Miracle-dz/UniFAR-FTUs huggingface dataset:
Structural changes in the membrane of vero cells infected with a paramyxovirus

Vero cells productively infected with the Halle strain of measles virus have been studied by means of surface replication, freeze-fracturing, and surface labeling with horseradish peroxidase-measles antibody conjugate in order to examine changes in the structure of the cell membrane during viral maturation. Early in infection, the surfaces of infected cells are embossed by scattered groups of twisted strands, and diffuse patches of label for viral antigens cover regions marked by these strands. At later stages, when numerous nucleocapsids become aligned under the plasmalemmal strands, the strands increase in number and width and become more convoluted. At this stage, label for viral antigens on the surface of the cell membrane is organized into stripes lying on the crests of strands. Finally, regions of the membrane displaying twisted strands protrude to form ridges or bulges, and the freeze-fractured membrane surrounding these protrusions is characterized by an abundance of particles small than those found on the rest of the cell membrane. The fractured membranes of viral buds are continuous sheets of these small particles, and the spacing between both nucleocapsids and stripes of surface antigen in buds is less than in the surrounding cell membrane. Detached virus is covered with a continuous layer of viral antigen, has unusually large but no small particles on its membrane surfaces exposed by freeze-fracturing, and no longer has nucleocapsids aligned under its surface. Thus, surface antigens, membrane particles, and nucleocapsids attached to the cell membrane are mobile within the plane of the membrane during viral maturation. All three move simutaneously in preparation for viral budding.
Automated Intrinsic Text Classification for Component Content Management Applications in Technical Communication

Classification models are used in component content management to identify content components for retrieval, reuse and distribution. Intrinsic metadata, such as the assigned information class, play an important role in these tasks. With the increasing demand for efficient classification of content components, the sector of technical documentation needs mechanisms that allow for an automation of such tasks. Vector space model based approaches can lead to sufficient results, while maintaining good performance, but they must be adapted to the peculiarities that characterize modular technical documents. In this paper we will present domain specific differences, as well as characteristics, that are special to the field of technical documentation and derive methods to adapt widespread classification and retrieval techniques for these tasks. We verify our approach with data provided from companies in the sector of manufacturing and mechanical engineering and use it for supervised learning and automated classification.
Stochastic modeling of EEG rhythms with fractional Gaussian Noise

This paper presents a novel approach to signal modeling for EEG signal rhythms. A new method of 3-stage DCT based multirate filterbank is proposed for the decomposition of EEG signals into brain rhythms: delta, theta, alpha, beta, and gamma rhythms. It is shown that theta, alpha, and gamma rhythms can be modeled as 1st order fractional Gaussian Noise (fGn), while the beta rhythms can be modeled as 2nd order fGn processes. These fGn processes are stationary random processes. Further, it is shown that the delta subband imbibes all the nonstationarity of EEG signals and can be modeled as a 1st order fractional Brownian motion (fBm) process. The modeling of subbands is characterized by Hurst exponent, estimated using maximum likelihood (ML) estimation method. The modeling approach has been tested on two public databases.
Efficient Synthesis of Linear Reversible Circuits

In this paper we consider circuit synthesis for n-wire linear reversible circuits using the C-NOT gate library. These circuits are an important class of reversible circuits with applications to quantum computation. Previous algorithms, based on Gaussian elimination and LU-decomposition, yield circuits with O(n^2) gates in the worst-case. However, an information theoretic bound suggests that it may be possible to reduce this to as few as O(n^2/log n) gates. We present an algorithm that is optimal up to a multiplicative constant, as well as Theta(log n) times faster than previous methods. While our results are primarily asymptotic, simulation results show that even for relatively small n our algorithm is faster and yields more efficient circuits than the standard method. Generically our algorithm can be interpreted as a matrix decomposition algorithm, yielding an asymptotically efficient decomposition of a binary matrix into a product of elementary matrices.
Age-Related Differences in Stepping Response When Stepping onto a Known Soft Surface under Dual Task Conditions

The purpose of this study was to investigate whether age-related differences in stepping response influence postural control when stepping onto a known soft surface under dual task conditions. Nine young and eleven older female adults participated. First, they stepped on a flat surface while grasping an empty cup (single task), and then they repeated the task while grasping a cup filled with water (dual task). For the second experiment, they stepped on a soft surface placed in front of them while performing the above tasks. The main result was that %DIP (initiation phase as a percentage of the total stepping task time) was significantly higher for older than for young adults during the dual task on the soft surface. In conclusion, caution due to previous experience may increase attentional demand during dual tasks and lengthen the time required for central nervous processing in order to avoid losing postural stability in older adults, resulting in reductions in step velocity and step length compared to those in young adults.
The Properties and the Evolution of the Highly Ionized Gas in MR2251-178

We present the first XMM-Newton observations of the radio-quiet quasar MR2251-178. We model the X-ray spectrum with two power laws, one at high energies with a slope of \Gamma=1.6 and the other to model the soft excess with a slope of \Gamma=2.9, both absorbed by at least two warm absorbers (WAs). The high-resolution grating spectrum shows emission lines from N VI, O VII, O VIII, Ne IX, and Ne X, as well as absorption lines from the low ionization ions O III, O IV, and O V. A study of the spectral variations in MR2251-178 over a period of 8.5 years yields that all X-ray observations can be fitted with the above model. Luminosity variations over timescales of years seem to correlate with the soft excess variations but not with the WA properties variations. The overall picture is that of a stratified WA that enters and disappears from the line-of-sight on timescales of several months. We also present the first FUSE spectrum of MR2251-178. The general characteristics of the UV and X-ray absorbers seem to be consistent.
Effects of Leaders Position and Shape on Aerodynamic Performances of V Flight Formation

The influences of the leader in a group of V – flight formation are dealt with. The investigation is focused on the effect of its position and shape on aerodynamics performances of a given V – flight formation. Vortices generated the wing tip of the leader moves downstream forming a pair of opposite rotating line vortices. These vortices are generally undesirable because they create a downwash that increases the induced drag on leader’s wing. However, this downwash is also accompanied by an upwash that can beneficial to the follower’s wing flying behind the leader’s one, namely a favorable lift for the follower’s wing. How much contributions of the leader’s wing to the follower’s wing in the V – formation flight is determined by the strength of tip vortices generated by the leader’s wing which is influenced by its position and shape including incidence angle, dihedral angle, aspect ratio and taper ratio. The prediction of aerodynamic performances of the V–flight formation including lift, drag and moment coefficients is numerically performed by solving Navier – Stokes equations with k - e turbulence model. The computational domain is defined with multiblock topology to capture the complex geometry arrangement of the V – flight formation.
Revised Level Set-Based Method for Topology Optimization and Its Applications in Bridge Construction

Abstract: To cure imperfections such as low accuracy and the lack of ability to nucleate hole in the conventional level set-based topology optimization method, a novel method using a trapezoidal method with discrete design variables is proposed. The proposed method can simultaneously accomplish topology and shape optimization. The finite element method is employed to obtain element properties and provide data for calculating design and topological sensitivities. With the aim of performing the finite element method on a non-conforming mesh, a relation between the level set function and the element densities field has to be clearly defined. The element densities field is obtained by averaging the Heaviside function values. The Lagrange multiplier method is exploited to fulfill the volume constraint. Based on topological and design sensitivity and the trapezoidal method, the Hamilton-Jacobi partial differential equation is updated recursively to find the optimal layout. In order to stabilize the iterations and improve the efficiency of the algorithm, re-initiation of the level set function is necessary. Then, the detailed process of a cantilever design is illustrated. To demonstrate the applications of the proposed method in bridge construction, two numerical examples of a pylon bridge design are introduced. It is shown that the results match practical designs very well, and the proposed method is a helpful tool in bridge design.
The Spatial Resolution of Visual Attention

Two tasks were used to evaluate the grain of visual attention, the minimum spacing at which attention can select individual items. First, observers performed a tracking task at many viewing distances. When the display subtended less than 1 degrees in size, tracking was no longer possible even though observers could resolve the items and their motions: The items were visible but could not be individuated one from the other. The limiting size for selection was roughly the same whether tracking one or three targets, suggesting that the resolution limit acts independently of the capacity limit of attention. Second, the closest spacing that still allowed individuation of single items in dense, static displays was examined. This critical spacing was about 50% coarser in the radial direction compared to the tangential direction and was coarser in the upper as opposed to the lower visual field. The results suggest that no more than about 60 items can be arrayed in the central 30 degrees of the visual field while still allowing attentional access to each individually. Our data show that selection has a coarse grain, much coarser than visual resolution. These measures of the resolution of attention are based solely on the selection of location and are not confounded with preattentive feature interactions that may contribute to measures from flanker and crowding tasks. The results suggest that the parietal area is the most likely locus of this selection mechanism and that it acts by pointing to the spatial coordinates (or cortical coordinates) of items of interest rather than by holding a representation of the items themselves.
The Persistent Sodium Current Generates Pacemaker Activities in the Central Pattern Generator for Locomotion and Regulates the Locomotor Rhythm

Rhythm generation in neuronal networks relies on synaptic interactions and pacemaker properties. Little is known about the contribution of the latter mechanisms to the integrated network activity underlying locomotion in mammals. We tested the hypothesis that the persistent sodium current (INaP) is critical in generating locomotion in neonatal rodents using both slice and isolated spinal cord preparations. After removing extracellular calcium, 75% of interneurons in the area of the central pattern generator (CPG) for locomotion exhibited bursting properties and INaP was concomitantly upregulated. Putative CPG interneurons such as commissural and Hb9 interneurons also expressed INaP-dependent (riluzole-sensitive) bursting properties. Most bursting cells exhibited a pacemaker-like behavior (i.e., burst frequency increased with depolarizing currents). Veratridine upregulated INaP, induced riluzole-sensitive bursting properties, and slowed down the locomotor rhythm. This study provides evidence that INaP generates pacemaker activities in CPG interneurons and contributes to the regulation of the locomotor activity.
Circadian Rhythms in Isolated Brain Regions

The suprachiasmatic nucleus (SCN) of the mammalian hypothalamus has been referred to as the master circadian pacemaker that drives daily rhythms in behavior and physiology. There is, however, evidence for extra-SCN circadian oscillators. Neural tissues cultured from rats carrying the Per-luciferase transgene were used to monitor the intrinsic Per1 expression patterns in different brain areas and their response to changes in the light cycle. Although many Per-expressing brain areas were arrhythmic in culture, 14 of the 27 areas examined were rhythmic. The pineal and pituitary glands both expressed rhythms that persisted for >3 d in vitro, with peak expression during the subjective night. Nuclei in the olfactory bulb and the ventral hypothalamus expressed rhythmicity with peak expression at night, whereas other brain areas were either weakly rhythmic and peaked at night, or arrhythmic. After a 6 hr advance or delay in the light cycle, the pineal, paraventricular nucleus of the hypothalamus, and arcuate nucleus each adjusted the phase of their rhythmicity with different kinetics. Together, these results indicate that the brain contains multiple, damped circadian oscillators outside the SCN. The phasing of these oscillators to one another may play a critical role in coordinating brain activity and its adjustment to changes in the light cycle.
Cholinergic Modulation of Stellate Cells in the Mammalian Ventral Cochlear Nucleus

The main source of excitation to the ventral cochlear nucleus (VCN) is from glutamatergic auditory nerve afferents, but the VCN is also innervated by two groups of cholinergic efferents from the ventral nucleus of the trapezoid body. One arises from collaterals of medial olivocochlear efferents, and the other arises from neurons that project solely to the VCN. This study examines the action of cholinergic inputs on stellate cells in the VCN. T stellate cells, which form one of the ascending auditory pathways to the inferior colliculus, and D stellate cells, which inhibit T stellate cells, are distinguished electrophysiologically. Whole-cell recordings from stellate cells in slices of the VCN of mice demonstrate that most T stellate cells are excited by cholinergic agonists through three types of receptors, whereas all D stellate cells tested were insensitive to cholinergic agonists. Nicotinic excitation in T stellate cells has two components. The faster component was blocked by α-bungarotoxin and methyllycaconitine, suggesting that receptors contained α7 subunits; the slower component was insensitive to both. Muscarinic receptors excite T stellate cells by blocking a voltage-insensitive, “leak” potassium conductance. Our results suggest that cholinergic efferent innervation enhances excitation by sounds of T stellate cells, opposing the inhibitory action of cholinergic innervation in the cochlea that is conveyed indirectly through the glutamatergic afferents. The inhibitory action of D stellate cells on their targets is probably not affected by cholinergic inputs. Excitation of T stellate cells by cholinergic efferents would be expected to enhance the encoding of spectral peaks in noise.
Tumor necrosis factor promoter polymorphism and susceptibility to lepromatous leprosy.

Genetically determined differences in immune responses to environmental agents may underlie susceptibility to many autoimmune and infectious diseases. Leprosy provides an example of a polarity in the type of immune response made to an infectious agent, and there is evidence that the major histocompatibility complex is genetically linked to leprosy type. It was found that HLA-DR2 is associated with both tuberculoid and lepromatous types of leprosy; however, a variant at position -308 of the promoter of the neighboring tumor necrosis factor (TNF) gene was increased in frequency in lepromatous (odds ratio = 3.0, P = .02) but not tuberculoid leprosy. Some studies have found higher serum levels of TNF in lepromatous than tuberculoid leprosy, and high TNF levels are found in malaria and leishmaniasis, which are also associated with this TNF allele. It is speculated that this association reflects genetic variability in cytokine production, which influences the immune response to and clinical outcome of leprosy.
Kam Tori and Absence of Diffusion of a wave-Packet in the 1D Random Dnls Model

When nonlinearity is added to an infinite system with purely discrete linear spectrum, Anderson modes become coupled with one another by terms of higher order than linear, allowing energy exchange between them. It is generally believed, on the basis of numerical simulations in such systems, that any initial wave-packet with finite energy spreads down chaotically to zero amplitude with second moment diverging as a power law of time, slower than standard diffusion (subdiffusion). We present results which suggest that the interpretation of spreading cannot be described as initially believed and that new questions arise and still remain opened. We show that an initially localized wave-packet with finite norm may generate two kinds of trajectories both obtained with nonvanishing probability. The first kind consists of KAM trajectories which are recurrent and do not spread. Empirical investigations suggest that KAM theory may still hold in infinite systems under two conditions: (1) the linearized spectrum is purely discrete, (2) the considered solutions are square summable and not too large in amplitude. We check numerically that in appropriate regions of the parameter space, indeed many initial conditions can be found with finite probability that generate (nonspreading) infinite dimension tori (almost periodic solutions) in a fat Cantor set in (projected) phase space. The second kind consists of trajectories which look initially chaotic and often spread over long times. We first rigorously prove that initial chaos does not necessarily imply complete spreading e.g. for large norm initial wave-packet. Otherwise, in some modified models, no spreading at all is proven to be possible, despite the presence of initial chaos in contradiction with early beliefs. The nature of the limit state is still unknown. However, we attempt to present empirical arguments suggesting that if a trajectory starts chaotically spreading, there will necessarily exist (generally large) critical spreading distances that depend on the disorder realization where the trajectory will be sticking to a dense set of KAM tori. This effect should induce drastic slowing down of the spreading which could be viewed as "inverse Arnold diffusion" since the trajectory approaches KAM tori regions instead of leaving them. We suggest that this effect should self-organize the chaotic behavior and that at long time, the wave-packet might not be spread down to zero, but could have a limit profile with marginal chaos (with singular continuous spectrum), despite a long spatial tail. Further analytical and numerical investigations are required.
Sputum YKL-40 Levels and Pathophysiology of Asthma and Chronic Obstructive Pulmonary Disease

Background: Recent evidence suggests that YKL-40, also called chitinase-3-like-1 protein, is involved in the pathogenesis of asthma and chronic obstructive pulmonary disease (COPD). Details of sputum YKL-40 in asthma and COPD, however, remain unknown. Objectives: To clarify associations of sputum YKL-40 levels with clinical indices in asthma and COPD. Methods: Thirty-nine patients with asthma, 14 age-matched never-smokers as controls, 45 patients with COPD, and 7 age-matched smokers as controls were recuited for this study. Sputum YKL-40 levels were measured and YKL-40 expression in sputum cells was evaluated by immunocytochemistry. Results: Sputum YKL-40 levels were higher in patients with COPD (346 ± 325 ng/ml) than in their smoker controls (125 ± 122 ng/ml; p < 0.05), but were not significantly different between patients with asthma (117 ± 170 ng/ml) and their controls (94 ± 44 ng/ml; p = 0.15). In patients with asthma only, sputum YKL-40 levels were positively correlated with disease severity (r = 0.34, p = 0.034) and negatively correlated with pre- and postbronchodilator %FEV1 (r = –0.47 and –0.42, respectively; p < 0.01) and forced mid-expiratory flow (r = –0.48 and –0.46, respectively, p < 0.01). Sputum YKL-40 levels were positively correlated with sputum neutrophil counts in asthma (r = 0.55, p < 0.001) and with neutrophil and macrophage counts in COPD (r = 0.45 and 0.65, respectively, p < 0.01). YKL-40 was expressed in the cytoplasm of sputum neutrophils and macrophages in all groups. Conclusions: Elevated sputum YKL-40 reflects airflow obstruction in asthma whereas the roles of YKL-40 in the proximal airways in COPD remain to be elucidated.
Variability in Regularity: Mining Temporal Mobility Patterns in London, Singapore and Beijing Using Smart-Card Data

To discover regularities in human mobility is of fundamental importance to our understanding of urban dynamics, and essential to city and transport planning, urban management and policymaking. Previous research has revealed universal regularities at mainly aggregated spatio-temporal scales but when we zoom into finer scales, considerable heterogeneity and diversity is observed instead. The fundamental question we address in this paper is at what scales are the regularities we detect stable, explicable, and sustainable. This paper thus proposes a basic measure of variability to assess the stability of such regularities focusing mainly on changes over a range of temporal scales. We demonstrate this by comparing regularities in the urban mobility patterns in three world cities, namely London, Singapore and Beijing using one-week of smart-card data. The results show that variations in regularity scale as non-linear functions of the temporal resolution, which we measure over a scale from 1 minute to 24 hours thus reflecting the diurnal cycle of human mobility. A particularly dramatic increase in variability occurs up to the temporal scale of about 15 minutes in all three cities and this implies that limits exist when we look forward or backward with respect to making short-term predictions. The degree of regularity varies in fact from city to city with Beijing and Singapore showing higher regularity in comparison to London across all temporal scales. A detailed discussion is provided, which relates the analysis to various characteristics of the three cities. In summary, this work contributes to a deeper understanding of regularities in patterns of transit use from variations in volumes of travellers entering subway stations, it establishes a generic analytical framework for comparative studies using urban mobility data, and it provides key points for the management of variability by policy-makers intent on for making the travel experience more amenable.