EXACT: a collaboration toolset for algorithm-aided annotation of images with annotation version control

In many research areas, scientific progress is accelerated by multidisciplinary access to image data and their interdisciplinary annotation. However, keeping track of these annotations to ensure a high-quality multi-purpose data set is a challenging and labour intensive task. We developed the open-source online platform EXACT (EXpert Algorithm Collaboration Tool) that enables the collaborative interdisciplinary analysis of images from different domains online and offline. EXACT supports multi-gigapixel medical whole slide images as well as image series with thousands of images. The software utilises a flexible plugin system that can be adapted to diverse applications such as counting mitotic figures with a screening mode, finding false annotations on a novel validation view, or using the latest deep learning image analysis technologies. This is combined with a version control system which makes it possible to keep track of changes in the data sets and, for example, to link the results of deep learning experiments to specific data set versions. EXACT is freely available and has already been successfully applied to a broad range of annotation tasks, including highly diverse applications like deep learning supported cytology scoring, interdisciplinary multi-centre whole slide image tumour annotation, and highly specialised whale sound spectroscopy clustering

Nutrition or Detoxification: Why Bats Visit Mineral Licks of the Amazonian Rainforest

Many animals in the tropics of Africa, Asia and South America regularly visit so-called salt or mineral licks to consume clay or drink clay-saturated water. Whether this behavior is used to supplement diets with locally limited nutrients or to buffer the effects of toxic secondary plant compounds remains unclear. In the Amazonian rainforest, pregnant and lactating bats are frequently observed and captured at mineral licks. We measured the nitrogen isotope ratio in wing tissue of omnivorous short-tailed fruit bats, Carollia perspicillata, and in an obligate fruit-eating bat, Artibeus obscurus, captured at mineral licks and at control sites in the rainforest. Carollia perspicillata with a plant-dominated diet were more often captured at mineral licks than individuals with an insect-dominated diet, although insects were more mineral depleted than fruits. In contrast, nitrogen isotope ratios of A. obscurus did not differ between individuals captured at mineral lick versus control sites. We conclude that pregnant and lactating fruit-eating bats do not visit mineral licks principally for minerals, but instead to buffer the effects of secondary plant compounds that they ingest in large quantities during periods of high energy demand. These findings have potential implications for the role of mineral licks for mammals in general, including humans

The K-theory of free quantum groups

In this paper we study the K -theory of free quantum groups in the sense of Wang and Van Daele, more precisely, of free products of free unitary and free orthogonal quantum groups. We show that these quantum groups are K -amenable and establish an analogue of the Pimsner–Voiculescu exact sequence. As a consequence, we obtain in particular an explicit computation of the K -theory of free quantum groups. Our approach relies on a generalization of methods from the Baum–Connes conjecture to the framework of discrete quantum groups. This is based on the categorical reformulation of the Baum–Connes conjecture developed by Meyer and Nest. As a main result we show that free quantum groups have a γ -element and that γ=1 . As an important ingredient in the proof we adapt the Dirac-dual Dirac method for groups acting on trees to the quantum case. We use this to extend some permanence properties of the Baum–Connes conjecture to our setting

Differences in acute phase response to bacterial, fungal and viral antigens in greater mouse-eared bats (Myotis myotis)

The acute phase response (APR) is an evolutionarily well-conserved part of the innate immune defense against pathogens. However, recent studies in bats yielded surprisingly diverse results compared to previous APR studies on both vertebrate and invertebrate species. This is especially interesting due to the known role of bats as reservoirs for viruses and other intracellular pathogens, while being susceptible to extracellular microorganisms such as some bacteria and fungi. To better understand these discrepancies and the reservoir-competence of bats, we mimicked bacterial, viral and fungal infections in greater mouse-eared bats (Myotis myotis) and quantified different aspects of the APR over a two-day period. Individuals reacted most strongly to a viral (PolyI:C) and a bacterial (LPS) antigen, reflected by an increase of haptoglobin levels (LPS) and an increase of the neutrophil-to-lymphocyte-ratio (PolyI:C and LPS). We did not detect fever, leukocytosis, body mass loss, or a change in the overall functioning of the innate immunity upon challenge with any antigen. We add evidence that bats respond selectively with APR to specific pathogens and that the activation of different parts of the immune system is species-specific

Pup vibrissae stable isotopes reveal geographic differences in adult female southern sea lion habitat use during gestation

Individuals within populations often differ substantially in habitat use, the ecological consequences of which can be far reaching. Stable isotope analysis provides a convenient and often cost effective means of indirectly assessing the habitat use of individuals that can yield valuable insights into the spatiotemporal distribution of foraging specialisations within a population. Here we use the stable isotope ratios of southern sea lion (Otaria flavescens) pup vibrissae at the Falkland Islands, in the South Atlantic, as a proxy for adult female habitat use during gestation. A previous study found that adult females from one breeding colony (Big Shag Island) foraged in two discrete habitats, inshore (coastal) or offshore (outer Patagonian Shelf). However, as this species breeds at over 70 sites around the Falkland Islands, it is unclear if this pattern is representative of the Falkland Islands as a whole. In order to characterize habitat use, we therefore assayed carbon (δ13C) and nitrogen (δ15N) ratios from 65 southern sea lion pup vibrissae, sampled across 19 breeding colonies at the Falkland Islands. Model-based clustering of pup isotope ratios identified three distinct clusters, representing adult females that foraged inshore, offshore, and a cluster best described as intermediate. A significant difference was found in the use of inshore and offshore habitats between West and East Falkland and between the two colonies with the largest sample sizes, both of which are located in East Falkland. However, habitat use was unrelated to the proximity of breeding colonies to the Patagonian Shelf, a region associated with enhanced biological productivity. Our study thus points towards other factors, such as local oceanography and its influence on resource distribution, playing a prominent role in inshore and offshore habitat use

Quantum simulation of battery materials using ionic pseudopotentials

Ionic pseudopotentials are widely used in classical simulations of materials to model the effective potential due to the nucleus and the core electrons. Modeling fewer electrons explicitly results in a reduction in the number of plane waves needed to accurately represent the states of a system. In this work, we introduce a quantum algorithm that uses pseudopotentials to reduce the cost of simulating periodic materials on a quantum computer. We use a qubitization-based quantum phase estimation algorithm that employs a first-quantization representation of the Hamiltonian in a plane-wave basis. We address the challenge of incorporating the complexity of pseudopotentials into quantum simulations by developing highly-optimized compilation strategies for the qubitization of the Hamiltonian. This includes a linear combination of unitaries decomposition that leverages the form of separable pseudopotentials. Our strategies make use of quantum read-only memory subroutines as a more efficient alternative to quantum arithmetic. We estimate the computational cost of applying our algorithm to simulating lithium-excess cathode materials for batteries, where more accurate simulations are needed to inform strategies for gaining reversible access to the excess capacity they offer. We estimate the number of qubits and Toffoli gates required to perform sufficiently accurate simulations with our algorithm for three materials: lithium manganese oxide, lithium nickel-manganese oxide, and lithium manganese oxyfluoride. Our optimized compilation strategies result in a pseudopotential-based quantum algorithm with a total runtime four orders of magnitude lower than the previous state of the art for a fixed target accuracy