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opencc-by-4.0Dec 2018View details →

FIG. 2 in Feasting among Venda-speakers of South Africa: the Late Iron Age fauna from Mutokolwe

FIG. 2. — Location of Mutokolwe and other sites mentioned in the text within South Africa (adapted from Fish [2000:71], and used with permission from the University of the Witwatersrand).

opencc-by-4.0Dec 2018View details →

FIG. 1 in Feasting among Venda-speakers of South Africa: the Late Iron Age fauna from Mutokolwe

FIG. 1. — Location of the study areas in north-eastern South Africa: DZ, Dzata; HU, Ha-Tshirundu; MU, Mutokolwe; TA, Tavhatshena; TH, Tshirululuni; TS, Tshitheme.

FIG. 12 in When ivory came from the seas. On some traits of the trade of raw and carved sea-mammal ivories in the Middle Ages

FIG. 12. — Olaus Magnus, Carta Marina, 1539, detail. Uppsala universitetsbibliotek (Photo Uppsala universitetsbibliotek).

FIG. 8 in When ivory came from the seas. On some traits of the trade of raw and carved sea-mammal ivories in the Middle Ages

FIG. 8. — Elder of the Apocalypse, Saint-Omer, c. 075-1100. Saint-Omer, musée de l'Hôtel Sandelin: Inv. 2484. Height: 12 cm. © Musées de Saint-Omer.

FIG. 6 in When ivory came from the seas. On some traits of the trade of raw and carved sea-mammal ivories in the Middle Ages

FIG. 6. — Tabernacle probably from Saint Pantaleon in Cologne, Cologne, c. 1180. London, Victoria and Albert Museum: 7650-1861. Height: 54.5 cm (Photo © Victoria and Albert Museum, London).

FIG. 2 in When ivory came from the seas. On some traits of the trade of raw and carved sea-mammal ivories in the Middle Ages

FIG. 2. — Walrus tusk found in Skara Brae,Orkney, 3100-2400 BC. National Museums Scotland: X.HA 168. Height:45 cm (Photo © National Museums Scotland).

FIG. 5 in When ivory came from the seas. On some traits of the trade of raw and carved sea-mammal ivories in the Middle Ages

FIG. 5. — Lewis Chessmen, Trondheim, third quarter of the 12th century. National Museums Scotland. Height: 6 to 10 cm (Photo © National Museums Scotland).

FIG. 1 in When ivory came from the seas. On some traits of the trade of raw and carved sea-mammal ivories in the Middle Ages

FIG. 1. — The Symmachi Panel. Rome, late 4th-early 5th century. Victoria and Albert Museum: 212-1865. Height: 29.6 cm (Photo © Victoria and Albert Museum, London).

FIG. 7. — 12 in When ivory came from the seas. On some traits of the trade of raw and carved sea-mammal ivories in the Middle Ages

FIG. 7. — 12th century seal matrix of a tax collector named Snorri. York Museums: YORYM 1973.5.29. Diameter: 3 cm (Photo York Museums, CC-BY SA 4.0).

FIG. 10 in When ivory came from the seas. On some traits of the trade of raw and carved sea-mammal ivories in the Middle Ages

FIG. 10. — Pair of ceremonial staffs carved in narwhal tusks, England, 2nd quarter of the 12th century. A, Victoria and Albert Museum: A. 79-136; B, National Museums Liverpool: 1995.42. Lengths: A, 117 cm (Photo © Victoria and Albert Museum); B, 110 cm (Photo © National Museums Liverpool).

opencc-by-4.0Jul 2018View details →

Revealing, examining, and critical understanding in the digital age

During the second Project Presentation Session on Friday 20.07.2018 the following 3 projects were presented: <ul> <li>Rasa Kasperienė (Vytautas Magnus University, Kaunas, Lithuania): "Application of Social Network & Content Analysis Methods for Facebook Groups Dynamics"</li> <li>Jeffrey Allan Kelly Lowenstein (Grand Valley State University, USA): "Gaming the Lottery: Anatomy of a Global Investigation"</li> <li>Erik Radisch, Gernot Howanitz, Bernhard Bermeitinger (University of Passau, Germany): "Contextualizing Bandera: A Distant Watching Approach"</li> </ul>

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Data from: Telomere heritability and parental age at conception effects in a wild avian population

Individual variation in telomere length is predictive of health and mortality risk across a range of species. However, the relative influence of environmental and genetic variation on individual telomere length in wild populations remains poorly understood. Heritability of telomere length has primarily been calculated using parent–offspring regression which can be confounded by shared environments. To control for confounding variables, quantitative genetic 'animal models' can be used, but few studies have applied animal models in wild populations. Furthermore, parental age at conception may also influence offspring telomere length, but most studies have been cross-sectional. We investigated within- and between- parental age at conception effects and heritability of telomere length in the Seychelles warbler using measures from birds caught over 20 years and a multi-generational pedigree. We found a weak negative within-paternal age at conception effect (as fathers aged, their offspring had shorter telomeres) and a weak positive between-maternal age at conception effect (females that survived to older ages had offspring with longer telomeres). Animal models provided evidence that heritability and evolvability of telomere length was low in this population, and that variation in telomere length was not driven by early-life effects of hatch period or parental identities. qPCR plate had a large influence on telomere length variation and not accounting for it in the models would have underestimated heritability. Our study illustrates the need to include and account for technical variation in order to accurately estimate heritability, as well as other environmental effects, on telomere length in natural populations.

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opencc-by-4.0Dec 2020View details →

Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive of novel ageing genes - Database of Physical gene-gene Interactions in young adult C.elegans.

This repository contains Supplementary Information for manuscript Suriyalaksh et al Gene Regulatory Network inference in long lived C.elegans reveals modular properties that are predictive  of novel ageing genes corresponding to the curation of physical gene-gene interactions for young adult C elegans worms  We manually curated 239,001 regulatory interactions from 289 young adult wild-type (WT) C.elegans datasets, consisting of 126 genes and 495 unique transcription factors (see TableS1_datasets_for_prior.csv for references).  This repository contains 3 different files: TableS1_datasets_for_prior.csv - contains datasets used as sources for physical gene-gene or TF-gene interactions TableS2_physical_priors.xlsx - contains three tabs: ChIPATAC - contains physical TF-gene interactions from 115 L4 or young-adult ChIP-seq datasets from modERN (Kudron et al., 2018) +  ChIP-seq datasets (GSE28350, GSE81521) from  (Hochbaum et. al, 2011, Li et. al, 2016). eY1HATAC- contains  3,501 TF-gene interactions from eY1H assay by Fuxman Bass et al. (2016). motifATAC - contains 202 unique TF DNA recognition motifs using “direct evidence” option from CiS-BP motif database (Weirauch et al., 2014), obtained through RTFBSDB R package (Wang et al., 2016) - see TableS1 TableS3_WT_functional_priors.csv - contains functional knockdown data that we use as gold standard to validate inferred networks in Suriyalaksh et al. (see TableS1_datasets_for_prior.csv for sources) --- Description of methodology to obtain regulatory interactions in TableS2: Regulatory sequences for each gene were acquired from ENSEMBL (Aken et al., 2017), obtained using biomaRt R package (accessed on 31st Oct 2017). This study used WBcel235/ce11 version of the C. elegans genome, and WormBase WS260 genome annotations. For motifs, TFs whose motifs overlapped with an open ATAC-seq region by at least one base pair were kept. For ChIP-seq, TF binding sites that overlapped with an open ATAC-seq region by at least one base pair were kept using bedtools intersect and bedtools merge commands. An interaction from a TF to a gene was inferred by aligning transcription start sites (TSS) using bedtools window commands with 1000 bp window size to the TF-binding locations from ChIP-seq and motifs. For eY1H data, an interaction is included if the TSS site of the target gene overlaps with an open ATAC-seq region by at least one base pair. For gene-gene interactions, of the 298 studies compiled in WormExp v1.0 database (Yang et al, 2016, updated 27/07/16), 98 studies were included in the database spanning 126 different genes (see Table S1 in this repository).

Fig. 3 in Magneto-biostratigraphic age constraints on the palaeoenvironmental evolution of the South Caspian basin during the Early-Middle Pleistocene (Kura basin, Azerbaijan)

Fig. 3. Sedimentary log, paleontological sampling points, microfauna assemblages and paleosalinity estimation in the Goychay section.

Fig. 8 in Magneto-biostratigraphic age constraints on the palaeoenvironmental evolution of the South Caspian basin during the Early-Middle Pleistocene (Kura basin, Azerbaijan)

Fig. 8. Sedimentary log, paleontological sampling points, microfauna assemblages and paleosalinity estimation in the Hajigabul section.

Fig. 7 in Magneto-biostratigraphic age constraints on the palaeoenvironmental evolution of the South Caspian basin during the Early-Middle Pleistocene (Kura basin, Azerbaijan)

Fig. 7. Magnetostratigraphy of the Goychay section. In columns, from left to right: Regional (local) stages; Depositional units; Lithological log; Biostratigraphic sampling points: green - mollusc samples, blue - microfauna samples; Magnetic susceptibility (plotted on a logarithmic scale; black line - values for each sample, red line - averaged 3); Inclination; Declination; Interpreted polarity (black - normal, white - reversed). The Akchagylian - Apsheronian transition is drawn based on microfauna (lower limit) and macrofauna (upper limit). (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 12 in Magneto-biostratigraphic age constraints on the palaeoenvironmental evolution of the South Caspian basin during the Early-Middle Pleistocene (Kura basin, Azerbaijan)

Fig. 12. Magnetostratigraphy of the Hajigabul section. In columns from left to right: Regional stages; Depositional units; Lithological log; Biostratigraphic sampling points, where green points are mollusc samples and blue points - microfauna samples; Magnetic susceptibility (plotted on a logarithmic scale)); Inclination; Declination; Interpreted polarity. (For interpretation of the references to colour in this figure legend, the reader is referred to the Web version of this article.)

Fig. 2 in Magneto-biostratigraphic age constraints on the palaeoenvironmental evolution of the South Caspian basin during the Early-Middle Pleistocene (Kura basin, Azerbaijan)

Fig. 2. Lithostratigraphic subdivision of the Goychay section (A) and the Hajigabul section (B). Logs, general view and characteristic photos of each sedimentary unit.

Fig. 1 in Magneto-biostratigraphic age constraints on the palaeoenvironmental evolution of the South Caspian basin during the Early-Middle Pleistocene (Kura basin, Azerbaijan)

Fig. 1. Location map of the Goychay and Hajigabul sections. Columns on the left: Global polarity time scale (Hilgen et al., 2012) Epoch/Age; Regional Stages: a* classical definition (Shantser, 1982; Arslanov et al., 1988; Nevesskaya et al., 2003, 2004), b* this study. Position of the studied sections in relation to the Caspian Sea (A) and to the Kura Basin (B) (The map base is taken from www.maps-for-free.com); Geological maps for the Goychay section (C) and the Hajigabul section (D) modified after Bairamov et al. (2008).

Fig. 13 in Magneto-biostratigraphic age constraints on the palaeoenvironmental evolution of the South Caspian basin during the Early-Middle Pleistocene (Kura basin, Azerbaijan)

Fig. 13. Correlation of polarity patterns to the Global Polarity Time Scale (GPTS), the main paleoenvironmental events and characteristic mollusc fauna in the Goychay and Hajigabul sections. Sedimentation rate curves: Hajigabul section (A), the Goychay section (B).