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Supplementary material 1 from: Yang L-L, Li H-H (2021) First report of the genus Pelecystola Meyrick (Lepidoptera, Tineidae) in China, with description of a new species. ZooKeys 1046: 189-206. https://doi.org/10.3897/zookeys.1046.68329
Table S1. Specimen data and GenBank accessions
Data from: Reporting tumor molecular heterogeneity in histopathological diagnosis
Background: Detection of molecular tumor heterogeneity has become of paramount importance with the advent of targeted therapies. Analysis for detection should be comprehensive, timely and based on routinely available tumor samples. Aim: To evaluate the diagnostic potential of targeted multigene next-generation sequencing (TM-NGS) in characterizing gastrointestinal cancer molecular heterogeneity. Methods: 35 gastrointestinal tract tumors, five of each intestinal type gastric carcinomas, pancreatic ductal adenocarcinomas, pancreatic intraductal papillary mucinous neoplasms, ampulla of Vater carcinomas, hepatocellular carcinomas, cholangiocarcinomas, pancreatic solid pseudopapillary tumors were assessed for mutations in 46 cancer-associated genes, using Ion Torrent semiconductor-based TM-NGS. One ampulla of Vater carcinoma cell line and one hepatic carcinosarcoma served to assess assay sensitivity. TP53, PIK3CA, KRAS, and BRAF mutations were validated by conventional Sanger sequencing. Results: TM-NGS yielded overlapping results on matched fresh-frozen and formalin-fixed paraffin-embedded (FFPE) tissues, with a mutation detection limit of 1% for fresh-frozen high molecular weight DNA and 2% for FFPE partially degraded DNA. At least one somatic mutation was observed in all tumors tested; multiple alterations were detected in 20/35 (57%) tumors. Seven cancers displayed significant differences in allelic frequencies for distinct mutations, indicating the presence of intratumor molecular heterogeneity; this was confirmed on selected samples by immunohistochemistry of p53 and Smad4, showing concordance with mutational analysis. Conclusions: TM-NGS is able to detect and quantitate multiple gene alterations from limited amounts of DNA, moving one step closer to a next-generation histopathologic diagnosis that integrates morphologic, immunophenotypic, and multigene mutational analysis on routinely processed tissues, essential for personalized cancer therapy.
FIGURES 5–7 Paracrias huberi 5 in Report of a novel biological association for Paracrias huberi Gumovsky (Hymenoptera: Eulophidae) with redescription of the female and description of the unknown male
FIGURES 5–7 Paracrias huberi 5. ♀ mesosoma, dorsal. 6. ♀ mesosoma, lateral. 7. ♂ mesosoma, dorsal.
Report HTA Mitrale PASCAL ACE
<p>Report HTA Mitrale PASCAL ACE</p> <p> </p>
REPORT HTA PASCAL ACE TRICUSPIDE
<p>REPORT HTA PASCAL ACE TRICUSPIDE</p>
Data from: Lack of activity of recombinant HIF prolyl hydroxylases (PHDs) on reported non-HIF substrates
Human and other animal cells deploy three closely related dioxygenases (PHD 1, 2 and 3) to signal oxygen levels by catalysing oxygen regulated prolyl hydroxylation of the transcription factor HIF. The discovery of the HIF prolyl-hydroxylase (PHD) enzymes as oxygen sensors raises a key question as to the existence and nature of non-HIF substrates, potentially transducing other biological responses to hypoxia. Over 20 such substrates are reported. We therefore sought to characterise their reactivity with recombinant PHD enzymes. Unexpectedly, we did not detect prolyl-hydroxylase activity on any reported non-HIF protein or peptide, using conditions supporting robust HIF-α hydroxylation. We cannot exclude PHD-catalysed prolyl hydroxylation occurring under conditions other than those we have examined. However, our findings using recombinant enzymes provide no support for the wide range of non-HIF PHD substrates that have been reported.
SimPhy configuration scripts for simulations reported in the study titled: Species tree inference methods intended to deal with incomplete lineage sorting are robust to the presence of paralogs
<p>Many recent phylogenetic methods have focused on accurately inferring species trees when there is gene tree discordance due to incomplete lineage sorting (ILS). For almost all of these methods, and for phylogenetic methods in general, the data for each locus is assumed to consist of orthologous, single-copy sequences. Loci that are present in more than a single copy in any of the studied genomes are excluded from the data. These steps greatly reduce the number of loci available for analysis. The question we seek to answer in this study is: What happens if one runs such species tree inference methods on data where paralogy is present, in addition to or without ILS being present? Through simulation studies and analyses of two large biological data sets, we show that running such methods on data with paralogs can still provide accurate results. We use multiple different methods, some of which are based directly on the multispecies coalescent (MSC) model, and some of which have been proven to be statistically consistent under it. We also treat the paralogous loci in multiple ways: from explicitly denoting them as paralogs, to randomly selecting one copy per species. In all cases the inferred species trees are as accurate as equivalent analyses using single-copy orthologs. Our results have significant implications for the use of ILS-aware phylogenomic analyses, demonstrating that they do not have to be restricted to single-copy loci. This will greatly increase the amount of data that can be used for phylogenetic inference.</p>
AI results complementing the 2020 Annual Report on surveillance for Avian Influenza in poultry and wild birds in Member States of the European Union - Luxembourg
<p>This dataset contains the results of the EU co-funded surveillance activities conducted in 2020, which consisted of:</p> <ul> <li>Serological surveys to monitor the circulation of AIV subtypes H5 and H7 in poultry (active surveillance). These surveys should preferentially target poultry species or production systems with increased risk for introduction of avian influenza (AI).</li> <li>Passive surveillance aiming at the virological detection of AI in wild birds found dead or moribund.</li> </ul>
Supplementary material 1 from: Bradshaw CJA, Hoskins AJ, Haubrock PJ, Cuthbert RN, Diagne C, Leroy B, Andrews L, Page B, Cassey P, Sheppard AW, Courchamp F (2021) Detailed assessment of the reported economic costs of invasive species in Australia. In: Zenni RD, McDermott S, García-Berthou E, Essl F (Eds) The economic costs of biological invasions around the world. NeoBiota 67: 511-550. https://doi.org/10.3897/neobiota.67.58834
Figures S1–S3 and Table S1
Figure 6 from: Pohjoismäki J, Bergström C (2021) Review of the Nordic Gymnocheta Robineau-Desvoidy (Diptera, Tachinidae) with report of two species new to Europe. ZooKeys 1053: 145-184. https://doi.org/10.3897/zookeys.1053.52761
Figure 6 Comparison of Gymnocheta spp. female sternites and terminalia A ventral view of the sternites and terminalia of iG. lucidaiiG. magnaiiiG. viridis and ivG. zhelochovtseviB detail of the female terminalia of iG. lucidaiiG. magnaiiiG. viridis and ivG. zhelochovtsevi. Note the long cerci in G. zhelochovtsevi. All photographs by J. Pohjoismäki.
Figure 2 from: Pohjoismäki J, Bergström C (2021) Review of the Nordic Gymnocheta Robineau-Desvoidy (Diptera, Tachinidae) with report of two species new to Europe. ZooKeys 1053: 145-184. https://doi.org/10.3897/zookeys.1053.52761
Figure 2 Gymnocheta spp. male heads in lateral (upper panels) and dorsal (lower panels) view AGymnocheta lucida Zimin BG. magna Zimin CG. viridis (Fallén) DG. zhelochovtsevi Zimin. Note the wide frons and strong outer vertical bristles. Scale bars: 1 mm. All photographs by Göran Liljeberg.
Figure 5 from: Pohjoismäki J, Bergström C (2021) Review of the Nordic Gymnocheta Robineau-Desvoidy (Diptera, Tachinidae) with report of two species new to Europe. ZooKeys 1053: 145-184. https://doi.org/10.3897/zookeys.1053.52761
Figure 5 Comparison of Gymnocheta spp. male terminalia A lateral view of the terminalia: iG. lucidaiiG. magnaiiiG. viridis and ivG. zhelochovtsevi – note the apical hook of the syncercus B dorsal view of the terminalia: iG. lucidaiiG. magnaiiiG. viridis and ivG. zhelochovtsevi, same specimen as in Fig. 4CC aedeagus and gonites of iG. lucidaiiG. magnaiiiG. viridis and ivG. zhelochovtsevi. Abbreviations: bph–basiphallus; dph–distiphallus; prg–pregonite; pog–postgonite. All photographs by J. Pohjoismäki.
Figure 1 from: Pohjoismäki J, Bergström C (2021) Review of the Nordic Gymnocheta Robineau-Desvoidy (Diptera, Tachinidae) with report of two species new to Europe. ZooKeys 1053: 145-184. https://doi.org/10.3897/zookeys.1053.52761
Figure 1 Gymnocheta spp. habitus A habitus Gymnocheta viridis ♂ B–ETachina viridis Fallén, holotype specimen B dorsal view C head in lateral view. Note the protruding lower facial margin (arrowhead) D detail of the right wing edge. Note the reduced costal spine (arrowhead) E sternite 5 of the holotype F labels associated with the holotype. All photographs by Göran Liljeberg.
Figure 3 from: Pohjoismäki J, Bergström C (2021) Review of the Nordic Gymnocheta Robineau-Desvoidy (Diptera, Tachinidae) with report of two species new to Europe. ZooKeys 1053: 145-184. https://doi.org/10.3897/zookeys.1053.52761
Figure 3 Gymnocheta spp. female heads in lateral (upper panels) and dorsal (lower panels) view AGymnocheta lucida Zimin BG. magna Zimin CG. viridis (Fallén) DG. zhelochovtsevi Zimin. Scale bars: 1 mm. All photographs by Göran Liljeberg.
Figure 4 from: Pohjoismäki J, Bergström C (2021) Review of the Nordic Gymnocheta Robineau-Desvoidy (Diptera, Tachinidae) with report of two species new to Europe. ZooKeys 1053: 145-184. https://doi.org/10.3897/zookeys.1053.52761
Figure 4 Fifth sternites of Gymnocheta spp. males AGymnocheta lucida male abdomen. Note the narrow profile of the posterior edge of the fifth sternite (arrow) B the edge of the fifth sternite in G. viridis is bulky and protruding beyond the tip of the abdomen, clearly recognisable from the side C the posterolateral lobe of G. zhelochovtsevi is somewhat subrectangular as in G. magna, but more rounded in profile. Note the apical hook of the syncercus D in contrast to G. zhelochovtsevi, posterior edge of fifth sternite in G. porphyrophora with well-developed median lobes (arrow) E dissected fifth sternites of Nordic Gymnocheta spp. in comparison: i) G. lucida, ii) G. magna, iii) G. viridis and iv) G. zhelochovtsevi. A distinct dorsomedial process present in G. magna and G. viridis Abbreviations: bpl–basal plate; dmp–dorsomedial process; mcl–median cleft; pll–posterolateral lobe; tms–transversal median stripe; wll–wart-like lobe (or median lobe). Photograph D by V. Neimorovets, rest by J. Pohjoismäki.
Figure 7 from: Pohjoismäki J, Bergström C (2021) Review of the Nordic Gymnocheta Robineau-Desvoidy (Diptera, Tachinidae) with report of two species new to Europe. ZooKeys 1053: 145-184. https://doi.org/10.3897/zookeys.1053.52761
Figure 7 Maximum likelihood tree of the Co1 sequences of the Nordic Gymnocheta spp. and related Ernestiini. Numbers at nodes indicate posterior probabilities and scale bar the relative sequence divergence. BOLD progress ID given before the species name and sample ID as well as GenBank access number given after it. The DNA barcodes do not differ between the Nordic G. zhelochovtsevi and G. viridis (BOLD:ACA6555) but differ significantly from G. lucida (BOLD:ACF3891) and G. magna (BOLD:ACA9848).
Figure 14 in The family Leucospidae (Hymenoptera: Chalcidoidea) from the South of Saudi Arabia, with the first report of the genus Micrapion and description of Leucospis arabica sp. nov.
Figure 14. Distribution map of leucospid species in Saudi Arabia and S. Sinai (Egypt).
MagNetUS 2021 - Day 3 - PC Report Out of Breakout Room Discussions, Discussion of Next Steps
<p>MagNetUS 2021 - Day 3</p> <p>PC Report Out of Breakout Room Discussions, Discussion of Next Steps</p>
FIGURES 1–2 in A report on Sipyloidea stigmata Redtenbacher (Diapheromeridae: Necrosciinae) as the first phasmid crop pest in India and its redescription
FIGURES 1–2. Sipyloidea stigmata: 1. female, 2. male.
FIGURES 10–12. Sipyloidea stigmata, egg. 10 in A report on Sipyloidea stigmata Redtenbacher (Diapheromeridae: Necrosciinae) as the first phasmid crop pest in India and its redescription
FIGURES 10–12. Sipyloidea stigmata, egg. 10. dorsal view; 11. lateral view; 12. operculum.
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.