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FIGURES 1–9. Chthonius agazzii Beier, 1966 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 1–9. Chthonius agazzii Beier, 1966, Buco delle Salamandre (Segusino, Treviso) (unless otherwise stated). 1, male, anterior margin of carapace; 2, female, id.; 3, male, (Grotta Faller, Sovramonte, Belluno), id.; 4, male, carapace; 5, male, right chelicera; 6, female, movable finger of right chelicera; 7, male, (Le Vette Feltrine, Pedavena, Belluno), id.; 8, male, right chelal hand, dorsal view; 9, female, id.
FIGURES 18–25. Chthonius agazzii Beier, 1966 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 18–25. Chthonius agazzii Beier, 1966, detail of dentition at the chelal fingers tip, antiaxial view (setae and sensilla af1-2, am1-2 omitted). 18, male holotype of C. malatestai, Mt. Pizzoc (Fregona, Treviso); 19, male, Milies (Treviso); 20, female, Pozzo Cima Alta (Velo d'Astico, Treviso); 21, female, near Trattoria della Moreieta (Arcugnano, Vicenza); 22, female, near Marezzane (Marano di Valpolicella, Verona); 23, male, Bus dei Tedeschi (San Pietro di Feletto, Treviso); 24, female, slope of Mt. Faverghera (Belluno); 25, female, near Buco delle Salamandre (Segusino, Treviso).
FIGURES 45–48. Chthonius caoduroi Callaini, 1987 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 45–48. Chthonius caoduroi Callaini, 1987, female, Grotta Sant'Angelo (Trecchina, Potenza). 45, right chela, antiaxial view; 46, detail of fingers at the chelal tip, antiaxial view; 47, detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 48, detail of fingers at level of trichobothrium sb, antiaxial view.
FIGURES 92–96. Chthonius comottii Inzaghi, 1987 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 92–96. Chthonius comottii Inzaghi, 1987, detail of chelal fingers dentition at level of trichobothria dx-et (top), it- est/t-st (middle) and b (bottom), antiaxial view (setae and sensilla af1-2, am1-2 omitted). 92, male, Sasso (Bordighera, Imperia); 93, female, Bocc d'la Mocia (Valduggia, Vercelli); 94, female, Chiappi (Castelmagno, Cuneo); 95, female, San Giacomo di Roburent (Cuneo); 96, female, Colle San Maurizio (Cervasca, Cuneo).
FIGURES 84–91. Chthonius comottii Inzaghi, 1987 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 84–91. Chthonius comottii Inzaghi, 1987, Baite Sedernello (Colzate, Bergamo). 84, male, right chela, antiaxial view; 85, male, detail of fingers at the chelal tip, antiaxial view; 86, male, detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 87, male, detail of fingers at level of trichobothrium sb, antiaxial view; 88, female, right chela, antiaxial view; 89, female, detail of fingers at the chelal tip, antiaxial view; 90, female, detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 91, female, detail of fingers at level of trichobothrium sb, antiaxial view.
FIGURES 77–83. Chthonius comottii Inzaghi, 1987 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 77–83. Chthonius comottii Inzaghi, 1987, Baite Sedernello (Colzate, Bergamo). 77, male, anterior margin of carapace; 78, female, id.; 79, male, carapace; 80, male, right chelicera; 81, female, movable finger of right chelicera; 82, male, right chelal hand, dorsal view; 83, female, id.
FIGURES 60–66. Chthonius carinthiacus Beier, 1951 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 60–66. Chthonius carinthiacus Beier, 1951, Rifugio Fonteghi (Imer, Trento) (unless otherwise stated). 60, male, anterior margin of carapace; 61, female, Mt. Gaverdina (Concei, Trento), id.; 62, male, carapace; 63, male, right chelicera; 64, female, Mt. Gaverdina (Concei, Trento), movable finger of right chelicera; 65, male, right chelal hand, dorsal view; 66, female, Mt. Gaverdina (Concei, Trento), id.
FIGURES 97–100. Chthonius densedentatus Beier, 1938 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 97–100. Chthonius densedentatus Beier, 1938, male, Omisalj (Krk, Croatia). 97, anterior margin of carapace; 98, carapace; 99, right chelicera; 100, right chelal hand, dorsal view.
FIGURES 110–116. Chthonius densedentatus Beier, 1938 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 110–116. Chthonius densedentatus Beier, 1938, Grotta Zinzulusa, 3.IV.2001 (Castro, Lecce) (unless otherwise stated). 110, female, right chela, antiaxial view; 111, female, detail of fingers at the right chelal tip, antiaxial view; 112, female, detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 113, female, detail of fingers at level of trichobothrium sb, antiaxial view; 114, female holotype, detail of dentition at the left chelal fingers tip, antiaxial view (setae and sensilla af1-2, am1-2 omitted); 115, female holotype, detail of fingers at level of trichobothria est-it and st-t, antiaxial view (setae omitted); 116, female holotype, detail of fingers at level of trichobothrium sb, antiaxial view (setae omitted).
FIGURES 101–104. Chthonius densedentatus Beier, 1938 in The Italian species of the Chthonius ischnocheles group (Arachnida, Pseudoscorpiones, Chthoniidae), with reference to neighbouring countries
FIGURES 101–104. Chthonius densedentatus Beier, 1938, male, Omisalj (Krk, Croatia). 101, right chela, antiaxial view; 102, detail of fingers at the chelal tip, antiaxial view; 103, detail of fingers at level of trichobothria est-it and st-t, antiaxial view; 104, detail of fingers at level of trichobothrium sb, antiaxial view.
Data from: A genomic reference panel for Drosophila serrata
Here we describe a collection of re-sequenced inbred lines of Drosophila serrata, sampled from a natural population situated deep within the species endemic distribution in Brisbane, Australia. D. serrata is a member of the speciose montium group whose members inhabit much of south east Asia and has been well studied for aspects of climatic adaptation, sexual selection, sexual dimorphism, and mate recognition. We sequenced 110 lines that were inbred via 17-20 generations of full-sib mating at an average coverage of 23.5x with paired-end Illumina reads. 15,228,692 biallelic SNPs passed quality control after being called using the Joint Genotyper for Inbred Lines (JGIL). Inbreeding was highly effective and the average levels of residual heterozygosity (0.86%) were well below theoretical expectations. As expected, linkage disequilibrium decayed rapidly, with r2 dropping below 0.1 within 100 base pairs. With the exception of four closely related pairs of lines which may have been due to technical errors, there was no statistical support for population substructure. Consistent with other endemic populations of other Drosophila species, preliminary population genetic analyses revealed high nucleotide diversity and, on average, negative Tajima's D values. A preliminary GWAS was performed on a cuticular hydrocarbon trait, 2-MeC28 revealing 4 SNPs passing Bonferroni significance residing in or near genes. One gene Cht9 may be involved in the transport of CHCs from the site of production (oenocytes) to the cuticle. Our panel will facilitate broader population genomic and quantitative genetic studies of this species and serve as an important complement to existing D. melanogaster panels that can be used to test for the conservation of genetic architectures across the Drosophila genus.
Data from: Genomics of Compositae crops: reference transcriptome assemblies, and evidence of hybridization with wild relatives
Although the Compositae harbours only two major food crops, sunflower and lettuce, many other species in this family are utilized by humans and have experienced various levels of domestication. Here we have used next generation sequencing technology to develop 15 reference transcriptome assemblies for Compositae crops or their wild relatives. These data allow us to gain insight into the evolutionary and genomic consequences of plant domestication. Specifically, we performed Illumina sequencing of Cichorium endivia, Cichorium intybus, Echinacea angustifolia, Iva annua, Helianthus tuberosus, Dahlia hybrida, Leontodon taraxacoides and Glebionis segetum, as well 454 sequencing of Guizotia scabra, Stevia rebaudiana, Parthenium argentatum and Smallanthus sonchifolius. Illumina reads were assembled using Trinity, and 454 reads were assembled using MIRA and CAP3. We evaluated the coverage of the transcriptomes using BLASTX analysis of a set of ultra-conserved orthologs (UCOs) and recovered most of these genes (88-98%). We found a correlation between contig length and read length for the 454 assemblies, and greater contig lengths for the 454 compared to the Illumina assemblies. This suggests that longer reads can aid in the assembly of more complete transcripts. Finally, we compared the divergence of orthologs at synonymous sites (Ks) between Compositae crops and their wild relatives and found greater divergence when the progenitors were self-incompatible. We also found greater divergence between pairs of taxa that had some evidence of post-zygotic isolation. For several more distantly related congeners, such as chicory and endive, we identified a signature of introgression in the distribution of Ks values.
Data from: Untangling taxonomy: a DNA barcode reference library for Canadian spiders
Approximately 1460 species of spiders have been reported from Canada, 3% of the global fauna. This study provides a DNA barcode reference library for 1018 of these species based upon the analysis of more than 30 000 specimens. The sequence results show a clear barcode gap in most cases with a mean intraspecific divergence of 0.78% vs. a minimum nearest-neighbour (NN) distance averaging 7.85%. The sequences were assigned to 1359 Barcode index numbers (BINs) with 1344 of these BINs composed of specimens belonging to a single currently recognized species. There was a perfect correspondence between BIN membership and a known species in 795 cases, while another 197 species were assigned to two or more BINs (556 in total). A few other species (26) were involved in BIN merges or in a combination of merges and splits. There was only a weak relationship between the number of specimens analysed for a species and its BIN count. However, three species were clear outliers with their specimens being placed in 11–22 BINs. Although all BIN splits need further study to clarify the taxonomic status of the entities involved, DNA barcodes discriminated 98% of the 1018 species. The present survey conservatively revealed 16 species new to science, 52 species new to Canada and major range extensions for 426 species. However, if most BIN splits detected in this study reflect cryptic taxa, the true species count for Canadian spiders could be 30–50% higher than currently recognized.
Data from: Long read reference genome-free reconstruction of a full-length transcriptome from Astragalus membranaceus reveals transcript variants involved in bioactive compound biosynthesis
Astragalus membranaceus, also known as Huangqi in China, is one of the most widely used medicinal herbs in Traditional Chinese Medicine. Traditional Chinese Medicine formulations from Astragalus membranaceus have been used to treat a wide range of illnesses, such as cardiovascular disease, type 2 diabetes, nephritis and cancers. Pharmacological studies have shown that immunomodulating, anti-hyperglycemic, anti-inflammatory, antioxidant and antiviral activities exist in the extract of Astragalus membranaceus. Therefore, characterising the biosynthesis of bioactive compounds in Astragalus membranaceus, such as Astragalosides, Calycosin and Calycosin-7-O-β-D-glucoside, is of particular importance for further genetic studies of Astragalus membranaceus. In this study, we reconstructed the Astragalus membranaceus full-length transcriptomes from leaf and root tissues using PacBio Iso-Seq long reads. We identified 27 975 and 22 343 full-length unique transcript models in each tissue respectively. Compared with previous studies that used short read sequencing, our reconstructed transcripts are longer, and are more likely to be full-length and include numerous transcript variants. Moreover, we also re-characterised and identified potential transcript variants of genes involved in Astragalosides, Calycosin and Calycosin-7-O-β-D-glucoside biosynthesis. In conclusion, our study provides a practical pipeline to characterise the full-length transcriptome for species without a reference genome and a useful genomic resource for exploring the biosynthesis of active compounds in Astragalus membranaceus.
Data from: Primary care follow-up and measured mental health outcomes among women referred for ultrasound assessment of pain and/or bleeding in early pregnancy: a quantitative questionnaire study
Objectives To examine the extent of primary care follow-up and mental health outcomes among women referred for ultrasound assessment of pain and/or bleeding in early pregnancy, including those whose pregnancy is found to be viable on ultrasound assessment. Design Questionnaire study with prospective follow-up. Setting Urgent gynaecology clinic in secondary care, England. Participants 57 women participated in the study. Entry criteria: referral to the urgent gynaecology clinic with pain and/or bleeding in early pregnancy; gestation less than 16 weeks (the clinic's own 'cut-off'); no previous attendance at the clinic during the current pregnancy. Exclusion criteria: inability to understand English or to provide informed consent. Primary and secondary outcome measures Incidence of primary care follow-up among women referred to the urgent gynaecology clinic; incidence of women with measured mental health scores suggesting significant symptoms of distress. Results Fewer than 1 in 10 women referred for ultrasound assessment of pain and/or bleeding in early pregnancy had follow-up arrangements made with their general practitioner (GP). Most women who had GP follow-up found it helpful and a significant minority of women who did not have GP follow-up felt that it would have been helpful. Following ultrasound assessment, more than one-third of women had significant symptoms of distress. Symptoms of distress, particularly anxiety, were present among those women found to have viable pregnancies, as well as among those with non-viable pregnancies. Conclusions GPs are advised to consider offering follow-up to all women referred for ultrasound assessment of pain and/or bleeding in early pregnancy. Researchers in this area are advised to consider the experiences of women with pain and/or bleeding in early pregnancy whose pregnancies are ultimately found to be viable on ultrasound scan.
Data from: Complete blood count reference intervals from a healthy adult urban population in Kenya
Background: There are racial, ethnic and geographical differences in complete blood count (CBC) reference intervals (RIs) and therefore it is necessary to establish RIs that are population specific. Several studies have been carried out in Africa to derive CBC RIs but many were not conducted with the rigor recommended for RI studies hence limiting the adoption and generalizability of the results. Method: By use of a Beckman Coulter ACT 5 DIFF CP analyser, we measured CBC parameters in samples collected from 528 healthy black African volunteers in a largely urban population. The latent abnormal values exclusion (LAVE) method was used for secondary exclusion of individuals who may have had sub-clinical diseases. The RIs were derived by both parametric and non-parametric methods with and without LAVE for comparative purposes. Results: Haemoglobin (Hb) levels were lower while platelet counts were higher in females across the 4 age stratifications. The lower limits for Hb and red blood cell parameters significantly increased after applying the LAVE method which eliminated individuals with latent anemia and inflammation. We adopted RIs by parametric method because 90% confidence intervals of the RI limits were invariably narrower than those by the non-parametric method. The male and female RIs for Hb after applying the LAVE method were 14.5−18.7 g/dL and 12.0−16.5 g/dL respectively while the platelet count RIs were 133−356 and 152−443 x103 per µL respectively. Conclusion: Consistent with other studies from Sub-Saharan Africa, Hb and neutrophil counts were lower than Caucasian values. Our finding of higher Hb and lower eosinophil counts compared to other studies conducted in rural Kenya most likely reflects the strict recruitment criteria and healthier reference population after secondary exclusion of individuals with possible sub-clinical diseases.
Data from: Genetic variation at aryl hydrocarbon receptor (AHR) loci in populations of Atlantic killifish (Fundulus heteroclitus) inhabiting polluted and reference habitats
Background: The non-migratory killifish Fundulus heteroclitus inhabits clean and polluted environments interspersed throughout its range along the Atlantic coast of North America. Several populations of this species have successfully adapted to environments contaminated with toxic aromatic hydrocarbon pollutants such as polychlorinated biphenyls (PCBs). Previous studies suggest that the mechanism of resistance to these and other "dioxin-like compounds" (DLCs) may involve reduced signaling through the aryl hydrocarbon receptor (AHR) pathway. Here we investigated gene diversity and evidence for positive selection at three AHR-related loci (AHR1, AHR2, AHRR) in F. heteroclitus by comparing alleles from seven locations ranging over 600 km along the northeastern US, including extremely polluted and reference estuaries, with a focus on New Bedford Harbor (MA, USA), a PCB Superfund site, and nearby reference sites. Results: We identified 98 single nucleotide polymorphisms within three AHR-related loci among all populations, including synonymous and nonsynonymous substitutions. Haplotype distributions were spatially segregated and F-statistics suggested strong population genetic structure at these loci, consistent with previous studies showing strong population genetic structure at other F. heteroclitus loci. Genetic diversity at these three loci was not significantly different in contaminated sites as compared to reference sites. However, for AHR2 the New Bedford Harbor population had significant FST values in comparison to the nearest reference populations. Tests for positive selection revealed ten nonsynonymous polymorphisms in AHR1 and four in AHR2. Four nonsynonymous SNPs in AHR1 and three in AHR2 showed large differences in base frequency between New Bedford Harbor and its reference site. Tests for isolation-by-distance revealed evidence for non-neutral change at the AHR2 locus. Conclusion: Together, these data suggest that F. heteroclitus populations in reference and polluted sites have similar genetic diversity, providing no evidence for strong genetic bottlenecks for populations in polluted locations. However, the data provide evidence for genetic differentiation among sites, selection at specific nucleotides in AHR1 and AHR2, and specific AHR2 SNPs and haplotypes that are associated with the PCB-resistant phenotype in the New Bedford Harbor population. The results suggest that AHRs, and especially AHR2, may be important, recurring targets for selection in local adaptation to dioxin-like aromatic hydrocarbon contaminants.
Data from: Response of ants to human-altered habitats with reference to seed dispersal of Corydalis giraldii Fedde (Papaveraceae)
Anthropogenic habitat disturbance has potential consequences for ant communities. However, there is limited information on the effects of ant responses on associated ecological processes such as seed dispersal. We investigated the effect of disturbance on the abundance, richness, and composition of ant communities and the resulting seed‐dispersal services for a herbaceous myrmecochore, Corydalis giraldii (Papaveraceae), in an undisturbed habitat (forest understory), moderately disturbed habitat (abandoned farm field), and highly disturbed habitat (road verge) on Qinling Mountains, China. In total, we recorded 13 ant species, and five out of these were observed to transport seeds. The community composition of dispersers was significantly different amongst habitats. The richness of the dispersers did not differ among the habitats, but their total abundance significantly varied across habitats and was recorded to decrease in the road verge by 21%, in comparison to abandoned farm fields. The major seed‐dispersing ant species in both the forest understory and abandoned farm field were large‐bodied (Myrmica sp. and Formica fusca, respectively), whereas the major seed‐dispersing ants found in the road verge were small‐bodied (Lasius alienus). This difference resulted in lower seed removal rates and dispersal distances in the road verge than in the other two habitats. The different dispersal patterns were attributed primarily to differences in dispersing ant abundance and identity, most likely in response to habitats with different degree of anthropogenic disturbance. The possible influence of disturbance on the ecological specialization of ant‐seed dispersal interaction was also discussed.
Data from: Correcting for cell-type effects in DNA methylation studies: reference-based method outperforms latent variable approaches in empirical studies
Based on an extensive simulation study, McGregor and colleagues recently recommended the use of surrogate variable analysis (SVA) to control for the confounding effects of cell-type heterogeneity in DNA methylation association studies in scenarios where no cell-type proportions are available. As their recommendation was mainly based on simulated data, we sought to replicate findings in two large-scale empirical studies. In our empirical data, SVA did not fully correct for cell-type effects, its performance was somewhat unstable, and it carried a risk of missing true signals caused by removing variation that might be linked to actual disease processes. By contrast, a reference-based correction method performed well and did not show these limitations. A disadvantage of this approach is that if reference methylomes are not (publicly) available, they will need to be generated once for a small set of samples. However, given the notable risk we observed for cell-type confounding, we argue that, to avoid introducing false-positive findings into the literature, it could be well worth making this investment.
Data from: Chromosome-level reference genome assembly and gene editing of the dead-leaf butterfly Kallima inachus
<p class="p">The leaf resemblance of <i><span>Kallima</span></i> (Nymphalidae) butterflies<i> </i>is an important ecological adaptive mechanism that increases survival. However, the genetic mechanism underlying ecological adaptation remains unclear owing to a dearth of genomic information. Herein, we revealed the karyotype (n = 31) of the dead-leaf butterfly <i><span>Kallima inach</span></i><i><span>us</span></i>, assembled its high-quality chromosome-level reference genome (568.92 Mb; contig N50: 19.20 Mb), and identified its Z and candidate W chromosomes. To our knowledge, this is the first study to report on these aspects of this species. In the assembled genome, 15,309 protein-coding genes and 49.86% repeat elements were annotated. Phylogenetic analysis showed that <i><span>K. inachus</span></i> diverged from <i><span>Melitaea cinxia </span></i>(no leaf resemblance), both of which are in Nymphalinae, around 40 million years ago. Demographic analysis indicated that the effective population size of <i><span>K. inach</span></i><i><span>us</span></i> decreased during the last interglacial period in the Pleistocene. The wings of adults with the pigmentary gene <i><span>ebony</span></i> knocked out using CRISPR/Cas9 showed phenotypes in which the orange dorsal region and entire ventral surface darkened, suggesting its vital role in the ecological adaption of dead-leaf butterflies. Our results provide important genome resources for investigating the genetic mechanism underlying protective resemblance in dead-leaf butterflies and insights into the molecular basis of protective coloration.</p>
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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.