BigFUSE: Global Context-Aware Image Fusion in Dual-View Light-Sheet Fluorescence Microscopy with Image Formation Prior

Light-sheet fluorescence microscopy (LSFM), a planar illumination technique that enables high-resolution imaging of samples, experiences defocused image quality caused by light scattering when photons propagate through thick tissues. To circumvent this issue, dualview imaging is helpful. It allows various sections of the specimen to be scanned ideally by viewing the sample from opposing orientations. Recent image fusion approaches can then be applied to determine in-focus pixels by comparing image qualities of two views locally and thus yield spatially inconsistent focus measures due to their limited field-of-view. Here, we propose BigFUSE, a global context-aware image fuser that stabilizes image fusion in LSFM by considering the global impact of photon propagation in the specimen while determining focus-defocus based on local image qualities. Inspired by the image formation prior in dual-view LSFM, image fusion is considered as estimating a focus-defocus boundary using Bayes Theorem, where (i) the effect of light scattering onto focus measures is included within Likelihood; and (ii) the spatial consistency regarding focus-defocus is imposed in Prior. The expectation-maximum algorithm is then adopted to estimate the focus-defocus boundary. Competitive experimental results show that BigFUSE is the first dual-view LSFM fuser that is able to exclude structured artifacts when fusing information, highlighting its abilities of automatic image fusion.Comment: paper in MICCAI 202

Floral scent evaluation of three cut flowers through sensorial and gas chromatography analysis

The main function of floral scent is to attract and guide pollinators, but it is also an important character in the ornamental plant industry. Several studies have considered the chemical evaluation of floral scent during vase life, but only a few have considered sensorial analysis of this character, which is a very important quality trait for the marketing of ornamental plants. This study focused on assessing the floral scent of three fragrant cut flowers of high economic importance: Lilium, chrysanthemum, and freesia. Eighty individuals were included in a sensorial analysis where the attributes of floral scent liking and intensity were evaluated. The composition of the floral scent was analyzed through the collection of headspace followed by gas chromatography-mass spectrometry (GC-MS). The floral scents of oriental lily and freesia were perceived as more intense, compared to chrysanthemum. A total of 28 volatile compounds were detected and the monoterpenes β-pinene (40.7 ± 1.8 μg·L−1), β-cis-ocimene (5552 ± 990 μg·L−1), and linalool (11,800 ± 220 μg·L−1) were the major volatile organic compounds (VOCs) present in chrysanthemum, lilium, and freesia, respectively. The results presented in this study confirm that the concentration and abundance of volatile compounds is not directly related to the human perception of floral scen

Odour dialects among wild mammals

Across multiple taxa, population structure and dynamics depend on effective signalling between individuals. Among mammals, chemical communication is arguably the most important sense, underpinning mate choice, parental care, territoriality and even disease transmission. There is a growing body of evidence that odours signal genetic information that may confer considerable benefits including inbreeding avoidance and nepotism. To date, however, there has been no clear evidence that odours encode population-level information in wild mammals. Here we demonstrate for the first time the existence of ‘odour dialects’ in genetically distinct mammalian subpopulations across a large geographical scale. We found that otters, Lutra lutra, from across the United Kingdom possess sex and biogeography-specific odours. Subpopulations with the most distinctive odour profiles are also the most genetically diverse but not the most genetically differentiated. Furthermore, geographic distance between individuals does not explain regional odour differences, refuting other potential explanations such as group odour sharing behaviour. Differences in the language of odours between subpopulations have the potential to affect individual interactions, which could impact reproduction and gene-flow

Sustainable and healthy diets: trade-offs and synergies : final scientific report

This project aimed at analysing trade-offs and synergies between healthy nutrition and sustainable food systems. First, we identified nutritional patters of the Swiss population based on representative consumption data. The health impacts of these nutritional patterns were then analysed based on a review of the scientific literature on health impacts of food commodities and diets and by calculating the Alternate Healthy Eating Index (AHEI), the Mediterranean Diet Score (MDS) and Disability Adjusted Life Years (DALYs) of the nutritional patterns. Second, we comprehensively analysed health, environmental, social and economic impacts and related trade-offs and synergies for a number of future scenarios of Swiss agricultural production and food consumption. For this, we used a modelling approach, linking three different models: a global mass flow model, a system dynamics model and an environmentally extended input-output model. We modelled ten different scenarios for the Swiss Food Sector in 2050. These scenarios were either developed in a participatory process during a series of interviews and group discussions with different groups of stakeholders or optimised environmental impacts while at the same time complying with different nutritional and agronomic restrictions. Three main scenarios were analysed with all three models in detail. Among these main scenarios was the SwissFoodPyramid2050 Scenario, which assumes a widespread implementation of the nutritional recommendations according to the Swiss Food Pyramid. The FeedNoFood2050 Scenario assumes an improved use of agricultural land by feeding only grass and by-products to livestock, which was not competing with direct human nutrition, i.e. did not require arable land (neither in Switzerland nor abroad). The third scenario was a reference scenario, which assumes no changes in diets until 2050 and which was used to compare the two alternative scenarios. The other scenarios were targeted at specific questions such as minimizing greenhouse gases. Our results illustrate two visions of how healthy diets and sustainable food systems could look like. Both the SwissFoodPyramid2050 and the FeedNoFood2005 scenarios would require similar dietary changes, such as a reduction of meat consumption and an increase of consumption of pulses. However, there are also fundamental differences between the diets in the two alternative scenarios, e.g. regarding the type of meat consumed. These differences can be interpreted as trade-offs which result from agronomic boundary conditions such as the coupled production of milk and meat, the availability of natural resources, such as grassland and co-products of food processing and health aspects of Swiss diets. Of primary importance in this respect was the use of permanent grasslands and the co-production of veal and beef with dairy production due to environmental reasons and reasons for optimally utilizing available resources. This means, if permanent grassland should be maintained as an ecosystem, dairy production would provide the basis for animal proteins. Thus, while in the FeedNoFood2050 Scenario veal and rather low-quality beef from dairy cows is consumed instead of meat from monogastrics, the SwissFoodPyramid2050 Scenario would result in a higher amount of meat from monogastrics. Our results imply that there is a lack of a comprehensive food systems view in the current discussion on healthy and sustainable diets. Stronger coherence between health, food and agricultural policy is needed to account for systemic boundary conditions and thus to allow for minimising trade-offs and maximise synergies. Current agricultural policies fail to address the health perspective. Financial support for meat and sugar producers, which lead to lower prices for those products and ultimately to a higher consumption than without these policies, are two obvious examples. Yet, comprehensive visions such as the SwissFoodPyramid scenario, the FeedNoFood Scenario or optimised scenarios would require an even more complex policy mix of incentives, regulations and information campaigns. This would probably need an adaptation of the current institutional setting and division of competences between the Federal Offices for Agriculture (FOAG) and for the Environment (FOEN), the State Secretariat for Economic Affairs (SECO) and the Federal Food Safety and Veterinary Office (FSVO). A commonly shared vision, including specific goals with respect to how the Swiss food system should look like, is urgently needed. Developing such a vision needs to involve all operators and stakeholders of the food system, as our results imply that more sustainable and healthy diets do not necessarily go along with financial benefits of both producers and consumers. These trade-offs and the knowledge of behavioural economics need to be considered for designing settings which create mutual benefits for operators in the food sector. For instance, neither the majority of consumers, food industry nor agricultural producers can be expected to respond altruistically as an entire sector in the long term. Therefore, policy needs to set financial incentives for internalising environmental and social externalities in order to push and pull the food system towards sustainability. Furthermore, it is crucial to account for agronomic boundary conditions and systemic aspects, such as the role of ruminants in utilizing grasslands and the unavoidable link of milk and meat production

In the human malaria parasite Plasmodium falciparum,polyamines are synthesized by a bifunctional ornithine decarboxylase, S-adenosylmethionine decarboxylase

The polyamines putrescine, spermidine, and spermine are crucial for cell differentiation and proliferation. Interference with polyamine biosynthesis by inhibition of the rate-limiting enzymes ornithine decarboxylase (ODC) andS-adenosylmethionine decarboxylase (AdoMetDC) has been discussed as a potential chemotherapy of cancer and parasitic infections. Usually both enzymes are individually transcribed and highly regulated as monofunctional proteins. We have isolated a cDNA from the malaria parasite Plasmodium falciparumthat encodes both proteins on a single open reading frame, with the AdoMetDC domain in the N-terminal region connected to a C-terminal ODC domain by a hinge region. The predicted molecular mass of the entire transcript is 166 kDa. The ODC/AdoMetDC coding region was subcloned into the expression vector pASK IBA3 and transformed into the AdoMetDC- and ODC-deficient Escherichia coli cell line EWH331. The resulting recombinant protein exhibited both AdoMetDC and ODC activity and co-eluted after gel filtration on Superdex S-200 at ~333 kDa, which is in good agreement with the molecular mass of ~326 kDa determined for the native protein from isolated P. falciparum. SDS-polyacrylamide gel electrophoresis analysis of the recombinant ODC/AdoMetDC revealed a heterotetrameric structure of the active enzyme indicating processing of the AdoMetDC domain. The data presented describe the occurrence of a unique bifunctional ODC/AdoMetDC in P. falciparum, an organization which is possibly exploitable for the design of new antimalarial drugs

Emergent properties arising from spatial heterogeneity influence fungal community dynamics

Community dynamics are mediated by species interactions, and within communities spatial heterogeneity and intransitive relationships promote coexistence. However, few experimental studies have assessed effects of heterogeneity on the interactions of competing individuals. Wood decay basidiomycete fungi are ideal for studying community structure and dynamics because they are easy to manipulate in laboratory microcosms, and communities resolve themselves rapidly. Most studies have only used simplistic pair-wise interactions in a 2-D plane, but here we investigate a three-species community in an environmentally realistic novel 3-dimensional system. We show how spatial heterogeneity and patch size dynamics are important for coexistence, and how competitive interactions change over different spatial dimensions. Emergent properties arose with increased spatial heterogeneity: the weakest competitor co-occurred with the community when its territory was less fragmented, and interactions became intransitive

3D-Printed Fluorescence Hyperspectral Lidar for Monitoring Tagged Insects

Insects play crucial roles in ecosystems, and how they disperse within their habitat has significant implications for our daily life. Examples include foraging ranges for pollinators, as well as the spread of disease vectors and pests. Despite technological advances with radio tags, isotopes, and genetic sequencing, insect dispersal and migration range remain challenging to study. The gold standard method of mark-recapture is tedious and inefficient. This paper demonstrates the construction of a compact, inexpensive hyperspectral fluorescence lidar. The system is based on off-the-shelf components and 3D printing. After evaluating the performance of the instrument in the laboratory, we demonstrate its efficient range-resolved fluorescence spectra in situ. We present daytime remote ranging and fluorescent identification of auto-powder-tagged honey bees. We also showcase range-, temporally- and spectrally-resolved free-flying mosquitoes, which were tagged through feeding on fluorescent-dyed sugar water. We conclude that violet light can efficiently excite administered sugar meals imbibed by flying insects. Our field experiences provide realistic expectations of signal-to-noise levels, which can be used in future studies. The technique is generally applicable and can efficiently monitor several tagged insect groups in parallel for comparative ecological analysis. This technique opens up a range of ecological experiments, which were previously unfeasible

Using volatile organic compounds to monitor shelf-life in rocket salad

Rocket salad (Diplotaxis tenuifolia or Eruca sativa) is a perishable product of increasing interest due to its high content of nutritionally relevant compounds including glucosinolates and vitamin C. There is an increasing consumption of ready-to-eat salads which are sold to the consumer in bags, often packed under modified atmosphere. Shelf-life and sell-by dates are commonly applied to these products and are usually dictated by the appearance of the product rather than its nutritional value. During shelf-life, postharvest deterioration leads to a loss of nutritionally relevant compounds such as vitamin C. This is accelerated by suboptimal conditions during storage and transport such as breaches of the cold-chain. Volatile organic compounds (VOCs) are easy and quick to sample use of thermal desorption gas chromatography time of flight mass spectroscopy (TD-GC-TOF-MS) enables remote sampling and a very sensitive analysis of VOC profiles. We have used TD-GC-TOF-MS to sample VOCs from rocket salad bags sourced from a local supermarket to assess changes during the shelf-life of the product. Using statistical analyses that treat the whole VOC profile as a single variable we show that it is possible to differentiate between day of purchase, use by date and time points beyond sale. We conclude that this methodology is therefore of use for assessing rocket salad quality through the supply chain

The order, shape and critical point for the quark-gluon plasma phase transition

The order, shape and critical point for the phase transition between the hadronic matter and quark-gluon plasma are considered in a thermodynamical consistent approach. The hadronic phase is taken as Van der Waals gas of all the known hadronic mass spectrum particles $m_H\le 2.0$ GeV as well as Hagedorn bubbles which correspond hadronic states with mass spectrum $m_H> 2.0$ GeV. The density of states for Hagedorn bubbles is derived by calculating the microcanonical ensemble for a bag of quarks and gluons with specific internal color-flavor symmetry. The mixed-grand and microcanonical ensembles are derived for massless and massive flavors. We find Hagedorn bubbles are strongly suppressed in the dilute hadronic matter and they appear just below the line of the phase transition. The order of the phase transition depends on Hagedorn bubble's internal color-flavor structure and the volume fluctuation as well. On the other hand, the highly compressed hadronic matter undergoes a smooth phase transition from the gas of known mass spectrum hadrons to another one dominated by Hagedorn bubbles with specific internal color-flavor structure before the phase transition to quark-gluon plasma takes place at last. The phase transition is found a first order for the intermediate and large chemical potentials. The existence of the tri-critical point depends on the modification of the bubble's internal structure specified by a phenomenological parameter $\gamma\propto\mu_B$ in the medium.Comment: 69 pages, 10 figure

Space and patchiness affects diversity–function relationships in fungal decay communities

The space in which organisms live determines health and physicality, shaping the way in which they interact with their peers. Space, therefore, is critically important for species diversity and the function performed by individuals within mixed communities. The biotic and abiotic factors defined by the space that organisms occupy are ecologically significant and the difficulty in quantifying space-defined parameters within complex systems limits the study of ecological processes. Here, we overcome this problem using a tractable system whereby spatial heterogeneity in interacting fungal wood decay communities demonstrates that scale and patchiness of territory directly influence coexistence dynamics. Spatial arrangement in 2- and 3-dimensions resulted in measurable metabolic differences that provide evidence of a clear biological response to changing landscape architecture. This is of vital importance to microbial systems in all ecosystems globally, as our results demonstrate that community function is driven by the effects of spatial dynamics