Animal board invited review: Improving animal health and welfare in the transition of livestock farming systems: Towards social acceptability and sustainability.

The need to integrate more clearly societal expectations on livestock farming has led the authors of this article to consider that livestock farming systems must be redesigned to position health and welfare at the heart of their objectives. This article proposes a vision of the advances in knowledge required at different scales to contribute to this transformation. After defining health and welfare of animals, the article emphasises the need to consider health in a broader perspective, to deepen the question of positive emotional experiences regarding welfare, and raises the question of how to assess these two elements on farms. The positive interactions between health and welfare are presented. Some possible tensions between them are also discussed, in particular when improving welfare by providing a more stimulating and richer environment such as access to outdoor increases the risk of infectious diseases. Jointly improving health and welfare of animals poses a number of questions at various scales, from the animal level to the production chain. At the animal level, the authors highlight the need to explore: the long-term links between better welfare and physiological balance, the role of microbiota, the psycho-neuro-endocrine mechanisms linking positive mental state and health, and the trade-off between the physiological functions of production, reproduction and immunity. At the farm level, in addition to studying the relationships at the group level between welfare, health and production, the paper supports the idea of co-constructing innovative systems with livestock farmers, as well as analysing the cost, acceptability and impact of improved systems on their working conditions and well-being. At the production chain or territory levels, various questions are raised. These include studying the best strategies to improve animal health and welfare while preserving economic viability, the labelling of products and the consumers' willingness to pay, the consequences of heterogeneity in animal traits on the processing of animal products, and the spatial distribution of livestock farming and the organisation of the production and value chain. At the level of the citizen and consumer, one of the challenges is to better inter-relate sanitary and health perspectives on the one hand, and welfare concerns on the other hand. There is also a need to improve citizens' knowledge on livestock farming, and to develop more intense and constructive exchanges between livestock farmers, the livestock industry and citizens. These difficult issues plead for interdisciplinary and transdisciplinary research involving various scientific disciplines and the different stakeholders, including public policy makers through participatory research.

Ex vivo radiation sensitivity assessment for individual head and neck cancer patients using deep learning-based automated nuclei and DNA damage foci detection.

Introduction: Tumor biopsy tissue response to ex vivo irradiation is potentially an interesting biomarker for in vivo tumor response, therefore, for treatment personalization. Tumor response ex vivo can be characterized by DNA damage response, expressed by the large-scale presence of DNA damage foci in tumor nuclei. Currently, characterizing tumor nuclei and DNA damage foci is a manual process that takes hours per patient and is subjective to inter-observer variability, which is not feasible in for clinical decision making. Therefore, our goal was to develop a method to automatically segment nuclei and DNA damage foci in tumor tissue samples treated with radiation ex vivo to characterize the DNA damage response, as potential biomarker for in vivo radio-sensitivity. Methods: Oral cavity tumor tissue of 21 patients was irradiated ex vivo (5 or 0 Gy), fixated 2 h post-radiation, and used to develop our method for automated nuclei and 53BP1 foci segmentation. The segmentation model used both deep learning and conventional image-analysis techniques. The training (22 %), validation (22 %), and test set (56 %) consisted of thousands of manually segmented nuclei and foci. The segmentations and number of foci per nucleus in the test set were compared to their ground truths. Results: The automatic nuclei and foci segmentations were highly accurate (Dice = 0.901 and Dice = 0.749, respectively). An excellent correlation (R2 = 0.802) was observed for the foci per nucleus that outperformed reported inter-observation variation. The analysis took âˆ¼ 8 s per image. Conclusion: This model can replace manual foci analysis for ex vivo irradiation of head-and-neck squamous cell carcinoma tissue, reduces the image-analysis time from hours to minutes, avoids the problem of inter-observer variability, enables assessment of multiple images or conditions, and provides additional information about the foci size. Thereby, it allows for reliable and rapid ex vivo radio-sensitivity assessment, as potential biomarker for response in vivo and treatment personalization.

Role of Spin-Orbit Coupling in High-Order Harmonic Generation Revealed by Supercycle Rydberg Trajectories.

High-harmonic generation is typically thought of as a sub-laser-cycle process, with the electron's excursion in the continuum lasting a fraction of the optical cycle. However, it was recently suggested that long-lived Rydberg states can play a particularly important role in high harmonic generation by atoms driven by the combination of the counterrotating circularly polarized fundamental light field and its second harmonic. Here we report direct experimental evidence of very long and stable Rydberg trajectories contributing to high-harmonic generation in such fields. We track their dynamics inside the laser pulse using the spin-orbit evolution in the ionic core, utilizing the spin-orbit Larmor clock. We confirm their effect on harmonic emission both via microscopic simulations and by showing how this radiation can lead to a well-collimated macroscopic far-field signal. Our observations contrast sharply with the general view that long-lived Rydberg orbits should generate negligible contribution to the macroscopic far-field high harmonic response of the medium.

Transcriptional Regulation of Jaw Osteoblasts: Development to Pathology.

Craniofacial and jaw bones have unique physiological specificities when compared to axial and appendicular bones. However, the molecular profile of the jaw osteoblast (OB) remains incomplete. The present study aimed to decipher the bone site-specific profiles of transcription factors (TFs) expressed in OBs in vivo. Using RNA sequencing analysis, we mapped the transcriptome of confirmed OBs from 2 different skeletal sites: mandible (Md) and tibia (Tb). The OB transcriptome contains 709 TF genes: 608 are similarly expressed in Md-OB and Tb-OB, referred to as "OB-core"; 54 TF genes are upregulated in Md-OB, referred to as "Md-set"; and 18 TF genes are upregulated in Tb-OB, referred to as "Tb-set." Notably, the expression of 29 additional TF genes depends on their RNA transcript variants. TF genes with no previously known role in OBs and bone were identified. Bioinformatics analysis combined with review of genetic disease databases and a comprehensive literature search showed a significant contribution of anatomical origin to the OB signatures. Md-set and Tb-set are enriched with site-specific TF genes associated with development and morphogenesis (neural crest vs. mesoderm), and this developmental imprint persists during growth and homeostasis. Jaw and tibia site-specific OB signatures are associated with craniofacial and appendicular skeletal disorders as well as neurocristopathies, dental disorders, and digit malformations. The present study demonstrates the feasibility of a new method to isolate pure OB populations and map their gene expression signature in the context of OB physiological environment, avoiding in vitro culture and its associated biases. Our results provide insights into the site-specific developmental pathways governing OBs and identify new major OB regulators of bone physiology. We also established the importance of the OB transcriptome as a prognostic tool for human rare bone diseases to explore the hidden pathophysiology of craniofacial malformations, among the most prevalent congenital defects in humans.

Agroecology landscapes.

Context: Agroecology combines agronomic and ecological concepts. It relies on the enhancement of biodiversity and related ecosystem services to support agricultural production. It is dependent on biological interactions for the design and management of agricultural systems in agricultural landscapes. Objectives: We review the role of landscape ecology to understand and promote biodiversity, pest regulation and crop pollination for the designing of "agroecology landscapes". We illustrate the use of landscape ecological methods for supporting agroforestry systems as an example of agroecological development, and we propose pathways to implement agroecology at landscape scale. Methods: The state of the art of how landscape ecology contributes to agroecology development is summarized based on a literature review. Results: Agroecology requires thinking beyond the field scale to consider the positioning, quality and connectivity of fields and semi-natural habitats at larger spatial scales. The spatial and temporal organisation of semi-natural elements and the crop mosaic interact. Understanding this interaction is the pre-requisite for promoting patterns and mechanisms that foster biodiversity and ecosystem service provision. Promoting agroecological practices beyond individual farm borders can be rooted in a bottom-up approach from agroecological lighthouse farms to farm networks to amplify agroecology adoption at the landscape scale. Conclusions: Achieving agricultural landscapes composed of fields and farms following agroecological management requires understanding of biodiversity patterns, biological interactions and mechanisms that determine and boost ecosystem functioning to improve services at landscape scale, involving farmers in a bottom-up and context-specific approach.

Spin Dynamics and Unconventional Coulomb Phase in Nd_{2}Zr_{2}O_{7}.

We investigate the temperature dependence of the spin dynamics in the pyrochlore magnet Nd_{2}Zr_{2}O_{7} by neutron scattering experiments. At low temperature, this material undergoes a transition towards an "all-in-all-out" antiferromagnetic phase and the spin dynamics encompass a dispersionless mode, characterized by a dynamical spin ice structure factor. Unexpectedly, this mode is found to survive above T_{N}≈300 mK. Concomitantly, elastic correlations of the spin ice type develop. These are the signatures of a peculiar correlated paramagnetic phase which can be considered as a new example of Coulomb phase. Our observations near T_{N} do not reproduce the signatures expected for a Higgs transition, but show reminiscent features of the "all-in-all-out" order superimposed on a Coulomb phase.

High-order parametric generation of coherent XUV radiation.

Extreme ultraviolet (XUV) radiation finds numerous applications in spectroscopy. When the XUV light is generated via high-order harmonic generation (HHG), it may be produced in the form of attosecond pulses, allowing access to unprecedented ultrafast phenomena. However, the HHG efficiency remains limited. Here we present an observation of a new regime of coherent XUV emission which has a potential to provide higher XUV intensity, vital for applications. We explain the process by high-order parametric generation, involving the combined emission of THz and XUV photons, where the phase matching is very robust against ionization. This introduces a way to use higher-energy driving pulses, thus generating more XUV photons.

From One- to Two-Magnon Excitations in the S=3/2 Magnet ß-CaCr_{2}O_{4}.

We apply neutron spectroscopy to measure the magnetic dynamics in the S=3/2 magnet ß-CaCr_{2}O_{4} (T_{N}=21 K). The low-energy fluctuations, in the ordered state, resemble large-S linear spin waves from the incommensurate ground state. However, at higher energy transfers, these semiclassical and harmonic dynamics are replaced by an energy and momentum broadened continuum of excitations. Applying kinematic constraints required for energy and momentum conservation, sum rules of neutron scattering, and comparison against exact diagonalization calculations, we show that the dynamics at high-energy transfers resemble low-S one-dimensional quantum fluctuations. ß-CaCr_{2}O_{4} represents an example of a magnet at the border between classical Néel and quantum phases, displaying dual characteristics.

Pollution by anthropogenic microfibers in North-West Mediterranean Sea and efficiency of microfiber removal by a wastewater treatment plant.

The widespread pollution from the release of microfibers is an emerging concern as they are a potential threat to the environment. Their identification in samples in terms of quantity and pathways remain a challenge as contamination can be a major source of error. A systematic study of synthetic microfibers (MFs) has been carried out in different environmental compartments of an urban area and in the surface waters of the northwestern Mediterranean. The quantity, size and type of polymer of MFs were recorded in air, in waste water from a domestic washing machine, at the inlet and outlet of the Haliotis urban wastewater treatment plant (WWTP) in Nice (Provence Alpes Côte-d'Azur, France) and in a variety of coastal and offshore areas. The results showed that MFs released by clothes during washing (on average of 13 × 106 MFs per m3) are an important emitter of microplastics. Despite its high removal efficiency (87.5% to 98.5%) by Haliotis, a large number of MFs, estimated at 4.3 billion, enter the marine environment daily from the treatment plant. The attenuated total reflectance Fourier-transform infrared spectroscopy (ATR-FTIR) characterization of the raw materials showed that 14 to 50% of fibers are synthetic, mostly polyester and polyamide, the remaining 35 to 72% being natural polymers (cotton, wool) or manufactured by processing natural polymers (especially cellulose). MFs were found in all environmental compartments studied and appear to be widespread in coastal and offshore surface waters with concentrations varying from 2.6 × 103 to 3.70 × 104 m-3. The sources of MFs in the marine environment are multiple, with laundry fibers discharges from WWTP and the atmospheric transport of urban fibers are among the main pathways.

Aurore: A platform for ultrafast sciences.

We present the Aurore platform for ultrafast sciences. This platform is based on a unique 20 W, 1 kHz, 26 fs Ti:sapphire laser system designed for reliable operation and high intensity temporal contrast. The specific design ensures the high stability in terms of pulse duration, energy, and beam pointing necessary for extended experimental campaigns. The laser supplies 5 different beamlines, all dedicated to a specific field: attosecond science (Aurore 1), ultrafast phase transitions in solids (Aurore 2 and 3), ultrafast luminescence in solids (Aurore 4), and femtochemistry (Aurore 5). The technical specifications of these five beamlines are described in detail, and examples of the recent results are given.

Absolute gas density profiling in high-order harmonic generation: erratum.

In this erratum, we correct two numerical errors due to conversion mistakes from our previous published manuscript [Opt. Express 26, 6001 (2018)]. In the original manuscript, the two errors compensated each other such that the conclusions remain perfectly unchanged.

Dimer Physics in the Frustrated Cairo Pentagonal Antiferromagnet Bi_{2}Fe_{4}O_{9}.

The research field of magnetic frustration is dominated by triangle-based lattices but exotic phenomena can also be observed in pentagonal networks. A peculiar noncollinear magnetic order is indeed known to be stabilized in Bi_{2}Fe_{4}O_{9} materializing a Cairo pentagonal lattice. We present the spin wave excitations in the magnetically ordered state, obtained by inelastic neutron scattering. They reveal an unconventional excited state related to local precession of pairs of spins. The magnetic excitations are then modeled to determine the superexchange interactions for which the frustration is indeed at the origin of the spin arrangement. This analysis unveils a hierarchy in the interactions, leading to a paramagnetic state (close to the Néel temperature) constituted of strongly coupled dimers separated by much less correlated spins. This produces two types of response to an applied magnetic field associated with the two nonequivalent Fe sites, as observed in the magnetization distributions obtained using polarized neutrons.

Phase-matching-free pulse retrieval based on transient absorption in solids.

In this paper, we introduce a pulse characterization technique that is free of phase-matching constraints, exploiting transient absorption in solids as an ultrafast optical switch. Based on a pump-probe setup, this technique uses pump pulses of sufficient intensity to induce the switch, while the pulses to characterize are probing the transmissivity drop of the photoexcited material. This enables the characterization of low-intensity ultra-broadband pulses at the detection limit of the spectrometer and within the transparency range of the solid. For example, by using zinc selenide (ZnSe), pulses with wavelengths from 0.5 to 20 µm can be characterized, denoting five octaves of spectral range. Using ptychography, we retrieve the temporal profiles of both the probe pulse and the switch. To demonstrate this approach, we measure ultrashort pulses from a titanium-sapphire (Ti-Sa) amplifier, which are compressed using a hollow core fiber setup, as well as infrared to mid-infrared pulses generated from an optical parametric amplifier (OPA). The characterized pulses are centered at wavelengths of 0.77, 1.53, 1.75, 4, and 10 µm, down to sub-two optical cycles duration, exceeding an octave of bandwidth, and with energy as low as a few nanojoules.

Cascaded harmonic generation from a fiber laser: a milliwatt XUV source.

Recent progresses in femtosecond ytterbium-doped fiber laser technology are opening new perspectives in strong field physics and attosecond science. High-order harmonic generation from these systems is particularly interesting because it provides high flux beams of ultrashort extreme ultraviolet radiation. A great deal of effort has been devoted to optimize the macroscopic generation parameters. Here we investigate the possibility of enhancing the single-atom response by producing high-order harmonics from the second, third and fourth harmonics of a turnkey 50 W, 166 kHz femtosecond Yb-fiber laser providing 135 fs pulses at 1030 nm. We show that the harmonic efficiency is optimal when the process is driven by the third harmonic, producing 6.6 ± 1.3 × 1014 photons/s at 18 eV in argon, which corresponds to 1.9 ± 0.4 mW average power.

Local pesticide use intensity conditions landscape effects on biological pest control.

Complex landscapes including semi-natural habitats are expected to favour natural enemies thereby enhancing natural pest biocontrol in crops. However, when considering a large number of situations, the response of natural biocontrol to landscape properties is globally inconsistent, a possible explanation being that local agricultural practices counteract landscape effects. In this study, along a crossed gradient of pesticide use intensity and landscape simplification, we analysed the interactive effects of landscape characteristics and local pesticide use intensity on natural biocontrol. During 3 years, using a set of sentinel prey (weed seeds, aphids and Lepidoptera eggs), biocontrol was estimated in 80 commercial fields located in four contrasted regions in France. For all types of prey excepted weed seeds, the predation rate was influenced by interactions between landscape characteristics and local pesticide use intensity. Proportion of meadow and length of interface between woods and crops had a positive effect on biocontrol of aphids where local pesticide use intensity was low but had a negative effect elsewhere. Moreover, the landscape proportion of suitable habitats for crop pests decreased the predation of sentinel prey, irrespectively of the local pesticide use intensity for weed seeds, but only in fields with low pesticide use for Lepidoptera eggs. These results show that high local pesticide use can counteract the positive expected effects of semi-natural habitats, but also that the necessary pesticide use reduction should be associated with semi-natural habitat enhancement to guarantee an effective natural biocontrol.

Real-time determination of enantiomeric and isomeric content using photoelectron elliptical dichroism.

The fast and accurate analysis of chiral chemical mixtures is crucial for many applications but remains challenging. Here we use elliptically-polarized femtosecond laser pulses at high repetition rates to photoionize chiral molecules. The 3D photoelectron angular distribution produced provides molecular fingerprints, showing a strong forward-backward asymmetry which depends sensitively on the molecular structure and degree of ellipticity. Continuously scanning the laser ellipticity and analyzing the evolution of the rich, multi-dimensional molecular signatures allows us to observe real-time changes in the chemical and chiral content present with unprecedented speed and accuracy. We measure the enantiomeric excess of a compound with an accuracy of 0.4% in 10 min acquisition time, and follow the evolution of a mixture with an accuracy of 5% with a temporal resolution of 3 s. This method is even able to distinguish isomers, which cannot be easily distinguished by mass-spectrometry.

Multiphoton photoelectron circular dichroism of limonene with independent polarization state control of the bound-bound and bound-continuum transitions.

Photoionization of randomly oriented chiral molecules with circularly polarized light leads to a strong forward/backward asymmetry in the photoelectron angular distribution. This chiroptical effect, referred to as Photoelectron Circular Dichroism (PECD), was shown to take place in all ionization regimes, from single photon to tunnel ionization. In the Resonance Enhanced Multiphoton Ionisation (REMPI) regime, where most of the table-top PECD experiments have been performed, understanding the role of the intermediate resonances is currently the subject of experimental and theoretical investigations. In an attempt to decouple the role of bound-bound and bound-continuum transitions in REMPI-PECD, we photoionized the (+)-limonene enantiomer using two-color laser fields in [1 + 1'] and [2 + 2'] ionization schemes, where the polarization state of each color can be controlled independently. We demonstrate that the main effect of the bound-bound transition is to break the sample isotropy by orientation-dependent photoexcitation, in agreement with recent theoretical predictions. We show that the angular distribution of PECD strongly depends on the anisotropy of photoexcitation to the intermediate state, which is different for circularly and linearly polarized laser pulses. On the contrary, the helicity of the pulse that drives the bound-bound transition is shown to have a negligible effect on the PECD.

Evidence for dynamic kagome ice.

The search for two-dimensional quantum spin liquids, exotic magnetic states remaining disordered down to zero temperature, has been a great challenge in frustrated magnetism over the last few decades. Recently, evidence for fractionalized excitations, called spinons, emerging from these states has been observed in kagome and triangular antiferromagnets. In contrast, quantum ferromagnetic spin liquids in two dimensions, namely quantum kagome ices, have been less investigated, yet their classical counterparts exhibit amazing properties, magnetic monopole crystals as well as magnetic fragmentation. Here, we show that applying a magnetic field to the pyrochlore oxide Nd2Zr2O7, which has been shown to develop three-dimensional quantum magnetic fragmentation in zero field, results in a dimensional reduction, creating a dynamic kagome ice state: the spin excitation spectrum determined by neutron scattering encompasses a flat mode with a six arm shape akin to the kagome ice structure factor, from which dispersive branches emerge.

Spin Fluctuations Drive the Inverse Magnetocaloric Effect in Mn_{5}Si_{3}.

Inelastic neutron scattering measurements are performed on single crystals of the antiferromagnetic compound Mn_{5}Si_{3} in order to investigate the relation between the spin dynamics and the magnetothermodynamics properties. It is shown that, among the two stable antiferromagnetic phases of this compound, the high temperature one has an unusual magnetic excitation spectrum where propagative spin waves and diffuse spin fluctuations coexist. Moreover, it is evidenced that the inverse magnetocaloric effect of Mn_{5}Si_{3}, the cooling by adiabatic magnetization, is associated with field induced spin fluctuations.