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International audience; A volumetric non-blind single image super-resolution technique using tensor factorization has been recently introduced by our group. That method allowed a 2-order-of-magnitude faster high-resolution image reconstruction with equivalent image quality compared to state-of-the-art algorithms. In this work a joint alternating recovery of the high-resolution image and of the unknown point spread function parameters is proposed. The method is evaluated on dental computed tomography images. The algorithm was compared to an existing 3D super-resolution method using low-rank and total variation regularization, combined with the same alternating PSF-optimization. The two algorithms have shown similar improvement in PSNR, but our method converged roughly 40 times faster, under 6 minutes both in simulation and on experimental dental computed tomography data

Available super-resolution techniques for 3D images are either computationally inefficient prior-knowledge-based iterative techniques or deep learning methods which require a large database of known low- and high-resolution image pairs. A recently introduced tensor-factorization-based approach offers a fast solution without the use of known image pairs or strict prior assumptions. In this article this factorization framework is investigated for single image resolution enhancement with an off-line estimate of the system point spread function. The technique is applied to 3D cone beam computed tomography for dental image resolution enhancement. To demonstrate the efficiency of our method, it is compared to a recent state-of-the-art iterative technique using low-rank and total variation regularizations. In contrast to this comparative technique, the proposed reconstruction technique gives a 2-order-of-magnitude improvement in running time -- 2 minutes compared to 2 hours for a dental volume of 282$\times$266$\times$392 voxels. Furthermore, it also offers slightly improved quantitative results (peak signal-to-noise ratio, segmentation quality). Another advantage of the presented technique is the low number of hyperparameters. As demonstrated in this paper, the framework is not sensitive to small changes of its parameters, proposing an ease of use., This work has been submitted to the IEEE for possible publication. Copyright may be transferred without notice, after which this version may no longer be accessible

National audience; Abstract:The resolution of ultrasound images is limited by the bandwidth of the imaging system and the features of the propagating medium. Using certain assumptions, image restoration can recover out-of-bandwidth data and improve resolution. Several resolution improvement methods have been reported in the literature. However, due to the lack of ground truth, their evaluation on experimental data remains an open issue. Indeed, to evaluate the performance of such methods, knowledge of the scattering function is necessary. Usually this is achieved with numerical simulations, since in traditional phantoms the exact distribution of scatterers is unknown. In the current work, based on a 3D-printed phantom, the feasibility of the evaluation of deconvolution is investigated. The deconvolution method used lp-norm-regularization terms with p=0.5 and p=2. Knowledge of the scattering function allows comparison of the deconvolved images with the ground truth. Thus, using the scattering function and the originally acquired B-mode image, performance of image restoration methods could be evaluated quantitatively through comparison of root mean square error and full width half maximum values. Preliminary results demonstrate the benefits of knowing the scattering function during experimental testing of image restoration methods. In summary, the current work shows the potential of an experimental method for evaluating the extent to which an image restoration method provides a faithful rendering of the underlying scattering structure.

The paper wishes to document a recent trend visible in the Hungarian independent theatre scene – a turn towards social, political issues, as well as a growing sensitivity towards the visible tensions in Hungarian political discourse. It does so through the analysis and the contextualization of two recent Hungarian independent theatrical productions. Studio K’s 2019 Sacra Hungarica is an in-your-face attempt to portray the current distortion of the language and the abuse language is used for, while Béla Pintér’s Blood Red, Off-White, Dark Green, a clever Oedipus Rex paraphrase that depicts marginalization, racism, and nationalism in a pointedly non-pc allegory. The essay introduces the status of independent theatre vis-à-vis politics after 1989 and will delineate the changes the conservative governments brought into the alternative scene. Then, through an in-depth analysis of the above-mentioned two productions, it discusses the various means of theatricality they use to comment on contemporary Hungary.

International audience; In recent years, magnetism has gained an enormous amount of interest among researchers for actuating different sizes and types of bio/soft robots, which can be via an electromagnetic-coil system, or a system of moving permanent magnets. Different actuation strategies are used in robots with magnetic actuation having a number of advantages in possible realization of microscale robots such as bioinspired microrobots, tetherless microrobots, cellular microrobots, or even normal size soft robots such as electromagnetic soft robots and medical robots. This review provides a summary of recent research in magnetically actuated bio/soft robots, discussing fabrication processes and actuation methods together with relevant applications in biomedical area and discusses future prospects of this way of actuation for possible improvements in performance of different types of bio/soft robots.

Infrared neural stimulation is a promising tool for stimulating the brain because it can be used to excite with high spatial precision without the need of delivering or inserting any exogenous agent into the tissue. Very few studies have explored its use in the brain, as most investigations have focused on sensory or motor nerve stimulation. Using intravital calcium imaging with the genetically encoded calcium indicator GCaMP6f, here we show that the application of infrared neural stimulation induces intracellular calcium signals in Layer 2/3 neurons in mouse cortex in vivo. The number of neurons exhibiting infrared-induced calcium response as well as the amplitude of those signals are shown to be both increasing with the energy density applied. By studying as well the spatial extent of the stimulation, we show that reproducibility of the stimulation is achieved mainly in the central part of the infrared beam path. Stimulating in vivo at such a degree of precision and without any exogenous chromophores enables multiple applications, from mapping the brain’s connectome to applications in systems neuroscience and the development of new therapeutic tools for investigating the pathological brain.

International audience; The ability of developing complex internal representations of the environment is considered a crucial antecedent to the emergence of humans’ higher cognitive functions. Yet it is an open question whether there is any fundamental difference in how humans and other good visual learner species naturally encode aspects of novel visual scenes. Using the same modified visual statistical learning paradigm and multielement stimuli, we investigated how human adults and honey bees ( Apis mellifera ) encode spontaneously, without dedicated training, various statistical properties of novel visual scenes. We found that, similarly to humans, honey bees automatically develop a complex internal representation of their visual environment that evolves with accumulation of new evidence even without a targeted reinforcement. In particular, with more experience, they shift from being sensitive to statistics of only elemental features of the scenes to relying on co-occurrence frequencies of elements while losing their sensitivity to elemental frequencies, but they never encode automatically the predictivity of elements. In contrast, humans involuntarily develop an internal representation that includes single-element and co-occurrence statistics, as well as information about the predictivity between elements. Importantly, capturing human visual learning results requires a probabilistic chunk-learning model, whereas a simple fragment-based memory-trace model that counts occurrence summary statistics is sufficient to replicate honey bees’ learning behavior. Thus, humans’ sophisticated encoding of sensory stimuli that provides intrinsic sensitivity to predictive information might be one of the fundamental prerequisites of developing higher cognitive abilities.

There are multiple definitions for low complexity regions (LCRs) in protein sequences, with all of them broadly considering LCRs as regions with fewer amino acid types compared to an average composition. Following this view, LCRs can also be defined as regions showing composition bias. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, and more generally the overlaps between different properties related to LCRs, using examples. We argue that statistical measures alone cannot capture all structural aspects of LCRs and recommend the combined usage of a variety of predictive tools and measurements. While the methodologies available to study LCRs are already very advanced, we foresee that a more comprehensive annotation of sequences in the databases will enable the improvement of predictions and a better understanding of the evolution and the connection between structure and function of LCRs. This will require the use of standards for the generation and exchange of data describing all aspects of LCRs. Short abstract There are multiple definitions for low complexity regions (LCRs) in protein sequences. In this critical review, we focus on the definition of sequence complexity of LCRs and their connection with structure. We present statistics and methodological approaches that measure low complexity (LC) and related sequence properties. Composition bias is often associated with LC and disorder, but repeats, while compositionally biased, might also induce ordered structures. We illustrate this dichotomy, plus overlaps between different properties related to LCRs, using examples.

The resolution of dental computed tomography (CT) images is limited by detector geometry, sensitivity, patient movement, the reconstruction technique and the need to minimize radiation dose. Recently, the use of convolutional neural network (CNN) architectures has shown promise as a resolution enhancement method. In the current work, two CNN architectures—a subpixel network and the so called U-net—have been considered for the resolution enhancement of 2-D cone-beam CT image slices of ex vivo teeth. To do so, a training set of 5680 cross-sectional slices of 13 teeth and a test set of 1824 slices of 4 structurally different teeth were used. Two existing reconstruction-based super-resolution methods using $\boldsymbol {\ell _{2}}$ -norm and total variation regularization were used for comparison. The results were evaluated with different metrics (peak signal-to-noise ratio, structure similarity index, and other objective measures estimating human perception) and subsequent image-segmentation-based analysis. In the evaluation, micro-CT images were used as ground truth. The results suggest the superiority of the proposed CNN-based approaches over reconstruction-based methods in the case of dental CT images, allowing better detection of medically salient features, such as the size, shape, or curvature of the root canal.

Visual Abstract, Transparent and flexible materials are attractive for a wide range of emerging bioelectronic applications. These include neural interfacing devices for both recording and stimulation, where low electrochemical electrode impedance is valuable. Here the conducting polymer poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) is used to fabricate electrodes that are small enough to allow unencumbered optical access for imaging a large cell population with two-photon (2P) microscopy, yet provide low impedance for simultaneous high quality recordings of neural activity in vivo. To demonstrate this, pathophysiological activity was induced in the mouse cortex using 4-aminopyridine (4AP), and the resulting electrical activity was detected with the PEDOT:PSS-based probe while imaging calcium activity directly below the probe area. The induced calcium activity of the neuronal network as measured by the fluorescence change in the cells correlated well with the electrophysiological recordings from the cortical grid of PEDOT:PSS microelectrodes. Our approach provides a valuable vehicle for complementing classical high temporal resolution electrophysiological analysis with optical imaging.

International audience; Electrical properties of neuronal processes are extraordinarily complex, dynamic, and, in the general case, impossible to predict in the absence of detailed measurements. To obtain such a measurement one would, ideally, like to be able to monitor electrical subthreshold events as they travel from synapses on distal dendrites and summate at particular locations to initiate action potentials. It is now possible to carry out these measurements at the scale of individual dendritic spines using voltage imaging. In these measurements, the voltage-sensitive probes can be thought of as transmembrane voltmeters with a linear scale, which directly monitor electrical signals. Amiram Grinvald and his colleagues were important early contributors to the methodology of voltage imaging, and they pioneered some of its significant results. In this study, we combined voltage imaging and glutamate uncaging using computer-generated holography (CGH). The results demonstrated that patterned illumination, by reducing the surface area of illuminated membrane, reduces photodynamic damage. Additionally, region-specific illumination practically eliminated the contamination of optical signals from individual spines by the scattered light from the parent dendrite. Finally, patterned illumination allowed one-photon uncaging of glutamate on multiple spines to be carried out in parallel with voltage imaging from the parent dendrite and neighboring spines.

Organic electrochemical transistors are integrated on depth probes to achieve localized electrical stimulation of neurons. The probes feature a mechanical delamination process which leaves only a 4 μm thick film with embedded transistors inside the brain. This considerably reduces probe invasiveness and correspondingly improves future brain-machine interfaces.

The paper investigates the collection-building strategies in the contemporary art museums of Central Europe. As its methodology, the study takes into consideration the collection-building principles and the way they are related to other activities of the institutions. It focuses on the role of the collection as an ensemble of musealized objects. The paper also intends to raise questions on how such institutions contribute, through their collections, to the participation of the given country in international discourse on contemporaneity. As a consequence of this collection-based observation conception, contemporary art centers and museums without collections are excluded from the observations. The observation focuses on the factors of national and international narratives intersecting each other in the process of modern and contemporary art museum-based national cultural policies.

The paper investigates the collection-building strategies in the contemporary art museums of Central Europe. As its methodology, the study takes into consideration the collection-building principles and the way they are related to other activities of the institutions. It focuses on the role of the collection as an ensemble of musealized objects. The paper also intends to raise questions on how such institutions contribute, through their collections, to the participation of the given country in international discourse on contemporaneity. As a consequence of this collection-based observation conception, contemporary art centers and museums without collections are excluded from the observations. The observation focuses on the factors of national and international narratives intersecting each other in the process of modern and contemporary art museum-based national cultural policies.

International audience; This paper presents a corpus-based study of the relative order between the direct object (DO) and the indirect object (IO) in the preverbal domain in Persian, a SOV language. The relative weight is one of the main factors stipulated in explaining constituent order preferences, namely several studies have pointed out the tendency to postpone heavy constituents (heavy NP shift). This weight effect is either accounted for in terms of parsing (Hawkins, 1994) or in terms of planning and production (Wasow 1997, Arnold et al. 2000, Stallings et al.1998, among others), planning or comprehending long and/or complex constituents requires more memory or resource than short and simple ones. Since this explanation lies on general principles of cognition, it has been sometimes assumed that “short-before-long” is universal. However, building on extensive data from typologically different languages, Hawkins have highlighted an asymmetry between VO and OV languages. The latter display the mirror image preference, i.e. “long-before-short”. Empirical corpus-based and experimental studies on Japanese, a consistent head-final language, have indeed confirmed this generalization (Yamashita & Chang, 2001). Our study shows a similar effect in Persian; however, relative length plays a secondary role, since the position of the DO mainly depends on its degree of determination.

Kisspeptin (KP) neurones in the rostral periventricular area of the third ventricle (RP3V) and arcuate nucleus (Arc) are important elements in the neuronal circuitry regulating gonadotropin-releasing hormone (GnRH) secretion. KP and co-synthesised neuropeptides/neurotransmitters act directly on GnRH perikarya and processes. GnRH neurones not only form the final output pathway regulating the reproductive functions of the anterior pituitary gland, but also provide neuronal input to sites within the hypothalamus. The current double-label immunohistochemical studies investigated whether GnRH-immunoreactive (IR) projections to the RP3V and/or Arc establish morphological connections with KP-IR neurones at these sites. To optimise visualisation of KP immunoreactivity in, respectively, the RP3V and Arc, ovariectomised (OVX) oestrogen-treated and OVX oil-treated female mice were studied. Confocal laser microscopic analysis of immunofluorescent specimens revealed GnRH-IR axon varicosities in apposition to approximately 25% of the KP-IR neurones in the RP3V and 50% of the KP-IR neurones in the Arc. At the ultrastructural level, GnRH-IR neurones were seen to establish asymmetric synaptic contacts, which usually reflect excitatory neurotransmission, with KP-IR neurones in both the RP3V and Arc. Together with previous data, these findings indicate reciprocal connectivity between both of the KP cell populations and the GnRH neuronal system. The functional significance of the GnRH-IR input to the two separate KP cell populations requires electrophysiological investigation.

International audience; Dès 1879 des milliers de terres-cuites figurées ont été découvertes sur les sites qu’occupaient dans l’antiquité les sanctuaires de Tarente. Malgré l’intérêt suscité par ces documents tant du point de vue artistique qu’iconographique, aucun classement exhaustif n’en avait jamais été tenté, alors qu’il s’agit du seul moyen de retracer l’histoire de cette production. On propose, donc, ici pour la première fois un catalogue systématique des types coroplastiques de l’époque archaïque, fondé sur l’examen direct des plus importantes collections de terres cuites tarentines.La période choisie correspond, dans l’ensemble du monde grec, à une recherche des formes d’expression artistique caractérisée par la concurrence entre plusieurs styles communautaires ; dans ce cadre, on s’est intéressé principalement à définir les traits qui peuvent caractériser le langage formel d’une colonie italiote telle que Tarente archaïque, à travers une classe de production quantitativement importante, susceptible de refléter les changements du goût d’une communauté. L’hypothèse d’une première phase éclectique qui aurait précédé l’émergence d’un véritable « style tarentin » est apparue comme une hypothèse de travail plausible, à partir de laquelle on a procédé à la reconnaissance des divers apports stylistiques extérieurs, qui contribuèrent, avant la fin de l’époque archaïque, à la naissance d’une culture artistique locale. A travers la reconnaissance des sources artistiques et de l’élaboration de la première forme « canonique » du type iconographique le plus important de la cité, celui du banqueteur couché, on est parvenu aussi à formuler une hypothèse concernant le culte, auquel il était lié.

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In rodents, a circadian signal from the suprachiasmatic nucleus (SCN) is essential for the pro-oestrous surge of gonadotrophin-releasing hormone (GnRH), which, in turn, induces luteinising hormone (LH) surge and ovulation. We hypothesised that kisspeptin (KP) neurones in the anteroventral periventricular and periventricular preoptic nuclei (AVPV/PeN) form part of the communication pathway between the SCN and GnRH neurones. In anterograde track tracing studies, we first identified vasopressin (VP)-containing axons of SCN origin in apposition to KP-immunoreactive (IR) neurones. Studies to quantify this input relied on the observation that VP-synthesising neurones in the SCN differ from other VP systems in their lack of galanin expression. In ovariectomised mice, 30.79 +/- 1.63% of KP-IR perikarya and proximal dendrites within the AVPV/PeN received galanin-negative VP-IR varicosities. Oestrogen-treatment significantly increased the number of KP-IR neurones, with their percentage apposed by galanin-negative VP-IR varicosities (46.95 +/- 1.88%) and the number of VP-IR appositions on individual KP-IR neurones. At the ultrastructural level, the VP-IR terminals formed symmetric synapses with KP-IR neurones, which was in accordance with the morphology of inhibitory synapses established by SCN neurones. By contrast to VP, vasoactive intestinal polypeptide (VIP), which is synthesised by a distinct subset of SCN neurones, occurred only rarely in axons apposed to KP-IR neurones. Altogether, our results are consistent with the hypothesis that KP neurones located in the mouse AVPV/PeN receive circadian information from the SCN via a vasopressinergic monosynaptic pathway, which is enhanced by oestrogen.

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Kisspeptin signaling via the kisspeptin receptor G-protein-coupled receptor-54 plays a fundamental role in the onset of puberty and the regulation of mammalian reproduction. In this immunocytochemical study we addressed the (i) topography, (ii) sexual dimorphism, (iii) relationship to gonadotropin-releasing hormone (GnRH) neurons and (iv) neurokinin B content of kisspeptin-immunoreactive hypothalamic neurons in human autopsy samples. In females, kisspeptin-immunoreactive axons formed a dense periventricular plexus and profusely innervated capillary vessels in the infundibular stalk. Most immunolabeled somata occurred in the infundibular nucleus. Many cells were also embedded in the periventricular fiber plexus. Rostrally, they formed a prominent periventricular cell mass (magnocellular paraventricular nucleus). Robust sex differences were noticed in that fibers and somata were significantly less numerous in male individuals. In dual-immunolabeled specimens, fine kisspeptin-immunoreactive axon varicosities formed axo-somatic, axo-dendritic and axo-axonal contacts with GnRH neurons. Dual-immunofluorescent studies established that 77% of kisspeptin-immunoreactive cells in the infundibular nucleus synthesize the tachykinin peptide neurokinin B, which is known to play crucial role in human fertility; 56 and 17% of kisspeptin fibers in the infundibular and periventricular nuclei, respectively, contained neurokinin B immunoreactivity. Site-specific co-localization patterns implied that kisspeptin neurons in the infundibular nucleus and elsewhere contributed differentially to these plexuses. This study describes the distribution and robust sexual dimorphism of kisspeptin-immunoreactive elements in human hypothalami, reveals neuronal contacts between kisspeptin-immunoreactive fibers and GnRH cells, and demonstrates co-synthesis of kisspeptins and neurokinin B in the infundibular nucleus. The neuroanatomical information will contribute to our understanding of central mechanisms whereby kisspeptins regulate human fertility.

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The Database of Intrinsically Disordered Proteins (DisProt, URL: https://disprot.org) is the major repository of manually curated annotations of intrinsically disordered proteins and regions from the literature. We report here recent updates of DisProt version 9, including a restyled web interface, refactored Intrinsically Disordered Proteins Ontology (IDPO), improvements in the curation process and significant content growth of around 30%. Higher quality and consistency of annotations is provided by a newly implemented reviewing process and training of curators. The increased curation capacity is fostered by the integration of DisProt with APICURON, a dedicated resource for the proper attribution and recognition of biocuration efforts. Better interoperability is provided through the adoption of the Minimum Information About Disorder (MIADE) standard, an active collaboration with the Gene Ontology (GO) and Evidence and Conclusion Ontology (ECO) consortia and the support of the ELIXIR infrastructure. © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

Small, cysteine-rich and cationic proteins with antimicrobial activity are produced by diverse organisms of all kingdoms and represent promising molecules for drug development. The ancestor of all industrial penicillin producing strains, the ascomycete Penicillium chryosgenum Q176, secretes the extensively studied antifungal protein PAF. However, the genome of this strain harbours at least two more genes that code for other small, cysteine-rich and cationic proteins with potential antifungal activity. In this study, we characterized the pafB gene product that shows high similarity to PgAFP from P. chrysogenum R42C. Although abundant and timely regulated pafB gene transcripts were detected, we could not identify PAFB in the culture broth of P. chrysogenum Q176. Therefore, we applied a P. chrysogenum-based expression system to produce sufficient amounts of recombinant PAFB to address unanswered questions concerning the structure and antimicrobial function. Nuclear magnetic resonance (NMR)-based analyses revealed a compact β-folded structure, comprising five β-strands connected by four solvent exposed and flexible loops and an “abcabc” disulphide bond pattern. We identified PAFB as an inhibitor of growth of human pathogenic moulds and yeasts. Furthermore, we document for the first time an anti-viral activity for two members of the small, cysteine-rich and cationic protein group from ascomycetes.

Extracting neuronal spiking activity from large-scale two-photon recordings remains challenging, especially in mammals in vivo, where large noises often contaminate the signals. We propose a method, MLspike, which returns the most likely spike train underlying the measured calcium fluorescence. It relies on a physiological model including baseline fluctuations and distinct nonlinearities for synthetic and genetically encoded indicators. Model parameters can be either provided by the user or estimated from the data themselves. MLspike is computationally efficient thanks to its original discretization of probability representations; moreover, it can also return spike probabilities or samples. Benchmarked on extensive simulations and real data from seven different preparations, it outperformed state-of-the-art algorithms. Combined with the finding obtained from systematic data investigation (noise level, spiking rate and so on) that photonic noise is not necessarily the main limiting factor, our method allows spike extraction from large-scale recordings, as demonstrated on acousto-optical three-dimensional recordings of over 1,000 neurons in vivo., Two-photon laser scanning microscopy allows functional calcium imaging of large neuronal populations in vivo, but the recorded signals typically suffer from low signal to noise. Here the authors develop an algorithm, MLspike, which estimates action potentials from noisy calcium signals, and benchmark it against existing methods.