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Quantification of faecal glucocorticoid metabolites as a measure of stress in the rock hyrax (Procavia capensis) living in an urban green space
<p>Despite the abundance of rock hyrax (<i>Procavia capensis</i>) within South Africa's urban areas, there is not much information available about the effect of anthropogenic activities on rock hyrax wellbeing. To determine the potential impact of anthropogenic disturbance on adrenocortical activity, we conducted an ACTH challenge to identify a suitable enzyme-immunoassay (EIA) for measuring faecal glucocorticoid metabolite (fGCM) concentrations in the rock hyrax. This study identified an 11β-hydroxyaetiocholanolone EIA as the most suitable assay in this regard. The fGCM levels measured, indicate the physiological stress response in different rock hyrax populations, living in an area with varying degrees of anthropogenic activity (low, medium, high) within the National Botanical Garden of Pretoria, South Africa. The species' habituation to human numbers <span>(weekly mean number of people</span>) was examined by determining individual flight initiation distance (FID). Seasonally, there were overall higher fGCM concentrations in late spring compared to winter. The fGCM concentrations, although not significantly different but possibly biologically relevant, in the section with the lowest anthropogenic disturbance were ~10% higher compared to those in the section with medium disturbance, and ~20% higher compared to those in the section with the highest disturbance. Animal FID did not differ significantly between seasons but they did differ significantly between sections, and decreased in accordance with fGCM concentrations. The non-invasive approach established in this study provides a foundation for assessing rock hyrax wellbeing, and can help better understand how anthropogenic presence is perceived as a stressor in this species.</p>
Determining the efficacy of camera traps, live capture traps, and detection dogs for locating cryptic small mammal species
<p>Metal box (e.g., Elliott, Sherman) traps and remote cameras are two of the most commonly employed methods presently used to survey terrestrial mammals. However, their relative efficacy at accurately detecting cryptic small mammals has not been adequately assessed. The present study therefore compared the effectiveness of metal box (Elliott) traps and vertically oriented, close range, white flash camera traps in detecting small mammals occurring in the Scenic Rim of eastern Australia. We also conducted a preliminary survey to determine effectiveness of a conservation detection dog (CDD) for identifying presence of a threatened carnivorous marsupial, <i>Antechinus arktos,</i> in present-day and historical locations, using camera traps to corroborate detections. 200 Elliott traps and 20 white flash camera traps were set for four deployments per method, across a site where the target small mammals, including <i>A. arktos</i>, are known to occur. Camera traps produced higher detection probabilities than Elliott traps for all four species. Thus, vertically mounted white flash cameras were preferable for detecting the presence of cryptic small mammals in our survey. The CDD, which had been trained to detect <i>A. arktos</i> scat, indicated in total 31 times when deployed in the field survey area, with subsequent camera trap deployments specifically corroborating <i>A. arktos</i> presence at 100% (3) indication locations. Importantly, the dog indicated twice within Border Ranges National Park, where historical (1980s-1990s) specimen-based records indicate the species was present, but extensive Elliott and camera trapping over the last 5-10 years have resulted in zero <i>A. arktos</i> captures. Camera traps subsequently corroborated <i>A. arktos</i> presence at these sites. This demonstrates that detection dogs can be a highly effective means of locating threatened, cryptic species, especially when traditional methods are unable to detect low-density mammal populations.</p>
FIGURE. In situ photos of Paphiopedilum charlesworthii var. lannaense. A. limestone mountain at 1,100–1,200 m elevation, B. P. charlesworthii var. lannaense living on vertical cliffs of limestone, C. P. charlesworthii var. lannaense plant, D. flowering plant with flower bud, E., F. flowering plant (flower color was faded because these photos were taken toward the end of flowering period) (photo. By S. Somboonphon) in Paphiopedilum charlesworthii var. lannaense, a new slipper orchid from Northern Thailand identified by morphological and AFLP analyses
FIGURE. In situ photos of Paphiopedilum charlesworthii var. lannaense. A. limestone mountain at 1,100–1,200 m elevation, B. P. charlesworthii var. lannaense living on vertical cliffs of limestone, C. P. charlesworthii var. lannaense plant, D. flowering plant with flower bud, E., F. flowering plant (flower color was faded because these photos were taken toward the end of flowering period) (photo. By S. Somboonphon)
Data for: Telomere length is highly repeatable and shorter in individuals with more elaborate sexual ornamentation in a short-lived passerine
<p>Quantifying an individual's state as fitness proxy has proven challenging, but accumulating evidence suggests that telomere length and attrition may indicate individual somatic state and success at self-maintenance, respectively. Sexual ornamentation is also thought to signal phenotypic quality, but links between telomeres and sexual ornamentation have been little explored. To address this issue, we examined whether telomere length and dynamics are predicted by the expression of a sexually selected ornament, the length of the outermost tail feathers (streamers), using longitudinal data from a population of European barn swallows (Hirundo rustica). In 139 adult individuals, each measured twice, we further assessed associations of telomere length with age, sex, breeding status and survival. Telomere length showed high individual repeatability (R = 0.97) across years while shortening with age in both sexes. Telomere length and dynamics were not significantly associated with survival to the next year, remaining lifespan, or reproduction status (comparing breeding and non-breeding yearlings). Tail streamer length, a sexually selected trait in barn swallows, was negatively associated with telomere length, independent of sex. Thus, telomere length may reflect the costs of carrying an elaborated sexual ornament, although ornament size did not significantly predict telomere shortening. In conclusion, telomere length in adult barn swallows is a highly consistent trait that shows a negative relationship with sexual ornamentation, suggesting a trade-off between sexual ornamentation and telomere length.</p>
◂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
Signature of long-lived memory CD8+ T cells in acute SARS-CoV-2 infection
<p>The datasets uploaded in this Zenodo entry were generated in the single cell RNA sequencing part of the project.</p> <p>For the scRNAseq analysis, cells from ten patients and the same time point were pooled together, generating four individual sample sets in total: (1) patients CoV2_T001- CoV2_T010, acute; (2) patients CoV2_T001- CoV2_T010, six months post-infection; (3) patients CoV2_T011- CoV2_T020, acute; (4) patients CoV2_T011- CoV2_T011-20, six months post-infection.</p> <p>We additionally generated two more sample sets: using 5000 unsorted PBMCs from each patient’s sample: (5) patients CoV2_T001- CoV2_T010, six months post-infection unsorted; (6) patients CoV2_T011- CoV2_T020, six months post-infection unsorted. The cells in these two sample sets were hashed.</p> <p>Finally, using PBMCs from four healthy donors, we generated sample set (7) by sorting and pooling 2000 CD8+ T cells from each healthy donor sample.</p> <p>We are here providing the pre-processed sets for each sample set (1-7), i.e. :<br> - "filtered feature bc matrix" files, as output from the ‘cellranger multi’ pipeline (Cell Ranger version 5.0.0), containing cell-RNA count matrices and cell-ADT matrices. ADTs comprise counts for TotalSeq antibodies and dCODE Dextramers.<br> - "filtered_contig_annotations.csv" files, as output from the ‘cellranger multi’ pipeline (Cell Ranger version 5.0.0), containing High-level annotations of each high-confidence, cellular contig for TCR clonal analysis. This file is not present for sets 5 and 6, because we did not perform TCR profiling for these samples.<br> - "clusters.tsv" files, as output from the souporcell SNP analysis (version 2). To cluster cells based on their patient specific genetic variants, we merged sample sets 1, 2 and 5 (comprising sorted cells from both time points of patients CoV2_T001- CoV2_T010 and unsorted cells of the same patients) and sets 3, 4 and 6 (comprising cells from both time points of patients CoV2_T011- CoV2_T020 and unsorted cells of the same patients). Then, we executed the souporcell pipeline with option <em>k=10 </em>(number of clusters to be determined) for each of the two merged sample sets.</p> <p>Together, these files allow to reproduce the analysis as reported in the paper.</p> <p>Additionally, we provide the Seurat Objects "Integrated.h5seurat" and "Integrated_NA_filtered.h5seurat" which can be used to skip the pre-processing steps of the data analysis. See the code provided on https://github.com/Moors-Code/SARS-CoV-2-Tcell-Boyman-collaboration for details.</p> <p> </p>
FIGURES 342–344. Amazonius elenae living. 342 in Taxonomic revision and cladistic analysis of the tarantula genera Tapinauchenius Ausserer, 1871, Psalmopoeus Pocock, 1985, and Amazonius n. gen. (Theraphosidae, Psalmopoeinae)
FIGURES 342–344. Amazonius elenae living. 342, female from Brazil, state of Acre, Senador Guiomard. 343, female from Peru, Loreto, Rio Momom, eating a Norops ortonii lizard. 344, male from Brazil, state of Acre, Cruzeiro do Sul. Photos: 342, Rogério Bertani; 343, Rick C. West; 344, Saymon Albuquerque.
FIGURES 288–292. Psalmopoeus irminia, living. 288 in Taxonomic revision and cladistic analysis of the tarantula genera Tapinauchenius Ausserer, 1871, Psalmopoeus Pocock, 1985, and Amazonius n. gen. (Theraphosidae, Psalmopoeinae)
FIGURES 288–292. Psalmopoeus irminia, living. 288, female from Venezuela, Amazonas, Cejal. 289, male from same locality. 290, female retreat, in cavity of a 10 cm living vine, same locality. 291, female from Brazil, state of Roraima, Amajari, Tepequém. 292, immature from pet trade. Photos: 288–290 Rick C. West, 291–292 Rogério Bertani.
FIGURES 305–306. Psalmopoeus langenbucheri, living. 305 in Taxonomic revision and cladistic analysis of the tarantula genera Tapinauchenius Ausserer, 1871, Psalmopoeus Pocock, 1985, and Amazonius n. gen. (Theraphosidae, Psalmopoeinae)
FIGURES 305–306. Psalmopoeus langenbucheri, living. 305, female from Venezuela, Aragua, Pittier National Park. 306, male from same locality. Photos: Rick C. West.
FIGURES 272–275. Psalmopoeus pulcher, living. 272 in Taxonomic revision and cladistic analysis of the tarantula genera Tapinauchenius Ausserer, 1871, Psalmopoeus Pocock, 1985, and Amazonius n. gen. (Theraphosidae, Psalmopoeinae)
FIGURES 272–275. Psalmopoeus pulcher, living. 272, female from Panama, Gamboa. 273, male from same locality. 274, subadult female, same locality. 275, immature from pet trade. Photos: 272–274 Rick C. West, 275 Rogério Bertani.
FIGURES 177–182. Psalmopoeus cambridgei, living. 177 in Taxonomic revision and cladistic analysis of the tarantula genera Tapinauchenius Ausserer, 1871, Psalmopoeus Pocock, 1985, and Amazonius n. gen. (Theraphosidae, Psalmopoeinae)
FIGURES 177–182. Psalmopoeus cambridgei, living. 177, female from Trinidad island, Arima. 178, male from same locality. 179, immature from pet trade. 180, female from Tobago Island, speyside. 181, female retreat in a fallen log, Trinidad Island, Arima. 182, same, opened with specimen inside. Photos: 177–178, 180–182 Rick C. West, 179 Leandro M. Borges.
FIGURES 58–62. Tapinauchenius plumipes, living. 58 in Taxonomic revision and cladistic analysis of the tarantula genera Tapinauchenius Ausserer, 1871, Psalmopoeus Pocock, 1985, and Amazonius n. gen. (Theraphosidae, Psalmopoeinae)
FIGURES 58–62. Tapinauchenius plumipes, living. 58, male from French Guiana, Montsinery-Tonnegrande. 59, female from same locality. (60–61) females from Brazil, Amazonas, Novo Airão, 61, in the wild, under a palm leaf retreat. 62, male from Brazil, Amazonas, Iranduba. Photos: 58, 59 Rick C. West, 60–62 Rogério Bertani.
FIGURE 8. Scolopsis curite, live individuals. A in The taxonomic identity of the monocle bream Scolopsis vosmeri species complex (Perciformes: Nemipteridae), with comments on molecular phylogenetic relationships within the genus Scolopsis
FIGURE 8. Scolopsis curite, live individuals. A: south-western Madagascar; B: Alameh, Socotra. Photos by G.R. Allen (A), S.V. Bogorodsky (B).
FIGURE 1. Scolopsis vosmeri, live individuals. A in The taxonomic identity of the monocle bream Scolopsis vosmeri species complex (Perciformes: Nemipteridae), with comments on molecular phylogenetic relationships within the genus Scolopsis
FIGURE 1. Scolopsis vosmeri, live individuals. A: Brunei; B: Sri Lanka; C: eastern Thailand. Photos by G.R. Allen (A & C), J.E. Randall (B).
The living heart: climate gradients predict desert mountain endemism
<p>Mountain regions are centres of biodiversity endemism at a global scale but the role of arid- zone mountain ranges in shaping biodiversity patterns is poorly understood. Focusing on three guilds of taxa from a desert upland refugium in Australia, we sought to determine: 1) the relative extent to which climate, terrain or geological substrate predict endemism, and 2) whether patterns of endemism are complimentary across broad taxonomic guilds. We mapped regional endemism for plants, land snails and vertebrates using combined Species Distribution Models (SDMs) for all endemic taxa (n=82). We then modelled predictors of endemism using Generalised Additive Models (GAMs) and geology, terrain and climate variables. We tested for the presence of inter- and intraguild hotspots of endemism. Many individual plant and land snail taxa were tightly linked with geology, corresponding to small distributions. Conversely, most vertebrate taxa were not constrained to specific geological substrates and occurred over larger areas. However, across all three guilds, climate was the strongest predictor of regional endemism, particularly for plants wherein discrete hotspots of endemism were buffered from extreme summer temperatures. Land snail and vertebrate endemism peaked in areas with the highest precipitation in the driest times of the year. Hotspots of endemism within each guild poorly predicted endemism in other guilds. We found an overarching signal that climatic gradients play a dominant role in the persistence of endemic taxa in an arid-zone mountain range system. An association with higher rainfall and cooler temperatures indicates that continuing trends towards hotter and drier climates may lead to range contractions in this, and potentially other, arid-zone mountain biotas. Contrasting patterns of endemism across guilds highlight the need to couple comprehensive regional planning for the protection of climate refugia, with targeted management of more localised and habitat specialist taxa.</p>
FIGURE 2. Living Trigonidiinae spp. A in New and little-known mute Trigonidiinae species from China (Orthoptera: Grylloidea: Trigonidiidae)
FIGURE 2. Living Trigonidiinae spp. A. Amusurgus (Usgmona) genji, B. Amusurgus (Amusurgus) fulvus, C. Amusurgus (Amusurgus) bispinosus, D. Metiochodes minor, E. Zilingxi danmai He sp. nov. a, male; b, female (photos by He Zhu-Qing).
FIGURE 8 in Leaf venation of living species of Persea (Lauraceae), with taxonomic and nomenclatural notes
FIGURE 8. Photomicrographs of Persea leaves. A. P. alba Nees & Mart. (Schwacke 5779). B. P. albida Kosterm. (House 1057). C. P. americana Mill. (Mori 10269). D. P. areolatocostae (C.K.Allen) van der Werff (Monteagudo 4714). E. P. aurata Miq. (Blanchet 3566). F. P. aurata Miq. (Gardner 4358). G. P. aurata Miq. (Pohl 2884). H. P. benthamiana Meisn. (Spruce 2766). I. P. borbonia (L.) Spreng. (Jones 23939). J. P. buchtienii O.C.Schmidt (Nee 42046). K. P. caerulea (Ruiz & Pav.) Mez (Ferrer-Pereira 699). L. P. caerulea (Ruiz & Pav.) Mez (Nee 42084). M. P. caerulea (Ruiz & Pav.) Mez (van der Werff 9473). N. P. caesia Meisn. (Moraes 4215). O. P. chamissonis Mez (García-Mendoza 1850). P. P. chrysophylla L.E.Kopp (Soejarto 3057). Q. P. croizatii van der Werff (Almeida 624). R. P. cuneata Meisn. (Escobar 7182). S. P. donnell-smithii Mez (Tenorio L. 14894). T. P. fastigiata L.E.Kopp (Maguire 36958). U. P. ferruginea Kunth (McPherson 13173). V. P. fuliginosa Nees & Mart. (Sellow 4313). W. P. fulva L.E.Kopp (Claussen 132). X. P. fulva L.E.Kopp (Glaziou 14203). Y. P. fulva L.E.Kopp (Harley 27826). Z. P. fulva L.E.Kopp (Warming s.n.). A'. P. fusca Mez (Glaziou 22068). B'. P. fusca Mez (Glaziou 22069). Bars = 250 μm.
FIGURE 7. X in Leaf venation of living species of Persea (Lauraceae), with taxonomic and nomenclatural notes
FIGURE 7. X-ray images (close-up) of the leaf venation of Persea. A. P. pumila P.L.R.Moraes & R.S.Pacheco (Moraes 3572). B. P. punctata Meisn. (Lund s.n.). C. P. rigida Nees & Mart. (Sellow 652). D. P. rufotomentosa Nees & Mart. (Moraes 3592). E. P. ruizii J.F.Macbr. (Solomon 15364). F. P. schiedeana Nees (Hammel 6966). G. P. sericea Kunth (Harling 23755). H. P. venosa Nees & Mart. (Herbarium Lusitanicum). I. P. venosa Nees & Mart. (Falkenberg 2971). J. P. veraguasensis Seem. (Davidse 24628). K. P. vesticula Standl. & Steyerm. (Hawkins 450). L. P. willdenovii Kosterm. (Sellow 5230 = H.I.B. 134). Bars = 5 mm.
FIGURE 12 in Leaf venation of living species of Persea (Lauraceae), with taxonomic and nomenclatural notes
FIGURE 12. Leaf venation of Caryodaphnopsis inaequalis (A.C.Sm.) van der Werff & H.G.Richt. A, D, G. Krukoff 4770. Machilus japonica Siebold & Zucc. ex Blume. B, E, H. Takagi 6. Machilus thunbergii Siebold & Zucc. C, F, I. Takagi 17. Bars: 1 cm (A–C), 5 mm (D–F), 250 μm (G–I).
FIGURE 9 in Leaf venation of living species of Persea (Lauraceae), with taxonomic and nomenclatural notes
FIGURE 9. Photomicrographs of Persea leaves. A. P. glabra van der Werff (Fróes 20022). B. P. glabra van der Werff (Harley 27205). C. P. glabra van der Werff (Moraes 2585). D. P. haenkeana Mez (Solomon 9293). E. P. humilis Nash (Kral 48093). F. P. hypoleuca (A.Rich.) Mez (Linden 1773). G. P. jariensis Vattimo-Gil (Silva 5395). H. P. jenmanii Mez (Steyermark 120). I. P. julianae van der Werff (Holmgren 54397). J. P. liebmannii Mez (Tenorio L. 6241). K. P. lingue Nees (Gay s.n.). L. P. longipes (Schltdl.) Meisn. (Schiede 59). M. P. meridensis L.E.Kopp (Marcano Berti 1730). N. P. meziana Rasingam & Karthig. (Santos Lima 342). O. P. meziana Rasingam & Karthig. (Moraes 5185). P. P. meziana Rasingam & Karthig. (Pereira 9869). Q. P. oblongifolia L.E.Kopp (Liogier 11380). R. P. obovata Nees & Mart. (Garcia 902). S. P. palustris (Raf.) Sarg. (Hansen 9993). T. P. pedunculosa Meisn. (Claussen 1774). U. P. perseiphylla (C.K.Allen) van der Werff (Boom 5743). V. P. peruviana Nees (Bernardi 16235). W. P. peruviana Nees (Spichiger 4749). X. P. povedae W.C.Burger (Herrera Ch. 435). Y. P. psammophila P.L.R.Moraes (Moraes 5358). Z. P. pseudofasciculata L.E.Kopp (Krukoff 11283). A'. P. pseudofasciculata L.E.Kopp (Krukoff 7080). B'. P. pumila P.L.R.Moraes & R.S.Pacheco (Moraes 3572). Bars = 250 μm.
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.