Artificial light at night alters predation on colour-polymorphic camouflaged prey

Artificial light at night (ALAN) disrupts biological processes across taxa and at all levels of organisation. Despite growing interest in this globally pervasive sensory pollutant, its impact on colour-guided processes remains largely unexplored. This is especially concerning given the rapid transition in recent years away from narrow-spectrum lighting and towards broad-spectrum options such as white LEDs, which are rich in the short wavelengths of light to which many taxa are particularly sensitive. Camouflage is particularly likely to be disrupted by broader spectra of ALAN due to changes in conspicuousness in background matching prey, which may alter prey recognition in visually guided predators. We simulated natural intensities of moonlight with and without ALAN, using both broad-spectrum (‘white’) ALAN and ALAN filtered to remove the characteristic short (blue) wavelength peak of broad-spectrum LEDs to test whether filtering might mitigate their effects. We tested how exposure to these light treatments impacted predator-prey interactions, using the intertidal crab Carcinus maenas and contrasting colour morphs of the colour-polymorphic snail Littorina obtusata as a model system. Exposure to broad-spectrum ALAN reduced overall predation and reversed the pattern of colour-based prey selection observed under control conditions. Snails were 55% less likely to be attacked under broad-spectrum ALAN than in control conditions, with likelihood decreasing over 70% for yellow snails. Yellow snails were over 26% more likely to be attacked than brown ones under control conditions, but brown snails were over 40% more likely to be attacked than yellow ones under broad-spectrum ALAN. Exposure to filtered ALAN removed any significant colour-based difference in prey recognition. Our results demonstrate that spectral composition is a crucial aspect of ALAN as a sensory pollutant, capable of instigating profound changes in predator-prey interactions that could drive changes in population demography and increase morphological homogeneity in species that depend on colour polymorphism for camouflage

Muon identification for the ATLAS experiment

The ATLAS experiment will efficiently reconstruct and identify muons, using data recorded by different sub-detectors. Muon tracks will be reconstructed in the inner tracking system and in the outermost muon spectrometer, exploiting both the solenoidal and the toroidal magnetic fields for momentum measurement; the corresponding energy deposits in the calorimeters will also be measured. Here we present the algorithms developed to combine these reconstructed quantities, in order to obtain a robust and precise muon identification capability. The peculiarities of each possible combined reconstruction technique will be discussed and the corresponding performance, evaluated on simulated samples, will be reported

Concepts, Design and Implementation of the ATLAS New Tracking (NEWT)

The track reconstruction of modern high energy physics experiments is a very complex task that puts stringent requirements onto the software realisation. The ATLAS track reconstruction software has been in the past dominated by a collection of individual packages, each of which incorporating a different intrinsic event data model, different data flow sequences and calibration data. Invoked by the Final Report of the Reconstruction Task Force, the ATLAS track reconstruction has undergone a major design revolution to ensure maintainability during the long lifetime of the ATLAS experiment and the flexibility needed for the startup phase. The entire software chain has been re-organised in modular components and a common Event Data Model has been deployed during the last three years. A complete new track reconstruction that concentrates on common tools aimed to be used by both ATLAS tracking devices, the Inner Detector and the Muon System, has been established. It has been already used during many large scale tests with data from Monte Carlo simulation and from detector commissioning projects such as the combined test beam 2004 and cosmic ray events. This document concentrates on the technical and conceptual details of the newly developed track reconstruction, also known as New Tracking

Blood ties: ABO is a trans-species polymorphism in primates

The ABO histo-blood group, the critical determinant of transfusion incompatibility, was the first genetic polymorphism discovered in humans. Remarkably, ABO antigens are also polymorphic in many other primates, with the same two amino acid changes responsible for A and B specificity in all species sequenced to date. Whether this recurrence of A and B antigens is the result of an ancient polymorphism maintained across species or due to numerous, more recent instances of convergent evolution has been debated for decades, with a current consensus in support of convergent evolution. We show instead that genetic variation data in humans and gibbons as well as in Old World Monkeys are inconsistent with a model of convergent evolution and support the hypothesis of an ancient, multi-allelic polymorphism of which some alleles are shared by descent among species. These results demonstrate that the ABO polymorphism is a trans-species polymorphism among distantly related species and has remained under balancing selection for tens of millions of years, to date, the only such example in Hominoids and Old World Monkeys outside of the Major Histocompatibility Complex.Comment: 45 pages, 4 Figures, 4 Supplementary Figures, 5 Supplementary Table

Editorial: Vagus nerve-mediated drive in supporting homeostasis: optimizing global health through monitoring and stimulating vagal function

Epigenetics encompasses the changes in gene expression triggered by environmental cues that occur without altering the underlying DNA sequences. Although epigenetics involves a limited number of identified mechanisms so far (DNA methylation, histone modifications and noncoding RNAs), the field of Epigenetics is spreading rapidly over integrated physiopathology (Jeffries, 2020). The importance of epigenetics has been acknowledged in cancer (Sun et al., 2022), sepsis (Binnie et al., 2020), autoimmune/inflammatory diseases (Surace and Hedrich, 2019), addiction (Hamilton and Nestler, 2019), aging (Pal and Tyler, 2016; Pérez et al., 2022), neurodegenerative diseases (Berson et al., 2018; Zhang et al., 2022) and even in neurodevelopmental (Esposito et al., 2018; Wu et al., 2020) and psychiatric diseases (Abdolmaleky et al., 2023). Likewise, a broad and expanding set of therapies in clinics have been potentialized by tuning the vagal complex of brainstem, i.e., the key neural node of homeostasis, via non-invasive Vagus Nerve Stimulation (VNS) (Hilz, 2022). Moreover, Heart Rate Variability (HRV), a physiologically validated and easily accessible read-out of the vagal tone (Lewis et al., 2012), is acknowledged as a polyvalent prognostic tool (Gidron et al., 2018; Mol et al., 2021). This is not surprising, since Epigenome is considered as a “mediator for host-microbiome crosstalk” (Peery et al., 2021) and since vagus nerve represents the fastest pathway of the Microbiota-Gut-brain Axis (Fülling et al., 2019). However, except for regulating neuro-inflammation (Chen et al., 2022), the mechanisms through which VNS influences peripheral and central nervous system plasticity are not well described yet, limiting therapeutic optimization (Morrison et al., 2020; Keute and Gharabaghi, 2021). Therefore, as the vagal complex (i.e., peripheral and brainstem components) is definitely prone to bring about epigenetic modulations, notably through neuro-endocrine stimuli (Gil et al., 2013), we questioned the epigenetic role of vagus nerve, in order to promote noninvasive VNS, guided by HRV monitoring, as a universal therapy to stay healthy

ATLAS Tracking Event Data Model

In this report the event data model (EDM) relevant for tracking in the ATLAS experiment is presented. The core component of the tracking EDM is a common track object which is suited to describe tracks in the innermost tracking sub-detectors and in the muon detectors in offline as well as online reconstruction. The design of the EDM was driven by a demand for modularity and extensibility while taking into account the different requirements of the clients. The structure of the track object and the representation of the tracking-relevant information are described in detail

Updates of the ATLAS Tracking Event Data Model (Release 13)

In a previous document we have presented the ATLAS tracking Event Data Model (EDM) that has been developed during the recent restructuring of the ATLAS offline track reconstruction. The tracking EDM has become a cornerstone of the new modular track reconstruction algorithms of both tracking devices of the ATLAS detector, the Inner Detector and the Muon System. Recently, some components have undergone yet another design evolution targeted at completing missing modules and at establishing anticipated functionality for the startup of the ATLAS experiment. One particular aspect of the EDM is that is does not only have to fulfill the requirements of today's algorithmic modules, but has to provide the flexibility for future developments. This document is based on ATLAS software release 13.0.0

ATLAS Inner Detector Event Data Model

The data model for event reconstruction (EDM) in the Inner Detector of the ATLAS experiment is presented. Different data classes represent evolving stages in the reconstruction data flow, and specific derived classes exist for the sub-detectors. The Inner Detector EDM also extends the data model for common tracking in ATLAS and is integrated into the modular design of the ATLAS high-level trigger and off-line software

Organization and management of ATLAS software releases

International audienceATLAS is one of the largest collaborations ever undertaken in the physical sciences. This paper explains how the software infrastructure is organized to manage collaborative code development by around 300 developers with varying degrees of expertise, situated in 30 different countries. We will describe how the succeeding releases of the software are built, validated and subsequently deployed to remote sites. Several software management tools have been used, the majority of which are not ATLAS specific; we will show how they have been integrated. ATLAS offline software currently consists of about 2 MSLOC contained in 6800 C++ classes, organized in almost 1000 packages

Organization and management of ATLAS offline software releases

ATLAS is one of the largest collaborations ever undertaken in the physical sciences. This paper explains how the software infrastructure is organized to manage collaborative code development by around 300 developers with varying degrees of expertise, situated in 30 different countries. ATLAS offline software currently consists of about 2 million source lines of code contained in 6800 C++ classes, organized in almost 1000 packages. We will describe how releases of the offline ATLAS software are built, validated and subsequently deployed to remote sites. Several software management tools have been used, the majority of which are not ATLAS specific; we will show how they have been integrated