Ceramic composition at Chalcolithic Shiqmim, northern Negev desert, Israel: investigating technology and provenance using thin section petrography, instrumental geochemistry and calcareous nannofossils

Technological innovations in ceramic production and other crafts are hallmarks of the Chalcolithic period (4500–3600 BCE) in the southern Levant, but details of manufacturing traditions have not been fully investigated using the range of analytical methods currently available. This paper presents results of a compositional study of 51 sherds of ceramic churns and other pottery types from the Chalcolithic site of Shiqmim in the northern Negev desert. By applying complementary thin section petrography, instrumental geochemistry and calcareous nannofossil analyses, connections between the raw materials, clay paste recipes and vessel forms of the selected ceramic samples are explored and documented. The study indicates that steps in ceramic manufacturing can be related to both technological choices and local geology. Detailed reporting of the resulting data facilitates future comparative ceramic compositional research that is needed as a basis for testable regional syntheses and to better resolve networks of trade/exchange and social group movement

Optic Neuritis and Retinal Ganglion Cell Loss in a Chronic Murine Model of Multiple Sclerosis

Multiple sclerosis (MS) and its animal model experimental autoimmune encephalomyelitis (EAE) are neurodegenerative diseases with characteristic inflammatory demyelination in the central nervous system, including the optic nerve. Neuronal and axonal damage is considered to be the main cause of long-term disability in patients with MS. Neuronal loss, including retinal ganglion cell (RGC) apoptosis in eyes with optic neuritis (ON), also occurs in EAE. However, there is significant variability in the clinical course and level of neuronal damage in MS and EAE. The current studies examine the mechanisms and kinetics of RGC loss in C57/BL6 mice immunized with myelin oligodendrocyte glycoprotein to induce a chronic EAE disease. Clinical progression of EAE was scored daily and vision was assessed by optokinetic responses. At various time points, RGCs were counted and optic nerves were examined for inflammatory cell infiltration. Almost all EAE mice develop ON by day 15 post-immunization; however, RGC loss is delayed in these mice. No RGC loss is detected 25 days post-immunization, whereas RGC numbers in EAE mice significantly and progressively decrease compared to controls from 35 to 50 days post-immunization. The delayed time course of RGC loss is in stark contrast to that reported in relapsing EAE, as well as in rats with chronic EAE. Results suggest that different clinical disease courses of optic nerve inflammation may trigger distinct mechanisms of neuronal damage, or RGCs in different rodent strains may have variable resistance to neuronal degeneration

Bugs as Features (Part II): A Perspective on Enriching Microbiome-Gut-Brain Axis Analyses with Multidisciplinary Techniques

The microbiome-gut-brain-axis field is multidisciplinary, benefiting from the expertise of microbiology, ecology, psychiatry, computational biology, and epidemiology amongst other disciplines. As the field matures and moves beyond a basic demonstration of its relevance, it is critical that study design and analysis are robust and foster reproducibility. In this companion piece to Bugs as Features (Part 1), we present techniques from adjacent and disparate fields to enrich and inform the analysis of microbiome-gut-brain-axis data. Emerging techniques built specifically for the microbiome-gut-brain axis are also demonstrated. All of these methods are contextualised to inform several common challenges: how do we establish causality? How can we integrate data from multiple 'omics techniques? How might we account for the dynamicism of host-microbiome interactions? This perspective is offered to experienced and emerging microbiome scientists alike, to assist with these questions and others, at the study conception, design, analysis and interpretation stages of research.Comment: For main text: 20 pages, 2 figures; for supplementary analysis: 31 pages and 6 figures. Supplementary analysis generated using Rmarkdown by Thomaz F. S. Bastiaanssen. arXiv admin note: substantial text overlap with arXiv:2207.1247

Bugs as Features (Part I): Concepts and Foundations for the Compositional Data Analysis of the Microbiome-Gut-Brain Axis

There has been a growing acknowledgement of the involvement of the gut microbiome - the collection of microbes that reside in our gut - in regulating our mood and behaviour. This phenomenon is referred to as the microbiome-gut-brain axis. While our techniques to measure the presence and abundance of these microbes have been steadily improving, the analysis of microbiome data is non-trivial. Here, we present a perspective on the concepts and foundations of data analysis and interpretation of microbiome experiments with a focus on the microbiome-gut-brain axis domain. We give an overview of foundational considerations prior to commencing analysis alongside the core microbiome analysis approaches of alpha diversity, beta diversity, differential feature abundance and functional inference. We emphasize the compositional data analysis (CoDA) paradigm. Further, this perspective features an extensive and heavily annotated microbiome analysis in R in the supplementary materials, as a resource for new and experienced bioinformaticians alike.Comment: For main text: 23 pages, 3 figures; for supplementary demonstration analysis: 31 pages and 12 figures. Supplementary demonstration analysis generated using Rmarkdown by Thomaz F. S. Bastiaanssen. Part I of a two-part piec

The age dependence of galaxy clustering

We construct mock galaxy catalogues to analyse clustering properties of a Λ cold dark matter universe within a cosmological dark matter simulation of sufficient resolution to resolve structure down to the scale of dwarfs. We show that there is a strong age-clustering correlation for objects likely to host luminous galaxies, which includes the satellite halo (subhalo) population. Older mock galaxies are significantly more clustered in our catalogue, which consists of satellite haloes as well as the central peaks of discrete haloes, selected solely by peak circular velocity. This age dependence is caused mainly by the age-clustering relation for discrete haloes, recently found by Gao et al., acting mostly on field members, combined with the tendency for older mock galaxies to lie within groups and clusters, where galaxy clustering is enhanced. Our results suggest that the clustering-age dependence is manifested in real galaxies. At small scales (less than ∼5 h−1 Mpc), the very simple assumption that galaxy colour depends solely on halo age is inconsistent with the strength of the observed clustering colour trends, where red galaxies become increasingly more clustered than blue galaxies towards smaller scales, suggesting that luminosity-weighted galaxy ages do not closely trace the assembly epoch of their dark matter hosts. The age dependence is present but is much weaker for satellite haloes lying within groups and clusters than for the global populatio

The Role of the Radial Orbit Instability in Dark Matter Halo Formation and Structure

For a decade, N-body simulations have revealed a nearly universal dark matter density profile, which appears to be robust to changes in the overall density of the universe and the underlying power spectrum. Despite its universality, the physical origin of this profile has not yet been well understood. Semi--analytic models by Barnes et al. (2005) have suggested that the density structure of dark matter halos is determined by the onset of the radial orbit instability (ROI). We have tested this hypothesis using N-body simulations of collapsing dark matter halos with a variety of initial conditions. For dynamically cold initial conditions, the resulting halo structures are triaxial in shape, due to the mild aspect of the instability. We examine how variations in initial velocity dispersion affect the onset of the instability, and find that an isotropic velocity dispersion can suppress the ROI entirely, while a purely radial dispersion does not. The quantity sigma^2/vc^2 is a criterion for instability, where regions with sigma^2/vc^2 <~1 become triaxial due to the ROI or other perturbations. We also find that the radial orbit instability sets a scale length at which the velocity dispersion changes rapidly from isotropic to radially anisotropic. This scale length is proportional to the radius at which the density profile changes shape, as is the case in the semi--analytic models; however, the coefficient of proportionality is different by a factor of ~2.5. We conclude that the radial orbit instability is likely to be a key physical mechanism responsible for the nearly universal profiles of simulated dark matter halos.Comment: 13 pages, 12 figures, accepted to Ap