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Two experiments showed that a photo frame placed at a distance from the photo itself enhances the apparent depth of contents within the photo. In Experiment 1, 32 observers rated the apparent depth of 60 successively presented photos of scenes with pictorial depth cues. In a separate block of trials, the photos were presented either with a frame in front of each photo or without a frame. Observers also assessed apparent depth of the same 60 photos by choosing the photo that had greater apparent depth when a framed and a frameless photo of the same scene were presented side by side. We found that mean depth ratings were higher for framed than for frameless photos, and framed photos were chosen more often than frameless photos. In Experiment 2, 12 observers rated the apparent depth of 20 different photos that were successively presented with or without a frame. The frame was placed in front of, at the same distance as, or behind each photo. Mean ratings for front-framed and behind-framed photos were higher than those for equidistant-framed or frameless photos, and mean ratings increased with the distance between the photo and the frame. We hypothesize that having to process the relative depth between a photo and a frame reduces the effectiveness of flatness information provided by the photo.

Chromatin-associated RNA (caRNA) is a vital component of the interphase nucleus; yet its distribution and role in the three-dimensional (3D) genome organization and function remain poorly understood. Here, we map caRNA’s spatial distribution on the 3D genome in human embryonic stem cells, fibroblasts, and myelogenous leukemia cells. We find that the relative abundance of trans-acting caRNA reflects the functional nuclear compartmentalization of the 3D genome, and the caRNA’s sequence features are predictive of its spatial localization. We observe extensive caRNA-genome interactions that span several hundred kilobases to several megabases. These caRNA domains correlate with chromatin loops and enhancer-promoter interactions. We report a tradeoff of caRNA’s promotive and suppressive roles to chromatin interactions. As a result, caRNA promotes chromatin interactions outside the anchors of chromatin loops, whereas caRNA exhibits an overall suppressive impact to chromatin interactions between loop anchors. Furthermore, caRNA suppresses chromatin loops’ number and strengths genome-wide, and this suppression depends on electric charge-mediated RNA interactions. These results reveal caRNA’s multifaced role in regulating 3D chromatin organization and highlight caRNA’s ability to modulate chromatin looping.

Knowledge of eye position in the brain is critical for localization of objects in space. To investigate the accuracy and precision of eye position feedback in an unreferenced environment, subjects with normal ocular alignment attempted to localize briefly presented targets during monocular and dichoptic viewing. In the task, subjects’ used a computer mouse to position a response disk at the remembered location of the target. Under dichoptic viewing (with red (right eye)–green (left eye) glasses), target and response disks were presented to the same or alternate eyes, leading to four conditions [green target–green response cue (LL), green–red (LR), red–green (RL), and red–red (RR)]. Time interval between target and response disks was varied and localization errors were the difference between the estimated and real positions of the target disk. Overall, the precision of spatial localization (variance across trials) became progressively worse with time. Under dichoptic viewing, localization errors were significantly greater for alternate-eye trials as compared to same-eye trials and were correlated to the average phoria of each subject. Our data suggests that during binocular dissociation, spatial localization may be achieved by combining a reliable versional efference copy signal with a proprioceptive signal that is unreliable perhaps because it is from the wrong eye or is too noisy.

Single-cell technology is a relatively new and promising way to obtain high-resolution transcriptomic data mostly used for animals during the last decade. However, several scientific groups developed and applied the protocols for some plant tissues. Together with deeply-developed cell-resolution imaging techniques, this achievement opens up new horizons for studying the complex mechanisms of plant tissue architecture formation. While the opportunities for integrating data from transcriptomic to morphogenetic levels in a unified system still present several difficulties, plant tissues have some additional peculiarities. One of the plants’ features is that cell-to-cell communication topology through plasmodesmata forms during tissue growth and morphogenesis and results in mutual regulation of expression between neighboring cells affecting internal processes and cell domain development. Undoubtedly, we must take this fact into account when analyzing single-cell transcriptomic data. Cell-based computational modeling approaches successfully used in plant morphogenesis studies promise to be an efficient way to summarize such novel multiscale data. The inverse problem’s solutions for these models computed on the real tissue templates can shed light on the restoration of individual cells’ spatial localization in the initial plant organ—one of the most ambiguous and challenging stages in single-cell transcriptomic data analysis. This review summarizes new opportunities for advanced plant morphogenesis models, which become possible thanks to single-cell transcriptome data. Besides, we show the prospects of microscopy and cell-resolution imaging techniques to solve several spatial problems in single-cell transcriptomic data analysis and enhance the hybrid modeling framework opportunities.

In MEG and EEG brain imaging research two popular approaches are often used for spatial localization of focal task- or stimuli-related brain activations. One is a so called MUSIC approach applied in the form of RAP or TRAP MUSIC algorithms. Another one is the beamformer approach, specifically multiple constrained minimum variance (MCMV) beamformer when dealing with significantly correlated activations. Either method is using its own source localizer functions. Considering simplicity, accuracy and computational efficiency both approaches have their advantages and disadvantages. In this study we introduce a novel set of so called Subspace MCMV (or SMCMV) beamformers whose localizer functions combine MUSIC and MCMV localizers. We show that in ideal situations where forward modeling, data recording and noise measurements are error-free, SMCMV localizers allow precise identification of n arbitrarily correlated sources irrespective to their strength in just n scans of the brain volume using RAP MUSIC type algorithm. We also demonstrate by extensive computer simulations that with respect to source localization errors and the total number of identified sources SMCMV outperforms both the TRAP MUSIC and MIA MCMV (which is the most accurate MCMV algorithm to our knowledge) in non-ideal practical situations, specifically when the noise covariance cannot be estimated precisely, signal to noise ratios are small, source correlations are significant and larger numbers of sources are involved.

Pseudevernia furfuracea (L.) Zopf (Parmeliaceae) is a well-known epiphytic lichen commonly used in Indian spice mixtures and food preparations such as curries. This study is an attempt to find the best extraction methodology with respect to extractive yield, total polyphenolic content (TPC), total flavonoid content and antioxidant activities of lichen P. furfuracea. Two phenolic compounds, atraric acid and olivetoric acid were isolated and quantified in their respective extracts with the aid of reverse phase high performance liquid chromatography (RP-HPLC). The highest concentration of both the compounds, atraric acid (4.89 mg/g DW) and olivetoric acid (11.46 mg/g DW) were found in 70% methanol extract. A direct correlation was also observed between the concentrations of these compounds with the free radical scavenging potential of the extracts which might contribute towards the antioxidant potential of the extract. Moreover, scanning electron microscopy and HPLC analysis which was used to study the effect of pre-processing on extraction process highlighted the capacity of a mixer grinder technique for improved separation of surface localized metabolites and enrichment of the fraction. An investigation of the chemical profile of the bioactive extract 70% methanol extract using UHPLC-DAD-MS lead to tentative identification of forty nine compounds. This extract was also assessed towards HEK 293 T cell line for cytotoxicity analysis. Concentration range of 0.156 to 100 µg/ml of PF70M extract exhibited no significant cell death as compared to control. Further, the active extract showed protective effect against hydroxyl radical’s destructive effects on DNA when assessed using DNA nicking assay. Based upon this, it can be concluded that optimization of extraction solvent, sample pre-proceesing and extraction techniques can be useful in extraction of specific antioxidant metabolites.

In this paper, we calculate the region of emergence of rogue waves in the Sasa–Satsuma equation by performing Penrose stability analysis. We consider Wigner-transformed Sasa–Satsuma equation and separate out unstable solutions, namely Penrose instability modes. We superpose these modes in a small region. With the help of marginal property of the Wigner transform, we identify the region in which rogue wave solution can emerge in the Sasa–Satsuma equation and calculate the amount of spatial localization. We also formulate a condition for the emergence of rogue wave solution in the Sasa–Satsuma equation.

Spectroscopic methods provide information on the spatial localization of biochemical components based on the analysis of vibrational spectra. Raman spectroscopy and Raman imaging can be used to analyze various types of human brain tumors and breast cancers. The objective of this study is to evaluate the Raman biomarkers to distinguish tumor types by Raman spectroscopy and Raman imaging. We have demonstrated that bands characteristic for carotenoids (1156 cm−1, 1520 cm−1), proteins (1004 cm−1), fatty acids (1444 cm−1, 1655 cm−1) and cytochrome (1585 cm−1) can be used as universal biomarkers to assess aggressiveness of human brain tumors. The sensitivity and specificity obtained from PLS-DA have been over 73%. Only for gliosarcoma WHO IV the specificity is lower and takes equal 50%. The presented results confirm clinical potential of Raman spectroscopy in oncological diagnostics.

Advances in the design and synthesis of nanomaterials with desired biophysicochemical properties can be harnessed to develop non-invasive neuromodulation technologies. Here, we demonstrate the reversible modulation of the electrical activity of neurons and cardiomyocytes using polydopamine (PDA) nanoparticles as photothermal nanotransducers. In addition to their broad light absorption and excellent photothermal activity, PDA nanoparticles are highly biocompatible and biodegradable, making them excellent candidates for both in vitro and in vivo applications. The modulation of the activity (i.e. spike rate of the neurons and beating rate of cardiomyocytes) of excitable cells could be finely controlled by varying the excitation power density and irradiation duration. Under optimal conditions, we demonstrate reversible suppression (~100%) of neural activity and reversible enhancement (two-fold) in the beating rate of cardiomyocytes. To improve the ease of interfacing of photothermal transducers with these excitable cells and enable spatial localization of the photothermal stimulus, we have realized a collagen/PDA nanoparticle foam, which can be used as an “add-on patch” for photothermal stimulation. The non-genetic optical neuromodulation approach using biocompatible and biodegradable nanoparticles represents a minimally-invasive method for controlling the activity of excitable cells with potential applications in nano-neuroscience and engineering.

Plant roots are composed of many differentiated tissue types, with each tissue exhibiting differential quantitative and qualitative accumulation of metabolites. The large-scale nontargeted metabolite profiles of these differentiated tissues are complex, which complicates the interpretation and development of hypotheses relative to the biological roles of differentially localized metabolites. Thus, we created a data visualization tool to aid in the visualization and understanding of differential metabolite accumulations in Medicago truncatula roots. This was achieved through the development of the Medicago truncatula Metabolite Atlas based upon an adaptation of the Arabidopsis Electronic Fluorescent Pictograph (eFP) Browser. Medicago truncatula roots were dissected into border cells, root cap, elongation zone, mature root, and root secretions. Each tissue was then analyzed by UHPLC-QTOF-MS and GC-Q-MS. Data were uploaded into a MySQL database and displayed in the Medicago truncatula Metabolite Atlas. The data revealed unique differential spatial localization of many metabolites, some of which are discussed here. Ultimately, the Medicago truncatula Metabolite Atlas compiles metabolite data into a singular, useful, and publicly available web-based tool that enables the visualization and understanding of differential metabolite accumulation and spatial localization.

Spectroscopic methods provide information on the spatial localization of biochemical components based on the analysis of vibrational spectra. Raman spectroscopy and Raman imaging can be used to analyze various types of human brain tissue. The objective of this study is employment of Raman spectroscopy and Raman imaging to evaluate the Raman biomarkers to distinguish tumor types. We have demonstrated that bands characteristic for carotenoids (1156 cm−1, 1520 cm−1), proteins (1004 cm−1), fatty acids (1444 cm−1, 1655 cm−1) and cytochrome (1585 cm−1) can be used as universal biomarkers to distinguish aggressiveness in human brain tumor. The sensitivity and specificity obtained from PLS-DA have been over 85%. Only for pituitary adenoma the specificity is lower and takes equal 46%. The presented results confirm the potential applications of vibrational spectroscopy methods in oncological diagnostics.

Synaptic active zone (AZ) contains multiple specialized release sites for vesicle fusion. The utilization of release sites is regulated to determine spatiotemporal organization of the two main forms of synchronous release, uni-vesicular (UVR) and multi-vesicular (MVR). We previously found that the vesicle-associated molecular motor myosin V regulates temporal utilization of release sites by controlling vesicle anchoring at release sites in an activity-dependent manner. Here we show that acute inhibition of myosin V shifts preferential location of vesicle docking away from AZ center toward periphery, and results in a corresponding spatial shift in utilization of release sites during UVR. Similarly, inhibition of myosin V also reduces preferential utilization of central release sites during MVR, leading to more spatially distributed and temporally uniform MVR that occurs farther away from the AZ center. Using a modeling approach, we provide a conceptual framework that unites spatial and temporal functions of myosin V in vesicle release by controlling the gradient of release site release probability across the AZ, which in turn determines the spatiotemporal organization of both UVR and MVR. Thus myosin V regulates both temporal and spatial utilization of release sites during two main forms of synchronous release.

International audience; As a subclass of interstitial lung diseases, nonspecific interstitial pneumonia (NSIP), defined by an association of inflammation and fibrotic lung lesions, leads to progressive loss of pulmonary function and premature mortality. Among fibrosis manifestations, traction bronchiectasis (TB) is one of the most critical, its presence being associated to poor prognosis. Accurate follow up is crucial to treatment decision and adaptation. In this paper we propose quantitative biomarkers for TB, associating spatial localization and severity measures. Bronchial tree segmentation and TB identification first exploited a semi-automatic approach for the definition of the ground truth, then used an automatic method involving a convolutional neural network. The CNN training/testing database included 73/18 patients respectively, with both baseline and follow up exams at one year; the detection performance was assessed in terms of precision, recall and F1-score. For both ground truth and CNN-segmented data, the following TB biomarkers were derived: TB ratio over total airway, airway volume, normalized tree length, and airway caliber (absolute and relative) deviation from the normal 2-power decrease law. A correlation study between the TB biomarkers and the initial and follow up pulmonary function tests was conducted. Among ground truth-based TB biomarkers, airway volume, normalized tree length, absolute caliber deviation and TB ratio over total airway showed significant negative correlation with both initial and follow-up pulmonary function parameters, manifesting as potential prognosis biomarkers. Among CNN-based TB biomarkers, airway volume, normalized tree length, relative and absolute caliber deviation showed significant negative correlation with follow-up pulmonary function parameters confirming their predictive potential.

Recent development of spatial transcriptomics (ST) is capable of associating spatial information at different spots in the tissue section with RNA abundance of cells within each spot, which is particularly important to understand tissue cytoarchitectures and functions. However, for such ST data, since a spot is usually larger than an individual cell, gene expressions measured at each spot are from a mixture of cells with heterogenous cell types. Therefore, ST data at each spot needs to be disentangled so as to reveal the cell compositions at that spatial spot. In this study, we propose a novel method, named deconvoluting spatial transcriptomics data through graph-based convolutional networks (DSTG), to accurately deconvolute the observed gene expressions at each spot and recover its cell constitutions, thus achieving high-level segmentation and revealing spatial architecture of cellular heterogeneity within tissues. DSTG not only demonstrates superior performance on synthetic spatial data generated from different protocols, but also effectively identifies spatial compositions of cells in mouse cortex layer, hippocampus slice and pancreatic tumor tissues. In conclusion, DSTG accurately uncovers the cell states and subpopulations based on spatial localization. DSTG is available as a ready-to-use open source software (https://github.com/Su-informatics-lab/DSTG) for precise interrogation of spatial organizations and functions in tissues.

Researchers worldwide are taking advantage of novel, commercially available, technologies, such as ion mobility mass spectrometry (IM-MS), for metabolomics and lipidomics applications in a variety of fields including life, biomedical, and food sciences. IM-MS provides three main technical advantages over traditional LC-MS workflows. Firstly, in addition to mass, IM-MS allows collision cross-section values to be measured for metabolites and lipids, a physicochemical identifier related to the chemical shape of an analyte that increases the confidence of identification. Second, IM-MS increases peak capacity and the signal-to-noise, improving fingerprinting as well as quantification, and better defining the spatial localization of metabolites and lipids in biological and food samples. Third, IM-MS can be coupled with various fragmentation modes, adding new tools to improve structural characterization and molecular annotation. Here, we review the state-of-the-art in IM-MS technologies and approaches utilized to support metabolomics and lipidomics applications and we assess the challenges and opportunities in this growing field.

Weakly supervised object localization is a challenging task in which the object of interest should be localized while learning its appearance. State-of-the-art methods recycle the architecture of a standard CNN by using the activation maps of the last layer for localizing the object. While this approach is simple and works relatively well, object localization relies on different features than classification, thus, a specialized localization mechanism is required during training to improve performance. In this paper, we propose a convolutional, multi-scale spatial localization network that provides accurate localization for the object of interest. Experimental results on CUB-200-2011 and ImageNet datasets show that our proposed approach provides competitive performance for weakly supervised localization., Comment: 8 pages, 9 figures

In this chapter, we describe the pipeline for multiplex immunohistochemical staining, multispectral image acquisition, and analysis. The protocol is dedicated for use on human formalin fixed paraffin embedded (FFPE) tissues and utilizes immune markers of dendritic cells, myeloid cells, and macrophages, as well as cytokeratin. This provides quantitative data of the (co-)expression levels and spatial localization of immune cell subtypes.

The article reveals the features of changing the scale and structure of production processes at industrial enterprises as a result of technological innovations. Historical peculiarities of the structural and large-scale transformation of industrial production systems under the influence of the consequences of scientific and technological progress are considered, the cyclical nature of such changes is reported in the article. The authors state that the main parameters of the analysis of large-scale changes are the concentration and spatial localization of production systems, the cyclical dependence of the localization and delocalization of industrial enterprises, depending on the type of new production technology being introduced. The expansion of the space of functional and technological interaction of the main production agents is substantiated on the basis of innovative changes. The tendency of the increase in the scale of production processes due to innovative changes and the introduction of new technological equipment, as well as its life cycle and service life are described in the article. It is proved that the growth of investment in fixed capital in recent years leads to a greater extent to the intensification of production processes without a significant impact on the large-scale dynamics of the size of industrial enterprises in the leading industries.

Visible light communication (VLC) is currently recognized as a relevant technology for a wealth of possible application scenarios. New classes of services can be designed in both outdoor and indoor environments, exploiting the directionality of the optical channel and the low attainable latencies. Such features allow VLC to offer both spatial localization of users and wireless communication by using widespread high-power LEDs as simultaneous illumination and information sources. In the indoor scenario, one of the most promising deployments is expected in museums, where digital data can be cast by the specific illumination system of each artwork and received by visitors placed nearby. This would enable a full set of services, aiming, e.g., at an immersive experience in the augmented reality approach or at real-time localization of visitors. In this work, we characterize for the first time the performance of a photodiode-based VLC system in a real museum environment, performing an extensive measurement campaign on several masterpieces (wall, canvas, and wood paintings) in the Basilica of Santa Maria Novella in Florence, Italy. In particular, we demonstrate the possibility of using indirect (diffused) illumination light to deliver specific information on each artwork to a visitor. We characterize the quality of such non-line-of-sight VLC links by performing packet error rate measurements as a function of angle and distance from the artwork, and we measure the effective field of view (FoV) of our receiving stage, as well as the influence of side displacements of the receiver on the transmission quality, demonstrating that diffusive VLC links can also be used for efficient localization of users in front of each artwork in museum applications. With observed baud rates up to 28 kbaud and FoV values up to 60° for realistic distances up to 6 m, we believe our work could pave the way for future studies involving VLC in a wealth of indoor applications, beyond the cultural heritage sector.

We describe multiscale geometrical changes via structured deformations $(g,G)$ and the non-local energetic response at a point $x$ via a function $\Psi$ of the weighted averages of the jumps $[u_{n}](y)$ of microlevel deformations $u_{n}$ at points $y$ within a distance $r$ of $x$. The deformations $u_{n}$ are chosen so that $\lim_{n\to \infty }u_{n}=g$ and $\lim_{n\to \infty }\nabla u_{n}=$ $G$. We provide conditions on $\Psi$ under which the upscaling "$n\to \infty$" results in a macroscale energy that depends through $\Psi$ on (1) the jumps $[g]$ of $g$ and the "disarrangment field" $\nabla g-G$, (2) the "horizon" $r$, and (3) the weighting function $\alpha _{r}$ for microlevel averaging of $[u_{n}](y)$. We also study the upscaling "$n\to \infty$" followed by spatial localization "$r\to 0$" and show that this succession of processes results in a purely local macroscale energy $I(g,G)$ that depends through $\Psi$ upon the jumps $[g]$ of $g$ and the "disarrangment field" $\nabla g-G$, alone. In special settings, such macroscale energies $I(g,G)$ have been shown to support the phenomena of yielding and hysteresis, and our results provide a broader setting for studying such yielding and hysteresis. As an illustration, we apply our results in the context of the plasticity of single crystals., Comment: 31 pages

In this work, we propose an interactive general instruction framework SketchMeHow to guidance the common users to complete the daily tasks in real-time. In contrast to the conventional augmented reality-based instruction systems, the proposed framework utilizes the user sketches as system inputs to acquire the users’ production intentions from the drawing interfaces. Given the user sketches, the designated task instruction can be analyzed based on the subtask division and spatial localization for each task. The projector-camera system is adopted in the projection guidance to the end-users with the spatial augmented reality technology. To verify the proposed framework, we conducted two case studies of domino arrangement and bento production. From our user studies, the proposed systems can help novice users complete the tasks efficiently with user satisfaction. We believe the proposed SketchMeHow can broaden the research topics in sketch-based real-world applications in human-computer interaction.

Road traffic safety is a social issue of widespread concern. It is important for traffic managers to understand the distribution patterns of road traffic accidents. To this end, this study examines the spatial and temporal patterns of road traffic accidents from both accident frequency and accident severity perspectives. Road traffic accident data from 2016 to 2018 in Harbin, China, were used for the analysis. First, the spatial localization of accidents was completed using geocoding, and the localized accident data were classified by season. Then, density analysis was performed both with and without considering road network density. The results of the density analysis showed that when road network density was considered, accidents were mainly distributed in urban centers, while accidents were more dispersed when road network density was not considered. Third, a cluster analysis considering accident severity found that low-severity accident clusters occurred mostly in urban centers. High-severity accident clusters were mostly present in suburban areas. Finally, the results of these two methods are shown by using the comap technique. Areas of the city with a high frequency and severity of crashes in each season were identified. This study will help traffic management to have a more visual and intuitive understanding of the urban traffic safety situation and to take targeted measures to improve it accordingly.

Recent progress has shown that Metal-organic Frameworks (MOFs) can be integrated with biomacromolecules. Depending on the synthesis protocol used, it is possible to control the spatial localization of the biomacromolecules in or on MOF biocomposites. When biomacromolecules are infiltrated or encapsulated within MOFs, the porous materials were found to form a protective coating around the bioactive entity, thus offering improved stability to non-native external environments that would normally lead to its degradation. When MOF particles are surface functionalized with biomacromolecules either via adsorption or grafting, enhanced targeting capabilities and improved biodistribution were observed. In this book chapter, we examine the principal synthetic methods for the preparation of MOF bio-composites. We discuss the progress toward combining the four main classes of biomacromolecules, such as proteins, carbohydrates, nucleic acids, and lipids, with MOFs, and disclose relevant examples for application to drug delivery, biopreservation, and biosensing. As MOF biocomposites composition has been extended from biomacromolecules to more complex biological systems, including viruses and cells, we illustrate how MOFs can be used for the preparation of protective exoskeletons for potential applications to vaccine transportation/delivery and regenerative medicine.

Nowadays, several low-cost yet productive video editing software tools have been developed due to which it is essential to check the genuineness of digital videos, before they can be used as legal evidences. Thus, detecting and localizing forgery in videos has become an important research field. In this paper we have proposed a solution to detect and localize spatio-temporal manipulation in videos using a deep learning approach involving an architecture based on LSTM or Long short-term memory. Our proposed model is able to perform temporal as well as spatial localization of forgery. The experiments are carried out on the REWIND dataset having 10 original and 10 forged videos. 16 videos are used for training and 4 are used for testing the model. The evaluation of model performance is done at pixel-level, frame-level and video-level for computing the spatial localization, temporal localization and forgery detection accuracy values respectively.

Recent work [M. H. Kolodrubetz et al, PRL 120, 150601] has demonstrated that periodically driven one-dimensional fermionic systems can support quantized energy pumping resulting from an adiabatic modulation of a second parameter. In this work, we explore this topological Floquet-Thouless energy pump in the quasiperiodic driving regime where the parametric driving occurs at finite frequency. We show that quantization of energy pumping persists for finite ramping frequencies, as long as they are incommensurate with the driving frequency, and the system remains localized by spatial disorder. Thus, the topological Floquet-Thouless energy pump is stable beyond the adiabatic regime, occupying a finite region of parameter space. Phase transitions away from these topological phases are accompanied by delocalization in position space, photon number (energy) space, or both. Using a dimensional reduction scheme, we demonstrate that a related phase can be realized with a cavity-qubit system driven by two incommensurate modes.

Enzymes are a class of protein that catalyze a wide range of chemical reactions, including the cleavage of specific peptide bonds. They are expressed in all cell types, play vital roles in tissue development and homeostasis, and in many diseases, such as cancer. Enzymatic activity is tightly controlled through the use of inactive pro-enzymes, endogenous inhibitors and spatial localization. Since the presence of specific enzymes is often correlated with biological processes, and these proteins can directly modify biomolecules, they are an ideal biological input for cell-responsive biomaterials. These materials include both natural and synthetic polymers, cross-linked hydrogels and self-assembled peptide nanostructures. Within these systems enzymatic activity has been used to induce biodegradation, release therapeutic agents and for disease diagnosis. As technological advancements increase our ability to quantify the expression and nanoscale organization of proteins in cells and tissues, as well as the synthesis of increasingly complex and well-defined biomaterials, enzyme-responsive biomaterials are poised to play vital roles in the future of biomedicine.

After an object disappears, the vanishing point is shifted in the direction of motion, a phenomenon known as representational momentum. The present study focused on the relationship between motion information and spatial location in a crossmodal setting. In two visuotactile experiments, we studied how motion information in one sensory modality affects the perceived final location of a motion signal (congruent vs. incongruent left-right motion direction) in another modality. The results revealed a unidirectional crossmodal influence of motion information on spatial localization performance. While visual motion information influenced the perceived final location of the tactile stimulus, tactile motion information had no influence on visual localization. These results therefore extend the existing literature on crossmodal influences on spatial location and are discussed in relation to current theories of multisensory perception.

The article considers systems of nonlinear reaction-diffusion models described by parabolic equations. It is shown that the models of the biological population consist in the limited nature and spatial localization of the outbreak. In the studied model, the corresponding approximations of self-similar solutions are found. The introduction of power nonlinearity in the processes of a biological population, as it turned out, in some cases leads to the same spatial dynamics as the coefficient of power nonlinearity in migration members.

Perceiving the spatial location and physical dimensions of objects that we touch is crucial for goal-directed actions. To achieve this, our brain transforms skin-based coordinates into a reference frame by integrating visual and proprioceptive cues, a process known as tactile remapping. In the current study, we examine the role of proprioception in the remapping process when information from the more dominant visual modality is withheld. We developed a new visual-to-touch sensory substitution device and asked participants to perform a spatial localization task in three different arm postures that included posture switches between blocks of trials. We observed that in the absence of visual information novel proprioceptive inputs can be overridden after switching postures. This behavior demonstrates effective top-down modulations of proprioception and points to the unequal contribution of different sensory modalities to tactile remapping.

The tumor immune microenvironment is a main contributor to cancer progression and a promising therapeutic target for oncology. However, immune microenvironments vary profoundly between patients and biomarkers for prognosis and treatment response lack precision. A comprehensive compendium of tumor immune cells is required to pinpoint predictive cellular states and their spatial localization. We generated a single-cell tumor immune atlas, jointly analyzing >500,000 cells from 217 patients and 13 cancer types, providing the basis for a patient stratification based on immune cell compositions. Projecting immune cells from external tumors onto the atlas facilitated an automated cell annotation system for a harmonized interpretation. To enable in situ mapping of immune populations for digital pathology, we applied SPOTlight, combining single-cell and spatial transcriptomics data and identifying striking spatial immune cell patterns in tumor sections. We expect the tumor immune cell atlas, together with our versatile toolbox for precision oncology, to advance currently applied stratification approaches for prognosis and immuno-therapy.

This paper introduces a new type of interface “3D Head Pointer” for operation of a wearable robot arm in 3D space. The developed system is aimed at assisting the user in execution of daily chores (e.g. opening an umbrella, stirring a pot) while concurrently operating wearable robot arm. Previous researches have demonstrated the difficulty in simultaneously controlling a robot arm while uninterruptedly performing another task with one's own hands. The proposed method uses a combination of the orientation of the face and head bobbing (a forward and backward movement of the head) to manipulate spatial localization in a polar coordinate system. In a Virtual Reality (VR) environment, the proposed system and its efficiency at adapting its operating magnification (IDF) by relying on the incremental changes in head bobbing were evaluated through measurement of the instructional accuracy and time demand. Experiments were conducted with 12 participants. Results displayed an accuracy of 1.3 cm with a 4 seconds time span necessary to communicate an instruction. These results, along with the confirmed ability of an individual to multi-task while operating, suggested the effectiveness of the operation method and IDF.

The current standard atomic collision theory cannot explain recent experiments on electron-ion collisional ionization processes in hot dense plasma. We suggest that the use of (distorted) plane waves for incident and scattered electrons is not adequate to describe dissipation during the ionization event. Random collisions with free electrons and ions in plasma cause electron matter waves to lose their phase, which results in partial decoherence of incident and scattered electrons. Such a plasma-induced transient spatial localization of the continuum-electron states significantly modifies the wave functions of continuum electrons, resulting in a strong enhancement of electron-ion collisional ionization of ions in plasma compared with isolated ions. We develop a theoretical formulation to calculate the differential and integral cross sections by incorporating the effects of plasma screening and transient spatial localization. The approach is then used to investigate electron-impact ionization of ions in solid-density magnesium plasma and gives results that are consistent with experiment. The correlation of continuum-electron energies is modified and the integral cross sections and rates increase considerably in hot dense plasma. For ionization of Mg9+ e+ 1s2 2s 2S → 1s2 1S + 2e, the ionization cross sections increase several-fold and the rates increase by one order of magnitude. Our findings shed new insight on collisional ionization and three-body recombination and should aid in investigations of the transport properties and nonequilibrium evolution of hot dense plasma.

The present work shows the spatial reliability of the diffuse optical tomography (DOT) system in a group of healthy subjects during a motor imagery task. Prior to imagery task performance, the subjects executed a motor task based on the finger to thumb opposition for motor training, and to corroborate the DOT spatial localization during the motor execution. DOT technology and data treatment allows us to distinguish oxy- and deoxyhemoglobin at the cerebral gyri level unlike the cerebral activations provided by fMRI series that were processed using different approaches. Here we show the DOT reliability showing functional activations at the cerebral gyri level during motor execution and motor imagery, which provide subtler cerebral activations than the motor execution. These results will allow the use of the DOT system as a monitoring device in a brain computer interface.

Immunohistochemistry (IHC) is a fundamental molecular technique that provides information on protein expression in the context of spatial localization and tissue morphology. IHC is used in all facets of pathology from identifying infectious agents or characterizing tumors in diagnostics, to characterizing cellular and molecular processes in investigative and experimental studies. Confidence in an IHC assay is primarily driven by the degree to which it is validated. There are many approaches to validate an IHC assay’s specificity including bioinformatics approaches using published protein sequences, careful design of positive and negative tissue controls, use of cell pellets with known target protein expression, corroboration of IHC findings with western blots and other analytical methods, and replacement of the primary antibody with an appropriate negative control reagent. Each approach has inherent strengths and weaknesses, and the thoughtful use of these approaches provides cumulative evidence, or a weight of evidence, to support the IHC assay’s specificity and build confidence in a study’s conclusions. Although it is difficult to be 100% confident in the specificity of any IHC assay, it is important to consider how validation approaches provide evidence to support or to question the specificity of labeling, and how that evidence affects the overall interpretation of a study’s results. In this review, we discuss different approaches for IHC antibody validation, with an emphasis on the characterization of antibody specificity in investigative studies. While this review is not prescriptive, it is hoped that it will be thought provoking when considering the interpretation of IHC results.

This thesis investigates different spatial hearing functions in 3 types of populations: Normal Hearing Subjects (NHS), Unilateral Hearing Loss patients (UHL) and Bilateral Hearing Loss patients ( BHL). To discover the mechanisms underlying the adaptive strategies that are observed in UHL with acquired deafness. The main aim of the thesis is to verify whether spatial Mismatch Negativity (MMN) could be a neuronal marker of spatial auditory plasticity observed in UHL patients, and to verify whether these neural correlates are consistent with the spatial auditory performance. Two types of investigations were applied to 20 NHS, 21 UHL and 14 BHL. The first investigation is a sound source identification task measured by the root mean square error (RMS). The second assessment is an electroencephalography (EEG) study where we analyzed the amplitude and latency of the MMN. MMN is defined as an auditory evoked potential that reflects the brain's ability to detect a change in one physical property of a sound. We used a standard sound in a reference position (50°) with three deviations from the standard (10° , 20°, and 100°), in binaural and monaural conditions. UHL patients were divided into 3 groups according to their spatial performances. The group of good performers (UHL {low rms}) showed better RMS scores in comparison with NHS with earplugs (NHS-mon), with performances similar to those of NHS subjects in binaural condition. A progressive increase of the MMN with the angle of deviation from the standard was noted in all groups. With a significant reduction of MMN amplitude in monaural NHS when the ear plug was applied on the ipsilateral side of the standard. MMN showed consistent variation with the behavioral observations, where UHL {low rms} patients had larger MMN amplitudes than those of monaural NHS and similar to those of binaural NHS. UHL patients have adaptive spatial auditory strategies. Our study was able to demonstrate that spatial auditory plasticity that occurs after deafness can be reflected by the MMN. Neural observations (i.e. the MMN) are correlated with behavioral observations of spatial source identification. This means that the spatial cortical plasticity, that took place in these subjects, is not limited to the functions of identification of the sound source, but exceeds these capacities towards more complex mechanisms such as deviance detection and short-term memory, that are involved in the spatial discrimination function., Cette thèse évalue les différentes fonctions d'audition spatiale chez 3 types de populations : Normaux entendants (NE), sourds unilatéraux (SU) et sourds bilatéraux (SB). Afin de découvrir les mécanismes qui soulignent les stratégies spatio-auditives adaptative qui sont observés chez les SU avec surdité acquise. Le but principal de la thèse est de vérifier si la MMN pourrait être un marqueur neuronal de la plasticité spatiale auditive observée chez les patients SU, et de vérifier se les corrélats neuronaux sont cohérentes avec les performances spatiales auditives. Deux types d'investigations ont été appliqués sur 20 sujets NE, 21 SU et 14 SB. La première investigation s'agit d'un test d'identification de source sonore mesuré par l'erreur quadratique moyenne (RMS). La deuxième évaluation est une étude électroencéphalographie qui sert à analyser la MMN. La MMN étant défini comme un potentiel évoqué qui reflète la capacité du cerveau à détecter un changement dans les propriétés physiques d'un son. Nous avons utilisé un son standard dans une position de référence (50°) avec 3 déviation par rapport au standard (10°, 20° et 100°) dans des conditions binaurales et monaurales. Les sujets sourds unilatéraux ont été divisé en 3 groupes selon leur performance spatiale. Le groupe des bons performeurs (SU low rms) a montré des meilleurs scores RMS en comparaison avec les NE munie d'un bouchon d'oreille (NE-mon), avec des performances similaires à ceux des sujets NE en binaurale. Une augmentation progressive de la MMN avec l'angle de la déviation par rapport au standard a été noté chez tous les groupes. Avec une réduction importante de la MMN chez les NH en monaurale quand le bouchon a été appliqué du côté du standard. La MMN a montré des résultats cohérents avec nos observations comportementales, ou les sujets SU avec un bon score RMS avait également des amplitudes de la MMN plus importantes que celles des sujets NE en condition monaurale et similaires à celles des NE en condition binaurale. Les sujets SU possèdent des stratégies adaptatives saptio-auditives. Notre étude a pu démontré que la plasticité corticale spatio-auditive qui a lieu suite à la surdité est reflété par la MMN. Les observations neuronales (MMN) sont corrélées avec les observations comportementaux de localisation spatiale. Ce qui signifie que la plasticité corticale qui a lieu chez ces sujets, n'est pas limités aux fonctions d'identification de la source sonores, mais dépasse ces capacités vers des mécanismes plus complexes tel que la détection de déviation et la mémoire à court terme, qui interviennent dans la fonction de discrimination spatiale des sons.

SIGNIFICANCE We validated a novel paradigm to measure aniseikonia across the visual field and used a mathematical approach that is able to describe the magnitude and shape of aniseikonia in a concise, clinically meaningful fashion. PURPOSE The measurement of aniseikonia has been performed clinically for more than half a century; however, amalgamation of field-wide local variations in binocular spatial localization into clinically applicable global metrics has yet to be attempted. Thus, the goal of the current study was twofold: first, to measure field-wide aniseikonia and second, to compare how local and global metrics each capture optically induced aniseikonia. METHODS Twelve visually normal observers performed a dichoptic localization task at 24 locations in the visual field. This was done in four conditions: (A) while wearing red-green filters, (B) while wearing green-red filters, (C) while wearing a monocular 5% overall size lens, and (D) while wearing a monocular 6% meridional size lens. The physical settings at perceptual equality were then used to compute both local (relative magnification) and global (coefficients for Zernike terms) descriptors of aniseikonia. RESULTS The comparison of each lens condition to the baseline condition confirmed predicted shifts in both the sign and magnitude of aniseikonia at both the local and global levels; however, the intraobserver levels of precision were moderate, and systematic underestimations were present across all locations in conditions C and D. CONCLUSIONS Local and global analyses derived from dichoptic localization data were both able to capture optically induced changes in binocular spatial perception; however, solutions that address the diagnostic and therapeutic challenges associated with this paradigm are needed before clinical implementation can proceed.

The possibilities for performing ureterocalicostomy significantly depend on the anatomy of the lower group of cups, which has not been examined yet from the point of view of this operation. The study included 115 patients who underwent multispiral computed tomography for various indications. The number of small cups of the lower group ranged from 1 to 5 (2.5 on average). We identified four main options for localizing renal cups in the region of the lower pole: I – one of the cups is localized in front, and the second along the vertical axis of the kidney (n = 13 / 11.3%); II – one of the cups is localized in front, and the second in the back (n = 35 / 30.4%); III – there is only one cup suitable for ureterocalicostomy, located along the vertical axis of the kidney (n = 18 / 15.7%); IV – one of the cups is localized at the back, and the second along the vertical axis of the kidney (n = 49 / 42.6%). The probability of damage to two cups with transverse resection of the kidney is 29.6%, while with oblique resection of kidney it is 12.2%. Information about the number of renal cups in the lower group and their spatial localization plays an important role in planning ureterocalicostomy. The proposed anatomical classification of cup anatomy allows choosing the type of renal resection in a particular patient and avoiding damage to adjacent cup structures.

International audience; It is nowadays well-accepted that the extracellular matrix (ECM) is not a simple reservoir for growth factors but is an organization center of their biological activity. In this review, we focus on the ability of the ECM to regulate the biological activity of BMPs. In particular, we survey the role of the ECM components, notably the glycosaminoglycans and fibrillary ECM proteins, which can be promoters or repressors of the biological activities mediated by the BMPs. We examine how a process called mechano-transduction induced by the ECM can affect BMP signaling, including BMP internalization by the cells. We also focus on the spatio-temporal regulation of the BMPs, including their release from the ECM, which enables to modulate their spatial localization as well as their local concentration. We highlight how biomaterials can recapitulate some aspects of the BMPs/ECM interactions and help to answer fundamental questions to reveal previously unknown molecular mechanisms. Finally, the design of new biomaterials inspired by the ECM to better present BMPs is discussed, and their use for a more efficient bone regeneration in vivo is also highlighted.