Miracle-dz/UniFAR-FTUs huggingface dataset:
Functional imaging of conduction dynamics in cortical and spinal axons

Mammalian axons are specialized for transmitting action potentials to targets within the central and peripheral nervous system. A growing body of evidence suggests that, besides signal conduction, axons play essential roles in neural information processing, and their malfunctions are common hallmarks of neurodegenerative diseases. The technologies available to study axonal function and structure integrally limit the comprehension of axon neurobiology. High-density microelectrode arrays (HD-MEAs) allow for accessing axonal action potentials at high spatiotemporal resolution, but provide no insights on axonal morphology. Here we demonstrate a method for electrical visualization of axonal morphologies based on extracellular action potentials recorded from cortical and motor neurons using HD-MEAs. The method enabled us to reconstruct up to 5-centimeter-long axonal arbors and directly monitor axonal conduction across thousands of recording sites. We reconstructed 1.86 meters of cortical and spinal axons in total and found specific features in their structure and function.
Reconstruction of the molecular evolution of Usutu virus in Germany: Insights into virus emersion and circulation

Usutu virus (USUV) is a mosquito-borne flavivirus that is widely distributed in southern and central Europe. The zoonotic virus circulates primarily between birds and mosquitoes, can, however, in rare cases infect other mammals including humans. In the past USUV has been associated with mass mortalities in birds, formerly blackbirds and owls. Birds commonly succumb either due to the peracute nature of the infection or due to severe encephalitis. In Germany, USUV has spread rapidly since its first detection in 2010 in mosquitoes under the presence of susceptible host and vector species. Nonetheless, there is to date limited access to whole genome sequences resulting in the absence of in-depth phylogenetic and phylodynamic analyses. In this study, 118 wild and captive birds were screened using a nanopore sequencing platform with prior target enrichment via amplicons. Due to the high abundancy of Europe 3 and Africa 3 in Germany an ample quantity of associated whole genome sequences was generated and the most recent common ancestor could be determined for each lineage. The corresponding clock phylogeny revealed an introduction of USUV Europe 3 and Africa 3 into Germany three years prior to their first isolation in the avifauna in 2011 and 2014, respectively. Based on the clustering and temporal history of the lineages, evidence exists for the genetic evolution of USUV within Germany as well as new introductions thereof into the country.
Polychaetoid/ZO-1 strengthens cell junctions under tension while localizing differently than core adherens junction proteins

During embryonic development dramatic cell shape changes and movements re-shape the embryonic body plan. These require robust but dynamic linkage between the cell-cell adherens junctions and the force-generating actomyosin cytoskeleton. Our view of this linkage has evolved, and we now realize linkage is mediated by a mechanosensitive multiprotein complex assembled via multivalent connections. Here we combine genetic, cell biological and modeling approaches to define the mechanism of action and functions of an important player, Drosophila Polychaetoid, homolog of mammalian ZO-1. Our data reveal that Pyd reinforces cell junctions under elevated tension, and facilitates cell rearrangements. Pyd is important to maintain junctional contractility and in its absence cell rearrangements stall. We next use structured illumination microscopy to define the molecular architecture of cell-cell junctions during these events. The cadherin-catenin complex and Cno both localize to puncta along the junctional membrane, but are differentially enriched in different puncta. Pyd, in contrast, exhibits a distinct localization to strands that extend out from the region occupied by core junction proteins. We then discuss the implications for the protein network at the junction-cytoskeletal interface, suggesting different proteins localize and function in distinct ways but combine to produce robust connections.
Development of a novel autonomous lower extremity exoskeleton robot for walking assistance

Today, exoskeletons are widely applied to provide walking assistance for patients with lower limb motor incapacity. Most existing exoskeletons are under-actuated, resulting in a series of problems, e.g., interference and unnatural gait during walking. In this study, we propose a novel intelligent autonomous lower extremity exoskeleton (Auto-LEE), aiming at improving the user experience of wearable walking aids and extending their application range. Unlike traditional exoskeletons, Auto-LEE has 10 degrees of freedom, and all the joints are actuated independently by direct current motors, which allows the robot to maintain balance in aiding walking without extra support. The new exoskeleton is designed and developed with a modular structure concept and multi-modal human-robot interfaces are considered in the control system. To validate the ability of self-balancing bipedal walking, three general algorithms for generating walking patterns are researched, and a preliminary experiment is implemented.
Simultaneous mapping of epigenetic inter-haplotype, inter-cell and inter-individual variation via the discovery of jointly regulated CpGs in pooled sequencing data

In the post-GWAS era, great interest has arisen in the mapping of epigenetic inter-individual variation towards investigating the emergence of phenotype in health and disease. Relevant DNA methylation methodologies – epigenome-wide association studies (EWAS), methylation quantitative trait loci (mQTL) mapping and allele-specific methylation (ASM) analysis – can each map certain sources of epigenetic variation and all depend on matching phenotypic/genotypic data. Here, to avoid these requirements, we developed Binokulars, a novel randomization test that identifies signatures of joint CpG regulation from reads spanning multiple CpGs. We tested and benchmarked our novel approach against EWAS and ASM on pooled whole-genome bisulfite sequencing (WGBS) data from whole blood, sperm and combined. As a result, Binokulars simultaneously discovered regions associated with imprinting, cell type- and tissue-specific regulation, mQTL, ageing and other (still unknown) epigenetic processes. To verify examples of mQTL and polymorphic imprinting, we developed JRC_sorter, another novel tool that classifies regions based on epigenotype models, which we deployed on non-pooled WGBS data from cord blood. In the future, this approach can be applied on larger pools to simultaneously map and characterise inter-haplotype, inter-cell and inter-individual variation in DNA methylation in a cost-effective fashion, a relevant pursuit towards phenome-mapping in the post-GWAS era.
Episodic live imaging of cone photoreceptor maturation in GNAT2-EGFP retinal organoids

Fluorescent reporter pluripotent stem cell (PSC) derived retinal organoids are powerful tools to investigate cell type-specific development and disease phenotypes. When combined with live imaging, they enable direct and repeated observation of cell behaviors within a developing retinal tissue. Here, we generated a human cone photoreceptor reporter line by CRISPR/Cas9 genome editing of WTC11-mTagRFPT-LMNB1 human induced pluripotent stem cells (iPSCs) by inserting enhanced green fluorescent protein (EGFP) coding sequences and a 2A self-cleaving peptide at the N-terminus of Guanine Nucleotide-Binding Protein Subunit Alpha Transducin 2 (GNAT2). In retinal organoids generated from these iPSCs, the GNAT2-EGFP allele robustly and exclusively labeled both immature and mature cones starting at culture day 34. Episodic confocal live imaging of hydrogel immobilized retinal organoids allowed tracking of morphological maturation of individual cones for >18 weeks and revealed inner segment accumulation of mitochondria and growth at 12.2 cubic microns per day from day 126 to day 153. Immobilized GNAT2-EGFP cone reporter organoids provide a valuable tool for investigating human cone development and disease.
Average-Case Complexity — Addendum

The discussion of completeness in Section 3 follows the treatment of Goldreich’s notes [Gol97]. The proof that the Bounded Halting problem is complete for 〈NP,PComp〉 presented in Section 3.2 is due to Gurevich [Gur91]. After we present the 〈NP,PComp〉-completeness of Bounded Halting, we do not discuss further completeness results, of which a few are known, including the Tiling problem studied in Levin’s [Lev86] foundational paper, a graph coloring problem [VL88, LV18], a matrix decomposition problem [Gur90, BG95], a bounded version of the Post correspondence problem [Gur91], and diophantine matrix problems [VR92].
Segmentación probabilística de carriles mediante parametrización lineal de baja dimensión

Lane detection is an important module for active safety systems, as it increases safety and reduces trafﬁc accidents caused by driver inattention. Illumination changes or occlusions make lane detection a challenging task, especially if the detection is performed from a single image. Consequently, this paper presents a probabilistic approach based on the Kalman ﬁlter, which using information from previous image frames manages to estimate the lane that could not be detected in the current image frame, considering uncertainty in the prediction as well as in the detection. To this end, a principal component analysis of the segmented curvature is introduced with the purposes of dimensionality reduction, moving from a large dimensional pixel representation to a considerably reduced space representation.
Feature extraction of SAR targets consisting of trihedral and dihedral corner reflectors

This paper studies feature extraction of targets consisting of both trihedral and dihedral corner reflectors via synthetic aperture radar. A mixed data model is introduced to describe the target features. The Cramer-Rao bounds (CRBs) for the parameter estimates of the data model are also derived. Two algorithms, the FFTB algorithm and the NLS algorithm, are devised to estimate the model parameters. Numerical examples show that the parameter estimates obtained with both algorithms reach the CRBs as the SNR increases. The parameter estimates obtained with the NLS algorithm start to achieve the CRB at a lower SNR than those with the FFTB algorithm, while the latter algorithm is computationally more efficient.
Glaucoma as a Neurodegenerative and Inflammatory Disease

Abstract Glaucoma is a neurodegenerative disease that leads to irreversible loss of vision through degeneration of the retinal ganglia cells (RGCs). Glaucoma is one of the most frequent causes of blindness in the world. Intraocular pressure is the main risk factor for the occurrence and development of this disease. Treatment is largely based on reducing internal optical pressure. However, some patients may deteriorate or become blind, despite normal or reduced internal optical pressure. The pathophysiological details are still unclear. Neuroinflammatory processes are also apparently an additional cause. In principle, innate or local responses of the adaptive immune system can be distinguished. The reaction of the innate immune system, particularly the local microglial cells, has long been studied. The macroglia with the astrocytes and Müller cells and their homeostatic effects have also long been known. On the other hand, it has long been thought that the retina with its RGZs was inert to adaptive immunological reactions – due to the function of the blood brain barrier. However, this system may be disturbed by antigen presentation, leading to a reaction of the adaptive immune system, with B cell and T cell responses. In this context, the key proteins are presumably heat shock proteins. We now know that neuroinflammation is important in glaucoma, as in other neurodegenerative diseases. It is important to increase our understanding of these phenomena. In this review article, we present our current knowledge of the role of the micro- and macroglia, the adaptive immune system, and the heat shock proteins.
On internal waves generated by travelling wind

Oceanic internal waves forced by a latitude-independent wind field travelling eastward at speed U is investigated, extending the hydrostatic f-plane model of Kundu & Thomson (1985). The ocean has a well-mixed surface layer overlying a stratified interior with a depth-dependent buoyancy frequency N(z), and f can vary with latitude. Solutions are found by decomposition into vertical normal modes. Problems discussed are (i) the response to a slowly moving line front, and (ii) the response in a variable f ocean. For the slowly moving line front assuming a depth-independent N, the trailing waves are found to have large frequencies, and the vertical acceleration ∂w/∂t is important (that is the dynamics are non-hydrostatic) if the frequency ω is larger than a few times (Nf)½. The wake contains waves associated with all vertical modes, in contrast to hydrostatic dynamics in which slowly moving line fronts do not generate trailing waves of low-order modes. It is argued that slowly moving wind fields can provide an explanation for the frequently observed broad peak in the spectrum of vertical motion at a frequency somewhat smaller than N, and of the vertical coherence of the associated waves in the upper ocean. To study lower-frequency internal waves, the hydrostatic constant-f model of Kundu & Thomson is extended to variable f. Various sections through such a flow clearly illustrate the development of a meridional wavelength λy = 2π/βt as predicted by D'Asaro (1989), in addition to the zonal wavelength λx due to translation of the wind. The two effects combine to cause a greater horizontal inhomogeneity, so that energy from the surface layer descends quickly, travelling equatorward and downward. Since waves at any point arrive from different latitudes, spectra no longer consist of discrete peaks but are more continuous and broader than those in the constant-f model. The waves are more intermittent because of the larger spectral width, and vertically less correlated in the thermocline because of a larger bandwidth of vertical modes. The vertical correlation in the deep ocean, however, is still high because the response is dominated by one or two low-order modes after 30 days of integration. As U decreases, the larger bandwidth of frequency increases the intermittency, and the larger bandwidth of vertical wavenumber decreases the vertical correlation. A superposition of travelling wind events intensifies the high-frequency end of the spectrum; a month-long travelling series of realistic strength can generate waves with amplitudes of order 4 cm/s in the deep ocean. It is suggested that propagating winds and linear dynamics are responsible for the generation of a large fraction of internal waves in the ocean at all depths. The main effect of nonlinearity and mean flow may be to shape the internal wave spectra to a ω-2 form.
Flows in Stenotic Vessels

▪ Abstract The relationship between flow in the arteries, particularly the wall shear stresses, and the sites where atherosclerosis develops has motivated much of the research on arterial flow in recent decades. It is now well accepted that it is sites where shear stresses are low, or change rapidly in time or space, that are most vulnerable. These conditions are likely to prevail at places where the vessel is curved; bifurcates; has a junction, a side branch, or other sudden change in flow geometry; and when the flow is unsteady. These flows, often but not always involving flow separation or secondary motions, are also the most difficult ones in fluid mechanics to analyze or compute. In this article we review the modeling studies and experiments on steady and unsteady, two-and three-dimensional flows in arteries, and in arterial geometries most relevant in the context of atherosclerosis. These include studies of normal vessels—to identify, on the basis of the fluid mechanics, lesion foci—and stenotic ves.
A two-model adaptive finite element method for plates

We introduce a goal-oriented adaptive finite element method, which combines the Kirchhoff and Mindlin-Reissner plate models. The lateral displacements are approximated by quadratic continuous polynomials, and the rotations of the midsurface are approximated by linear discontinuous polynomials. A duality-based a posteriori error representation separates the discretization and modeling errors, and in this sense local mesh and model refinement are independent. The target quantity of interest is an arbitrary linear functional of the displacement and/or rotation errors.
Dynamic Articulatory Model of Speech Production

A dynamic articulatory model of speech production is described. From a discrete phonemic input, it generates a continuous description of the configuration of the articulatory mechanism in a midsagittal section. The model is divided into a “state” and “operators,” which act as agents for modifying the state by trying to manipulate it (i.e., responding articulatory structures) toward abstract “goals. ” This bifurcation allows many of the constraints of the real system to be included in the model in a natural manner. By this means, the contextual effects of connected speech can be generated by less ad hoc methods than usually required by other schemes of speech modeling and/or synthesis. The present model concerns itself only with vowels and stops, but it is felt that the general methodologies are applicable to all speech sounds. A motion‐picture film of model action, as simulated on a large time‐shared computer system, is shown. [Work supported in part by the U. S. Air Force Cambridge Research Laboratories, .
An Exact Formulation for Dual-Band Composite Right/Left-Handed Transmission Line Design

Abstract This article presents an exact formulation for dual-band composite right/left-handed transmission line design. Because of using an approximation, the previously introduced formulation for the design of such transmission lines is not exact. Furthermore, the accuracy of the previous formulation depends on the homogeneity of the structure; i.e., accurate results are obtained only if the phase shift of each cell is small. To derive the new formulation, the transmission matrices of the composite right/left-handed transmission line at two desired frequencies are set equal to the transmission matrices corresponding to the desired phase shifts and characteristic impedances. Using some mathematical calculations, closed-form relations for unknown parameters of composite right/left-handed transmission lines are obtained. In this derivation, no approximation is used, and hence, the final formulation, independent of the structure homogeneity, is exact.
Site occupancy in the Re-W sigma phase

C. Berne, M. Sluiter, Y. Kawazoe, T. Hansen, and A. Pasturel Commissariat a l’Energie Atomique, Direction de la Recherche Technologique, Departement des Techniques des Energies Nouvelles, 17 Rue des Martyrs, 38054 Grenoble-Cedex 09, France Institute for Materials Research, Tohoku University, Sendai 980-8577, Japan Institut Laue Langevin, BP 156, 38042 Grenoble-Cedex 09, France Laboratoire de Physique et Modelisation des Milieux Condenses, Maison des Magisteres, BP 166 CNRS, 38042 Grenoble-Cedex 09, France ~Received 23 April 2001; published 19 September 2001!
Does Diabetes Influence Adherence in Glaucoma Patients ?

With chronic diseases, patient adherence plays a crucial role in delaying disease progression and in determining the success of therapy. Problems arise not only from low medication adherence, but also non-adherence to recommended follow-up examinations. Obtaining an accurate estimate of adherence is difficult, especially in glaucoma patients, due to the fact that most antihypertensive drugs are administered in the form of eye drops. There is great variability in the published adherence values for glaucoma patients. Most studies report an average medication adherence of approximately 70%, with around 50% of patients having good adherence (at least 80% of medication administered as planned). Furthermore, 6.8– 31.4% of the eye drops do not end up in the patientʼs eye, which means there is even less active ingredient to achieve a therapeutic effect. Glaucoma patients also show low persistence and adherence to follow-up appointments. Since diabetes increases the risk for POAG and secondary glaucoma and given that diabetics have particularly low adherence, the question arose whether a diabetes diagnosis is associated with reduced adherence in glaucoma patients. Previous studies found no significant association between diabetes and reduced adherence in glaucoma patients, although a significant impact of elevated HbA1c on adherence in glaucoma patients was found in one study. However, this connection still needs to be examined more closely in studies with larger samples.
A Preliminary Study of the Auditory Stimulation Relieving Mental Fatigue Behaviours

Mental fatigue, which is common in aviation, is one of the representative symptoms of depression and affects work efficiency and long-term mental health. There have been a lot of studies on musical treatments, yet few are concerned about the effects of acoustic waves on mental fatigue. It is necessary to investigate the effects of auditory stimulation on mental fatigue. This study used a 24-hour-restraint mouse model with mental fatigue symptoms as animal subjects. The 24-hour-restraint mice were divided into a control group and two acoustic groups. Two auditory stimulation, i.e., pink noise with 5kHz pure tone and pink noise with 10kHz pure tone, were generated for each acoustic group. Each acoustic group was exposed to one stimulus at 60 dB(A) for 1h per day. After 7 days, we carried out the open field test and the forced swimming test. We found increased total distance and latency to abandon and decreased immobility time in the auditory stimulation groups compared to the control group. The pink noise with high-frequency tones may have positive effects on relieving mental fatigue behaviours.
An Efficient Machine Learning Approach for Hardware Trojan Detection

As outsourcing of IC manufacturing has become a global phenomenon, the risk of ICs being infested with Trojans has increased more than ever. In this paper, we propose a circuit gate level netlist based Trojan detection using supervised machine learning approaches. A number of features are extracted from the netlist that delivers a sophisticated dataset for the approximately trained model to deliver a higher true positive detection rate. The netlist is analyzed in 45 nm technology to generate features and Monte Carlo simulation is performed to generate two thousand virtual netlists, including one thousand Trojan infested netlists. We experiment with the s27 benchmark circuit netlist to evaluate our approach. Different types of sequential and combinational types of Trojans from literature are inserted into the netlist to evaluate the proposed approach. The results show significant Trojan detectability in different machine learning approaches.