter registers. To achieve this goal representative samples from each one of the volumes were selected and transcribed in order to train a specialized HTR model able to propose a high quality automatic transcription. The collected ground-truth released on this repository currently has <strong>512 pages from the 26 registers</strong> of the cathedral chapter preserved in the National Archives (LL105 - LL128, <strong>1326-1504</strong>). The transcriptions were manually completed in <strong>two rounds</strong> by a group of 12 contributors, historians and paleographers, over the course of 2021-2022 using <a href="https://escriptorium.paris.inria.fr/">eScriptorium </a>as annotation environment. </p> <p> </p> <p><strong>Ground-truth features :</strong></p> <p><br> <em>Number of hands </em>: according to our estimates no fewer than 18 main hands were involved in the writing of the registers during the medieval period. </p> <p><em>Language</em> : More than 98% of the content of the registers was written in Latin, the rest in French. The exact percentage is hard to estimate because the vernacular language is often used in formulae, notes and comments. It is rare to find entire pages or blocks written in French. </p> <p><em>Script family</em> : The registers were written using a Cursive script (ca. late XIIIe - XVIe).</p> <p><em>Documental typology</em> : The volumes containing the chapter conclusions were conceived to serve as memorial records, but above all as documents for regular use and consultation in the daily practice of administration and management. In diplomatics the notion of "documentary manuscripts" is used to describe this kind of sources also by opposition to books and litterary or normative manuscripts.</p> <table align="center"> <caption><strong>Ground truth statistics</strong></caption> <tbody> <tr> <th>Text units</th> <th>Count</th> </tr> <tr> <td>Pages</td> <td>512</td> </tr> <tr> <td>Annotated regions (see section 2)</td> <td>2448</td> </tr> <tr> <td>Lines of text</td> <td>34231</td> </tr> <tr> <td>Tokens</td> <td>205083</td> </tr> <tr> <td>Characters</td> <td>3320407</td> </tr> </tbody> </table> <p> </p> <p><strong>Rules of transcription :</strong></p> <ul> <li>The abbreviations have been resolved, both those by suspension (<code>facimꝰ</code> ---> <code>facimus</code>) and by contraction (<code>dñi</code> --> <code>domini</code>). Likewise, those using conventional signs (<code>⁊</code> --> <code>et</code> ; <code>ꝓ</code> --> <code>pro</code>) have been resolved. </li> <li>The named entities (names of persons, places and institutions) have been <code>capitalized</code>. The beginning of a block of text as well as the original capitals used by the notary are also capitalized.</li> <li>The consonantal <code>i</code> and <code>u</code> characters have been transcribed as <code>j</code> and <code>v</code> in both French and Latin.</li> <li>The punctuation marks used in the text: <code>.</code> and <code>/</code> have been transcribed, but the transcription has not been standardized with modern punctuation.</li> <li>Corrections and words that appear cancelled in the manuscript have been transcribed surrounded by the sign <code>$</code> at the beginning and at the end.</li> <li>More specific transcription rules can be found into the file <code>transcription_guidelines.pdf</code></li> </ul> <p> </p> <p><strong>Section 2. e-NDP Layout Segmentation.</strong></p> <p>Layout segmentation is a compulsory step before HTR recognition in order to distinguish sections and regions inside a document. This process intend to separate interdependant page zones to produce a recognition in a section-sequence order and not in a line-sequence order which mix textual and peri-textual content.</p> <p>The regions of 364 pages (see <code>GT-layout_list</code>) of the e-NDP corpus were annotated using a 5 sections vocabulary (see <code>endp_layout_regions</code>) in order to describe the page distribution in all the 26 volumes :</p> <ol> <li><em>Block</em> : All the central text blocks, that normally corresponds to the main content called "conclusions" in registers.</li> <li><em>Liste</em> : List of names of the canons who were present during the meeting. Normally located before the <em>conclusions</em>.</li> <li><em>Entrée</em> : Marginal notes or entries to inform about the content of <em>conclusions</em>.</li> <li><em>Date</em> : Paragraph contending the date. Normally at the head of a <em>conclusion</em>, but separate of the main body.</li> <li><em>Numérotation</em> : Page numbers in roman or arabic. Usually appear in the top corners of the pages.</li> </ol> <table align="center"> <caption><strong>Layout GT statistics</strong></caption> <tbody> <tr> <th>Region</th> <th>Count</th> </tr> <tr> <td>block</td> <td>833</td> </tr> <tr> <td>liste</td> <td>431</td> </tr> <tr> <td>date</td> <td>448</td> </tr> <tr> <td>entrée</td> <td>205</td> </tr> <tr> <td>numérotation</td> <td>531</td> </tr> </tbody> </table> <p> </p> <p><strong>Section 3. The e-NDP HTR modeling.</strong></p> <p>The e-NDP project has progressively trained several HTR models adapted to work on late medieval cursive in order to accelerate the production of ground truth. Currently the best model delivers an average <strong>CER (Character error ratio) of 9.7%</strong> in handwriting recognition on the 26 registers (see <code>endp_learning_curve</code>) and can serve as generalist model for other manuscripts of the same period and similar script family. These models and their training implementation details can be found in the project's github <a href="https://github.com/chartes/e-NDP_HTR">repository</a>. </p> <p>Additionally, the automatic HTR transcriptions of the 26 registers (14k pages, 4.5M tokens) enriched with lexical and semantical information has been the subject of a first <a href="https://nosketch-engine.lamop.fr/#dashboard?corpname=endp">online publication</a> using the NoSketch engine that allows advanced data mining based on the combination of data, metadata and NLP features. </p> <p> </p> <p><strong>Section 4. Dataset content.</strong></p> <p>This zip dataset contains :</p> <p>- <code>HTR_ground_truth</code> : Two folders containing the jpg / jpeg images and their curated transcriptions in PAGE XML format.</p> <p>- <code>images_docs</code> : 4 files illustrating the different phases of the project (list of GT for layout segmentation, layout ontologie, transcription guideline and HTR evaluation curves)</p>
Bibliography of the Systematic Literature Review of the IPBES Global Assessment, Chapter 4
<p>Bibliographies from the systematic literature review in Chapter 4 of the IPBES Global Assessment</p> <p>DOI: 10.5281/zenodo.3553579</p>
Fig. 1-2. Eremohaplomydas desertorum n in Chapter XVIII. Diptera (Brachycera): Mydaidae
Fig. 1-2. Eremohaplomydas desertorum n. sp. ♀. — 1 A. Tête face, péristome, orifice buccal, antennes, prosternum. - 1 B. Partie postéro-latérale gauche de Porifice buccal. — 2. Aile.
The Acoustic Environment of York Minster's Chapter House
<p>This repository contains the data set related to the paper “The Acoustic Environment of York Minster's Chapter House”, published in "Acoustics" as part of the "Special Issue Historical Acoustics: Relationships between People and Sound over Time" and available at: DOI: 10.3390/acoustics2010003</p> <p>This dataset contains the B-format Room Impulse Responses (RIR) in the Waveform Audio File standard Format (.wav) measured and simulated at a selected set of source-receiver combinations in the York Minster's Chapter House, used for the acoustical analysis performed as part of the CATHEDRAL ACOUSTICS project (CA-MRIR-YM-CH and CA-SRIR-YM-CH folders respectively). The .xls spreadsheets (CA-YM-CH-MRIR-ResultData-EnergyParameters and CA-YM-CH-SRIR-ResultData-EnergyParameters) include the results derived for the measured and simulated RIR used for the discussion presented in the manuscript.</p> <p>LICENCE.txt, METADATA.txt and README.txt contain a brief description of the folder contents, authors, other useful information.</p> <p>Details on the acoustic measurement campaigns and simulations can be found in the manuscript.</p> <p>Please cite both the paper and dataset if used.</p> <p>--------------------------------------------------</p> <p>This work is license under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License (CC BY-NC-SA 4.0). (see https://creativecommons.org/licenses/by-nc-sa/4.0/)</p> <p>--------------------------------------------------</p> <p>Dataset curated by Lidia Álvarez-Morales, Theatre, Film, Television and Interactive Media Department, University of York.<br> Contact: lidia.alvarezmorales@york.ac.uk; lidiaalvarezmorales@gmail.com</p> <p>-------------------------------------------------</p> <p>Funding was provided by the European Union’s Horizon 2020 research and innovation programme (http://dx.doi.org/10.13039/501100007601) under the Marie Sklodowska-Curie grant agreement No 797586</p>
Mateo-Ramírez et al Species_Chapter 25_Alboran Sea-Ecosystems and Marine Resources
<p>Lists of species include in conservation agreements or relevant by their singularity present in MPA and KBA of Alboran Sea and adjacent areas. </p> <p>This dataset is part of the Chapter 25 Marine Protected Areas and Key Biodiversity Areas of the Alboran Sea and Adjacent Areas. In J. C. Baéz et al. (eds.), Alboran Sea - Ecosystems and Marine Resources, https://doi.org/10.1007/978-3-030-65516-7_25</p>
ROER4D Chapter 11 - Appendix 1
<p>This document serves as the Appendix 1 of the ROER4D edited volume<em> Chapter 11: Cultural-historical factors influencing OER adoption in Mongolia’s higher education sector</em>. It contains the aggregated data that underly the analysis presented in the chapter.</p>
Dissertation Chapter 1 Supplemental Tables
<p>Supplementary tables for first chapter of dissertation: "<span>A haplotype-resolved chromatin landscape connects cis-regulatory variants to trait variation in Citrus"</span></p>
Supplemental Material for Z. S. Cooper Dissertation Chapter 4 - Marinobacter Pangenomics
<p>This dataset contains main and supplemental data tables for a chapter of the doctoral dissertation by Zachary S. Cooper at the University of Washington School of Oceanography. The chapter is titled "Chapter 4: Evolutionary divergence of <em>Marinobacter </em>strains in cryopeg brines as revealed by pangenomics". Briefly, this chapter contains pangenomic analyses of novel genomes of the bacterial genus <em>Marinobacter</em> that are compared with representative species of the genus to discern evolutionary history and functional capabilities of this species in the extreme cryopeg environment. The main data tables include lists of genomes used in the analyses and their characteristics as described in the dissertation chapter. The supplemental data tables include gene cluster annotations with COGs (S1), functional frequencies across the pangenome (S2), functional enrichment analysis (S3), KEGG annotations (S4), KEGG pathway completion values (S5), average nucleotide identity values (S6), alignment coverage values (S7), and horizontal gene transfer analysis summaries (S8). The tables were produced from the combination of outputs of the bioinformatic programs Anvi'o, KEGG KofamKOALA, KEGG Decoder, PyANI, and HGTector2. Details on the methods and interpretations of this data are included in the dissertation.</p>
Text-fig. 1. Location of Wiesa fossil site in eastern Germany and other fossil sites for comparison. Explanation for map b: all fossil sites – black circles; grey circles – cities; topographic names in italics – German states (Länder). For bio- and lithostratigraphic data of fossil sites, see chapter Methodologies and material and Text-fig. 3. in Assessment Of Phytogeographic Reference Regions For Cenozoic Vegetation: A Case Study On The Miocene Flora Of Wiesa (Germany)
Text-fig. 1. Location of Wiesa fossil site in eastern Germany and other fossil sites for comparison. Explanation for map b: all fossil sites – black circles; grey circles – cities; topographic names in italics – German states (Länder). For bio- and lithostratigraphic data of fossil sites, see chapter Methodologies and material and Text-fig. 3.
Chapter 3 and 4
<p>The files consist of raw data consisting of DDR and non-DDR genes</p>
Course material-- DATA for ClathrinCLEM chapter
<p>Course material associated to NEUBIAS chapter "Resolving the process of Clathrin mediatedendocytosis using Correlative Light and Electron Microscopy.</p> <p>This is the data needed to follow this workflow chapter.</p>
Text-fig. 1. Geographic situation of the source area of the Glenarea cretacea holotype. a, Řetenice locality of A. E. Reuss, b, Teplice-Stínadla locality, c, Teplice-Písečný vrch locality. For detail, see 'type locality of Glenarea cretacea' chapter. in The Scleractinian Coral Genus Glenarea (Bohemian Cretaceous Basin)
Text-fig. 1. Geographic situation of the source area of the Glenarea cretacea holotype. a, Řetenice locality of A. E. Reuss, b, Teplice-Stínadla locality, c, Teplice-Písečný vrch locality. For detail, see 'type locality of Glenarea cretacea' chapter.
Fig. 23.6 in Chapter 23: Tedford's Gerbils from Afghanistan
Fig. 23.6. Postcrania of Abudhabia radinskyi, AMNH 133509. A, B, Left pes and left tibia, drawn by Margaret Stevens. C, Femur, added for comparison. All to same scale.
Fig. 24.1 in Chapter 24 Another Molar of the Miocene Hominid Griphopithecus suessi from the Type Locality at Sandberg, Slovakia
Fig. 24.1. Map indicating Sandberg locality (circled 1 at Sandberg sandpit), with respect to Devínska Nová Ves (formerly Neudorf or Neudorf an der March).
Fig. 23.1 in Chapter 23: Tedford's Gerbils from Afghanistan
Fig. 23.1. Locality map adapted from the field map used by Tedford and Radinsky, Fairchild Aerial Surveys sheet 510 D1, original scale 1:50,000. The local hill, Tor Ghar, exceeding 1750 m is indicated. A, Locality of Abudhabia. B, Approximate location of fossils collected by the French team of Heintz et al. (1978; see also Flynn et al., 1983). Black rectangles are dwellings; hatching indicates fields.
Fig. 23.4 in Chapter 23: Tedford's Gerbils from Afghanistan
Fig. 23.4. Five dentitions of Abudhabia radinskyi. A, Right upper dentition of AMNH 133507, holotype. B, C, Right and left upper dentitions of AMNH 133509. D, Right lower dentition of AMNH 133507. E, Left lower dentition of AMNH 133508. Anterior is upward.
Fig. 22.1 in Chapter 22: Rodents from the Chinese Neogene: Biogeographic Relationships with Europe and North America
Fig. 22.1. Distribution of Neogene rodent localities in China. , Early Miocene (Xiejian + Shanwangian): 1, Suosuoquan; 2, Xiejia; 3, Gaolanshan; 4, Zhangjiaping; 5, Gashunyinadege; 6, Wuertu; 7, Shanwang; 8, Sihong (Songlinzhuang, Zhengji, Shuanggou); 9, Fangshan. v, Middle Miocene (Tunggurian): 10, Halamagai; 11, Quantougou; 12, Lierpu (Qijia, Danshuilu); 13, Dingjiaergou; 14, Tunggur; 15, Tairum Nor. M, Late Miocene (Baodean): 16, Songshan; 17, Bulong; 18, Jilong; 19, Qingyang; 20, Baode; 21, Lantian (Bahe); 22, Amuwusu; 23, Shala; 24, Baogedawula; 25, Ertemte (Harr Obo); 26, Shihuiba; 27, Yuanmou. ·, Pliocene (Yushean): 28, Bilike; 29, Jingle; 30, Dingcun; 31, Youhe; 32, Daodi; 33, Zhoukoudian (Cap Travertine); 34, Yinan; 35, Zhaotong; 36, Wushan.., Late Miocene + Pliocene: 37, Yushe (Mahui; Gaozhuang; Mazegou; Haiyan; Jiayucun); 38, Lingtai (Wenwanggou).
Fig. 25.2 in Chapter 25 Mimotricentes tedfordi, a New Arctocyonid from the Late Paleocene of California
Fig. 25.2. Mimotricentes tedfordi, epoxy cast of RAM 6908, maxillary fragment with right P4–M3, holotype, Tiffanian, Goler Formation, Kern County, California. A, Labial view. B, Stereo occlusal view. C, Lingual view. Scale bar equals 4 mm.
ScienceDex guides
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
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)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
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.