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Fig. 1 in A Long-Term Comparison Of Laying Date And Clutch Size In The Red-Backed Shrike (Lanius Collurio) In Silesia, Southern Poland
Fig. 1. The number of Red-backed Shrike clutches laid during successive five-day periods (1 = 6–10 May) in the two study periods. For sample size – see text
Fig. 10 in Two new species of Metacyclops Kiefer, 1927 (Copepoda, Cyclopoida) from Thailand and an up-to-date key to the species recorded in Asia
Fig. 10. Metacyclops brancelji sp. nov., paratype, ♀ (A; ZMB 34231a) and holotype, ♀ (B−D; ZMB 34231 slide No. 5124). A. Habitus, dorsal view. B. Fifth pedigerous somite and genital double-somite, lateral view. C−D. Two last abdominal somites and caudal rami, dorsal and lateral views, respectively. Scale bars: A = 100 μm; B−D = 50 μm.
Fig. 7 in Two new species of Metacyclops Kiefer, 1927 (Copepoda, Cyclopoida) from Thailand and an up-to-date key to the species recorded in Asia
Fig. 7. Metacyclops sakaeratensis sp. nov., holotype, ♀ (ZMB 34230 slide No. 5120). A. P1, frontal view. B. P2, frontal view. C. Frontal view of intercoxal sclerite of P3. D. P3 exp-1. E. P4, frontal view. Arrows indicate hook-like expansion. In C and E, the spinule row is on the caudal surface of intercoxal sclerite and coXa. Scale bar = 50 μm.
Fig. 9 in Two new species of Metacyclops Kiefer, 1927 (Copepoda, Cyclopoida) from Thailand and an up-to-date key to the species recorded in Asia
Fig. 9. Metacyclops sakaeratensis sp. nov., paratype, ♂ (A−D; ZMB 34230 slide No. 5123) and allotype, ♂ (E−G; ZMB 34230 slide No. 5121). A−D. Intercoxal sclerites of P1, P2, P3 and P4, respectively, frontal view. E−F. Right and left P5, respectively, ventral view. G. P6, lateral view. In C−D, the spinule row is on the caudal surface of intercoXal sclerite. Scale bar = 50 μm.
Fig. 12 in Two new species of Metacyclops Kiefer, 1927 (Copepoda, Cyclopoida) from Thailand and an up-to-date key to the species recorded in Asia
Fig. 12. Metacyclops brancelji sp. nov., holotype, ♀ (ZMB 34231 slide No. 5124). A. Antennule. B. Antenna, caudal view. C. Mandible. D. Maxillule, frontal view. E. Maxilla, frontal view. F. Maxilliped, frontal view. Scale bar = 50 μm.
Fig. 3 in Two new species of Metacyclops Kiefer, 1927 (Copepoda, Cyclopoida) from Thailand and an up-to-date key to the species recorded in Asia
Fig. 3. Metacyclops sakaeratensis sp. nov., holotype, ♀ (ZMB 34230 slide No. 5120). A−B. Fifth pedigerous somite and genital double-somite, ventral and lateral views, respectively. C. Caudal ramus, lateral view (arrows indicate spinules). D−E. P5, lateral and ventral views, respectively (arrows in D indicate rows of spinules on the lateral surface of the fifth pedigerous somite). Scale bars = 50 μm.
Fig. 2 in Two new species of Metacyclops Kiefer, 1927 (Copepoda, Cyclopoida) from Thailand and an up-to-date key to the species recorded in Asia
Fig. 2. Metacyclops sakaeratensis sp. nov., paratype, ♀ (A, C; ZMB 34230) and holotype, ♀ (B, D; ZMB 34230 slide No. 5120). A. Habitus, dorsal view. B. Rostrum, frontal view. C. Integumental pits and posterior margins of cephalothorax and two subsequent pedigerous somites, dorsal view. D. Urosome, dorsal view (black and open arrows indicate spinules and transverse suture, respectively). Scale bars: A, C = 100 μm; B, D = 50 μm.
Fig. 1 in Two new species of Metacyclops Kiefer, 1927 (Copepoda, Cyclopoida) from Thailand and an up-to-date key to the species recorded in Asia
Fig. 1. Geographical location and details of the sampling sites. A. Map of Thailand and a location of Nakhon Ratchasima, Satun and Songkhla Provinces. B–C. Location (indicated by a black circle with no. 1) and sampling point of headwater stream in Nakhon Ratchasima Province. D. Locations of caves in Satun and Songkhla Provinces (indicated by black circles with nos 2, 3, 4). E–F. Sampling points in Phupha Phet Cave. G–H. Sampling points in Rakhang Thong Cave and Khao Nui Cave, respectively.
Fig. 6 in Two new species of Metacyclops Kiefer, 1927 (Copepoda, Cyclopoida) from Thailand and an up-to-date key to the species recorded in Asia
Fig. 6. Metacyclops sakaeratensis sp. nov., holotype, ♀ (ZMB 34230 slide No. 5120). A−B. Right and left mandibles, respectively (the mandibular palp of the right mandible was lost during dissection). C. Maxillule, caudal view. D. Maxilla, caudal view. E. MaXilliped, frontal view. Scale bar = 50 μm.
Fig. 15 in Two new species of Metacyclops Kiefer, 1927 (Copepoda, Cyclopoida) from Thailand and an up-to-date key to the species recorded in Asia
Fig. 15. Metacyclops brancelji sp. nov., paratype, ♂ (A−D; ZMB 34231 slide No. 5127) and allotype, ♂ (E−G; ZMB 34231 slide No. 5125). A−D. Intercoxal sclerites of P1, P2, P3 and P4, respectively, frontal view. E−F. Right and left P5, respectively, ventral view. G. P6, ventral view. In C−D, the spinule row is on the caudal surface of intercoXal sclerite. Scale bar = 50 μm.
Fig. 5 in Two new species of Metacyclops Kiefer, 1927 (Copepoda, Cyclopoida) from Thailand and an up-to-date key to the species recorded in Asia
Fig. 5. Metacyclops sakaeratensis sp. nov., holotype, ♀ (A−B; ZMB 34230 slide No. 5120) and paratype, ♀ (C−D; ZMB 34230 slide No. 5122). A. Antennule (arrows indicate aesthetascs). B. Antenna, frontal surface. C. Coxobasis of antenna, caudal surface. D. Labrum, inner side. Scale bar = 50 μm.
Fig. 11 in Two new species of Metacyclops Kiefer, 1927 (Copepoda, Cyclopoida) from Thailand and an up-to-date key to the species recorded in Asia
Fig. 11. Metacyclops brancelji sp. nov., SEM photographs of additional material (Rakhang Thong Cave, Satun Province, collection of the third author CB), ♂ (A, C−E) and ♀ (B). A. Second and third pedigerous somites, lateral view (arrow indicates distal margin of third pedigerous somites). B. Genital double-somite and second abdominal somite, dorsal view (arrow indicates posterior margin of the transverse suture). C. Caudal ramus, lateral view (arrows indicate spinules). D. P5, lateral view. E. Male P6, lateral view.
Fig. 13 in Two new species of Metacyclops Kiefer, 1927 (Copepoda, Cyclopoida) from Thailand and an up-to-date key to the species recorded in Asia
Fig. 13. Metacyclops brancelji sp. nov., holotype, ♀ (ZMB 34231 slide No. 5124). A. P1, frontal view. B. P2, frontal view. C. Frontal view of intercoxal sclerite of P3. D. P4, frontal view. E−F. Right and left P5, respectively, ventral view. In C−D, the spinule row is on the caudal surface of intercoxal sclerite and coXa. Scale bars = 50 μm.
Dates and 500 hPa geopotential height of P90, P95 and P99 blocking days
<p>These .mat files contain the dates of blocking days over two domains around the Antarctic Peninsula: a domain located to the west (150-90ºW, 50-70ºW) and a domain located over and to the east of the Peninsula (90-30ºW, 50-70ºW). Extreme blocking on each domain occurs when the mean 500 hPa geopotential height, averaged over the domain, is larger than the 90% percentile. Very extreme blocking occurs when the mean 500 hPa geopotential height, averaged over the domain, is larger than the 95% and 99% percentiles.</p> <p>Variables included within each file:</p> <p>- date_500mb_p90</p> <p>- date_500mb_p95</p> <p>- date_500mb_p99</p> <p>They represent the dates of extreme and very extreme blocking on each domain</p> <p>- geo_h500mb_p90</p> <p>- geo_h500mb_p95</p> <p>- geo_h500mb_p99</p> <p>They represent the corresponding 500 hPa mean geopotential height averaged over each domain during extreme (values larger than 90% percentile) and very extreme (values larger than the 95% and 99% percentiles) blocking days.</p> <p>Also included on each file are variables:</p> <p>- date_500mb_p90_sor</p> <p>- date_500mb_p95_sor</p> <p>- date_500mb_p99_sor</p> <p>which are just the dates of extreme and very extreme blocking days sorted in ascending order.</p> <p>For more details on this dataset, see </p> <p><strong>J. C. Marín</strong>, D. Bozkurt, Barrett, B., 2022: Atmospheric blocking trends and seasonality around the Antarctic Peninsula. Accepted in Journal of Climate.</p>
Bacterial community composition of bulk soil from date palm (Phoenix dactylifera) farm depend on irrigation water salinity
<p>Non-saline and saline ground water irrigation is extensively used in the arid regions of United Arab Emirates (UAE) for date palm (<em>Phoenix</em> <em>dactylifera</em>) cultivation without knowing its effect on bulk soil bacterial communities. Bulk soil acts as a supply base for microbes and nutrients that are accessed by date palm roots. We collected soil samples from date farms across UAE and performed V3-V4 16s rRNA metabarcoding analysis to understand how bulk soil bacterial diversity and communities respond to irrigation water sources (non-saline and saline groundwater irrigation). There was no significant variation in bulk bacterial diversity (Shannon diversity, richness as well as evenness). But bulk bacterial communities differed between irrigation water sources and irrigation water electrical conductivity was the significant factor that explained a part of community variation. Out of total 5089 OTUs, saline bulk soil harbored only 21.3% of total OTUs compared to 31.5% OTUs in non-saline bulk soil, while 47.15% OTUs shared between both types of irrigation. Proteobacteria abundance was higher in saline bulk soil, while Actinobacteriota abundance was enhanced in non-saline bulk soil. Similar selection was observed at genus level, wherein saline bulk soil showed increase in abundance of <em>Subgroup_10, Nitrospira </em>and<em> Mycobacterium</em>, whereas <em>Microvirga, Ammoniphilus, Nitrospira</em> and <em>Lysinibacillus </em>were elevated in non-saline bulk soil. Saline (<em>Novibacillus</em> and <em>Bauldea</em>) and non-saline bulk soil (<em>Microvirga</em>, <em>Marmoricola</em>, <em>Domibacillus</em>, <em>Oceanobacillus</em>, <em>Bhargavaea</em> and <em>Solirubrobacter</em>) showed significant selection of indicator taxa (P < 0.05). This indicate that bacterial communities colonizing bulk soil differ depending on irrigation water source and it is affected by irrigation water EC.</p>
Data from: Skyline fossilized birth-death model is robust to violations of sampling assumptions in total-evidence dating
<p>Several total-evidence dating studies under the fossilized birth-death (FBD) model have produced very old age estimates, which are not supported by the fossil record. This phenomenon has been termed "deep root attraction (DRA)". For two specific datasets, involving divergence time estimation for the early radiations of ants, bees and wasps (Hymenoptera) and of placental mammals (Eutheria), it has been shown that the DRA effect can be greatly reduced by accommodating the fact that extant species in these trees have been sampled to maximize diversity, so called diversified sampling. Unfortunately, current methods to accommodate diversified sampling only consider the extreme case where it is possible to identify a cut-off time such that all splits occurring before this time are represented in the sampled tree but none of the younger splits. In reality, the sampling bias is rarely this extreme, and may be difficult to model properly. Similar modeling challenges apply to the sampling of the fossil record. This raises the question of whether it is possible to find dating methods that are more robust to sampling biases. Here, we show that the skyline FBD (SFBD) process, where the diversification and fossil-sampling rates can vary over time in a piecewise fashion, provides age estimates that are more robust to inadequacies in the modeling of the sampling process and less sensitive to DRA effects. In the SFBD model we consider, rates in different time intervals are either considered to be independent and identically distributed, or assumed to be autocorrelated following an Ornstein-Uhlenbeck (OU) process. Through simulations and reanalyses of the Hymenoptera and Eutheria data, we show that both variants of the SFBD model unify age estimates under random and diversified sampling assumptions. The SFBD model can resolve DRA by absorbing the deviations from the sampling assumptions into the inferred dynamics of the diversification process over time. Although this means that the inferred diversification dynamics must be interpreted with caution, taking sampling biases into account, we conclude that the SFBD model represents the most robust approach available currently for addressing DRA in total-evidence dating.</p>
Dated and Datable Manuscripts: dataset
<p>This data set encompasses 101 transcriptions of digital images of dated medieval manuscripts</p> <p>The original data set was created as part of the <a href="https://anr.fr/Project-ANR-12-CORP-0010">ANR ORIFLAMMS (ANR-12-CORP-0010)</a> project. Texts were transcribed by Irene Ceccherini in the original TEI-XML format, rendering both abbreviated and expanded forms of the original text. The transcriptions were revised at the end of the project by Dominique Stutzmann, and the alignement data was produced by merging coordinates created through the Oriflamms software and coordinates produced by A2IA for words, and corrected at word level by Dominique Stutzmann.</p> <p> A new version was prepared in March 2022 as part of the research for a joint paper on HTR diversity for the<br> DH 2022 conference (Tokyo). In particular, (1) the coordinates of lines were corrected through a complete new layout segmetation with the Transkribus software; (2) several ALTO files were generated with different versions of the edited text (normalized or not normalized / abbreviations expanded or not).<br> <br> <strong>Folders</strong><br> The present data set gathers different folders with different types of information.<br> The folder schema and file format used in the ORIFLAMMS is described in:</p> <ul> <li>Consortium Oriflamms. « Spécification du format XML-TEI pour l’alignement texte-image. 1. Structure et convention de nommage ». *Écriture médiévale & numérique*, 11 Sept. 2016. [<a href="http://oriflamms.hypotheses.org/1442">http://oriflamms.hypotheses.org/1442</a>].</li> <li>Consortium Oriflamms. « Spécification du format XML-TEI pour l’alignement texte-image. 2. Bonnes pratiques d’encodage ». *Écriture médiévale & numérique*, 12 Sept. 2016. [<a href="http://oriflamms.hypotheses.org/1510">http://oriflamms.hypotheses.org/1510</a>].</li> </ul> <p><br> <strong>img</strong><br> Folder with 101 images.<br> These images are scans of actual printed photographs at scale. The source of the photograph, i.e. the shelfmark<br> of the medieval manuscript and the folio number, is handwritten on the picture. It is also formalized as TEI <msIdentifier/> element in the files of the /texts/ folder.<br> These images are also integrated in the <a href="https://bvmm.irht.cnrs.fr/">BVMM (Bibliothèque Virtuelle des Manuscrits Médiévaux)</a> as IIIF compliant images.</p> <p><strong>texts</strong><br> Original TEI-XML edition with identifiers for all paragraphs, lines, words in the `texts/mss-dates-w.xml` file, and also for characters in the `mss-dates-c.xml` file.<br> The additional file named `texts/mss-dates-w-merged.xml` does not correspond to the ORIFLAMMS specification. It is a XML-TEI file with the same structure as `mss-dates-w.xml` but with following additions:</p> <ol> <li>the zones coordinates are integrated in a `<facsimile/>` element within each concerned `<TEI/>` element;</li> <li>the `@xml:id` attributes within `<milestone/>` elements are renamed to avoid multiple occurrences;</li> <li>he `<lb/>` and `<w/>` elements are enhanced with a `@facs` attribute pointing to the corresponding `<zone/>` element;</li> <li>the `<w/>` elements are enhanced with a `@corresp` attribute containing the string value of the word without expansion nor normalization.</li> </ol> <p><strong>/zones/, /img_links/</strong><br> zones described as coordinates on the images (/img/ folder) and files linking between the edition in /texts/ folder and coordinates in the /zones/ folder.</p> <p><strong>/ontologies/, /ontologies_link/, /oriflamms/</strong><br> Here, folders are present, but the data is not created.</p> <p><strong>/alto/</strong><br> ALTO files were created from the preexisting TEI files and combine the coordinates and the text in single files where the text is flat and rendered at a line level, with/without normalization and with/without abbrevations.</p>
Tracing Maize History in Northern Iroquoia through Radiocarbon Date Summed Probability Distributions Data
<p>These files contain the data used in the radiocarbon summed probability distribution and complementary analyses to create a history of maize (<em>Zea mays</em> ssp. <em>mays</em>) in Northern Iroquoia. Results piublished in:</p> <p>Hart, John P.. "Tracing Maize History in Northern Iroquoia Through Radiocarbon Date Summed Probability Distributions" <em>Open Archaeology</em>, vol. 8, no. 1, 2022, pp. 594-607. <a href="https://doi.org/10.1515/opar-2022-0256">https://doi.org/10.1515/opar-2022-0256</a></p> <p> </p>
DateLife: leveraging databases and analytical tools to reveal the dated Tree of Life
<p>Achieving a high-quality reconstruction of a phylogenetic tree with branch lengths proportional to absolute time (chronogram) is a difficult and time-consuming task. But the increased availability of fossil and molecular data, and time-efficient analytical techniques has resulted in many recent publications of large chronograms for a large number and wide diversity of organisms. Knowledge of the evolutionary time frame of organisms is key for research in the natural sciences. It also represent valuable information for education, science communication, and policy decisions. When chronograms are shared in public, open databases, this wealth of expertly-curated and peer-reviewed data on evolutionary timeframe is exposed in a programatic and reusable way, as intensive and localized efforts have improved data sharing practices, as well as incentivizited open science in biology. Here we present DateLife, a service implemented as an R package and an R Shiny website application available at www.datelife.org, that provides functionalities for efficient and easy finding, summary, reuse, and reanalysis of expert, peer-reviewed, public data on time frame of evolution. The main DateLife workflow constructs a chronogram for any given combination of taxon names by searching a local chronogram database constructed and curated from the Open Tree of Life Phylesystem phylogenetic database, which incorporates phylogenetic data from the TreeBASE database as well. We implement and test methods for summarizing time data from multiple source chronograms using supertree and congruification algorithms, and using age data extracted from source chronograms as secondary calibration points to add branch lengths proportional to absolute time to a tree topology. DateLife will be useful to increase awareness of the existing variation in alternative hypothesis of evolutionary time for the same organisms, and can foster exploration of the effect of alternative evolutionary timing hypotheses on the results of downstream analyses, providing a framework for a more informed interpretation of evolutionary results.</p>
Text-fig. 4. Porechye open pit coal mine. a: photography of the Lipovtsy Formation section; b: stratigraphic column, 1 – sandstone, 2 – conglomerate, 3 – coal, 4 – tuff dated by U-Th-Pb geochronology, 5 – siltstone, 6 – mudstone, 7 – palynological samples with angiosperm pollen, 8 – dispersed angiosperm cuticles. in Angiosperm Diversification In The Early Cretaceous Of Primorye, Far East Of Russia
Text-fig. 4. Porechye open pit coal mine. a: photography of the Lipovtsy Formation section; b: stratigraphic column, 1 – sandstone, 2 – conglomerate, 3 – coal, 4 – tuff dated by U-Th-Pb geochronology, 5 – siltstone, 6 – mudstone, 7 – palynological samples with angiosperm pollen, 8 – dispersed angiosperm cuticles.
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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.