From Archive to GIS: Recovering Spatial Information for Tholos IV at the Palace of Nestor from the Notebooks of Lord William Taylour

This article is a case study in doing new things with old data. In 1953 Lord William Taylour directed the excavation of a monumental vaulted tholos tomb known as 'Tholos IV' at the site of ancient Pylos, Messenia, Greece. The excavation was conducted over two months, during which detailed notes were recorded in three notebooks now kept in the Archives of the American School of Classical Studies at Athens. The formal publication of Tholos IV, however, contains only a basic narrative of the excavation, offering neither precise detail on stratigraphy, object find spots, nor even a complete inventory of small finds. The present study goes back to the original notebooks kept by Taylour and combines the data contained in them with a new digital survey of Tholos IV to produce a comprehensive and accurate 3D GIS model for the excavation. Furthermore, the GIS has been produced in such a way that its dataset is compatible with new excavation data currently generated in the ongoing Palace of Nestor Excavations (PONEX) project, bringing together two excavation campaigns conducted under very different circumstances, methodologies, and recording protocols. Discussion follows on how the production of this GIS deepens our understanding not just of the legacy excavation, but also of the site and its wider landscape.Loy’s contribution to the project in 2018 and 2019 was supported jointly by the Arts and Humanities Research Council (AHRC) and Pembroke College Cambridge, award number AH/L503897/1, with further funding for travel made available by the Louise Taft Semple Fund of the Department of Classics of the University of Cincinnat

Late Bronze Age climate change and the destruction of the Mycenaean Palace of Nestor at Pylos

This paper offers new high-resolution oxygen and carbon isotope data from Stalagmite S1 from Mavri Trypa Cave, SW Peloponnese. Our data provide the climate background to the destruction of the nearby Mycenaean Palace of Nestor at Pylos at the transition from Late Helladic (LH) IIIB to LH IIIC, similar to 3150-3130 years before present (before AD 1950, hereafter yrs BP) and the subsequent period. S1 is dated by 24 U-Th dates with an averaged precision of +/- 26 yrs (2s), providing one of the most robust paleoclimate records from the eastern Mediterranean for the end of the Late Bronze Age (LBA). The delta O-18 record shows generally wetter conditions at the time when the Palace of Nestor at Pylos was destroyed, but a brief period of drier conditions around 3200 yrs BP may have disrupted the Mycenaean agricultural system that at the time was likely operating close to its limit. Gradually developing aridity after 3150 yrs BP, i.e. subsequent to the destruction, probably reduced crop yields and helped to erode the basis for the reinstitution of a central authority and the Palace itself

Quantitative chest computed tomography combined with plasma cytokines predict outcomes in COVID-19 patients

Despite extraordinary international efforts to dampen the spread and understand the mechanisms behind SARS-CoV-2 infections, accessible predictive biomarkers directly applicable in the clinic are yet to be discovered. Recent studies have revealed that diverse types of assays bear limited predictive power for COVID-19 outcomes. Here, we harness the predictive power of chest computed tomography (CT) in combination with plasma cytokines using a machine learning and k-fold cross-validation approach for predicting death during hospitalization and maximum severity degree in COVID-19 patients. Patients (n = 152) from the Mount Sinai Health System in New York with plasma cytokine assessment and a chest CT within five days from admission were included. Demographics, clinical, and laboratory variables, including plasma cytokines (IL-6, IL-8, and TNF-α), were collected from the electronic medical record. We found that CT quantitative alone was better at predicting severity (AUC 0.81) than death (AUC 0.70), while cytokine measurements alone better-predicted death (AUC 0.70) compared to severity (AUC 0.66). When combined, chest CT and plasma cytokines were good predictors of death (AUC 0.78) and maximum severity (AUC 0.82). Finally, we provide a simple scoring system (nomogram) using plasma IL-6, IL-8, TNF-α, ground-glass opacities (GGO) to aerated lung ratio and age as new metrics that may be used to monitor patients upon hospitalization and help physicians make critical decisions and considerations for patients at high risk of death for COVID-19

Realising consilience: How better communication between archaeologists, historians and natural scientists can transform the study of past climate change in the Mediterranean

This paper reviews the methodological and practical issues relevant to the ways in which natural scientists, historians and archaeologists may collaborate in the study of past climatic changes in the Mediterranean basin. We begin by discussing the methodologies of these three disciplines in the context of the consilience debate, that is, attempts to unify different research methodologies that address similar problems. We demonstrate that there are a number of similarities in the fundamental methodology between history, archaeology, and the natural sciences that deal with the past (“palaeoenvironmental sciences”), due to their common interest in studying societal and environmental phenomena that no longer exist. The three research traditions, for instance, employ specific narrative structures as a means of communicating research results. We thus present and compare the narratives characteristic of each discipline; in order to engage in fruitful interdisciplinary exchange, we must first understand how each deals with the societal impacts of climatic change. In the second part of the paper, we focus our discussion on the four major practical issues that hinder communication between the three disciplines. These include terminological misunderstandings, problems relevant to project design, divergences in publication cultures, and differing views on the impact of research. Among other recommendations, we suggest that scholars from the three disciplines should aim to create a joint publication culture, which should also appeal to a wider public, both inside and outside of academia.This paper emerged as a result of a workshop at Costa Navarino and the Navarino Environmental Observatory (NEO), Greece in April 2014, which addressed Mediterranean Holocene climate and human societies. The workshop was co-sponsored by IGBP/PAGES, NEO, the MISTRALS/PaleoMex program, the Labex OT-Med, the Bolin Centre for Climate Research at Stockholm University, and the Institute of Oceanography at the Hellenic Centre for Marine Research. We also acknowledge funding from the National Science Centre, Poland, within the scheme of the Centre's postdoctoral fellowships (DEC-2012/04/S/HS3/00226 (A.I)); the Swedish Research Council (grant numbers 421-2014-1181 (E.W.) and 621-2012-4344 (K.H.)); CSIC-Ramón y Cajal post-doctoral program RYC-2013-14073 and Clare Hall College, Cambridge, Shackleton Fellowship (B.M.); the EU/FP7 Project ‘Sea for Society’ (Science and Society - 2011-1, 289066)

MicroMotility: State of the art, recent accomplishments and perspectives on the mathematical modeling of bio-motility at microscopic scales

Mathematical modeling and quantitative study of biological motility (in particular, of motility at microscopic scales) is producing new biophysical insight and is offering opportunities for new discoveries at the level of both fundamental science and technology. These range from the explanation of how complex behavior at the level of a single organism emerges from body architecture, to the understanding of collective phenomena in groups of organisms and tissues, and of how these forms of swarm intelligence can be controlled and harnessed in engineering applications, to the elucidation of processes of fundamental biological relevance at the cellular and sub-cellular level. In this paper, some of the most exciting new developments in the fields of locomotion of unicellular organisms, of soft adhesive locomotion across scales, of the study of pore translocation properties of knotted DNA, of the development of synthetic active solid sheets, of the mechanics of the unjamming transition in dense cell collectives, of the mechanics of cell sheet folding in volvocalean algae, and of the self-propulsion of topological defects in active matter are discussed. For each of these topics, we provide a brief state of the art, an example of recent achievements, and some directions for future research

Epigenome-wide association study of serum urate reveals insights into urate co-regulation and the SLC2A9 locus

Elevated serum urate levels, a complex trait and major risk factor for incident gout, are correlated with cardiometabolic traits via incompletely understood mechanisms. DNA methylation in whole blood captures genetic and environmental influences and is assessed in transethnic meta-analysis of epigenome-wide association studies (EWAS) of serum urate (discovery, n = 12,474, replication, n = 5522). The 100 replicated, epigenome-wide significant (p < 1.1E–7) CpGs explain 11.6% of the serum urate variance. At SLC2A9, the serum urate locus with the largest effect in genome-wide association studies (GWAS), five CpGs are associated with SLC2A9 gene expression. Four CpGs at SLC2A9 have significant causal effects on serum urate levels and/or gout, and two of these partly mediate the effects of urate-associated GWAS variants. In other genes, including SLC7A11 and PHGDH, 17 urate-associated CpGs are associated with conditions defining metabolic syndrome, suggesting that these CpGs may represent a blood DNA methylation signature of cardiometabolic risk factors. This study demonstrates that EWAS can provide new insights into GWAS loci and the correlation of serum urate with other complex traits

Meta-analyses identify DNA methylation associated with kidney function and damage

Chronic kidney disease is a major public health burden. Elevated urinary albumin-to-creatinine ratio is a measure of kidney damage, and used to diagnose and stage chronic kidney disease. To extend the knowledge on regulatory mechanisms related to kidney function and disease, we conducted a blood-based epigenome-wide association study for estimated glomerular filtration rate (n = 33,605) and urinary albumin-to-creatinine ratio (n = 15,068) and detected 69 and seven CpG sites where DNA methylation was associated with the respective trait. The majority of these findings showed directionally consistent associations with the respective clinical outcomes chronic kidney disease and moderately increased albuminuria. Associations of DNA methylation with kidney function, such as CpGs at JAZF1, PELI1 and CHD2 were validated in kidney tissue. Methylation at PHRF1, LDB2, CSRNP1 and IRF5 indicated causal effects on kidney function. Enrichment analyses revealed pathways related to hemostasis and blood cell migration for estimated glomerular filtration rate, and immune cell activation and response for urinary albumin-to-creatinineratio-associated CpGs

Plasma lipid profiles discriminate bacterial from viral infection in febrile children

Fever is the most common reason that children present to Emergency Departments. Clinical signs and symptoms suggestive of bacterial infection are often non-specific, and there is no definitive test for the accurate diagnosis of infection. The 'omics' approaches to identifying biomarkers from the host-response to bacterial infection are promising. In this study, lipidomic analysis was carried out with plasma samples obtained from febrile children with confirmed bacterial infection (n = 20) and confirmed viral infection (n = 20). We show for the first time that bacterial and viral infection produces distinct profile in the host lipidome. Some species of glycerophosphoinositol, sphingomyelin, lysophosphatidylcholine and cholesterol sulfate were higher in the confirmed virus infected group, while some species of fatty acids, glycerophosphocholine, glycerophosphoserine, lactosylceramide and bilirubin were lower in the confirmed virus infected group when compared with confirmed bacterial infected group. A combination of three lipids achieved an area under the receiver operating characteristic (ROC) curve of 0.911 (95% CI 0.81 to 0.98). This pilot study demonstrates the potential of metabolic biomarkers to assist clinicians in distinguishing bacterial from viral infection in febrile children, to facilitate effective clinical management and to the limit inappropriate use of antibiotics