Find research datasets worth reusing

opencc-by-4.0Feb 2018View details →

Table S1 - Table S7: Integrated meta-omic analyses of the gastrointestinal tract microbiome in patients undergoing allogeneic stem cell transplantation

Table S1. Number of reads per prokaryotic operational taxonomic unit (OTU) and sample from the cohort. Table S2. Number of reads per eukaryotic operational taxonomic unit (OTU) and sample from the cohort. Table S3. Blood cell counts and clinical data from patient A07. Table S4. Number of reads per operational taxonomic unit (OTU) and sample from patient A07. Table S5. Numbers of identified antibiotic resistance genes and total number of genes. Numbers of identified antibiotic resistance genes in relation to total numbers of genes in samples from patient A07 before and after allo-HSCT and from four healthy individuals. Table S6. Statistics of the metagenomic and metatranscriptomic datasets and the co-assembled contigs. Table S7. Antibiotic resistance genes in population-level genomes and their expression in the pre- and post-treatment sample.

opennotspecifiedNov 2023View details →

FIGURE 2 in Ultrastructural observation of digestive tract and the adaptative characteristics of dietary habits for ground-dwelling and omnivorous insects

FIGURE 2. Scanning electron microscope observation of the L. taicoun. A–D. Crop (Cr). (The long and thin spines on the inner surface of the crop are pointed out with arrows.) E–M. Proventriculus (Pv). (ST: Sclerotized lobes; MT: Median tooth; SL: Sclerotized lobes) N–P. Gastric caecum (Gc). Q–S. Midgut. T–U. Ileum. V–Y. Malpighian tubules (MTs). (The micro-tracheae and internal microvilli are pointed out with arrows.) Z–BB. Colon. CC–DD. Rectum.

opennotspecifiedNov 2023View details →

FIGURE 4 in Ultrastructural observation of digestive tract and the adaptative characteristics of dietary habits for ground-dwelling and omnivorous insects

FIGURE 4. Scanning electron microscope observation of the V. micado. A–D. Crop (Cr). (The long and thin spines on the inner surface of the crop are pointed out with arrows.) E–L. Proventriculus (Pv). (ST: Sclerotized lobes; MT: Median tooth; SL: Sclerotized lobes) M–N. Gastric caecum (Gc). O–Q. Midgut. R–T. Ileum. U. Malpighian tubules (MTs). (The micro-tracheae are pointed out with arrows.) V–W. Colon. X–Y. Rectum.

opencc-by-4.0Oct 2024View details →

Dataset on the content of Cu, Ni Cd, Pb, Zn, Ag, Mg, Fe, Co and Ca in the carcass, gastrointestinal tract tissues and the whole body of nestlings of a small passerine bird, the Eurasian Reed Warbler Acrocephalus scirpaceus

The data include the description of the age and the concentrations of Cu, Ni Cd, Pb, Zn, Ag, Mg, Fe, Co and Ca measured in the isolated, emptied gastrointestinal tract, the whole body, and carcass of the each individual nestling of a different age and hence a different stage of post-natal development. The dataset includes also some additional information on the breeding biology of the focal species.

opencc-by-4.0Jan 2022View details →

Grammar [IO Islamic 2392] Anthology, including tracts in Persian

<ul> <li>Grammar.</li> <li>This manuscript is now IO Islamic 2392 in the India Office collections.</li> <li>[metadata:<a href="https://de.wikipedia.org/wiki/Otto_Loth"> Otto Loth, </a><a href="http://doi.org/10.5281/zenodo.3923636">A Catalogue of the Arabic Manuscripts in the Library of the India Office</a>, (volume 1), no. 990 here with further notations and hyperlinks].</li> </ul> <a href="https://archive.org/details/catalogueofarabi01greauoft/page/274/mode/2up?view=theater">990</a>. 2392. Size 71/4 in. by 43/4 in.; foll. 175. Nineteen lines in a page. I. Foll. 2-9. Glosses on Zamakhsharî’s رسالة التصرفات ( see the <a href="https://doi.org/10.5281/zenodo.5827788">preceding no</a>.) by an unknown author. Imperfect at the end. Beginning: قوله فصل فى الحروف تجر الاسماء فان قلت لم لم يصدر الشيخ رحمة الله عليه هذه الرسالة بالحمد لله الخ Written in a small Nasta’lîḳ hand. II. Foll. 10-49. ‘ISMAT ALLAH’S Commentary on the same treatise, identical with no. <a href="https://doi.org/10.5281/zenodo.5827788">989</a>. Clearly written in Nasta’lîḳ, by ترسن (؟) محمد اندخودى . Corrections and notes by the author on the margin. Injured by damp. III. Foll. 67v.-82. A Commentary ( ممزوج ) on Shams al-dîn Miṣrî’s treatise on Conjugation. It is entitled الرسالة البرهانية . The author is not known. Begins: الحمد لله الذى خلق الاشياء بقدرته ... و بعد فان كتاب الصرف للامام شمس الملة و الدين المصرى الخ The original treatise commences: الحمد لله على نعمائة .... و بعد فهذه جملة من تصريف الافعال الخ Written like no. I. IV. Foll. 83-160. A Commentary ( ممزوج ) on <a href="http://worldcat.org/identities/lccn-n82231797/">‘Izz al-dîn ‘Abd al-wahhâb </a><a href="http://worldcat.org/identities/lccn-n82231797/">Zanjânî</a>’s (d. A.H. 655) treatise on Conjugation, مختصر التصريف , by (Sa’d al-dîn) Mas’ûd b. ‘Omar TAFTÂZÂNÎ (d. A.H.792). See <a href="https://en.wikipedia.org/wiki/Kashf_al-Zunun">Ḥ. Kh.</a> iv. 208; Cat. <a href="https://doi.org/10.5281/zenodo.6827074">St. Petersb. </a>150; Cat. Bodl. ii. 186 ; Aumer, <a href="https://catalog.lib.uchicago.edu/vufind/Turnstile/Challenge?context=eyJwb2xpY3lJZCI6ImdlbmVyYWwiLCJkZXN0aW5hdGlvbiI6IlwvdnVmaW5kXC9SZWNvcmRcLzcxMTQyOCJ9">Hdss</a>. Münch . 336. Printed at Constantinople, A.H. 1253. Cf. no. <a href="https://doi.org/10.5281/zenodo.5810635">955</a>, regarding the original work. Plainly written, by Pîr Muḥammad b. ׳Ârif Shaikh Nasafî. Dated Dhu’l-ḥijjah, 973 [= June/July 1566]. Corrections and some notes on the margin. Worm-eaten. Foll. 50-67 and 161-175. Persian tracts. [<a href="http://worldcat.org/identities/lccn-n83184096/">Sir Charles Wilkins</a>.]

opennotspecifiedJan 2022View details →

◂Fig. 8 Light microscope images of living specimens of Ramisyllis kingghidorahi n. sp. A Branching point. B, E–G Posterior ends showing pygidia. C, D, H, I Midbody segments in regions of long dorsal cirri. Arrows point to the ventral blood vessel in H and the digestive tract in I.A, D, E, and I in dorsal view. B, C, F and H in ventral view. G In lateral view. Scale bars: 500 µm A, E, 200 µm B, C, D, 100 µm F, H, I, and 50 µm G in Ramisyllis kingghidorahi n. sp., a new branching annelid from Japan

◂Fig. 8 Light microscope images of living specimens of Ramisyllis kingghidorahi n. sp. A Branching point. B, E–G Posterior ends showing pygidia. C, D, H, I Midbody segments in regions of long dorsal cirri. Arrows point to the ventral blood vessel in H and the digestive tract in I.A, D, E, and I in dorsal view. B, C, F and H in ventral view. G In lateral view. Scale bars: 500 µm A, E, 200 µm B, C, D, 100 µm F, H, I, and 50 µm G

Fig. 2. A in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts

Fig. 2. A maximum-likelihood phylogenetic tree reconstructed using core genes (n=100) identified from whole-genome sequences, showing the evolutionary relationships among five novel Limosilactobacillus species, six L. reuteri subspecies and other recognized species in the genus Limosilactobacillus. GenBank or JGI accession numbers of these genomes are provided in parentheses. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. Strains of five novel Limosilactobacillus species are labelled by different colours; labels of six L. reuteri subspecies are colour representing vertebrate host origin: green for rodents, red for pigs, blue for humans and orange for poultry. The tree was drawn with iTOL [54].

Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts

Fig. 1. A maximum-likelihood phylogenetic tree reconstructed using 16S rRNA gene sequences. GenBank or JGI accession numbers of these genomes are provided in parentheses. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. Strains of five novel Limosilactobacillus species are labelled by different colours; labels of six L. reuteri subspecies are colour representing vertebrate host origin: green for rodents, red for pigs, blue for humans and orange for poultry. The tree was drawn with iTOL [54].

Fig. 3. A in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts

Fig. 3. A maximum-likelihood phylogenetic tree reconstructed using core genes (n=100) identified from whole-genome sequences, showing the evolutionary relationships among six L. reuteri subspecies. The tree was reconstructed using 33 L. reuteri genomes available in public databases (n=6 for L. reuteri subsp. kinnaridis, n=2 for L. reuteri subsp. porcinus, n=5 for L. reuteri subsp. murium, n=10 for L. reuteri subsp. reuteri, n=5 for L. reuteri subsp. suis and n=5 for L. reuteri subsp. rodentium) and L. balticus BG-AF3-AT was used as an outgroup. Further information on the involved genome sequences is listed in Table S1. The tree was inferred based on the GTR+G model with 1000 bootstrap replicates and only bootstrap values above 60% are shown. The tree was drawn with iTOL [54].

Fig. 4 in Limosilactobacillus balticus sp. nov., Limosilactobacillus agrestis sp. nov., Limosilactobacillus albertensis sp. nov., Limosilactobacillus rudii sp. nov. and Limosilactobacillus fastidiosus sp. nov., five novel Limosilactobacillus species isolated from the vertebrate gastrointestinal tract, and proposal of six subspecies of Limosilactobacillus reuteri adapted to the gastrointestinal tract of specific vertebrate hosts

Fig. 4. Pairwise average nucleotide identity values (ANI; %) of genome sequences belonging to the same or different L. reuteri subspecies. ANI values within the same subspecies and between different subspecies were calculated for 33 L. reuteri genomes available in public databases (n=6 for L. reuteri subsp. kinnaridis, n=2 for L. reuteri subsp. porcinus, n=5 for L. reuteri subsp. murium, n=10 for L. reuteri subsp. reuteri, n=5 for L. reuteri subsp. suis and n=5 for L. reuteri subsp. rodentium). Further information on the involved genome sequences is listed in Table S1.

opencc-by-4.0Feb 2022View details →

Miscellanies [IO Islamic 2686] Tracts with interlinear Javanese translations

<ul> <li>Miscellanies.</li> <li>This manuscript is now IO Islamic 2686 in the India Office collections.</li> <li>[metadata:<a href="https://de.wikipedia.org/wiki/Otto_Loth"> Otto Loth, </a><a href="http://doi.org/10.5281/zenodo.3923636">A Catalogue of the Arabic Manuscripts in the Library of the India Office</a>, (volume 1), no. 1046 here with further notations and hyperlinks].</li> </ul> <a href="https://archive.org/details/catalogueofarabi01greauoft/page/300/mode/2up?view=theater">1046</a>. 2686. Size 101/2 in. by 71/2 in.; foll. 222. Fourteen lines in a page. I. Foll.1-11. SAMARḲANDÎ’S Catechism (see nos. <a href="https://doi.org/10.5281/zenodo.5000618">381</a> and 470, i.). Ends: تمة الکتاب المسمّی بسمرقندی غفر الله ذنوب من کتب هذا الخ II. Foll. 12-32. AḤMAD B. AL-‘ABBÂS’s Sixty Questions (see no. <a href="https://doi.org/10.5281/zenodo.5196738">470</a>, ii). III. Foll. 33-37. Explanation of the confession of faith, identical with Cat. Mus. Brit. 393b, no. iv. IV. Foll. 38-63. SANSÛÎ’S Articles of Faith (see no. <a href="https://doi.org/10.5281/zenodo.5196738">470</a>, vi.). V. Foll.64-78. Elements of Faith, the same as no. <a href="https://doi.org/10.5281/zenodo.5196738">470</a>, iii., but without the commentary. VI. Foll. 79-99. A mystic treatise on Religious Duties. Begins: الحمدلله رب العالمین....فامّا بعد اسعدکم الله تعالی فی الدَرین (!) دنیا و اُخرً (!) فاعلم ان الامور المشروعة عند اهل السنة و الجماعة ثلثة مراتیب (!) عبادة و عبودیة و عبودة الخ VII. Foll. 100-118. A short treatise on Prayer. Begins: اعلم ان الشروع فی الصلوة بالعلم الخ. VIII. Foll. 119-140. A treatise on Ṣûfism. Begins: الحمدلله کاشف السر بالاسرار...قال الشیخ الامام العارف الفقیر الضعیف رحمة الله علیه قال یوسف ابن مُکِیَّةٍ (!) قد قدس الله روحه العزیز فی بیان الشریعة الخ IX. Foll. 141-169. A tract of the same kind. Begins: الحمدلله رب العالمین الذی (!) خلق الله تعالی باهلها و اسرارها....و بعد الاوّل طریق الی الله تعالی ان یعوف ذاته و صفاته الخ X. Foll. 170-188. A similar tract. Begins: الحمدلله رب العالمین ...و بعد فالعالم مرآة غیر مصقولة الخ Ends: تمت کتاب الرسالة المبارکة النافعة المسمّاة باب التحیّة(؟)1 XI. Foll. 189-222. Another mystic treatise, imperfect at the end. Begins: الحمدلله ...اما بعد فاعلم ارشدک الله ان کل تکلیف مأمور بمعرفة الله الخ All these tracts are accompanied by an interlinear translation in Javanese, written in the Arabic character. Written in a large plain hand, on rice-paper.   1 The last word is corrupt. It might also be المحبّة.

dryad32/100

Data from: Whistling shares a common tongue with speech: bioacoustics from real-time MRI of the human vocal tract

Most human communication is carried by modulations of the voice. However, a wide range of cultures has developed alternate forms of communication that make use of a whistled sound source. For example, whistling is used as a highly salient signal for capturing attention, can have iconic cultural meanings such as the cat-call, enact a formal code as in boatswain's calls, or stand as a proxy for speech in whistled languages. We used real-time magnetic resonance imaging to examine the muscular control of whistling to describe a strong association between the shape of the tongue and the whistled frequency. This bioacoustic profile parallels the use of the tongue in vowel production. This is consistent with the role of whistled languages as proxies for spoken languages, in which one of the acoustical features of speech sounds are substituted with a frequency modulated whistle. Furthermore, previous evidence that non-human apes may be capable of learning to whistle from humans suggests that these animals may have similar sensorimotor abilities to those that are used to support speech in humans.

opencc-zeroSep 2019View details →

opencc-by-4.0Jul 2022View details →

In vivo probabilistic atlas of white matter tracts of the human subthalamic area combining track density imaging and optimized diffusion tractography

Sample code to reproduce the results of the paper "In vivo probabilistic atlas of white matter tracts of the human subthalamic area combining track density imaging and optimized diffusion tractography", by Basile et al., Brain Structure and Function 2022.  The repository also includes the probabilistic atlas of the human subthalamic area.

opennotspecifiedMar 2013View details →

Distribution. SW Tanzania, known only from the Udzungwa Mts, a few small tracts of forest between the Little Ruaha and Ulanga rivers (S of Iringa), and several forest patches of the Kilombero Valley at the E base of the Udzungwa Mts (Magombera, Kiwanga, Kalunga, and in gallery forest along the Msolwa River S of the railway to its confluence with the Kilombero River, including the Ibiki and Msitu ya Kinjugu forests). in Cercopithecidae

Distribution. SW Tanzania, known only from the Udzungwa Mts, a few small tracts of forest between the Little Ruaha and Ulanga rivers (S of Iringa), and several forest patches of the Kilombero Valley at the E base of the Udzungwa Mts (Magombera, Kiwanga, Kalunga, and in gallery forest along the Msolwa River S of the railway to its confluence with the Kilombero River, including the Ibiki and Msitu ya Kinjugu forests).

opennotspecifiedAug 2022View details →

FIGURE 9. Atopida, female genital tract. A in Revision of Atopida White, 1846 (Coleoptera: Scirtoidea: Scirtidae)

FIGURE 9. Atopida, female genital tract. A) A. insularis sp. nov., B) A. villosa. Abbreviations: bscl—bursal sclerite, gla— gland, sVIII—sternite VIII, tVIII—tergite VIII.

FIGURE 1. Protrelleta floridana Chitwood, 1932. Female. A. Oesophageal region, lateral view. B. Cephalic end, optical section. C. Tail, lateral view. D. Egg. E. Genital tract, lateral view. F in Morphological and molecular characterization of two species of nematodes (Oxyuridomorpha: Thelastomatoidea: Protrelloididae, Thelastomatidae) parasitic in the cockroach Blaberus discoidalis Serville (Blattaria: Blaberidae) from Cuba

FIGURE 1. Protrelleta floridana Chitwood, 1932. Female. A. Oesophageal region, lateral view. B. Cephalic end, optical section. C. Tail, lateral view. D. Egg. E. Genital tract, lateral view. F. Habitus, lateral view.

FIGURE 5. Thurstonia nilotica n in Four new species of Hysterocinetida (Protozoa: Ciliophora) from the digestive tract of earthworms collected to the lower Nyong estuary (South Coast, Cameroon)

FIGURE 5. Thurstonia nilotica n. sp. A. General morphology after double staining by DAPI (blue) and immunofluorescence microscopy (IF) using FITC-conjugated anti-tubulin antibody (green); B. General morphology (Drawings after silver staining); C. Ciliature of the upper face; D. Ciliature of the lower face; BA. Buccal Apparatus; Ma. Macronucleus; Mi. micronucleus; Su. Sucker. Scale bar: 20 μm.

FIGURE 4. Thurstonia emini n in Four new species of Hysterocinetida (Protozoa: Ciliophora) from the digestive tract of earthworms collected to the lower Nyong estuary (South Coast, Cameroon)

FIGURE 4. Thurstonia emini n. sp. A. General morphology after double staining by DAPI (blue) and immunofluorescence microscopy (IF) using FITC-conjugated anti-tubulin antibody (green); B. General morphology (Drawings after silver staining); C. Ciliature of the upper face; D. Ciliature of the lower face; BA. Buccal Apparatus; Ma. Macronucleus; Mi. micronucleus; Su. Sucker. Scale bar: 20 μm.

FIGURE 2. Preptychostomum donendaensis n in Four new species of Hysterocinetida (Protozoa: Ciliophora) from the digestive tract of earthworms collected to the lower Nyong estuary (South Coast, Cameroon)

FIGURE 2. Preptychostomum donendaensis n. sp. A. General morphology after double staining by DAPI (blue) and immunofluorescence microscopy (IF) using FITC-conjugated anti-tubulin antibody (green); B. General morphology (Drawings after silver staining); C. Ciliature of the upper face; D. Ciliature of the lower face; BA. Buccal Apparatus; Ma. Macronucleus; Mi. micronucleus; Su. Sucker. Scale bar: 20 μm.

FIGURE 3. Proptychostomum gigas n in Four new species of Hysterocinetida (Protozoa: Ciliophora) from the digestive tract of earthworms collected to the lower Nyong estuary (South Coast, Cameroon)

FIGURE 3. Proptychostomum gigas n. sp. A. General morphology after double staining by DAPI (blue) and immunofluorescence microscopy (IF) using FITC-conjugated anti-tubulin antibody (green); B. General morphology (Drawings after silver staining); C. Ciliature of the upper face; D. Ciliature of the lower face; BA. Buccal Apparatus; Ma. Macronucleus; Mi. micronucleus; Su. Sucker. Scale bar: 20 μm.