A proposed division of the family Picornaviridae into subfamilies based on phylogenetic relationships and functional genomic organization

The highly diverse virus family Picornaviridae presently comprises 68 approved genera with 158 species plus many unassigned viruses. In order to better match picornavirus taxonomy to the functional and genomic groupings between genera, the establishment of five subfamilies (Caphthovirinae, Kodimesavirinae, Ensavirinae, Paavivirinae and Heptrevirinae) is proposed. The subfamilies are defined by phylogenetic analyses of 3CD (precursor of virus-encoded proteinase and polymerase) and P1 (capsid protein precursor) coding sequences and comprise between 7 and 22 currently approved virus genera. Due to the high within-subfamily and between-subfamily divergences of the picornavirus genera, p-distance estimates are unsuited for the demarcation of subfamilies. Members of the proposed subfamilies typically show some commonalities in their genome organisations, including VP1/2A cleavage mechanisms and possession of leader proteins. Other features, such as internal ribosomal entry site types, are more variable within and between members of genera. Some subfamilies are characterised by homology of proteins 1A, 2A, 2B and 3A encoded by members, which do not belong to the canon of orthologous picornavirus proteins. The proposed addition of a subfamily layer to the taxonomy of picornaviruses provides a valuable additional organisational level to the family that acknowledges the existence of higher-level evolutionary groupings of its component genera.

Labelling the past: data set creation and multi-label classification of Dutch archaeological excavation reports

The extraction of information from Dutch archaeological grey literature has recently been investigated by the AGNES project. AGNES aims to disclose relevant information by means of a web search engine, to enable researchers to search through excavation reports. In this paper, we focus on the multi-labelling of archaeological excavation reports with time periods and site types, and provide a manually labelled reference set to this end. We propose a series of approaches, pre-processing methods, and various modifications of the training set to address the often low quality of both texts and labels. We find that despite those issues, our proposed methods lead to promising results.

Using a Bayesian Modelling Approach to the Understand the Redistribution of Pottery to Romano-British Rural Sites

The vast majority of inhabitants of Roman Britain lived in the countryside. However, the redistribution of pottery to Romano-British rural sites is poorly understood. To address this issue, a Bayesian approach (Integrated Nested Laplace Approximation, INLA) is used to model the count of pottery recovered from rural sites. Through model selection, the redistribution of pottery was identified to be driven by small towns and pottery production sites. Findings also suggest that the redistribution of pottery was not homogenous across site types, with Roman roads and local trackways playing an important role.

Clonal variation in coppiced and uncoppiced growth, root-sprout stem formation, and biomass partitioning in Salix interior on two highly disturbed site types

Salix interior Rowlee (INT), a wide-ranging North American willow from the small taxonomic group Salix sect. Longifoliae, is notable for its ability to form multi-stemmed vegetative stem colonies arising via root sprouts (RS) from a shallow horizontal root network. This study quantifies biomass production for both 1-yr-old coppiced plants and the original 4-yr-old plants, as well as for the RS stems associated with each ortet (original mother plant) using eight selected genotypes established on two distinct site types. Significantly greater coppiced and uncoppiced ortet stem dry mass was recorded on the coarse-textured, shale rock overburden (SO); possibly due to significantly greater fertility, compared to adjacent gravel outwash deposits (GD), which had greater RS stem mass. Significant clonal differences, as well as site type × clone interactions, were found for ortet stem dry mass, especially on SO sites, When expressed as a fraction of total stem dry mass produced on 2 m × 2 m biomass plots, the RS component represented a significant 57% of total stem dry mass per plot on GD sites. The use of colony-forming willows such as INT minimizes the need for periodic replanting, providing a cost advantage over conventional short-rotation, coppice-based woody biomass plantations using species that do not have the ability to reproduce via root sprouting.

Was pike on the menu? Exploring the role of freshwater fish in medieval England

Historical sources report that some species of freshwater fish were considered luxury food items in England during the Middle Ages. The high retail price associated with species such as pike, salmon and sturgeon, as well as restrictions of fishing rights on rivers, estuaries and natural and artificial ponds, proves their exclusivity and role as symbols of social privilege. In this work, the zooarchaeological evidence from 11 English sites dated between the 11th and the 15th c. AD is discussed. This paper explores the differences between the ranges of freshwater species recovered from different site types, by looking at specific features that could define these fishes as luxury items: in particular, species selection and fish size are investigated as potentially meaningful variables. The size of fish will be used as an indicator of status and interpreted in view of the increasing phenomenon of fishing from artificial fishponds.

Bryophytes as key indicators of ecosystem function and structure of northern peatlands

Bryophytes play a number of important roles in the functioning and structure of northern peatlands where they form the ground layer of fens and bogs. Sphagnum, dominant in bogs and poor fens, and brown mosses, dominant in rich fens, make up a large percentage of the organic matter that is stored as deep deposits of peat. In this paper we review the mechanisms of resistance to decay in these two moss groups. We then document a case study of a rich fen dominated mostly by Hamatocaulis vernicosus, that has remained stable for over 8000 calendar years. At this site, we use macrofossil abundances, including bryophyte habitat positions on water level and chemistry gradients, to infer past environmental conditions. Lastly, we provide a new ecohydrologic framework for wetland classes centered on bryophyte abundances across water level, nutrient, and salinity gradients and argue that bryophyte species are among the most significant indicators for classifying wetland site-types.

Dioxygen Activation Kinetics over Distinct Cu Site Types in Cu-CHA Zeolites

Cu-exchanged zeolites activate dioxygen to form active sites for partial methane oxidation (PMO), nitrogen oxide decomposition, and carbon monoxide oxidation. Apparent rates of O₂ activation depend both on the intrinsic kinetics of distinct Cu site types and the distributions of such sites within a given zeolite, which depend on the density and arrangement of the framework Al atoms. Here, we use hydrothermal synthesis methods to control the arrangement of framework Al sites in chabazite (CHA) zeolites and, in turn, the distinct Cu site types formed. Time-resolved in situ resonance Raman spectroscopy reveals the kinetics of O₂ adsorption and activation within these well-defined Cu-CHA materials and the concomitant structural evolution of copper-oxygen (Cu_xO_y) complexes, which are interpreted alongside Cu(I) oxidation kinetics extracted from in situ X-ray absorption spectroscopy (XAS). Raman spectra of several plausible CuxOy species simulated using density functional theory suggest that experimental spectra (λ_ex = 532 nm) capture the formation of mono(μ-oxo)dicopper species (ZCuOCuZ). Transient experiments show that the timescales required to form Cu_xO_y structures that no longer change in Ra-man spectra correspond to the durations of oxidative treatments that maximize CH₃OH yields in stoichiometric PMO cycles (approximately 2 h). Yet, these periods extend well beyond the timescales for the complete conversion of the initial Cu(I) intermediates to their Cu(II) states (<0.3 h, reflected in XANES spectra), which demonstrates that Cu_xO_y complexes continue to evolve structurally following rapid oxidation. The dependence of ZCuOCuZ formation rates on O₂ pressure, H₂O pressure, and temperature are consistent with a mechanism in which ZCuOH reduce to form ZCu⁺ sites that bind molecular oxygen and form ZCu-O₂ intermediates. Subsequent reaction with proximate ZCu⁺ form bridging peroxo dicopper complexes that cleave O-O bonds to form ZCuOCuZ in steps facilitated by water. These data and interpretations provide evidence for the chemical processes that link rapid and kinetically irrelevant Cu oxidation steps (frequently probed by XAS and UV-Vis spectroscopy) to the relatively slow genesis of reactive Cu complexes that form CH₃OH during PMO. In doing so, we reveal previously unrec-ognized complexities in the processes by which Cu ions in zeolites activate O₂ to form active Cu_xO_y complexes, which under-score the insight afforded by judicious combinations of experimental and theoretical techniques.

Dioxygen Activation Kinetics over Distinct Cu Site Types in Cu-CHA Zeolites

Cu-exchanged zeolites activate dioxygen to form active sites for partial methane oxidation (PMO), nitrogen oxide decomposition, and carbon monoxide oxidation. Apparent rates of O₂ activation depend both on the intrinsic kinetics of distinct Cu site types and the distributions of such sites within a given zeolite, which depend on the density and arrangement of the framework Al atoms. Here, we use hydrothermal synthesis methods to control the arrangement of framework Al sites in chabazite (CHA) zeolites and, in turn, the distinct Cu site types formed. Time-resolved in situ resonance Raman spectroscopy reveals the kinetics of O₂ adsorption and activation within these well-defined Cu-CHA materials and the concomitant structural evolution of copper-oxygen (Cu_xO_y) complexes, which are interpreted alongside Cu(I) oxidation kinetics extracted from in situ X-ray absorption spectroscopy (XAS). Raman spectra of several plausible CuxOy species simulated using density functional theory suggest that experimental spectra (λ_ex = 532 nm) capture the formation of mono(μ-oxo)dicopper species (ZCuOCuZ). Transient experiments show that the timescales required to form Cu_xO_y structures that no longer change in Ra-man spectra correspond to the durations of oxidative treatments that maximize CH₃OH yields in stoichiometric PMO cycles (approximately 2 h). Yet, these periods extend well beyond the timescales for the complete conversion of the initial Cu(I) intermediates to their Cu(II) states (<0.3 h, reflected in XANES spectra), which demonstrates that Cu_xO_y complexes continue to evolve structurally following rapid oxidation. The dependence of ZCuOCuZ formation rates on O₂ pressure, H₂O pressure, and temperature are consistent with a mechanism in which ZCuOH reduce to form ZCu⁺ sites that bind molecular oxygen and form ZCu-O₂ intermediates. Subsequent reaction with proximate ZCu⁺ form bridging peroxo dicopper complexes that cleave O-O bonds to form ZCuOCuZ in steps facilitated by water. These data and interpretations provide evidence for the chemical processes that link rapid and kinetically irrelevant Cu oxidation steps (frequently probed by XAS and UV-Vis spectroscopy) to the relatively slow genesis of reactive Cu complexes that form CH₃OH during PMO. In doing so, we reveal previously unrec-ognized complexities in the processes by which Cu ions in zeolites activate O₂ to form active Cu_xO_y complexes, which under-score the insight afforded by judicious combinations of experimental and theoretical techniques.

The Human Impact on Changes in the Forest Range of the Silesian Beskids (Western Carpathians)

Changes in forest range are caused by human activity in many regions of the world. The aim of this paper is an attempt to determine the impact of pastoral and forest management on changes in forest cover and their fragmentation in the Silesian Beskids (southern Poland) in 1848–2015. Historical maps and landscape metrics were used to study changes in forest cover. Using a digital map of forests, analyses of the distribution of forest communities, site types and their condition were conducted. Since 1848 the forest area has increased by 11.8%, while the area of forest core zones has increased by 16.2%, accompanied by a 4.5% reduction in the forest’s internal buffer zone. From the mid-nineteenth century, the forest range has been systematically growing from 82.1 to 93.9% because of the pastureland abandonment and forest regeneration, despite temporary logging resulting in forest fragmentation. Minor changes in core area index (CAI) from 80.41 to 87.55 indicate that pastoral economy did not result in considerable fragmentation of forests. The impact of forest management was greater as the sites characterised by natural condition occupy only 28% of the forest land and anthropogenically transformed ones dominate occupying over 50%. An artificial spruce monoculture was died-off and large felling areas were created at the beginning of the twenty-first century covering almost 40% of the study area.