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134 results for “1788”
Multiple Sequence Alignment of a diverse dataset with 1788 Mycobacterium tuberculosis isolates
<p><strong>Multiple Sequence Alignment of a diverse dataset with 1788 <em>Mycobacterium tuberculosis</em> isolates used for <a href="https://github.com/insapathogenomics/ReporTree">ReporTree</a> benchmarking</strong></p> <p>The dataset comprises whole-genome sequence data published by <a href="https://doi.org/10.1016/S1473-3099(15)00062-6">Walker et al. 2015</a>. For the multiple sequence analysis, we proceeded as follows:</p> <ol> <li>Reads were downloaded from ENA BioProject <a href="https://www.ncbi.nlm.nih.gov/bioproject/PRJNA282721">PRJNA282721</a> (accessed on March 16<sup>th</sup>, 2023) and trimmed using Trimmomatic (<a href="https://pubmed.ncbi.nlm.nih.gov/24695404/">Bolger et al., 2014</a>) with <a href="https://github.com/B-UMMI/INNUca">INNUca</a> default settings;</li> <li>Quality-processed reads were individually mapped against the H37Rv reference genome (Genbank accession: <a href="https://www.ncbi.nlm.nih.gov/nuccore/NC_000962.3/">NC_000962.3</a>) using <a href="https://github.com/tseemann/snippy">Snippy</a> v4.5.1 and SNP-calling was performed on variant sites with the following criteria: a minimum proportion of reads differing from the reference of 70%, a minimum mapping quality of 30 and a minimum coverage for SNP calling of 10;</li> <li>A full alignment was extracted using Snippy’s core module (snippy-core), with masking of SNPs falling within known <em>M. tuberculosis</em> genomic regions with high GC content, repetitive elements and resistance-associated positions (corresponding to ~8% of the genome), as previously described for surveillance purposes (<a href="https://pubmed.ncbi.nlm.nih.gov/30948181/">Macedo et al., 2019</a>);</li> <li><em>M. tuberculosis </em>lineages were determined using tb-profiler v4.4.1 (<a href="https://pubmed.ncbi.nlm.nih.gov/31234910/">Phelan et al., 2019</a>), with samples from the <em>M. tuberculosis</em> complex other than <em>M. tuberculosis</em>, representing a mix of multiple lineages, or with less than 95% of mapped positions in the reference, being excluded;</li> <li>A filtered alignment comprising the maximum number of informative sites (88,562 nucleotide sites with at least one mutation in a given sequence) was extracted from the full alignment using the alignment_processing.py v1.1.0 (default settings) of <a href="https://github.com/insapathogenomics/ReporTree">ReporTree</a>, and then used as input for the benchmarking.</li> </ol> <p>In this repository, we provide two alignment files:</p> <ul> <li>Core_MTB_1787_strs.full.aln: this corresponds to the full multiple sequence alignment comprising 1787 samples and the reference (corresponding to the point 4 of the methodology).</li> <li>MTb_original_align_profile.fasta: this corresponds to the multiple sequence alignment comprising 1787 samples and the reference and only presenting the alignment informative sites (corresponding to the point 5 of the methodology)</li> </ul>
FIG. 12 in L'histoire de la description du squale bouclé Echinorhinus brucus (Bonnaterre, 1788) (Echinorhinidae) et la redécouverte des illustrations du type perdu
FIG. 12. — Manuscrit de Blainville (Ms BLA 60) donnant la description du « Squalus spinosus » et ses observations de l'holotype publiées dans sa Faune française (Blainville 1825: 66-68). Crédits: Muséum national d'Histoire naturelle.
FIG. 10 in L'histoire de la description du squale bouclé Echinorhinus brucus (Bonnaterre, 1788) (Echinorhinidae) et la redécouverte des illustrations du type perdu
FIG. 10. — « Genre Echinorhine, Echinorhinus, Blainv. ». Extrait du registre des anciennes collections d'Ichtyologie du Muséum national d'Histoire naturelle (Anonyme: 43) révélant la présence de cinq spécimens conservés montés, dont deux ont une origine inconnue (nos 376,377) et dont deux furent réformés /détruits (nos 376, 378).
FIG. 11 in L'histoire de la description du squale bouclé Echinorhinus brucus (Bonnaterre, 1788) (Echinorhinidae) et la redécouverte des illustrations du type perdu
FIG. 11. — Illustration originale de l'holotype sec d'Echinorhinus brucus par Blainville ([1809]-1821, Ms BLA 60) vu du profil gauche au crayon et à l'encre sur papier vergé (A, en haut) et détail de ses dents et de sa tête (B), (femelle, 195 cm). Cette illustration aurait dû servir de modèle aux figures de la planche 16 non éditée de sa Faune française. Crédits: Muséum national d'Histoire naturelle.
FIG. 13 in L'histoire de la description du squale bouclé Echinorhinus brucus (Bonnaterre, 1788) (Echinorhinidae) et la redécouverte des illustrations du type perdu
FIG. 13. — Estampe du « Squale bouclé » publiée par Lacepède (1798: 30, pl. 3, fig. 2) dans son Histoire naturelle des poissons; sans mention d'illustrateur et de graveur. Il s'agit de la première figure publiée d'un squale bouclé.
FIG. 8 in L'histoire de la description du squale bouclé Echinorhinus brucus (Bonnaterre, 1788) (Echinorhinidae) et la redécouverte des illustrations du type perdu
FIG. 8. — Description du « Broucut de Biarritz » par Duhamel du Monceau (1781: 329),suivant les propos de Bordas, publiée dans son Traité général des pesches.
FIG. 7 in L'histoire de la description du squale bouclé Echinorhinus brucus (Bonnaterre, 1788) (Echinorhinidae) et la redécouverte des illustrations du type perdu
FIG. 7. — Copie manuscrite du Mémoire sur les différentes espèces de chiens de mer publié par Broussonet (1780: 672-673) dans lequel est décrit pour la première fois le Squale bouclé: A, page du titre; B, description du « Bouclé ». (Broussonet [1780], Ms 2570). Crédits: Muséum national d'Histoire naturelle.
FIG. 6 in L'histoire de la description du squale bouclé Echinorhinus brucus (Bonnaterre, 1788) (Echinorhinidae) et la redécouverte des illustrations du type perdu
FIG. 6. — Calque annoté du dessin original « Le Brucus » de La Hire (cf. Fig. 4) réalisé par Valenciennes entre 1826 et 1838 (Valenciennes in Cuvier & Valenciennes, Ms 1015). Crédits: Muséum national d'Histoire naturelle.
FIG. 5 in L'histoire de la description du squale bouclé Echinorhinus brucus (Bonnaterre, 1788) (Echinorhinidae) et la redécouverte des illustrations du type perdu
FIG. 5. — Verso du feuillet présentant « Le Brucus » disséqué et illustré par Du Verney et La Hire en 1680 (cf. Fig. 4). Légendes des dissections anatomiques illustrées au recto de la planche et représentant le système digestif, le système reproducteur, des denticules dermiques, la dentition et un oeil (planche 23 du manuscrit de Du Verney & La Hire 1679-1680, Ms 244). Format: 460 × 310 mm. Crédits: Muséum national d'Histoire naturelle.
FIG. 3 in L'histoire de la description du squale bouclé Echinorhinus brucus (Bonnaterre, 1788) (Echinorhinidae) et la redécouverte des illustrations du type perdu
FIG. 3. — Frontispice du manuscrit intitulé Dissections de divers poissons faites [par ordre du Roy] sur les costes de France pendant les années 1679 et 1680 [par MM. Joseph-Guichard Du Verney et Philippe de La Hire, membres de l'Académie Royale des Sciences] (Du Verney & La Hire 1679-1680, Ms 244); suite à la Révolu- tion française les mentions royales et les noms des auteurs ont été découpées dans le titre. Format 460 × 310 mm. Crédits: Muséum national d'Histoire naturelle.
FIG. 2 in L'histoire de la description du squale bouclé Echinorhinus brucus (Bonnaterre, 1788) (Echinorhinidae) et la redécouverte des illustrations du type perdu
FIG. 2. — Extrait du procès-verbal de l'Assemblée de l'Académie Royale des Sciences du 15 avril 1682, de la main de Jean-Baptiste Du Hamel, prouvant que le « Bruchus » a été dessiné par La Hire durant son séjour à Bayonne en 1680 (ARS 1679-1683a: 96, Manuscrit 2B10 ou 2B5*).
FIG. 4 in L'histoire de la description du squale bouclé Echinorhinus brucus (Bonnaterre, 1788) (Echinorhinidae) et la redécouverte des illustrations du type perdu
FIG. 4. — « Le Brucus » disséqué et illustré par Du Verney et La Hire en 1680 sur la côte de Bayonne. Femelle adulte, 7 pieds de long (223 cm), correspondant au dessin redécouvert de l'holotype (l'iconotype) d'Echinorhinus brucus (Bonnaterre, 1788) (planche 23 du manuscrit de Du Verney & La Hire 1679-1680, Ms 244). Format: 460 × 310 mm. Crédits: Muséum national d'Histoire naturelle.
FIG. 1 in L'histoire de la description du squale bouclé Echinorhinus brucus (Bonnaterre, 1788) (Echinorhinidae) et la redécouverte des illustrations du type perdu
FIG. 1. — Vignette parue dans les ouvrages de Perrault (1671, 1676: préfaces) mettant en scène des académiciens autour de la « dissection du renard », réalisée le 28 avril 1668 selon le registre de l'Académie (ARS 1668: 11'-13'), dans la salle des squelettes donnant sur le Jardin royal des Plantes. Apparaissent au premier plan, à droite, Claude Perrault assis consultant un texte, derrière lui Sébastien Leclerc montrant au jeune Joseph-Guichard Du Verney l'épreuve d'une planche des Mémoires pour servir à l'histoire naturelle des animaux. Jean-Baptiste Du Hamel, assis à la table une plume à la main, rédige le procès-verbal de cette assemblée. Scène gravée par Leclerc, 106 × 260 mm (Schiller 1964: 102; Préaud 1980: 240, 241). Crédits: Muséum national d'Histoire naturelle.
Jewish Soldiers of the Habsburg Army (1788-1820)
<p><strong>Version 3 (18 September 2025)</strong><span lang="EN-GB"> contains a further <strong>393</strong> service itineraries. <strong>44 </strong>entries from the previous versions have been updated. Currently the database has material for <strong>2,251</strong> Jewish soldiers, <strong>522 </strong>wives, and more than <strong>100 </strong>children. Archival records covered since the last update, include:</span></p> <ul> <li><span lang="EN-GB">The transport detachments of the 17 Border Infantry Regiments (including the 11 Regiments of the Croatian Military Frontier) during the last Habsburg-Ottoman War (1788-1791). </span></li> <li>The entire surviving manpower reports for the 24<sup>th</sup> Line Infantry Regiment between 1802 and 1811. Originally the Vienna house regiment, the 24<sup>th</sup> was transferred in summer 1808 to Galicia and allocated the Bereschany District as its main recruitment area. Currently, the database has 15 Jewish soldiers from <span lang="EN-GB">that town, and a total of 78 from the entire district (Pl: Brzeżany/ Ukr: Бережани/ Yi: </span><span dir="RTL" lang="HE">ברעזשאַן</span><span lang="EN-GB">).</span></li> <li>The 10<sup>th</sup> <em>Hauptfeldspital</em> - the main military hospital allocated to the Austrian Army operating against the Grand Duchy of Warsaw during the 1809 War. The hospital<span lang="EN-GB"> and its entire staff were taken prisoner when the Poles took Krakow on 16<sup>th</sup> July.</span></li> <li>The records of the 11<sup>th</sup><span> Bohemian Line Infantry Regiment ‘Archduke Rainer’ for 1819 and 1820. In that period, the Regiment was based in the Kouřim District, but its soldiers also came from Čáslav and the northern part of Tabor districts</span></li> </ul> <p>In addition, following new features are now added:</p> <ul> <li><span lang="EN-GB">A glossary is added as a separate sheet covering the professions of the Jewish soldiers and acronyms used to denote their military unit. As the database has grown, the pop-up notes used for that purpose until now have become too small.<span> </span></span></li> <li>Following the discovery of the first Jewish <em>Fourier </em>(military clerk), Joseph Wahhla from Prague, who enlisted into the 11<sup>th</sup><span> Line Infantry Regiment in 1814, a column has been added for that category. It compares interestingly to the established stereotypes of Jews in the army. This happened 25 years since after the original conscription edict. According the materials of our database, there were Jewish infantryman since 1789, cavalrymen since 1799, artilleryman since 1802, and a first major intake of Jewish surgeons in 1809. </span><span> </span></li> </ul> <p><strong>ORIGINAL VERSION 1 (18 September 2024)</strong></p> <p>With more than <strong>1,500 individual entries</strong>, this is the inaugural instalment of my research database collated in the framework of the Project <a href="https://www.oeaw.ac.at/en/ihb/research-units/history-of-the-habsburg-monarchy/research/jewish-soldiers"><strong>Forgotten Soldiers: Jewish Military Experience in the Habsburg Monarchy</strong></a>. This is an open access database, and everyone is welcome to use it according to their own scholarly and personal interests. In <strong>1,189</strong> cases we have official documented records confirming the soldiers were Jewish. In another <strong>313 </strong>entries I was able to identify likely Jewish soldiers based on circumstantial evidence cross-referencing names and places of birth, with the presence of confirmed Jewish soldiers drafted into the same units as part of the same recruitment drive. This dataset further includes evidence for <strong>156 spouses</strong> and <strong>47 children</strong>. While military records do mentions these, their number suggests that the Habsburg army preferred to enlist unmarried men.</p> <p>The database is structured in a similar way to an official individual entry in the Habsburg military records. These were arranged in tables, with soldiers listed by seniority. Name, place and land of birth are followed by age and religion. This latter rubric allows identifying the bulk of the Jewish soldiers. Also included in the record is marital status, profession (if any), number, names and ages of children (if any), followed by a short summary text of the soldier’s service itinerary. While not always consistent in detail, these texts mention enlistment dates, transfers between units, promotions, desertions, periods as prisoner of war and military awards (if any). I have taken the material from the personal records and added several additional parameters:</p> <ul> <li>The soldiers are entered into the database according to their date of enlistment. This is followed by a colour-coded table showing their years of service. To see the meaning of the different colours employed, scroll to the legend at the end of the dataset.</li> <li>Following the years of service, we see the date when the soldier left service (final year in service for incomplete service records). When known, the reason the soldier left the army is given (discharge/ death/ desertion etc).</li> <li>Then come the three most important columns within the table: service record, primary sources and units. At first glance, these columns have only a few letters and numbers, but bring your mouse courser onto the relevant field marked with red triangles. An additional window will then open:</li> </ul> <p>a. <em>Service Record</em>: Shows the entire service record of the soldier arranged by date. I use original German as it appears in the archival records. If you see spelling differences with modern German – they are there for a reason.</p> <p>b. <em>Primary Sources</em>: Provides the information on all the archival records consulted to reconstruct the service itinerary. The number in the field denotes the number of the archival cartons consulted.</p> <p>c<em>. Units</em>: Number of units in which a soldier serves. Bringing the cursor on to the field will open their list. Most Jewish soldiers served in the line infantry (<strong>IR</strong>) and the Military Transport Corps (<strong>MFWK</strong> or <strong>MFK</strong>). However, there were also Jewish sharpshooters, cavalrymen, gunners and even a few members of the nascent Austrian Navy.</p> <ul> <li>The next two columns provide entries of the soldier’s conduct and medical condition, which in Habsburg military jargon was referred to rather callously as <em>Defekten</em>. I note the original medical diagnoses verbatim. When possible to identify, I note the modern medical term.</li> <li>General database-wide parameters are then noted in the next part of the table. Among others, it provides information on enlistment type (conscript/ volunteer?), main branches of service (such as Infantry/ Cavalry/ Artillery), and roles within the military (such as non-commissioned officers/ drummers/ medics).</li> <li>Concluding this part of the table are columns covering desertions, periods as prisoner of war and awards of the army cannon cross (for veterans of 1813-14) and other military awards.</li> <li>The last column provides the original German outtake rubric as to how the soldier left service. In special cases, additional service notes are provides on the right.</li> </ul> <p><strong>How to use this dataset</strong></p> <p>This depends on what you are looking for. Firstly, download the dataset on to your computer via the link provided below. It is a simple Excel file which is easy to work with. If you wish to find out whether one of your ancestors served in the Habsburg army, use a simple keyword search. Please note that in our period there was no single accepted orthography meaning that some letters were used interchangeably (for instance B/P; D/T). There were also various patronymic suffices used in different parts of the monarchy (<em>-witz</em> in German/ <em>-wicz </em>in Polish/ <em>-vits</em> in Hungarian). Habsburg military clerks were mostly German speakers who often recorded the name phonetically. For instance, <em>Jankel</em>/ <em>Jankl</em>/ <em>Jacob</em>/ <em>Jacobus</em> all denote the same name. A Jewish teenager who identified himself as <em>Moische </em>when first reporting to duty, may have stayed so in the military records for decades, even if he was already a non-commissioned officer whose subordinates referred to as <em>Herr Corporal</em>. </p> <p>If you study the history of concrete Jewish communities, use the keyword search and the filter option to find entries in the database where this locality is mentioned. Some places like Prague and Lublin could be identified effortlessly. In other cases (and see the above point on German-speaking clerks), place names were recorded phonetically. The military authority usually stuck to official Polish names in Galicia, and Hungarian in the Lands of the Crown of St. Stephan. In reality, a Jewish recruit from Transcarpathian Ruthenia could have his place of birth recorded in Hungarian, Romanian or Rusin. When I could not identify the place in question, I marked it with italics. Do you think you identified something I could not? Excellent! Then please write me, and I will correct the entry in the next instalment of this database.</p> <p>I should stress that, currently, the database is not statistically representative. I have worked chronologically, meaning that there are disproportionally more entries for Jewish soldiers from the Turkish War, the first two Coalition Wars, and the Wars of 1805 and 1809. If you look at some of my other databases (for instance, that of the <a href="../doi/10.5281/zenodo.11180076">1st Line Infantry Regiment 'Kaiser'</a>), you will find least as many Jews who served in the wars of 1813-15. I will cover these in due course. This said, using the filter option of the Excel sheet, you can already make some individual queries. For instance, did Jewish grenadiers meet the minimal height requirement to be eligible for transfer into the elite infantry? (Hint: they did not!) If you are interested in the historical study of nutritional standards, compare the height of the soldiers with their year and place of birth. In my other project, I made calculations of the average height of Habsburg soldiers and I can already reveal that Jewish conscripts were, on average, several centimetres smaller than their non-Jewish comrades drafted in the same annual intake. Whatever stereotypes said, most Jews in the Habsburg Monarchy around 1800 were very poor and the sad fact of malnutrition as a child is reflected in their height as adults.</p> <p>I should stress that this is a cumulative database. ZENODO has an excellent feature allowing updated versions to supersede earlier files while retaining the same DOI (Digital Object Identifier) and metadata. As my research progresses, I plan to upload new versions of this database bi-annually. This includes not only adding new entries, but also expanding and correcting existing ones. It might well be that the service record of a soldier covered up to 1806 will be brought to a later date, possibly even to his discharge from the army. If you have not found whom you are looking for, or if you want to work with larger samples for your research, visit this page again in a few months’ time. And if you do use this database for scholarly research (by all means, please do), do not forget to cite it as you would cite any other item in your bibliography! If you are a museum professional and you want to employ material from your database to illustrate your exhibitions, you are welcome, but please cite this resource for others to learn. Links to this database will also be appreciated.</p>
FIG. 44 in An inventory of Bramble sharks Echinorhinus brucus (Bonnaterre, 1788) (Elasmobranchii, Echinorhinidae) in natural history collections worldwide for conservation status assessment
FIG. 44. — Echinorhinus brucus (Bonnaterre, 1788) in Venezuelan (Cumaná) collections: A-D, TNEC-MT (Entry 233).
FIG. 43 in An inventory of Bramble sharks Echinorhinus brucus (Bonnaterre, 1788) (Elasmobranchii, Echinorhinidae) in natural history collections worldwide for conservation status assessment
FIG. 43. — Echinorhinus brucus (Bonnaterre, 1788) in United States (Gainesville, Cambridge, Raleigh, New Port Richey and Washington D.C.) collections: A, B, UF103000 (Entry 223); B, UF 103001 (Entry 224); C, MCZ 39633 (Entry 225); D-H, NCSM 44134 (Entry 226); I, coll. PMH223-9 (Entry 228); J, coll. PMH223- 10 (Entry 229); K, USNM RAD107112-001 (Entry 232).
FIG. 42 in An inventory of Bramble sharks Echinorhinus brucus (Bonnaterre, 1788) (Elasmobranchii, Echinorhinidae) in natural history collections worldwide for conservation status assessment
FIG. 42. — Echinorhinus brucus (Bonnaterre, 1788) in United Kingdom (Penzance, London and Cambridge) collections (continuation): A, PZNAS unregistered (Entry 216); B, RCSL 1311Ba (Entry 220); C-F, UMZC CH50.1/1 (Entry 222).
FIG. 41 in An inventory of Bramble sharks Echinorhinus brucus (Bonnaterre, 1788) (Elasmobranchii, Echinorhinidae) in natural history collections worldwide for conservation status assessment
FIG. 41. — Echinorhinus brucus (Bonnaterre, 1788) in United Kingdom (Oxford) collections (continuation): A, OUMNH.ZC.314b (Entry 202); B, OUMNH.ZC.497a (Entry 203); C, OUMNH.ZC.499a (Entry 204); D, OUMNH.ZC.499b (Entry 205); E, OUMNH.ZC.896c (Entry 206); F, OUMNH.ZC.1099a (Entry 207); G, OUMNH. ZC.1099b (Entry 208); H, OUMNH.ZC.1396a (Entry 209); I, OUMNH.ZC.1396b (Entry 210); J, OUMNH.ZC.4319 (Entry 211), K, OUMNH.ZC.5428 (Entry 212); L, OUMNH registers; M, OUMNH.ZC.17347 (Entry 213); N, O, OUMNH.ZC.17618 (Entry 214).
FIG. 38 in An inventory of Bramble sharks Echinorhinus brucus (Bonnaterre, 1788) (Elasmobranchii, Echinorhinidae) in natural history collections worldwide for conservation status assessment
FIG. 38. — Echinorhinus brucus (Bonnaterre, 1788) in United Kingdom (London) collections (continuation): A, B, BMNH 1856.12.10.654 (Entry 188); C, BMNH register (Entries 188-193); D, BMNH 1909.9.3.26 (Entry 194).
FIG. 37 in An inventory of Bramble sharks Echinorhinus brucus (Bonnaterre, 1788) (Elasmobranchii, Echinorhinidae) in natural history collections worldwide for conservation status assessment
FIG. 37. — Echinorhinus brucus (Bonnaterre, 1788) in United Kingdom (Glasgow, Liverpool, London and Sheffield) collections (continuation): A, GMRC 1909.97 (Entry 183); B, LIVCM unregistered (Entry 184); C-E, MEFC unregistered (Entry 186); F, MSHF D.4.1.75-2 (Entry 187).
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