Miracle-dz/UniFAR-FTUs huggingface dataset:
Evaluation of the EndoPAT as a Tool to Assess Endothelial Function

Endothelial dysfunction is a potential target for (pharmaceutical) intervention of several systemic pathological conditions. We investigated the feasibility of the EndoPAT to evaluate acute changes in endothelial function with repeated noninvasive measurements and assessed its discriminating power in different populations. Endothelial function was stable over a longer period of time in renally impaired patients (coefficient of variation 13%). Endothelial function in renally impaired and type 2 diabetic patients was not decreased compared to healthy volunteers (2.9 ± 1.4 and 1.8 ± 0.3, resp., versus 1.8 ± 0.5, P > 0.05). The EndoPAT did not detect an effect of robust interventions on endothelial function in healthy volunteers (glucose load: change from baseline 0.08 ± 0.50, 95% confidence interval −0.44 to 0.60; smoking: change from baseline 0.49 ± 0.92, 95% confidence interval −0.47 to 1.46). This suggests that at present the EndoPAT might not be suitable to assess (changes in) endothelial function in early-phase clinical pharmacology studies. Endothelial function as measured by the EndoPAT could be physiologically different from endothelial function as measured by conventional techniques. This should be investigated carefully before the EndoPAT can be considered a useful tool in drug development or clinical practice.
Chromatin structure shapes the search process of transcription factors

The diffusion of regulatory proteins within the nucleus plays a crucial role in the dynamics of transcriptional regulation. The standard model assumes a 3D plus ID diffusion process: regulatory proteins either move freely in solution or slide on DNA. This model however does not considered the 3D structure of chromatin. Here we proposed a multi-scale stochastic model that integrates, for the first time, high-resolution information on chromatin structure as well as DNA-protein interactions. The dynamics of transcription factors was modeled as a slide plus jump diffusion process on a chromatin network based on pair-wise contact maps obtained from high-resolution Hi-C experiments. Our model allowed us to uncover the effects of chromatin structure on transcription factor occupancy profiles and target search times. Finally, we showed that binding sites clustered on few topological associated domains leading to a higher local concentration of transcription factors which could reflect an optimal strategy to efficiently use limited transcriptional resources.
Locomotion Without a Brain: Physical Reservoir Computing in Tensegrity Structures

Embodiment has led to a revolution in robotics by not thinking of the robot body and its controller as two separate units, but taking into account the interaction of the body with its environment. By investigating the effect of the body on the overall control computation, it has been suggested that the body is effectively performing computations, leading to the term morphological computation. Recent work has linked this to the field of reservoir computing, allowing one to endow morphologies with a theory of universal computation. In this work, we study a family of highly dynamic body structures, called tensegrity structures, controlled by one of the simplest kinds of “brains. ” These structures can be used to model biomechanical systems at different scales. By analyzing this extreme instantiation of compliant structures, we demonstrate the existence of a spectrum of choices of how to implement control in the body-brain composite. We show that tensegrity structures can maintain complex gaits with linear feedback control and that external feedback can intrinsically be integrated in the control loop. The various linear learning rules we consider differ in biological plausibility, and no specific assumptions are made on how to implement the feedback in a physical system.
A new fractionator principle with varying sampling fractions: exemplified by estimation of synapse number using electron microscopy

The quantification of ultrastructure has been permanently improved by the application of new stereological principles. Both precision and efficiency have been enhanced. Here we report for the first time a fractionator method that can be applied at the electron microscopy level. This new design incorporates a varying sampling fraction paradigm. The method allows for systematic random sampling from blocks of variable slab thickness, thereby eliminating the need for exhaustive serial sectioning through an entire containing space. This novel approach acknowledges the inaccuracy inherent in estimating the total object number using section sampling fractions based on the average thickness of sections of variable thicknesses. As an alternative, this approach estimates the correct particle section sampling probability based on an estimator of the Horvitz–Thompson type, resulting in a theoretically more satisfying and accurate estimate of the expected number of particles for the defined containing space.
Crossing the border twice: Reimporting prepositions to alleviate L1-specific transfer errors

We present a data-driven approach which exploits word alignment in a large parallel corpus with the objective of identifying those verb- and adjective-preposition combinations which are difficult for L2 language learners. This allows us, on the one hand, to provide language-specific ranked lists in order to help learners to focus on particularly challenging combinations given their native language (L1). On the other hand, we provide extensive statistics on such combinations with the objective of facilitating automatic error correction for preposition use in learner texts. We evaluate these lists, first manually, and secondly automatically by applying our statistics to an error-correction task.
Exploring ion beam lithography with the EUT singletron:construction of a waveguide in PMMA

Potential successors to optica! lithography are known as next generation lithograpbies (NGLs). They include X-ray lithography, electron beam lithography and ion beam lithography. Ion beam lithography (IBL) with MeV ionsis an interesting option due to its potential high resolution and ability to write high aspect ratio structures. In this study, IBL with the nuclear mieroprobe at the Singletron at the Eindhoven University of Technology is explored. In IBL light ions are used to irradiate a resist in which a latent image is formed that is subsequently chemically developed. The interaction between the ions and the resist, PMMA, can cause scissioning or cross-linking of this polymer resulting in a change of molecular weight. The main factors in determining whether scissioning or cross-linking takes place are the energy deposited during ion irradiation and the polymer structure. Depending on the polymer structure either one or two activated sites are required for scissioning or cross-linking. A scissioned polymer has a lower molecular weight compared to the unirradiated PMMA. In a well chosen developer scissioned PMMA can be dissolved faster than pristine PMMA. Hansen solubility parameters were combined with Flory-Huggins theory to obtain insight in the parameters that determine the selectivity in polymer dissolution. Dissalution kinetics were found to inftuence the solubility rate. In this work the ion ftuence required to achieve scissioning was determined and a suitable developer was selected. It was found that a deposited energy in the range of 1.6 1010 to 3.2 1011 eV/Jlm3 is needed in the irradiation ofPMMA to dissolve the irradiated part completely in the developer MIBK:IPA 1:3. This deposited energy corresponds toa ftuence range of 1.2 106 to 2.4107 3 Me V H+ ions/Jlm2. A waveguide is constructed in PMMA using IBL and qualitatively examined as an example of one of the many applications of this technique.
Aciculin interacts with filamin C and Xin and is essential for myofibril assembly, remodeling and maintenance

ABSTRACT Filamin C (FLNc) and Xin actin-binding repeat-containing proteins (XIRPs) are multi-adaptor proteins that are mainly expressed in cardiac and skeletal muscles and which play important roles in the assembly and repair of myofibrils and their attachment to the membrane. We identified the dystrophin-binding protein aciculin (also known as phosphoglucomutase-like protein 5, PGM5) as a new interaction partner of FLNc and Xin. All three proteins colocalized at intercalated discs of cardiac muscle and myotendinous junctions of skeletal muscle, whereas FLNc and aciculin also colocalized in mature Z-discs. Bimolecular fluorescence complementation experiments in developing cultured mammalian skeletal muscle cells demonstrated that Xin and aciculin also interact in FLNc-containing immature myofibrils and areas of myofibrillar remodeling and repair induced by electrical pulse stimulation (EPS). Fluorescence recovery after photobleaching (FRAP) experiments showed that aciculin is a highly dynamic and mobile protein. Aciculin knockdown in myotubes led to failure in myofibril assembly, alignment and membrane attachment, and a massive reduction in myofibril number. A highly similar phenotype was found upon depletion of aciculin in zebrafish embryos. Our results point to a thus far unappreciated, but essential, function of aciculin in myofibril formation, maintenance and remodeling.
Visibility of individual packet losses in MPEG-2 video

The ability of a human to visually detect whether a packet has been lost during the transport of compressed video depends heavily on the location of the packet loss and the content of the video. In this paper, we explore when humans can visually detect the error caused by individual packet losses. Using the results of a subjective test based on 1080 packet losses in 72 minutes of video, we design a classifier that uses objective factors extracted from the video to predict the visibility of each error. Our classifier achieves over 93% accuracy.
Perspective on the Discovery and Scientific Impact of p38 MAP Kinase

It has now been almost 20 years since the discovery of p38 MAP kinase and its role in inflammatory cytokine synthesis through reverse pharmacology and its subsequent exploration as a potential target for autoimmune and other diseases. At the time of its discovery, the use of cell-based phenotypic screens to identify new molecular targets was at its infancy, and while p38 MAP kinase was not the first target to be identified this way, it provides a useful model for reviewing the pros and cons of this approach and the subsequent impact it can have on discovering new medicines.
Discriminative learning of I2C distance for image classification

In order to improve image classification performance of the Image-To-Class (I2C) distance, a new distance learning method is proposed to improve the discrimination of I2C distance by learning the parameters in a regularized logistic regression framework in this paper. To generate a more discriminative I2C distance, we use the spatial layout of the individual features to further improve our learned distance. Meanwhile, a new kernel by making use of the output of the regression model can further enhance its complementary to the widely used bag-of-features based approaches. Experimental results can show that the proposed method can significantly outperform other I2C methods in several prevalent image datasets.
Pedagogic data as a basis for Web service fault models

This paper outlines our method for deriving fault models for use with our WS-FIT tool that can be used to assess the dependability of SOA. Since one of the major issues with extracting these heuristic rules and fault models is the availability of software systems we examine the use of systems constructed through pedagogic activities to provide one source of information.
Brain-computer interface technology for speech recognition: A review

This paper presents an overview of the studies that have been conducted with the purpose of understanding the use of brain signals as input to a speech recogniser. The studies have been categorised based on the type of the technology used with a summary of the methodologies used and achieved results. In addition, the paper gives an insight into some studies that examined the effect of the chosen stimuli on brain activities as an important factor in the recognition process. The remaining part of this paper lists the limitations of the available studies and the challenges for future work in this area.
Interplay between Two Allosteric Sites and Their Influence on Agonist Binding in Human μ Opioid Receptor

Allostery is a widespread mechanism that allows for precise protein tuning. Its underlying mechanisms are elusive, particularly when there are multiple allosteric sites at the protein. This concerns also G-protein-coupled receptors (GPCRs), which are targets for a vast part of currently used drugs. To address this issue, we performed molecular dynamics simulations of a GPCR-human μ opioid receptor (MOR) in a native-like environment, with full agonist (R)-methadone, Na(+) ions, and a positive modulator BMS986122 in various configurations. We found that MOR's seventh transmembrane helix (TM VII) is central for allosteric signal transmission, and modulators affect its bending and rotation. The PAM stabilizes favorable agonist interactions, while Na(+) tends to disrupt agonist binding. We identified two residues involved in allosteric signal transmission: Trp 7.35 at the top and Tyr 7.53 at the bottom of TM VII.
Investigations into the Effects of Biofuel Contaminants on Solid Oxide Fuel Cells

Solid Oxide Fuel Cells (SOFCs) have gathered considerable attention as a clean, highly efficient conversion device for the production of both electricity and heat from fuels. Due to their high operating temperatures, SOFCs do not require pure hydrogen as fuel, but exhibit a high fuel flexibility, a major advantage concerning the high cost of hydrogen production. Nonetheless, certain requirements apply in terms of fuel purity. The presence of contaminants such as sulfur compounds, siloxanes, halogens, volatile organic compounds and tars within the fuel stream, even at trace levels can significantly reduce the lifetime of key components such as the fuel cell stack and reformer. Cleaning technologies can remove harmful impurities from the biofuels so as to meet the cleanliness requirements of SOFC stacks, though these come at higher cost. The purpose of this study is to provide guidelines regarding the maximum impurity concentrations in the biofuels which SOFCs can tolerate. This work has two principal aims: (i) to identify any threshold tolerance limits of different contaminants, if they exist and (ii) to investigate degradation mechanisms caused by contaminants. Siloxane D4, hydrogen chloride and sulfur were selected as biogas impurities. In addition, the effect of toluene (a common impurity in wood gasifier product gas) was also investigated on the performance of Ni-YSZ SOFCs. Short tests lasting 100-500 h were carried out to study the influence of the selected impurities on state-of-the-art Ni anode-supported SOFCs. Experiments were performed on single cells provided by Topsoe Fuel Cell (TOFC) and SOLIDpower and in some cases on 11-cell short stacks, provided by TOFC. Contamination tests were performed on simple hydrogen feed and more complex feeds such as simulated biogas or reformed biogas. Furthermore, in the cases of contamination with siloxane D4 and hydrogen chloride, single cell results were compared with those of short stacks. In-situ (electrochemical impedance spectroscopy- EIS) and ex-situ (electron microscopy and chemical analysis) characterization methods were used to identify the prevailing degradation mechanisms. Suggestions were made, which Ni-YSZ anode processes are affected by each contaminant. Siloxane deposit as SiO2 and block electrode pores and TPB (triple-phase-boundary) electrochemical reaction zone; HCl adsorbs on Ni particles to hinder the electrochemical reaction; sulfur, both from H2S and thiophene, adsorbs reversibly on Ni and leads to an immediate sharp cell voltage drop, which remains small at low S-concentrations. It was found that the complete removal of siloxanes is necessary, that S-compounds are acceptable to a level of 0.5 ppm and that there is no need to remove HCl and tar compounds from the biogas, for the concentration levels in which they are expected to be found in anaerobic digester gas.
Navigation and Control for Micro Aerial Vehicles in GPS-Denied Environments

Micro-air vehicles have been increasingly employed in diverse research projects in both military and civilian applications. That is because their high maneuverability and accurate mobility. Many of them have been successfully used in outdoor areas, while some have been operated indoors. However, very few have dedicated especial attention to the case of high pitch and roll movements while doing scan-line based odometry. In this paper, we present a general approach consisting of algorithms that enable small aerial robots to fly indoors. We solve the overall problem of large movement change in pitch and roll angles by improving the standard scan matching algorithm. We also validate the effectiveness of the upgraded algorithm by a set of experiments that demonstrate the ability of a small quad-rotor to autonomously operate in cluttered indoor scenarios.
Ductile Behavior of Timber Structures under Strong Dynamic Loads

Due to their comparatively low mass that implies reduced horizontal dynamic loads even during strong earthquakes, wood-made buildings might be a good choice in seismic prone regions. To meet the modern design philosophy requirements, however, such structures should be able to behave in a ductile way under exceptional events. By presenting a brief review of the latest developments in the field, this chapter investigates on when and to what extent historical and modern timber buildings may exhibit a ductile and dissipative behavior. A special focus is given to the crucial role of connections and to the difficulties involved by their mechanical model when carrying out codebased non-linear dynamic analyses. Although a ductile behavior is typically required under strong earthquakes, it is to note that a well-designed ductile structure may also be able to withstand other exceptional events as, for instance, tornadoes or blasts.
Brief Definitive Report Identification of a Human T Lymphocyte Surface Protein Associated with the E-rosette Receptor

Human thymus-dependent lymphocytes (T cells) are defined by their ability to form spontaneous rosettes (E-rosettes) with sheep erythrocytes (SRBC) (1-3). Recently , several murine monoclonal antibodies that recognize distinct differentiation antigens on human T cells have been described (4-11). We report here a monoclonal antibody, designated 9.6, that identifies a 50,000-dalton surface protein that appears to be present on all E-rosette-forming cells. Blocking and lysostripping experiments indicate that this monoclonal antibody reacts either with the E receptor itself or with a closely associated structure. Materials and Methods Cells. Mononuclear cells from peripheral blood (PBL) or bone marrow were obtained from normal volunteers and isolated by centrifugation over Ficoll-Hypaque (LSM; Litton Bionetics Inc., Kensington, Md.). T cells were enumerated by rosetting with 2-aminoethylisothiouronium bromide hydrobromide (AET)-treated SRBC (SRBC^v.r) in medium (RPMI-1640) with 12% fetal calf serum (12). For the isolation of purified T cells, PBL were passed over nylon wool (11) and then incubated with SRBCA~-v. Rosette-forming T cells (E +) were separated from non-T cells (E-) by centrifugation over Ficoll-Hypaque. T cells were recovered from the rosettes by lysis of SRBC in Tris-buffered 0.83% ammonium chloride. Normal human thymocytes were prepared from thymus specimens obtained in the course of corrective open heart surgery from children < 14 yr old. Long-term-cultured T cells, stimulated by alloantigen, were maintained in medium supplemented with T cell growth factor (TCGF) (13). A selected panel of cultured lymphoid cell lines was used for serological analysis. Included were leukemic T cell lines (CEM, HSB2, 8402, Jurkat, Molt-4F, and KE37), the leukemic pre-B cell line NALM-6, Epstein-Barr virus-transformed B-lymphoid cell lines (PA-3, SB, 8392, HA, Swei), and the Burkitt's lymphoma ceil line Daudi. Leukemic blasts from peripheral blood of patients with acute lymphocytic leukemia (ALL), were separated over Ficoll-Hypaque, and cryopreserved. Cells were obtained either at presentation or relapse when the leukocyte count was >20,000/mm s and >90% of the cells were blasts. Subdivision of ALL into T and null cell types was based on the clinical criterion of a thymic mass, and on determination of whether the leukemic blasts formed E-rosettes or expressed ia-like antigen. Immunizations, Fusion, and Screening. The clone of hybrid cells producing the antibody described here was isolated from a previously described fusion experiment (9). Briefly, spleen cells from BALB/c mice immunized with human peripheral blood lymphocytes were fused with BALB/c MOPC21 NSI/1 myeloma cells. Antibody production by hybrid cells was assayed by …
Concept-Level Knowledge Visualization For Supporting Self-Regulated Learning

Mastery Grids is an intelligent interface that provides access to different kinds of practice content for an introductory programming course. A distinctive feature of the interface is a parallel topic-level visualization of student progress and the progress of their peers. This contribution presents an extended version of the original system that features a fine-grained visualization of student knowledge on the level of the detailed concepts that are associated with the course. The student model is based on a Bayesian-network which is built using students performance history in the learning activities.
Crystal structure of 2-cyano-1-methylpyridinium bromide

In the title molecular salt, C7H7N2 +·Br−, all the non-H atoms lie on crystallographic mirror planes. The packing consists of (010) cation–anion layers, with the cations forming dimeric units via very weak pairwise C—H⋯N interactions. Weak C—H⋯Br interactions link the cations to the anions.
iWatcher: efficient architectural support for software debugging

Recent impressive performance improvements in computer architecture have not led to significant gains in ease of debugging. Software debugging often relies on inserting run-time software checks. In many cases, however, it is hard to find the root cause of a bug. Moreover, program execution typically slows down significantly, often by 10-100 times. To address this problem, this paper introduces the Intelligent Watcher (iWatcher), novel architectural support to monitor dynamic execution with minimal overhead, automatically, and flexibly. iWatcher associates program-specified monitoring functions with memory locations. When any such location is accessed, the monitoring function is automatically triggered with low overhead. To further reduce overhead and support rollback, iWatcher can leverage Thread-Level Speculation (TLS). To test iWatcher, we use applications with various bugs. Our results show that iWatcher detects many more software bugs than Valgrind, a well-known open-source bug detector. Moreover, iWatcher only induces a 4-80% execution overhead, which is orders of magnitude less than Valgrind. Even with 20% of the dynamic loads monitored in a program, iWatcher adds only 66-174% overhead. Finally, TLS is effective at reducing overheads for programs with substantial monitoring.