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Quantitative results of the analysis of human bioengineered tissues corresponding to the work "Generation of tissue-like models of human bilayered tissues functionalized with olive oil components"
<p>This file contains the raw dataset generated in the work entitled "GENERATION OF NOVEL TISSUE-LIKE MODELS OF HUMAN BILAYERED TISSUES FUNCTIONALIZED WITH BIOACTIVE COMPONENTS OBTAINED FROM OLIVE OIL". These results correspond to the quantification of the histological results obtained in this work.</p>
Quantitative results of the analysis of two types of bone particles corresponding to the work "A comprehensive analysis of two types of xenogeneic bone particles for use in maxillofacial bone regeneration therapies"
<p>This dataset corresponds to the quantitative data generated in the work entitled "A comprehensive analysis of two types of xenogeneic bone particles for use in maxillofacial bone regeneration therapies".</p> <p>Regeneration of maxillofacial bone structures is challenging. One of the strategies applied to bone damage repair is the use of bone filler particles, and different types of these particles have been tested. In this work, we analyzed the regenerative potential of deproteinized bone particles (DP) and collagen-based bone particles (CP) to determine the potential of each biomaterial in bone repair. Results of the structural analysis using scanning electron microscopy and 3D scanning showed that DP and CP were structurally similar, and consisted of a heterogeneous mixture of bone particles of different sizes and shapes. Then, ex vivo analyses using morphological evaluation, LIVE & DEAD and quantification of DNA released to the medium demonstrated that CP and DP were highly biocompatible when used in direct and in indirect contact with human cells, at 24, 48 and 72h of follow-up. Then, when both particles were grafted for 2 months on Wistar rats in which a critical defect had been generated at the mandible bone. Results of the computed tomography analysis showed a significant reduction of the bone defect in the CP group, but not in the DP group, as compared with negative controls devoid of any bone particles. Histological analysis of the graft area revealed that both particles were biocompatible in vivo, and a regenerative tissue with collagen fibers and mineralized spots was found in CP and DP, with higher number of mineralized spots in DP. Histochemistry and immunohistochemistry analyses confirmed the presence of collagen, proteoglycans and osteocalcin at the regeneration area of CP and DP. In general, these results confirm the biocompatibility of both types of particles and that both were able to induce maxillofacial bone regeneration, especially in the case of CP. Future studies should determine their clinical usefulness in patients with cleft palate, mandibular damage and other maxillofacial applications.</p>
FIG. 4. — A, B, Sphaerocypraea tardivelae n in Nouveaux taxons et discussion de la systématique des genres correspondants d'Ovulidae (Mollusca, Caenogastropoda) de l'Éocène inférieur de Gan (France)
FIG. 4. — A, B, Sphaerocypraea tardivelae n. sp., vue ventrale et vue latérale externe, holotype (déformé) MNHN-LP n° R63014 (coll. D. Ledon), h. 48,8 mm, Gan (La Tuilerie); C, D, Sphaerocypraea incomparabilis (Briano, 1993), vue ventrale et détail du pli terminal, spécimen USNM, h. 80,3 mm, « off Somalia » (« north-western Indian Ocean »); E, Sphaerocypraea jacksonensis (Johnson, 1899), détail du pli terminal, spécimen MNHN-BIMM (coll. L. & C. Dolin), h. 85 mm, Jackson (Town Creek), Hinds County (Mississippi), détail. Échelles: 5 mm.
FIG. 2 in Nouveaux taxons et discussion de la systématique des genres correspondants d'Ovulidae (Mollusca, Caenogastropoda) de l'Éocène inférieur de Gan (France)
FIG. 2. — Analyse biométrique du rapport entre hauteur et diamètre maximal (A) et du rapport entre hauteur/diamètre maximal et diamètre maximal/nombre de dents labrales (B) chez Cypraea kerniana (Anderson & Hanna, 1925) synonyme junior de Prionovolva (Grovesia) mathewsonii (Gabb, 1869) () et chez P. (G.) ganensis n. sp. ().
FIG. 1. — A-D in Nouveaux taxons et discussion de la systématique des genres correspondants d'Ovulidae (Mollusca, Caenogastropoda) de l'Éocène inférieur de Gan (France)
FIG. 1. — A-D, Prionovolva (Grovesia) ganensis n. sp.; A, B, vue ventrale et vue latérale externe, holotype MNHN-LP n° R63009 (coll. L. & T. Dolin), h. 13,4 mm, Gan (La Tuilerie); C, D, vue ventrale et détail du pli teminal, paratype MNHN-LP n° R63011a (coll. D. Merle), h. 13 mm, Gan (La Tuilerie); E, F, Prionovolva (Prionovolva) nubeculata (Adams, 1854), vue ventrale et détail du pli terminal, spécimen MNHN-BIMM (coll. L. Dolin), h. 18,6 mm, Nouméa (chenal îlot Maître), Nouvelle-Calédonie; G, Habuprionovolva umbilicata (Sowerby, 1849), vue ventrale, spécimen MNHN-BIMM (coll. L. Dolin), h. 9,5 mm, Honshu Isl. (Kii channel), Wakayama Prefecture (Japon). Échelles: 5 mm.
FIG. 5. — A, B, Simnia pacaudi n in Nouveaux taxons et discussion de la systématique des genres correspondants d'Ovulidae (Mollusca, Caenogastropoda) de l'Éocène inférieur de Gan (France)
FIG. 5. — A, B, Simnia pacaudi n. sp., vue ventrale et vue latérale externe, holotype MNHN-LP n° R63015 (coll. J.-M. Pacaud), h. 18,9 mm, Gan (La Tuilerie); C, D, Sandalia vibrayana (Raincourt, 1870), vue ventrale et détail du pli terminal, spécimen MNHN-BIMM (coll. L. Staadt), h. 10,2 mm, Mons-en-Laonnois (hameau des Creuttes), Aisne (France); E, F, Simnia brevirostris (Schumacher, 1817), vue ventrale et détail du pli terminal, spécimen MNHN-BIMM (coll. L. Dolin), h. 21,3 mm, Cebu Isl. (off Punta Engaño), Philippines; G, Phenacovolva angasi (Reeve, 1865), vue ventrale, spécimen MNHN-BIMM (coll. L. Dolin), h. 15,9 mm, Cebu Isl. (off Punta Engaño), Philippines. Échelles: 5 mm.
FIG. 3. — A-C, Luponovula merlei n in Nouveaux taxons et discussion de la systématique des genres correspondants d'Ovulidae (Mollusca, Caenogastropoda) de l'Éocène inférieur de Gan (France)
FIG. 3. — A-C, Luponovula merlei n. sp.; A, B, vue ventrale et vue latérale externe, holotype MNHN-LP n° R63012 (coll. L. & T. Dolin), h. 39 mm, Gan (La Tuilerie); C, vue ventrale reconstituant (tirés) le galbe initial, paratype (comprimé latéralement) MNHN-LP n° R63013 (coll. J.-M. Pacaud), h. 45,5 mm, Gan (La Tuilerie); D, E, Luponovula normalis (Gregorio, 1880), vue ventrale et détail du pli terminal, spécimen (incomplet, pédomorphisé) MNHN-LP n°J 03872 (coll. E. Hébert & E. Munier-Chalmas), h. 46,4 mm, San Giovanni Ilarione (Bosco del Prete), Vicenza (Italie). Échelles: 5 mm.
FIG. 2. — Analyse factorielle des correspondances. Projection des 77 in Révision de Flabellipecten solarium (Lamarck, 1819) (Mollusca, Bivalvia, Pectinidae) du Miocène moyen et supérieur de l'Ancien Monde
FIG. 2. — Analyse factorielle des correspondances. Projection des 77 individus (73 principaux et 4 supplémentaires,) et des 10 variables (voir Fig. 1) dans le plan factoriel 1-2., Gigantopecten ligerianus (Dollfus & Dautzenberg, 1906);, Gigantopecten gigas (Schlotheim, 1813);, Flabellipecten solarium (Lamarck, 1819). Les contours et profils de quelques valves ont été ajoutés pour illustrer les résultats de l'analyse. Abréviations: cdp, coup de pouce (pour G. ligerianus) CMD, profondeur de la valve ou convexité maximale; DAP, diamètre antéro-postérieur; DUP, diamètre umbono-palléal (cette variable de référence est un indicateur de taille car prise dans la direction de croissance au niveau du plan directeur de la coquille); HOA, hauteur de l'oreille antérieure; HOP, hauteur de l'oreille postérieure; HPL, demi-hauteur postérieure, mesurée de la ligne cardinale au maximum de la largeur; LAH, demi-longueur antérieure prise au maximum ventral de la hauteur; LIC, longueur de la ligne cardinale; RAD, renfoncement antérieur du disque; RPD, renfoncement postérieur du disque (ces deux dernières variables permettent de caractériser la forme du disque: étiré dans le sens antéro-postérieur, donc plus ou moins ovale, lorsque ces renfoncements sont importants, plus arrondi lorsqu'ils sont plus faibles). Échelle: 2 cm.
FIG. 1. — Correspondance d in Nouveautés nomenclaturales et taxinomiques introduites par Alcide d'Orbigny dans le Prodrome (1850, 1852) pour les espèces du Paléocène et de l'Éocène
FIG. 1. — Correspondance d'A. Gaudry à E. Hébert datée du 5 août 1858 mentionnant le catalogue de la collection d'Orbigny: « Il paraît que le Ministère est peu disposé à faire faire un catalogue scientifique […] Je sais que je n'ai point besoin de vous recommander une collection qui intéresse autant la Science que l'honneur même du nom de d'Orbigny […] ».
Text-fig. 4. Dorsal view of endocranium of a Devonian osteolepiform (Eusthenopteron foordi). Derivatives of the teniform cartilages blue (cf. fig. 7 in Bjerring 2015). ab: anterolateral bar of otico-occipital (Jarvik 1954) which corresponds to the orbitoparietal commissure of the armadillo; rfsa: endoskeleton above the supra-auditive fossa which corresponds to the parietal lamina of the armadillo; tn: tectum nasi; to: tectum orbitae which corresponds to the orbital cartilage and the orbitonasal commissure of the armadillo. in Cartilago Teniformis And Its Derivatives: Additional Information On The Basic Composition And Evolution Of The Skull
Text-fig. 4. Dorsal view of endocranium of a Devonian osteolepiform (Eusthenopteron foordi). Derivatives of the teniform cartilages blue (cf. fig. 7 in Bjerring 2015). ab: anterolateral bar of otico-occipital (Jarvik 1954) which corresponds to the orbitoparietal commissure of the armadillo; rfsa: endoskeleton above the supra-auditive fossa which corresponds to the parietal lamina of the armadillo; tn: tectum nasi; to: tectum orbitae which corresponds to the orbital cartilage and the orbitonasal commissure of the armadillo.
Text-fig. 5. Upper part of the stratigraphic section at the Omanitherium type locality. B–D correspond to the beds identified in the stratigraphic section (Text-fig. 3). The workers are excavating at the type locality. in Large Mammals From The Rupelian Of Oman - Recent Finds
Text-fig. 5. Upper part of the stratigraphic section at the Omanitherium type locality. B–D correspond to the beds identified in the stratigraphic section (Text-fig. 3). The workers are excavating at the type locality.
Text-fig. 3. Scatter diagram of mean L/W values of selected Spermophilinus upper first molars (M1 and M2) from Switzerland and south Germany. The crosses correspond to the minimum and maximum values of the length and width. The intersection gives the value of the mean. Comparative data are after Ziegler and Fahlbusch (1986), Bolliger (1992), Kälin (1993), Ziegler (1995, 2005), Kälin and Engesser (2001), Prieto (2007), Prieto et al. (2009, 2017), Seehuber (2009). Blue: localities younger than ~14 Ma (S. bredai); Green: localities ranging from ~14 Ma to ~15Ma (S. bredai); Red: localities ranging from ~15 Ma to ~16 Ma (S. besana); Yellow: older localities (most S. besana). in Dental Anomaly In A Middle Miocene Fossil Of The Genus Spermophilinus (Rodentia, Sciuridae) From Southern Germany
Text-fig. 3. Scatter diagram of mean L/W values of selected Spermophilinus upper first molars (M1 and M2) from Switzerland and south Germany. The crosses correspond to the minimum and maximum values of the length and width. The intersection gives the value of the mean. Comparative data are after Ziegler and Fahlbusch (1986), Bolliger (1992), Kälin (1993), Ziegler (1995, 2005), Kälin and Engesser (2001), Prieto (2007), Prieto et al. (2009, 2017), Seehuber (2009). Blue: localities younger than ~14 Ma (S. bredai); Green: localities ranging from ~14 Ma to ~15Ma (S. bredai); Red: localities ranging from ~15 Ma to ~16 Ma (S. besana); Yellow: older localities (most S. besana).
FIG. 18. Longitudinal correspondence among Amazonian Shield versants. A in The Fishes Of The Amazon: Distribution And Biogeographical Patterns, With A Comprehensive List Of Species
FIG. 18. Longitudinal correspondence among Amazonian Shield versants. A. Red area delimits the distribution pattern of western basins (Trombetas and Tapajós); yellow area the western basins pattern (Jari, Xingu, and Tocantins). B. Sartor gr. elongatus (records from MZUSP). C. Bryconexodon spp. (records from MZUSP). D. Bivibranchia velox (records from MZUSP).
Example variant files and corresponding annotations for GnomAD v3.1.1 on a subset of chromosome 22
<p>Example variant files and corresponding hg38 annotations for `chr22:15518158-20127355`.</p> <p>Sources:</p> <ul> <li><a href="http://dx.doi.org/10.1093/nar/gky955">Gencode v34 (hg38)</a></li> <li><a href="https://doi.org/10.1038/s41586-020-2308-7">GnomAD v3.1.1</a></li> </ul>
Respirometry data for cactus mice (Peromyscus eremicus) corresponding to Colella et al. 2021
<p>Metabolism is a complex phenotype shaped by natural environmental rhythms, as well as behavioral, morphological, and physiological adaptations. Metabolism has been historically studied under constant environmental conditions, but new methods of continuous metabolic phenotyping now offer a window into organismal responses to dynamic environments, and enable identification of abiotic controls and the timing of physiological responses relative to environmental change. We use indirect calorimetry to characterize metabolic phenotypes of the desert-adapted cactus mouse (<i>Peromyscus eremicus</i>) in response variable environmental conditions that mimic their native environment versus those recorded under constant warm and constant cool conditions, while using a constant photoperiod and full access to resources. We found significant sexual dimorphism, with males being more prone to dehydration than females. Under circadian environmental variation, most metabolic shifts occurred prior to physical environmental change and the timing was disrupted under both constant temperature-humidity treatments. The ratio of CO<sub>2</sub> produced to O<sub>2</sub> consumed (the respiratory quotient) reached greater than 1.0, only during the light phase under diurnally variable conditions, a pattern that strongly suggests that<i> </i>lipogenesis is contributing to the production of energy and endogenous water. Our results are consistent with historical descriptions of circadian torpor in this species (torpid by day, active by night), but reject the hypothesis that torpor is initiated by food restriction or negative water balance.</p>
On the correspondence between the transcriptomic response of a compound and its effects on its targets
<p>Dataset used in the manuscript "On the correspondence between the transcriptomic response of a compound and its effects on its targets".</p> <p>More info at https://github.com/enveda/transcriptomic-target-correlation</p>
Data corresponding to: Evaluation of sequencing and PCR-based methods for the quantification of the viral genome formula
<p>Viruses show great diversity in their genome organisation. Multipartite viruses package their genome segments into separate particles, most or all of which are required to initiate infection in the host cell. The benefits of such seemingly inefficient genome organization are not well understood. One hypothesised benefit of multipartition is that it allows for flexible changes in gene expression by altering the frequency of each genome segment in different environments, such as encountering different host species. The ratio of the frequency of segments is termed the genome formula (GF). Thus far, formal studies quantifying the GF have been performed for well-characterised virus-host systems in experimental settings using RT-qPCR. However, to understand GF variation in natural populations or novel virus-host systems, a comparison of several methods for GF estimation including high-throughput sequencing (HTS) based methods is needed. Currently, it is unclear how HTS-methods compare a golden standard, such as RT-qPCR. Here we show a comparison of multiple GF quantification methods (RT-qPCR, RT-digital PCR, Illumina RNAseq and Nanopore direct RNA sequencing) using three host plants (<em>Nicotiana tabacum</em>, <em>Nicotiana benthamiana</em>, and <em>Chenopodium quinoa</em>) infected with cucumber mosaic virus (CMV), a tripartite RNA virus. Our results show that all methods give roughly similar results, though there is a significant method effect on genome formula estimates. While the RT-qPCR and RT-dPCR GF estimates are congruent, the GF estimates from HTS methods deviate from those found with PCR. Our findings emphasise the need to tailor the GF quantification method to the experimental aim, and highlight that it may not be possible to compare HTS and PCR-based methods directly. The difference in results between PCR-based methods and HTS highlights that the choice of quantification technique is not trivial.</p>
Textual Process Descriptions and Corresponding BPMN Models
<p>This dataset provides an archive with 24 textual process descriptions in different granularities, each with 8-11 BPMN models, that represent possible solutions for modelling the description. Each BPMN model has an assigned score of 0..5 which describes how good a human expert deemed the solution.</p>
Annotated Video Dataset of Fencing Movements and Corresponding Error Patterns
<p>Video dataset containing 1289 videos and their augmentation of four fencing movements, performed by a variety of fencers. The main actions included are counterattack, lunge, flèche and parry. For each movement samples with typical error patterns are included and annotated. Additionally labels for mulit-labelling are documented. The corresponding paper "Mastering Fencing Techniques with Machine Learning: A Video-Based Classification and Correction System" is published at the 10th IEEE Swiss Conference on Data Science (SDS 2023)</p>
Dataset corresponding to the publication: Friction and slip measured at the bed of an Antarctic ice stream
<p>The following data is included here, which comprises the data presented in the publication:<br> Hudson, T. S., Kufner, S., Brisbourne, A. M., Kendall, J., Smith, A. M., Arthern, R., & Alley, R. (2023). Friction and slip measured at the bed of an Antarctic ice stream. Nature Geoscience.</p> <p>Files included are:<br> all_icequakes_2018to2019.csv - A catalogue of the icequakes used in the study.<br> cluster_????.csv - csv files containing the results for each icequake, grouped by cluster (i.e. one csv file per cluster).<br> slip_rate_movie.mp4 - A movie of slip-rate for each icequake through time.</p> <p>Headers for the files are as follows:<br> ------------------------------------- all_icequakes_2018to2019.csv file -------------------------------------<br> origin_time - Origin time of icequake, in UTC time.<br> Mw - Moment magnitude.<br> Mw_err - Error in Mw.<br> fc - Corner frequency (Hz).<br> fc_err - Error in corner frequency.<br> Q - Quality factor (measure of attenuation).<br> Q_err - Error in Q.<br> inter-event_time_s - Inter-event time between this icequake and the previous icequake (s).<br> stress_drop - Stress-drop of icequake (Pa).<br> stress_drop_err - error in stress-drop.<br> lat - Latitude (decimal degrees).<br> lon - Longitude (decimal degrees).<br> x (km) - x grid location (km).<br> y (km) - y grid location (km).<br> z (km bsl) - Depth (km bsl).<br> x_err (km) - Error in x (km).<br> y_err (km) - Error in y (km).<br> z_err (km) - Error in z (km).</p> <p>------------------------------------- cluster_XXXX.csv file -------------------------------------<br> mean_Mw - Mean moment magnitude for icequake from all receivers.<br> mean_fc - Corner frequency for icequake from all receivers (Hz).<br> stdev_Mw - Standard deviation in Mw.<br> stdev_fc - Standard deviation in corner-frequency.<br> mean_Q - Mean Q for icequake from all receivers.<br> stdev_Q - Standard deviation in Q.<br> n_obs - Number of receivers used to calculate above means.<br> lat - Latitude of icequake.<br> lons - Longitude of icequake.<br> depths - Depth of icequake (km bsl).<br> x - x location of icequake (km).<br> y - y location of icequake (km).<br> zs - z location of icequake (km bsl).<br> origin_time - Origin time of icequake (UTC time).<br> origin_time_days - Origin time in days relative to 1st January 2019 (days).<br> inter-event_time_s - Inter-event time from previous to current event (s).<br> stress_drop - Stress drop (Pa)<br> uncertainty_stress_drop - Uncertainty in stress-drop.<br> M_0 - Seismic moment release (Nm).<br> uncertainty_M_0 - Uncertainty in M_0.<br> fault_radius_m - Fault radius, in metres.<br> uncertainty_fault_radius_m - Uncertainty in fault radius (m).<br> slip_ice_m - Slip in the ice (m).<br> slip_till_m - Slip in the till (m).<br> uncertainty_slip_ice_m - Uncertainty in slip_ice_m.<br> uncertainty_slip_till_m - Uncertainty in slip_till_m.<br> RSF_v/v_0 - v/v_0 calculated for the rate-and-state model.<br> RSF_sigma - Normal stress calculated for the rate-and-state model (Pa).<br> RSF_tau - Shear-stress calculated for the rate-and-state model (Pa).<br> uncertainty_RSF_v/v_0 - Uncertainty in RSF_v/v_0.<br> uncertainty_RSF_sigma - Uncertainty in RSF_sigma.<br> uncertainty_RSF_tau - Uncertainty in RSF_tau.<br> RSF_G* - Effective shear-modulus calculated for the rate-and-state model (Pa).<br> RSF_Gb - Bed shear modulus calculated for the rate-and-state model (Pa).<br> RSF_slip_m - Slip calculated for the rate-and-state model (Pa).<br> uncertainty_RSF_G* - Uncertainty in RSF_G*.<br> uncertainty_RSF_Gb - Uncertainty in RSF_Gb.<br> uncertainty_RSF_slip_m - Uncertainty in RSF_slip_m.</p>
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.