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opencc-by-4.0Dec 2020View details →

Vector sequences in early WIV SRA sequencing data of SARS-CoV-2 inform on a potential large-scale security breach at the beginning of the COVID-19 pandemic

DESCRIPTION Sequences identified as Influenza A virus, Spodoptera frugiperda rhabdovirus and Nipah henipavirus have been previously identified within the early HiSeq 1000 and HiSeq 3000 sequencing data of SARS-CoV-2, SRR11092059,SRR11092060,SRR11092061 and SRR11092062, and were being used to support the hypothesis that a "simultaneous outbreak of multiple zoonotic viruses" have happened in the Huanan Seafood market. https://doi.org/10.31219/osf.io/s4td6 However, a closer examination of these sequences revealed that they were not sequences of actual wild viruses, but were in stead fragments left behind from PCR products and cloning vectors harboring both cDNA clones and infectious clones of such viruses, with evidence of viral sequences being joined directly to DNA sequences of vector and non-human origin within the same short reads. Here are the vector sequences and PCR product-like sequences recovered from the earliest WIV SRA sequencing data of Human SARS-CoV-2 from dataset SRR11092059,SRR11092060,SRR11092061,SRR11092062. Sequences associated with Vectors and PCR products from 3 distinct viral species have been obtained: The 3'-end of a Nipah Henipahvirus with fusion to a Hepatitis D virus Ribozyme, a T7 terminator and a Tetracycline resistance gene, The 5'-end of the same Nipah Henipahvirus with fusion to sequences found in diverse vectors, A complete vector genome encoding the HA gene of Influenza A virus subtype H7N9 under a CMV promoter and a bgH polyA terminator, and 221 Contiguous sequences corresponding to the Spodoptera frugiperda rhabdovirus reference genome fused to sequences that were homologous to multiple Plastid sequences and Notably Mitochondrial sequences of Rodents. As sequences corresponding to a rescued infectious clone of a BSL-4 organism (Nipah Henipahvirus) were found in sample sequences that supposedy represents patient samples that were obtained from Hospital ICU and sequenced in a pathogen diagnosis laboratory (which is separate from the Virology Research laboratory which is implied by the context of an Infectious Clone of such an organism, evident by the 3'-HDV ribozyme and T7 terminator fused directly to the 3'-terminus of the Nipah Henipahvirus reads), The discovery of artifact-containing sequences of at least 3 different pathogen species that are phylogenetically and methodologically distinct from each other in samples that were supposedly submitted by a laboratory that is Separate from the virological research laboratories that could have hosted such clone sequences imply extensive crosstalk and cross-contamination between the various laboratories within the Wuhan Institute of Virology, which includes at least one BSL-4 laboratory with evidence of containment breach of a BSL-4 organism and it's subsequent introduction into RNA-seq samples that were processed by a laboratory of distinct and separate purposes than the basic virological research evidenced by the Infectious Clone of the Hipah Henipahvirus. Such a discovery therefore likely imply a major security breach happening within the Wuhan institute of Virology at the time when the first sequences of SARS-CoV-2 was sampled and sequenced, which have important implications on the origins of the SARS-CoV-2 virus itself. METHODS The metagenomic sequencing datasets, SRR11092059,SRR11092060,SRR11092061 and SRR11092062 were first analyzed using the NCBI phylogenetic analysis tool, which identified viral sequences that is not related to SARS-CoV-2 itself. These include Influenza A virus (IAV, subtype H7N9), Spodoptera frugiperda rhabdovirus and Nipah Henipahvirus. The datasets were then subjected to BLAST search using MEGABLAST against the reference sequences of such viruses to verify the existence of the viral sequences and determine the exact sybtype of such viruses and the closest sequences on GenBank that corresponds to the reads. There seuqences are MH926031.1 for the  Spodoptera frugiperda rhabdovirus,  KY199425.1 for the Influenza A virus and AY988601.1 for the Nipah Henipahvirus. A second round BLAST analysis with these identified sequences were then performed, which unexpectedly revealed numerous reads corresponding to Cloning vectors and non-human Mitochondrial and Plastid sequences being fused directly to the sequences of the identified viral species. Reads were then downloaded and subjected to assembly using the CAP3 sequence assembly program and the EGASSEMBLER tool. Contig sequences were then queried against the NCBI nr/nt database which unanimously identified the original sample sequences as viral sequences inserted into cloning vectors. The complete sequence of the Influenza A virus Haemagluttinin (HA) gene clone was obtained from SRR11092061,SRR11092062 using multiple rounds of BLAST search and sequence assembly expansion on the existing vector-virus junction contigs, and a partial sequence corresponding the 3'-end of Nipah Henipahvirus AY988601.1 fused to a 3'-HDV ribozyme, T7 terminator and a Tet resistance gene was obtained from SRR11092059. In addition, 221 Contig sequences corresponding to the Rhabdovirus MH926031.1 fused to Chloroplast sequence MN524635.1 and Rodent Mitochondrial sequence MT241668.1 have been recovered from SRR11092061. We then performed a BLAST search using the identified vector sequences on SRR11092059,SRR11092060,SRR11092061 and SRR11092062, which confirms the existence of these two vetor sequences in all 4 datasets.

opencc-zeroNov 2020View details →

aquila (Whalen & Carter in Carter, Whalen & Guex, 1998), Orbuk-32; R, Pseudoeucyrtis busuangaensis (Yeh & Cheng, 1998), Orbuk-32; S, Farcus graylockensis Pessagno, Whalen & Yeh, 1986, Orbuk-32; T-U, Farcus sp. A, Orbuk-26; V, Farcus sp. B, Orbuk-27; W-X, Anaticapitula anatiformis (De Wever, 1982); W, Orbuk-32; X, Orbuk-38; Y, Saitoum sp. aff. S. triumphense Whalen & Carter in Carter, Whalen & Guex, 1998, Orbuk-32. Scale bar: A-C, K-L, T-U, W-Y, 100 µm; D-J, M-O, 120 µm; P-S, V, 150 µm. in Late Triassic to Early Jurassic radiolarian, conodont and ammonite assemblages from the Tavuscayiri block, Mersin Mélange, southern Turkey: Time constraints for the T/J boundary and sedimentary evolution of the southern margin of the northern Neotethys

aquila (Whalen & Carter in Carter, Whalen & Guex, 1998), Orbuk-32; R, Pseudoeucyrtis busuangaensis (Yeh & Cheng, 1998), Orbuk-32; S, Farcus graylockensis Pessagno, Whalen & Yeh, 1986, Orbuk-32; T-U, Farcus sp. A, Orbuk-26; V, Farcus sp. B, Orbuk-27; W-X, Anaticapitula anatiformis (De Wever, 1982); W, Orbuk-32; X, Orbuk-38; Y, Saitoum sp. aff. S. triumphense Whalen & Carter in Carter, Whalen & Guex, 1998, Orbuk-32. Scale bar: A-C, K-L, T-U, W-Y, 100 µm; D-J, M-O, 120 µm; P-S, V, 150 µm.

opencc-by-4.0Jan 2021View details →

Model intercomparison of COSMO 5.0 and IFS 45r1 at kilometer-scale grid spacing

Simulation output data from COSMO and IFS used to produce the figures in the model intercomparison paper (https://doi.org/10.5194/gmd-2021-31), as well as the data used for initializing the soil in COSMO. The output data is partitioned into different parts: <ol> <li>cosmo_hordiff.tar: Model output from COSMO for the horizontal diffusion experiment.</li> <li>cosmo_standard.tar: Model output from COSMO for the standard experiment.</li> <li>ifs_standard.tar: Model output from IFS for the standard experiment.</li> <li>soil_cosmo_ini_vergara2021_avg_mayjune_12km.nc: Initial conditions for the soil model used in COSMO.</li> </ol>

Fig. 4 in Identification of nurseries areas of juvenile Prochilodus lineatus (Valenciennes, 1836) (Characiformes: Prochilodontidae) by scale and otolith morphometry and microchemistry

Fig. 4. Relative warp (RW) analysis based on landmark coordinates. Thin plate spline transformation grids for the extreme points of RW are shown; these were superimposed on the shapes predicted when the average landmark configuration of all scales was deformed into that of a hypothetical scale positioned at the extreme of the RW of interest. A) RW2 vs. RW1; B) RW3 vs. RW1.

Fig. 1 in Identification of nurseries areas of juvenile Prochilodus lineatus (Valenciennes, 1836) (Characiformes: Prochilodontidae) by scale and otolith morphometry and microchemistry

Fig. 1. Study area. The red circles indicate the streaked prochilod (Prochilodus lineatus) collection sites.

Fig. 2 in Identification of nurseries areas of juvenile Prochilodus lineatus (Valenciennes, 1836) (Characiformes: Prochilodontidae) by scale and otolith morphometry and microchemistry

Fig. 2. Lapilli otolith of a streaked prochilod (Prochilodus lineatus). a) Right otolith of one of the sampled individuals, internal view (age 0+); b) right otolith section through the core (age 0+); c) example view of growth rings in an adult fish (age 8+). Abbreviations: A, anterior; D, dorsal; P, posterior; V, ventral; Ext, exterior; Int, interior.

Fig. 3 in Identification of nurseries areas of juvenile Prochilodus lineatus (Valenciennes, 1836) (Characiformes: Prochilodontidae) by scale and otolith morphometry and microchemistry

Fig. 3. Landmark definitions used in the fish scales. Abbreviations: A, anterior; D, dorsal; P, posterior; V, ventral.

opencc-by-4.0Jun 2021View details →

Millimeter- to Decimeter-Scale Surface Slope and Roughness of the Moon at the Chang'e-4 Exploration Region

The datasets related to the work of Millimeter- to Decimeter-Scale Surface Slope and Roughness of the Moon at the Chang'e-4 Exploration Region. Cite the following references if using the DEM data. Wu, B., Li, Y., Liu, W. C., Wang, Y., Li, F., Zhao, Y., and Zhang, H. (2021), Centimeter-resolution topographic modeling and fine-scale analysis of craters and rocks at the Chang’E-4 landing site, Earth Planet. Sci. Lett., 553, 116666. <a href="https://doi.org/10.1016/j.epsl.2020.116666">https://doi.org/10.1016/j.epsl.2020.116666</a> Guo, D., Fa, W., Wu, B., Li, Y., & Liu, Y. (2021). Millimeter- to Decimeter-Scale Surface Slope and Roughness of the Moon at the Chang’e-4 Exploration Region. Geophysical Research Letters, 48, e2021GL094931. <a href="https://doi.org/10.1029/2021GL094931">https://doi.org/10.1029/2021GL094931</a>

opencc-by-4.0Jun 2021View details →

Downscaled surface mass balance in Antarctica: impacts of subsurface processes and large-scale atmospheric circulation

Here is the surface mass balance calculated from a offline subsurface model, that is used in the paper Downscaled surface mass balance in Antarctica: impacts of subsurface processes and large-scale atmospheric circulation. More data are available by contacting nichsen@space.dtu.dk

opencc-by-4.0Jun 2021View details →

Data from "Multi-wavelength continuum sizes of protoplanetary discs: scaling relations and implications for grain growth and radial drift"

Table 1, Table 2, and Table 3 from Tazzari et al., 2021, "Multi-wavelength continuum sizes of protoplanetary discs: scaling relations and implications for grain growth and radial drift", Monthly Notices of the Royal Astronomical Society, arXiv:2010.02249 Both tables are available in IPAC format, which is in human- and machine-readable: <pre><code class="language-python">from astropy.io import ascii tb = ascii.read('Table1.txt', format='ipac')</code></pre> Table comments (stored at the beginning of the ASCII file as lines starting with "/") can be read as: <pre><code class="language-python">tb.meta['comments'] </code></pre>

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Data from: Enriching the ant tree of life: enhanced UCE bait set for genome-scale phylogenetics of ants and other Hymenoptera

1. Targeted enrichment of conserved genomic regions (e.g., ultraconserved elements or UCEs) has emerged as a promising tool for inferring evolutionary history in many organismal groups. Because the UCE approach is still relatively new, much remains to be learned about how best to identify UCE loci and design baits to enrich them. 2. We test an updated UCE identification and bait design workflow for the insect order Hymenoptera, with a particular focus on ants. The new strategy augments a previous bait design for Hymenoptera by (a) changing the parameters by which conserved genomic regions are identified and retained, and (b) increasing the number of genomes used for locus identification and bait design. We perform in vitro validation of the approach in ants by synthesizing an ant-specific bait set that targets UCE loci and a set of "legacy" phylogenetic markers. Using this bait set, we generate new data for 84 taxa (16/17 ant subfamilies) and extract loci from an additional 17 genome-enabled taxa. We then use these data to examine UCE capture success and phylogenetic performance across ants. We also test the workability of extracting legacy markers from enriched samples and combining the data with published data sets. 3. The updated bait design (hym-v2) contained a total of 2,590-targeted UCE loci for Hymenoptera, significantly increasing the number of loci relative to the original bait set (hym-v1; 1,510 loci). Across 38 genome-enabled Hymenoptera and 84 enriched samples, experiments demonstrated a high and unbiased capture success rate, with the mean locus enrichment rate being 2,214 loci per sample. Phylogenomic analyses of ants produced a robust tree that included strong support for previously uncertain relationships. Complementing the UCE results, we successfully enriched legacy markers, combined the data with published Sanger data sets, and generated a comprehensive ant phylogeny containing 1,060 terminals. 4. Overall, the new UCE bait design strategy resulted in an enhanced bait set for genome-scale phylogenetics in ants and likely all of Hymenoptera. Our in vitro tests demonstrate the utility of the updated design workflow, providing evidence that this approach could be applied to any organismal group with available genomic information.

opencc-by-4.0Oct 2019View details →

Fig. 10. Middle Pleistocene Didacna species from the Hajigabul section. Scale bar 5 in Magneto-biostratigraphic age constraints on the palaeoenvironmental evolution of the South Caspian basin during the Early-Middle Pleistocene (Kura basin, Azerbaijan)

Fig. 10. Middle Pleistocene Didacna species from the Hajigabul section. Scale bar 5 mm. A-B. Didacna bergi (1954 m, early Khazarian); C-G. D. parvula (1795 m, Late Bakunian); H-I. D. cf carditoides (1795 m, Late Bakunian); J-K. Didacna sp (1795 m, Late Bakunian).

opencc-by-4.0Jun 2016View details →

Internal and Predictive Validity of the French Health of the Nation Outcome Scales Dataset

This dataset is related to Golay P, Basterrechea L, Conus P, Bonsack C (2016). Internal and Predictive Validity of the French Health of the Nation Outcome Scales: Need for Future Directions. PLoS ONE 11(8): e0160360. doi:10.1371/journal.pone.0160360. http://journals.plos.org/plosone/article/related?id=10.1371%2Fjournal.pone.0160360 It includes 19 variables and 2722 cases.

opencc-zeroDec 2004View details →

FIGURES 37 – 41. Trichodes tugelanus. FIGURE 37. Aedeagus ventrally. FIGURE 38. Aedeagus laterally. FIGURE 39. Male sternum VIII. FIGURE 40. Pygidium. Scale 1 in Revision of the Afrotropical species of the genus Trichodes HERBST, 1792 (Coleoptera, Cleridae)

FIGURES 37 – 41. Trichodes tugelanus. FIGURE 37. Aedeagus ventrally. FIGURE 38. Aedeagus laterally. FIGURE 39. Male sternum VIII. FIGURE 40. Pygidium. Scale 1 mm. FIGURE 41. Distri

FIGURE 7 in Scale ontogeny in the cardinalfish family Apogonidae

FIGURE 7. SEM images of scales of (a) Rhabdamia nigrimentum SAIAB 69337, 37.1 mm, mid-body scale, and (b) Taeniamia pallida, SAIAB 96247, 57.2 mm, mid-body scale. LM images of scales of (c) Apistus carinatus SAIAB 87086, 61.8 mm SL, scale between pelvic-fin bases. (d) Cheilodactylus pixii, uncatalogued, 115 mm, scale next to upper pectoral-fin base. fo = focus.

FIGURE 6 in Scale ontogeny in the cardinalfish family Apogonidae

FIGURE 6. SEM images of scales from different parts of the fish body showing variability in scale shape and size of the posterior field. Scales of the platycephalid Cociella heemstrai SAIAB 1508, 85 mm SL: (a) Body scale 2 rows above lateral line below 2 nd dorsal-fin spine; and (b) Scale immediately above 1 st anal-fin ray. Scales of the epigonid Florenciella lugubris SAIAB 14088, 97.5 mm SL: (c) scale immediately below lateral line. (d) scale above 3 rd anal-fin ray. fo = scale focus.

FIGURE 5 in Scale ontogeny in the cardinalfish family Apogonidae

FIGURE 5. SEM images of scales sampled from selected scorpaenid species. (a, b) Parascorpaena mossambica SAIAB 35158, 12.8 mm and 14.6 mm, respectively. (c) Pterois mombassae SAIAB 68969, 14.9 mm and SAIAB 14532, 71.5 mm. (d) Scorpaenopsis venosa SAIAB 40271, 17.9 mm. (e) Dendrochirus brachypterus SAIAB 87001, 35.8 mm. (f) D. brachypterus SAIAB 4163, 77 mm. (g) Scorpaenodes guamensis SAIAB 98510, 14.0 mm and 43.5 mm. fo = scale focus.

FIGURE 2 in Scale ontogeny in the cardinalfish family Apogonidae

FIGURE 2. SEM images of juvenile spinoid scales of species representing selected apogonid genera: (a) Ostorhinchus doederleini AMS I. 30881 - 019, 11.0 mm. (b) Cheilodipterus intermedius AMS I. 33273 - 010, 12 mm. (c) Unidentified apogonid AMS I. 41401 - 010, 14.8 mm. (d) Fowleria sp. AMS I. 42791 - 033, 14.8 mm. (e) Taeniamia pallida SAIAB 96212, 18.4 mm. (f) Ostorhinchus cookii 15.5 mm.

FIGURE 4 in Scale ontogeny in the cardinalfish family Apogonidae

FIGURE 4. SEM images of scales of selected species of the Pempheridae, Kurtidae and Gobiidae. (a) Pemperis sp. SAIAB 9521, 46.6 mm SL. (b) Pempheris flavicycla SAIAB 77805, 119 mm SL. (c) Cycloid scale of Kurtus gulliveri SAIAB 70522, 148 mm. Peripheral ctenoid scales of: (d) Bathygobius cocosensis SAIAB 56733, 38.5 mm. (e) Gnatholepis anjerensis SAIAB 2576, 83.5 mm. (f) Caffrogobius saldanha PEM 20130111, 14.5 mm.

FIGURE 3 in Scale ontogeny in the cardinalfish family Apogonidae

FIGURE 3. Ontogeny of transforming ctenoid scales in Taeniamia pallida. (a) Cycloid stage (SAIAB 96212, 18.4 mm). (b) & (c) Spinoid and early ctenoid stage showing baseline of spines and first row of ctenii with no truncation (SAIAB 96212, 20 & 25.5 mm, respectively). (d) adult scale with spines and first row of ctenii truncated (SAIAB 96247, 57.2 mm).