Art, Creativity and Automation. From Charters to Shared 3D Visualization Practices

In this study, we introduce the themes of the Special Issue on Art, Creativity and Automation. Sharing 3D Visualization Practices in Archaeology, and present the most important outcomes of a roundtable session involving prominent researchers in the field, organized by the authors during the Archon Winter School in February 2020. By assessing the diversity of research aims, artistic projects, creative practices and technology used in the contributions to the Special Issue, and drawing on the thoughts and perspectives generated during the roundtable discussion, we seek to identify shared challenges within the community of visualizers which could ultimately pave the way to shared practices. In this light, we assess whether established charters and guidelines are still relevant in a now matured digital archaeology, where visualization techniques have attained a central position in archaeological knowledge production. Although parts of the guidelines have become common practice, the remainder did not keep up with the fast pace of development of digital practice and its current fundamental role in archaeology, and as a result some of the guidelines risk becoming obstructive in archaeological creative practice.Material Culture Studie

The ‘ForensOMICS’ approach for postmortem interval estimation from human bone by integrating metabolomics, lipidomics, and proteomics

The combined use of multiple omics allows to study complex interrelated biological processes in their entirety. We applied a combination of metabolomics, lipidomics and proteomics to human bones to investigate their combined potential to estimate time elapsed since death (i.e., the postmortem interval [PMI]). This 'ForensOMICS' approach has the potential to improve accuracy and precision of PMI estimation of skeletonized human remains, thereby helping forensic investigators to establish the timeline of events surrounding death. Anterior midshaft tibial bone was collected from four female body donors before their placement at the Forensic Anthropology Research Facility owned by the Forensic Anthropological Center at Texas State (FACTS). Bone samples were again collected at selected PMIs (219-790-834-872days). Liquid chromatography mass spectrometry (LC-MS) was used to obtain untargeted metabolomic, lipidomic, and proteomic profiles from the pre- and post-placement bone samples. The three omics blocks were investigated independently by univariate and multivariate analyses, followed by Data Integration Analysis for Biomarker discovery using Latent variable approaches for Omics studies (DIABLO), to identify the reduced number of markers describing postmortem changes and discriminating the individuals based on their PMI. The resulting model showed that pre-placement metabolome, lipidome and proteome profiles were clearly distinguishable from post-placement ones. Metabolites in the pre-placement samples suggested an extinction of the energetic metabolism and a switch towards another source of fuelling (e.g., structural proteins). We were able to identify certain biomolecules with an excellent potential for PMI estimation, predominantly the biomolecules from the metabolomics block. Our findings suggest that, by targeting a combination of compounds with different postmortem stability, in the future we could be able to estimate both short PMIs, by using metabolites and lipids, and longer PMIs, by using proteins

The legacy of 1300 years of land use in Jamaica

Despite decades of archaeological research on Jamaica, little is known about how settlers influenced landscape change on the island over time. Here, we examine the impact of human occupation through a multi-proxy approach using phytolith, charcoal, and stratigraphic analyses. White Marl was a continuously inhabited village settlement (ca. 1050–450 cal yrs BP) with large mounded midden areas, precolonial house structures, and human landscape management practices. We have shown that the local vegetation at White Marl was directly affected by human settlement through the use of agroforestry and burning, and suggest that fire was used to modify vegetation. Manioc phytoliths were found throughout human occupation and are broadly associated with increases in evidence for burning, suggesting fire was used to modify the landscape and clear vegetation for crop cultivation. The phytolith assemblages relate to three distinct temporal vegetation phases: (1) the earliest occupation dominated by arboreal vegetation (pre-ca. 870 cal yrs BP); (2) a transition to palm-dominated vegetation (ca. 870–670 cal yrs BP); and (3) the latest occupation representing European colonization associated with a more open, grass-dominated landscape (after ca. 670 cal yrs BP). These transitions occur independent of changes in paleoclimate records, suggesting humans were the dominant driver of vegetation change.Introduction Archaeological context Archaeobotany in Jamaica The White Marl site Materials and methods - Sampling, stratigraphic analysis, and recording - Phytoliths - Phytolith extraction - Phytolith identification, counting, and quantification - Charcoal extraction and quantification Results - Vegetation phase 1: Arboreal-dominated canopy - Vegetation phase 2: Palm-dominated canopy - Vegetation phase 3: Open grassland-dominated landscape - Crops - Burning indicators - Vegetation changes and climate Discussion Conclusio

Annexin A2 Binds RNA and Reduces the Frameshifting Efficiency of Infectious Bronchitis Virus

Annexin A2 (ANXA2) is a protein implicated in diverse cellular functions, including exocytosis, DNA synthesis and cell proliferation. It was recently proposed to be involved in RNA metabolism because it was shown to associate with some cellular mRNA. Here, we identified ANXA2 as a RNA binding protein (RBP) that binds IBV (Infectious Bronchitis Virus) pseudoknot RNA. We first confirmed the binding of ANXA2 to IBV pseudoknot RNA by ultraviolet crosslinking and showed its binding to RNA pseudoknot with ANXA2 protein in vitro and in the cells. Since the RNA pseudoknot located in the frameshifting region of IBV was used as bait for cellular RBPs, we tested whether ANXA2 could regulate the frameshfting of IBV pseudoknot RNA by dual luciferase assay. Overexpression of ANXA2 significantly reduced the frameshifting efficiency from IBV pseudoknot RNA and knockdown of the protein strikingly increased the frameshifting efficiency. The results suggest that ANXA2 is a cellular RBP that can modulate the frameshifting efficiency of viral RNA, enabling it to act as an anti-viral cellular protein, and hinting at roles in RNA metabolism for other cellular mRNAs

Qualitative Release Assessment to Estimate the Likelihood of Henipavirus Entering the United Kingdom

The genus Henipavirus includes Hendra virus (HeV) and Nipah virus (NiV), for which fruit bats (particularly those of the genus Pteropus) are considered to be the wildlife reservoir. The recognition of henipaviruses occurring across a wider geographic and host range suggests the possibility of the virus entering the United Kingdom (UK). To estimate the likelihood of henipaviruses entering the UK, a qualitative release assessment was undertaken. To facilitate the release assessment, the world was divided into four zones according to location of outbreaks of henipaviruses, isolation of henipaviruses, proximity to other countries where incidents of henipaviruses have occurred and the distribution of Pteropus spp. fruit bats. From this release assessment, the key findings are that the importation of fruit from Zone 1 and 2 and bat bushmeat from Zone 1 each have a Low annual probability of release of henipaviruses into the UK. Similarly, the importation of bat meat from Zone 2, horses and companion animals from Zone 1 and people travelling from Zone 1 and entering the UK was estimated to pose a Very Low probability of release. The annual probability of release for all other release routes was assessed to be Negligible. It is recommended that the release assessment be periodically re-assessed to reflect changes in knowledge and circumstances over time

Dental calculus evidence of Taï Forest Chimpanzee plant consumption and life history transitions

Dental calculus (calcified dental plaque) is a source of multiple types of data on life history. Recent research has targeted the plant microremains preserved in this mineralised deposit as a source of dietary and health information for recent and past populations. However, it is unclear to what extent we can interpret behaviour from microremains. Few studies to date have directly compared the microremain record from dental calculus to dietary records, and none with long-term observation dietary records, thus limiting how we can interpret diet, food acquisition and behaviour. Here we present a high-resolution analysis of calculus microremains from wild chimpanzees (Pan troglodytes verus) of Taï National Park, Côte d"Ivoire. We test microremain assemblages against more tan two decades of field behavioural observations to establish the ability of calculus to capture the composition of diet. Our results show that some microremain classes accumulate as long-lived dietary markers. Phytolith abundance in calculus can reflect the proportions of plants in the diet, yet this pattern is not true for starches. We also report microremains can record information about other dietary behaviours, such as the age of weaning and learned food processing techniques like nutcracking

Diseases and Causes of Death in European Bats: Dynamics in Disease Susceptibility and Infection Rates

Bats receive increasing attention in infectious disease studies, because of their well recognized status as reservoir species for various infectious agents. This is even more important, as bats with their capability of long distance dispersal and complex social structures are unique in the way microbes could be spread by these mammalian species. Nevertheless, infection studies in bats are predominantly limited to the identification of specific pathogens presenting a potential health threat to humans. But the impact of infectious agents on the individual host and their importance on bat mortality is largely unknown and has been neglected in most studies published to date.) were collected in different geographic regions in Germany. Most animals represented individual cases that have been incidentally found close to roosting sites or near human habitation in urban and urban-like environments. The bat carcasses were subjected to a post-mortem examination and investigated histo-pathologically, bacteriologically and virologically. Trauma and disease represented the most important causes of death in these bats. Comparative analysis of pathological findings and microbiological results show that microbial agents indeed have an impact on bats succumbing to infectious diseases, with fatal bacterial, viral and parasitic infections found in at least 12% of the bats investigated.Our data demonstrate the importance of diseases and infectious agents as cause of death in European bat species. The clear seasonal and individual variations in disease prevalence and infection rates indicate that maternity colonies are more susceptible to infectious agents, underlining the possible important role of host physiology, immunity and roosting behavior as risk factors for infection of bats