Miracle-dz/UniFAR-FTUs huggingface dataset:
Microscopic observation and mechanism discussion for the changes of mouse skin after interacted by intense pulse light

The technologies based on Differential Interference Contrast microscopy (DIC), Laser Scanning Confocal Microscopy (LSCM), Two Photon Emission Laser Scanning Microscopy (TPELSM) and Optical Coherent Tomography (OCT) were used to study the changes of mouse skin after irradiated by Intense Pulse Light (IPL). The experimental results were compared and analyzed by different microscopic observation tools. The relations of the epithelial or dermal interaction with IPL in different energy density were given, and the morphologic changes of mouse skin were observed before and after days irradiated respectively. The function of dermal collagen during the renovating of the tissue and the key factors were presented.
Syntactically-Informed Semantic Category Recognizer for Discharge Summaries

Semantic category recognition (SCR) contributes to document understanding. Most approaches to SCR fail to make use of syntax. We hypothesize that syntax, if represented appropriately, can improve SCR. We present a statistical semantic category (SC) recognizer trained with syntactic and lexical contextual clues, as well as ontological information from UMLS, to identify eight semantic categories in discharge summaries. Some of our categories, e.g., test results and findings, include complex entries that span multiple phrases. We achieve classification F-measures above 90% for most categories and show that syntactic context is important for SCR.
Tool use as distributed cognition: how tools help, hinder and define manual skill

Our thesis in this paper is that, in order to appreciate the interplay between cognitive (goal-directed) and physical performance in tool use, it is necessary to determine the role that representations play in the use of tools. We argue that rather being solely a matter of internal (mental) representation, tool use makes use of the external representations that define the human–environment–tool–object system. This requires the notion of Distributed Cognition to encompass not simply the manner in which artifacts represent concepts but also how they represent praxis. Our argument is that this can be extended to include how artifacts-in-context afford use and how this response to affordances constitutes a particular form of skilled performance. By artifacts-in-context, we do not mean solely the affordances offered by the physical dimensions of a tool but also the interaction between the tool and the object that it is being used on. From this, “affordance” does not simply relate to the physical appearance of the tool but anticipates subsequent actions by the user directed towards the goal of changing the state of the object and this is best understood in terms of the “complimentarity” in the system. This assertion raises two challenges which are explored in this paper. The first is to distinguish “affordance” from the adaptation that one might expect to see in descriptions of motor control; when we speak of “affordance” as a form of anticipation, don’t we just mean the ability to adjust movements in response to physical demands? The second is to distinguish “affordance” from a schema of the tool; when we talk about anticipation, don’t we just mean the ability to call on a schema representing a “recipe” for using that tool for that task? This question of representation, specifically what knowledge needs to be represented in tool use, is central to this paper.
Point cloud data filtering and downsampling using growing neural gas

3D sensors provide valuable information for mobile robotic tasks like scene classification or object recognition, but these sensors often produce noisy data that makes impossible applying classical keypoint detection and feature extraction techniques. Therefore, noise removal and downsampling have become essential steps in 3D data processing. In this work, we propose the use of a 3D filtering and downsampling technique based on a Growing Neural Gas (GNG) network. GNG method is able to deal with outliers presents in the input data. These features allows to represent 3D spaces, obtaining an induced Delaunay Triangulation of the input space. Experiments show how GNG method yields better input space adaptation to noisy data than other filtering and downsampling methods like Voxel Grid. It is also demonstrated how the state-of-the-art keypoint detectors improve their performance using filtered data with GNG network. Descriptors extracted on improved keypoints perform better matching in robotics applications as 3D scene registration.
Electron microscopic studies on the attachment of Mycoplasma pneumoniae to guinea pig erythrocytes

A mechanism of pathogenicity of Mycoplasma pneumoniae is its ability to attach to the surface of mammalian cells. It has previously been demonstrated by others that M. pneumoniae adheres with a specialized terminal structure, the "tip," to ciliated epithelial cells of the respiratory tract. In this report we show by electron microscopy that M. pneumoniae adsorbs with membrane sites other than the tip to guinea pig erythrocytes.
Estimating the number of graphs containing very long induced paths

Let P(n, k) denote the number of graphs on n + k vertices that contain Pn, a path on n vertices, as an induced subgraph. In this note we will find upper and lower bounds for P(n, k). Using these bounds we show that for k fixed, P(n, k) behaves roughly like an exponential function of n as n gets large.
Overexpression of the cellular retinoic acid binding protein-I (CRABP- I) results in a reduction in differentiation-specific gene expression in F9 teratocarcinoma cells

Treatment of F9 teratocarcinoma stem cells with retinoic acid (RA) causes their irreversible differentiation into extraembryonic endoderm. To elucidate the role of the cellular retinoic acid binding protein-I (CRABP-I) in this differentiation process, we have generated several different stably transfected F9 stem cell lines expressing either elevated or reduced levels of functional CRABP-I protein. Stably transfected lines expressing elevated levels of CRABP-I exhibit an 80- 90% reduction in the RA induced expression of retinoic acid receptor (RAR) beta, laminin B1, and collagen type IV (alpha 1) mRNAs at low exogenous RA concentrations, but this reduction is eliminated at higher RA concentrations. Thus, greater expression of CRABP-I reduces the potency of RA in this differentiation system. Moreover, transfection of a CRABP-I expression vector into F9 cells resulted in five- and threefold decreases in the activation of the laminin B1 RARE (retinoic acid response element) and the RAR beta RARE, respectively, as measured from RARE/CAT expression vectors in transient transfection assays. These results support the idea that CRABP-I sequesters RA within the cell and thereby prevents RA from acting to regulate differentiation specific gene expression. Our data suggest a mechanism whereby the level of CRABP-I can regulate responsiveness to RA during development.
Single-crystal nickel-based superalloys developed by numerical multi-criteria optimization techniques: design based on thermodynamic calculations and experimental validation

A method for finding the optimum alloy compositions considering a large number of property requirements and constraints by systematic exploration of large composition spaces is proposed. It is based on a numerical multi-criteria global optimization algorithm (multistart solver using Sequential Quadratic Programming), which delivers the exact optimum considering all constraints. The CALPHAD method is used to provide the thermodynamic equilibrium properties, and the creep strength of the alloys is predicted based on a qualitative numerical model considering the solid solution strengthening of the matrix by the elements Re, Mo and W and the optimum morphology and fraction of the γ′-phase. The calculated alloy properties which are required as an input for the optimization algorithm are provided via very fast Kriging surrogate models. This greatly reduces the total calculation time of the optimization to the order of minutes on a personal computer. The capability of the multi-criteria optimization method developed was experimentally verified with two new single crystal superalloys. Their compositions were designed such that the content of expensive elements was reduced. One of the newly designed alloys, termed ERBO/13, is found to possess creep strength of only 14 K below CMSX-4 in the high-temperature/low-stress regime although it is a Re-free alloy.
A Neural Network-Based Gait Phase Classification Method Using Sensors Equipped on Lower Limb Exoskeleton Robots

An exact classification of different gait phases is essential to enable the control of exoskeleton robots and detect the intentions of users. We propose a gait phase classification method based on neural networks using sensor signals from lower limb exoskeleton robots. In such robots, foot sensors with force sensing registers are commonly used to classify gait phases. We describe classifiers that use the orientation of each lower limb segment and the angular velocities of the joints to output the current gait phase. Experiments to obtain the input signals and desired outputs for the learning and validation process are conducted, and two neural network methods (a multilayer perceptron and nonlinear autoregressive with external inputs (NARX)) are used to develop an optimal classifier. Offline and online evaluations using four criteria are used to compare the performance of the classifiers. The proposed NARX-based method exhibits sufficiently good performance to replace foot sensors as a means of classifying gait phases.
Evolution of the Antigen-Specific CD8+ TCR Repertoire across the Life Span: Evidence for Clonal Homogenization of the Old TCR Repertoire

Defects in T cell responses against pathogens and reduced diversity of TCRs have been described at both extremes of the life span. Yet, we still lack information on how Ag-specific T cell populations are maintained and/or altered from birth to old age. In this study, for the first time to our knowledge, we provide insight into Ag-specific TCR repertoire changes over the life span at the single-cell level. We have examined the TCR diversity of the primary CD8+ T cell response to the immunodominant HSV-1 epitope HSV glycoprotein B 495–502 (HSV gB498–505; SSIEFARL) (gB-8p) in neonatal, adult, and old C57BL/6 mice. The global distinctive features of the gB-8p–specific TCR repertoire were preserved in mice of different ages. However, both old and especially neonatal mice exhibited significant decreases in TCR diversity compared with that of adult mice. Still, although the neonatal Ag-specific repertoire comprised expectedly shorter germline-biased CDR3β lengths, the repertoire was surprisingly complex, and only a minority of responding cells lacked random nucleotide additions. Changes with aging included increased use of the already dominant TCRVβ10 family, a trend for lower content of the TCR containing the germline WG motif in the CDR3, and a remarkable sharing of one dominant clonotype between individual old mice, implying operation of selective mechanisms. Implications for the rational design of vaccines for neonates and the elderly are discussed.
Anthrax lethal toxin and Salmonella elicit the common cell death pathway of caspase-1-dependent pyroptosis via distinct mechanisms

Caspase-1 cleaves the inactive IL-1β and IL-18 precursors into active inflammatory cytokines. In Salmonella-infected macrophages, caspase-1 also mediates a pathway of proinflammatory programmed cell death termed “pyroptosis. ” We demonstrate active caspase-1 diffusely distributed in the cytoplasm and localized in discrete foci within macrophages responding to either Salmonella infection or intoxication by Bacillus anthracis lethal toxin (LT). Both stimuli triggered caspase-1-dependent lysis in macrophages and dendritic cells. Activation of caspase-1 by LT required binding, uptake, and endosome acidification to mediate translocation of lethal factor (LF) into the host cell cytosol. Catalytically active LF cleaved cytosolic substrates and activated caspase-1 by a mechanism involving proteasome activity and potassium efflux. LT activation of caspase-1 is known to require the inflammasome adapter Nalp1. In contrast, Salmonella infection activated caspase-1 through an independent pathway requiring the inflammasome adapter Ipaf. These distinct mechanisms of caspase-1 activation converged on a common pathway of caspase-1-dependent cell death featuring DNA cleavage, cytokine activation, and, ultimately, cell lysis resulting from the formation of membrane pores between 1.1 and 2.4 nm in diameter and pathological ion fluxes that can be blocked by glycine. These findings demonstrate that distinct activation pathways elicit the conserved cell death effector mechanism of caspase-1-mediated pyroptosis and support the notion that this pathway of proinflammatory programmed cell death is broadly relevant to cell death and inflammation invoked by diverse stimuli.
A performance comparison of flat-panel imager-based MV and kV cone-beam CT.

The use of cone-beam computed tomography (CBCT) has been proposed for guiding the delivery of radiation therapy, and investigators have examined the use of both kilovoltage (kV) and megavoltage (MV) x-ray beams in the development of such CBCT systems. In this paper, the inherent contrast and signal-to-noise ratio (SNR) performance for a variety of existing and hypothetical detectors for CBCT are investigated analytically as a function of imaging dose and object size. Theoretical predictions are compared to the results of experimental investigations employing largearea flat-panel imagers (FPIs) at kV and MV energies. Measurements were performed on two different FPI-based CBCT systems: a bench-top prototype incorporating an FPI and kV x-ray source (100 kVp x rays), and a system incorporating an FPI mounted on the gantry of a medical linear accelerator (6 MV x rays). The SNR in volume reconstructions was measured as a function of dose and found to agree reasonably with theoretical predictions. These results confirm the theoretically predicted advantages of employing kV energy x rays in imaging soft-tissue structures found in the human body. While MV CBCT may provide a valuable means of correcting 3D setup errors and may offer an advantage in terms of simplicity of mechanical integration with a linear accelerator (e.g., implementation in place of a portal imager), kV CBCT offers significant performance advantages in terms of image contrast and SNR per unit dose for visualization of soft-tissue structures. The relatively poor SNR performance at MV energies is primarily a result of the low x-ray quantum efficiencies (approximately a few percent or less) that are currently achieved with FPIs at high energies. Furthermore, kV CBCT with an FPI offers the potential of combined volumetric and radiographic/fluoroscopic imaging using the same device.
Fault‐tolerant control of nonlinear process systems subject to sensor faults

The problem of control of nonlinear process systems subject to input constraints and sensor faults (complete failure or intermittent unavailability of measurements) is considered. A fault-tolerant controller is designed that utilizes reconfiguration (switching to an alternate control configuration) in a way that accounts for the process nonlinearity, the presence of constraints and the occurrence of sensor faults. To clearly illustrate the importance of accounting for the presence of input constraints, first the problem of sensor faults that necessitate sensor recovery to maintain closed-loop stability is considered. We address the problem of determining, based on stability region characterizations for the candidate control configurations, which control configuration should be activated (reactivating the primary control configuration may not preserve stability) after the sensor is rectified. We then consider the problem of asynchronous measurements, that is of intermittent unavailability of measurements. To address this problem, the stability region (that is, the set of initial conditions starting from where closed-loop stabilization under continuous availability of measurements is guaranteed), as well as the maximum allowable data loss rate which preserves closed-loop stability for the primary and the candidate backup configurations are computed. This characterization is utilized in identifying the occurrence of a destabilizing sensor fault, and in activating a suitable backup configuration that preserves closed-loop stability. The proposed method is illustrated using a chemical process example and demonstrated via application to a polyethylene reactor. 2007 American Institute of Chemical Engineers AIChE J, 53: 654–668, 2007
Crystal structure of Hop2–Mnd1 and mechanistic insights into its role in meiotic recombination

In meiotic DNA recombination, the Hop2−Mnd1 complex promotes Dmc1-mediated single-stranded DNA (ssDNA) invasion into homologous chromosomes to form a synaptic complex by a yet-unclear mechanism. Here, the crystal structure of Hop2−Mnd1 reveals that it forms a curved rod-like structure consisting of three leucine zippers and two kinked junctions. One end of the rod is linked to two juxtaposed winged-helix domains, and the other end is capped by extra α-helices to form a helical bundle-like structure. Deletion analysis shows that the helical bundle-like structure is sufficient for interacting with the Dmc1-ssDNA nucleofilament, and molecular modeling suggests that the curved rod could be accommodated into the helical groove of the nucleofilament. Remarkably, the winged-helix domains are juxtaposed at fixed relative orientation, and their binding to DNA is likely to perturb the base pairing according to molecular simulations. These findings allow us to propose a model explaining how Hop2−Mnd1 juxtaposes Dmc1-bound ssDNA with distorted recipient double-stranded DNA and thus facilitates strand invasion.
AN ONTOLOGY FOR COORDINATION

Independent agents that interact within open, distributed, and decentralized environments need to collaboratively regulate their activities in order to facilitate the harmonious and successful achievement of possibly conflicting tasks. Coordination is the process of managing these interactions by identifying and possibly resolving the interdependencies occurring between such activities. A successful coordination mechanism facilitates mutually beneficial interdependencies (e.g., by ensuring activities are not duplicated) while avoiding adverse outcomes (e.g., by preventing two processes simultaneously accessing the same non-shareable resource, potentially causing deadlock). However, for such a mechanism to work effectively within open systems, agents need to communicate and reason about activities, resources, and their properties; i.e., to commit to a shared ontology of coordination that defines the semantics underlying the different coordination regimes. This article describes an ontological approach to coordination in which agents dynamically manage the interdependencies that arise during their interactions. A proof-of-concept implementation in the insurance domain is described and empirically evaluated.
Implementation of on-line clutch pressure estimation for stepped automatic transmissions

On-line estimation of clutch pressures in hydraulically powered stepped automatic transmissions can be useful for on-line diagnostics or development of closed-loop transmission control to improve shift quality. This paper presents the development and implementation of a model-based sliding mode observer to provide on-line estimates of clutch pressures for the clutches involved in gear shifts. The estimation of transmission input torque (torque converter turbine torque), which is needed by the observer for accurate clutch pressure estimation but is not available, is also addressed here and implemented using an adaptive sliding mode observer. The resulting observers are validated via off-line simulation tests, as well as on-line tests at different sampling frequencies on a test vehicle, in order to demonstrate observer performance and establish the feasibility of the approach.
Potrace : a polygon-based tracing algorithm

Black-on-white images can be represented either as a bitmap or as a vector outline. A bitmap represents an image as a grid of black or white pixels. A vector outline describes an image via an algebraic description of its contours, typically in the form of Bezier curves. The advantage of representing an image as a vector outline is that it can be scaled to any size without loss of quality. Outline images are independent of the resolution of any particular output device. They are particularly popular in the description of fonts, which must be reproducible at many different sizes. Examples of outline font formats include PostScript Type 1 fonts, TrueType, and Metafont. On the other hand, most actual input and output devices, such as scanners, displays, and printers, ultimately produce or consume bitmaps. The process of converting a vector outline to a bitmap is called rendering. The converse process of turning bitmaps into outlines is called tracing. It is clear that no tracing algorithm can be perfect in an absolute sense, as there are in general many possible outlines that can give rise to the same bitmap. The process of tracing cannot be used to generate information that is not already present. On the other hand, out of the many possible outlines that could give rise to a given bitmap, clearly some are more plausible or aesthetically pleasing than others. For example, a common way of rendering bitmaps at a high resolution is to draw each black pixel as a precise square, which gives rise to “jaggies” or staircase patterns. Clearly, jaggies are neither pleasant to look at, nor are they particularly plausible interpretations of the original image. There is probably no absolute measure of what constitutes a good tracing algorithm, but it seems clear that some algorithms give better results than others. In this paper, we describe a tracing algorithm that is simple, efficient, and tends to produce excellent results. The algorithm is called Potrace, which stands for polygon tracer. However, the output of the algorithm is not a polygon, but a smooth contour made from Bezier curves. The name of the algorithm derives from the fact that it uses polygons as an intermediate representation of images. The Potrace algorithm is designed to work well on high resolution images. Thus, a typical application is to produce a vector outline from a company or university logo that has been scanned at a high resolution. Another possible application is the conversion of bitmapped fonts to outline fonts, if the original bitmapped fonts are available at a high enough resolution. No tracing algorithm will work well on very small scales, such as
Overview of Protein Folds in the Immune System

The rapid advancement of X‐ray crystallography and nuclear magnetic resonance techniques in recent years has resulted in the solution of macromolecular structures at an unprecedented rate. This review aims at providing a comprehensive description of structures and folds related to the function of the immune system. Focus is placed on immunologically relevant proteins such as immunoreceptors and major histocompatibility complexes. Information is also provided regarding protein structure data banks.