gebhart/patrepeval huggingface dataset:
Quantitative nanoparticle structures from electron crystallography data (2010)

We describe the quantitative refinement of nanoparticle structures from gold nanoparticles probed by electron diffraction in the ultrafast electron crystallography (UEC) geometry. We establish the equivalence between the modified radial distribution function employed in UEC and the atomic pair distribution function (PDF) used in x-ray and neutron powder-diffraction analysis. By leveraging PDF refinement techniques, we demonstrate that UEC data are of sufficient quality to differentiate between cuboctahedral, decahedral, and icosahedral nanoparticle models for the ground-state (dark) structures of the gold nanoparticles. Furthermore, we identify the signatures of systematic errors that may occur during data reduction and show that atomic positions refined from UEC are robust to these errors. This work serves as a foundation for reliable quantitative structural analysis of time-resolved laser-excited nanoparticle states.
Performance assessment of industrial control system during pre-sales uncertain context using automatic Colored Petri Nets model generation (2016)

Industrial control systems (ICS) are defined with hardware and software components dedicated to control and monitoring tasks for factory process. Proper functioning of ICS architectures is mainly linked to the performance they offer. System integrators (SI) must know performance of the architecture they propose to the customers by assessing them. Many methodologies have already proven their capabilities to assess ICS architecture performance. One of them is colored Petri Nets (CPN). To assess the performance of ICS architecture using CPN involve defining manually the model. Pre-sales uncertain context involves problematic making this manual model definition challenging. This paper introduces a concept allowing automatic CPN model generation by instantiation and parameterization. However before introducing the concept, the paper shows the problematic involved by the pre-sales context. Then shows why CPN methodology is a relevant solution for assessing the performance of ICS in this context.
Haptic feedback designs in teleoperation systems for minimal invasive surgery (2005)

One of the major shortcomings of state-of-the-art robotic systems for minimal invasive surgery is the lack of haptic feedback for the surgeon. In order to provide haptic information, sensors and actuators have to be added to the master and slave device. A control system should process the data and make a coupling between slave and master. Despite the significant amount of research on haptic devices, this control design problem is, largely, an open problem. This paper reports the results on three model-based control designs. Using the formalism of passivity, a robust controller has been designed, and is compared to a gain scheduled controller (LPV) which is adaptable for changes in the tissue characteristics.
Observer Kalman Filter Identification of Suspen‐Dome (2017)

A number of Suspen‐Dome structures have been built, but there is some difficulty in using experimental data to obtain good modal parameters, especially modal damping. In this paper, an ANSYS numerical simulation of the 35.4 m span Suspen‐Dome is presented. Firstly, the natural vibration characteristics of Suspen‐Dome and dynamic response under some random forces were obtained. Then the results of the numerical simulation established that 60 modes are sufficient for a reasonable dynamic model. This model is used to represent the Suspen‐Dome dynamic behavior, and OKID is then used to try to identify a model from simulated data. A 400‐order model generated from OKID is shown to contain the 60 modes from ANSYS and is shown to give good predictions of the dynamic behavior of Suspen‐Dome. The results of this paper can confirm that it can be a very efficient tool for the identification of models of Suspen‐Dome dynamics.
Therapy with a Purified Plasminogen Concentrate in an Infant with Ligneous Conjunctivitis and Homozygous Plasminogen Deficiency (1998)

Ligneous conjunctivitis is a rare disease characterized by acute or chronic recurrent conjunctivitis in which the conjunctival membranes acquire a wood-like consistency, due primarily to deposits of fibrin.1,2 Corneal involvement and chronic obstruction of the eye may lead to blindness. The disease is frequently associated with nasopharyngitis, tracheobronchial obstruction, otitis media, vulvovaginitis, and defective wound healing.2–9 Pseudomembranous conjunctivitis was first described in 1847 by Bouisson,10 and the term “conjunctivitis lignosa” was introduced by Borel in 1933.11 More than 100 cases have been reported in the literature, but no satisfactory treatment has yet been found. The results of therapy . . .
iPSC-Derived Platelets Depleted of HLA Class I Are Inert to Anti-HLA Class I and Natural Killer Cell Immunity (2019)

The ex vivo production of platelets depleted of human leukocyte antigen class I (HLA-I) could serve as a universal measure to overcome platelet transfusion refractoriness caused by HLA-I incompatibility. Here, we developed human induced pluripotent cell-derived HLA-I-deficient platelets (HLA-KO iPLATs) in a clinically applicable imMKCL system by genetic manipulation and assessed their immunogenic properties including natural killer (NK) cells, which reject HLA-I downregulated cells. HLA-KO iPLATs were deficient for all HLA-I but did not elicit a cytotoxic response by NK cells in vitro and showed circulation equal to wild-type iPLATs upon transfusion in our newly established Hu-NK-MSTRG mice reconstituted with human NK cells. Additionally, HLA-KO iPLATs successfully circulated in an alloimmune platelet transfusion refractoriness model of Hu-NK-MISTRG mice. Mechanistically, the lack of NK cell-activating ligands on platelets may be responsible for evading the NK cell response. This study revealed the unique non-immunogenic property of platelets and provides a proof of concept for the clinical application of HLA-KO iPLATs.
Core–shell protein clusters comprising haemoglobin and recombinant feline serum albumin as an artificial O₂ carrier for cats (2018)

This report describes the synthesis and structure of core–shell protein clusters comprising haemoglobin (Hb) at the centre and recombinant feline serum albumin (rFSA) at the exterior, named as haemoglobin–albumin clusters (Hb–rFSA₃). Specifically, we highlight their capability as an artificial O₂ carrier that can be used as a red blood cell (RBC) substitute for cats, the most populous pet animal in the world. First, rFSA was expressed by genetic engineering using Pichia yeast. The proteins show identical features to the native FSA derived from feline plasma. Single crystals of rFSA were prepared under a microgravity environment on the international space station (ISS), from which the structure was first revealed at 3.4 A resolution. Subsequently, bovine Hb was wrapped covalently by rFSA using an α-succinimidyl-e-maleimide crosslinker, yielding Hb–rFSA₃ clusters. Three rFSA entities enfolded the Hb nuclei satisfactorily, giving the protein clusters a negative surface net charge (pI = 4.7) and preventing an immunological response against anti-Hb antibodies. The O₂ affinity was higher (P₅₀ = 9 Torr) than that of the native Hb. The Hb–rFSA₃ clusters are anticipated for use as an alternative material for RBC transfusion, and as an O₂ therapeutic reagent that can be exploited in various veterinary medicine scenarios.
Activins regulate 17β-hydroxysteroid dehydrogenase type I transcription in murine gonadotrope cells (2009)

Activins are pleiotropic members of the TGFbeta superfamily and were initially characterized based on their abilities to stimulate FSH synthesis and secretion by gonadotrope cells of the anterior pituitary gland. Here, we identified the gene encoding the steroidogenic enzyme, 17beta-hydroxysteroid dehydrogenase type I (17beta-HSD1; Hsd17b1), as an activin-responsive gene in immortalized gonadotrope cells, LbetaT2. 17beta-HSD1 catalyzes the conversion of estrone to the more active 17beta-estradiol, and activin A stimulated an increase in this enzymatic activity in these cells. We demonstrated that activins signaled via the type I receptor, activin receptor-like kinase (ALK4), and the intracellular signaling protein, SMAD2, to regulate Hsd17b1 transcription in immediate-early fashion. Critical cis-elements, including a minimal SMAD-binding element, were mapped to within 100 bp of the start of transcription. Activin/ALK4 signaling also regulated Hsd17b1 transcription in both immortalized and primary cultured murine granulosa cells. The promoter regions mediating basal and activin/ALK4-regulated promoter activity were generally conserved across the different cell types. The data show that activin A rapidly regulates Hsd17b1 transcription in gonadotrope and granulosa cells and may thereby regulate local 17beta-estradiol synthesis.
Antigenic Properties of Bacteriophage φ29 Structural Proteins (1973)

Serological methods and electron microscopy were used to study the structural proteins of the small Bacillus subtilis bacteriophage phi29. This virus has a large number of fibers attached at both ends of its prolate head. A complex neck assembly is comprised of 12 symmetrically arranged appendages as the outer component. Head fibers, neck appendages, and the head surface bind anti-phi29 antibodies. Immune sera absorbed with defective lysates of suppressor-sensitive (sus) mutants have been used to determine the genetic control of neck appendages production. Studies on the serum-blocking power of lysates defective in different tail components showed that appendages contain the main serum-blocking protein. This finding suggests an essential role of the neck appendages in phage adsorption or DNA injection.
Purification and Crystallization of the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) (2004)

The cystic fibrosis transmembrane conductance regulator (CFTR) is a membrane protein that is mutated in patients suffering from cystic fibrosis. Here we report the purification and first crystallization of wild-type human CFTR. Functional characterization of the material showed it to be highly active. Electron crystallography of negatively stained two-dimensional crystals of CFTR has revealed the overall architecture of this channel for two different conformational states. These show a strong structural homology to two conformational states of another eukaryotic ATP-binding cassette transporter, P-glycoprotein. In contrast to P-glycoprotein, however, both conformational states can be observed in the presence of a nucleotide, which may be related to the role of CFTR as an ion channel rather than a transporter. The hypothesis that the two conformations could represent the "open" and "closed" states of the channel is considered.
Degrees of Freedom and Synthetic Functions in the Analysis of Large Antennas (2004)

The Synthetic Function Expansion (SFX) method reduces the complexity of the MoM analysis of antenna and scattering problems by dividing the overall structure into portions, recognizing that the degrees of freedom of the field coupling between the solution on these portions are limited, and building basis that exploit this property. THE AGGREGATE-FUNCTION PARADIGM This work belongs to a class of methods that end up in reducing the actual size of the final algebraic problem associated with the Method-of-Moment (MoM) analysis of antennas and scatterers. These methods can in turn be divided into two major classes: those employing basis of higher polynomial order and with larger spatial support, and those that group basis (typically of low polynomial order) into functions defined over portions of the structure that are significantly larger than one cell of the initial mesh. The present method belongs to the second class. A large part of the functions approaches can be traced back to the so-called diakoptic approach (1, and references therein), originally developed for structures that are naturally or artificially broken down in sub-structures interconnected by ports. One (or two) are introduced per each port, that are essentially the solution of the sub-structure in isolation, and these are used to compact the MoM matrix. In order to reach convergence and/or accuracy, one or more iterations are employed, in which the interactions between the various regions of definition of the macro-basis are included. Various versions exists of the technique, with improvements of the above basic idea, e.g. (1), (2). Finally, it is noted that a recent addition to this list is the powerful characteristic basis function (CBF) technique outlined in (3). Another starting point in generating aggregate for electrically large structures is based on asymp- totic (high-frequency) solutions; an example of this approach is described in (4) for large and finite periodic arrays; similar constructs have been employed in (5). In the past years these authors have likewise worked on a reduced-complexity strategy, employing a few, global unknowns defined on different portions of the structure, with different strategies in the generation and use of these global basis (6, 7, 8). It can be observed that the underlying question behind the aggregate-function quest is what is the number of degrees of freedom of the solution we are looking for on each portion, and the implicit assumption that this number should be much smaller than the number of basis involved in discretizing the problem in the conventional way. In the present paper, this question is addressed explicitly from the offstart, and the problem of representing the unknown field quantities is accordingly phrased.
A relation prediction method based on PU learning (2017)

This paper studies relation prediction in heterogeneous information networks under PU learning context. One of the challenges of this problem is the imbalance of data number between the positive set P (the set of node pairs with the target relation) and the unlabeled set U (the set of node pairs without the target relation). We propose a K-means and voting mechanism based technique SemiPUclus to extract the reliable negative set RN from U under a new relation prediction framework PURP. The experimental results show that PURP achieves better performance than comparative methods in DBLP co-authorship network data.
Abstraction of the Hydrogen Atom of Methane by Iron−Oxo Species:  The Concerted Reaction Path Is Energetically More Favorable (1998)

Two kinds of H-atom abstractions from methane by iron−oxo complexes with different charges are discussed from density functional theory calculations. A concerted H-atom abstraction via a four-centered transition state is shown to be energetically more favorable than a direct H-atom abstraction via a transition state with a linear C−H−O array. Iron(IV)−oxo complexes appear to be the most effective for the cleavage of the C−H bond of alkanes in the concerted mechanism, which is rationalized from qualitative orbital interaction analyses. The results of this paper support the establishment of the two-step concerted mechanism that we have proposed for alkane hydroxylations by iron−oxo species. The proposed reaction mechanism may have relevance to our understanding of some catalytic and enzymatic processes concerning alkane hydroxylations if coordinatively unsaturated transition-metal oxides are responsible for such important chemical reactions.
Wear Studies for Development of an Intervertebral Disc Prosthesis (1992)

Two long-term wear behavior studies used in part of the process of selecting the best materials for a new all-metal orthopaedic spinal implant are presented. The relative and absolute wear volume rates of candidate metals were investigated through simulation of two bearing regions of an intervertebral disc prosthesis. It was determined gravimetrically that hot isostatically pressed Co-Cr-Mo alloy provided the lowest Co-Cr-Mo alloy wear debris generation. It had an average wear volume rate of 0.093 mm3/million cycles from a spring-in-pocket simulation and 0.126 mm3/million cycles from a hinge (pin-in-slot) simulation. The estimated total wear volume of a hot isostatically pressed intervertebral disc prosthesis with titanium-6%Al-4%V alloy springs was 2.9 mm3/million cycles.
Biliary necrosis due to hepatic involvement with hereditary hemorrhagic telangiectasia. (1998)

Biliary necrosis due to hepatic involvement with hereditary hemorrhagic telangiectasia.B McInroy, A B Zajko and A D PinnaAudio Available | Share
Shape Memory Alloy Research and Development at NASA Glenn - Current and Future Progress (2015)

Shape memory alloys (SMAs) are a unique class of multifunctional materials that have the ability to recover large deformations or generate high stresses in response to thermal, mechanical and or electromagnetic stimuli. These abilities have made them a viable option for actuation systems in aerospace, medical, and automotive applications, amongst others. However, despite many advantages and the fact that SMA actuators have been developed and used for many years, so far they have only found service in a limited range of applications. In order to expand their applications, further developments are needed to increase their reliability and stability and to address processing, testing and qualification needed for large-scale commercial application of SMA actuators.
Gate-level simulation of quantum circuits (2003)

Simulating quantum computation on a classical computer is a difficult problem. The matrices representing quantum gates, and vectors modeling qubit states grow exponentially with an increase in the number of qubits. However, by using a new data structure called the Quantum Information Decision Diagram (QuIDD) that exploits the structure of quantum operators, many of these matrices and vectors can be represented in a form that grows polynomially. Using QuIDDs, we implemented a general-purpose quantum computing simulator in C++ called QuIDDPro and tested it on Grover's algorithm. Our QuIDD technique asymptotically outperforms other known simulation techniques.
Quantitative Determination of Perfluorochemicals in Sediments and Domestic Sludge (2005)

Perfluorochemicals (PFCs) are the subject of increasingly intense environmental research. Despite their detection both in biota and in aqueous systems, little attention has been paid to the possible presence of this class of compounds in solid environmental matrixes. The limited available data indicate that some PFCs such as perfluorooctane sulfonate (PFOS) may strongly sorb to solids, and sewage sludge is widely suspected as a major sink of PFCs entering municipal waste streams. A quantitative analytical method was developed that consists of liquid solvent extraction of the analytes from sediments and sludge, cleanup via solid-phase extraction, and injection of the extracts with internal standards into a high-performance liquid chromatography (HPLC) system coupled to a tandem mass spectrometer (LC/MS/MS). The limits of detections of the method were analyte and matrix dependent, but ranged from 0.7 to 2.2 ng/g and 0.041 to 0.246 ng/g (dry weight) for sludge and sediment, respectively. A demonstration of the method was performed by conducting a limited survey of domestic sludge and sediments. The concentration of PFCs in domestic sludge ranged from 5 to 152 ng/g for total perfluorocarboxylates and 55 to 3370 ng/g for total perfluoroalkyl sulfonyl-based chemicals. Data from a survey of San Francisco Bay Area sediments suggest widespread occurrence of PFCs in sediments at the low ng/g to sub-ng/g level. Furthermore, substances that may be transformed to PFOS, such as 2-(N-ethylperfluorooctanesulfonamido) acetic acid (N-EtFOSAA) and 2-(N-methylperfluorooctanesulfonamido) acetic acid (N-MeFOSAA), are present in both sediments and sludge at levels often exceeding PFOS.
Finite Element Studies of Skid Resistance under Hot Weather Condition (2018)

The skid resistance of a pavement surface is an important characteristic that influences traffic safety. Previous studies have shown that skid resistance varies with temperature. However, relatively limited work has been carried out to study the effect of temperature on skid resistance in hot climates. Recent developments in computing and computational methods have encouraged researchers to analyze the mechanics of the tire-pavement interaction phenomenon. The aim of this paper is to develop a thermo-mechanical tire pavement interaction model that would allow more robust and realistic modeling of skid resistance using the Finite Element (FE) method. The results of this model were validated using field tests that were performed in the State of Qatar. Consequently, the validated FE model was used to quantify the effect of factors such as speed, inflation pressure, wheel load, and ambient temperature on the skid resistance/braking distance. The developed model and analysis methods are expected to be valuable for road engineers to evaluate the skid resistance and braking distance for pavement management and performance prediction purposes.
Experimental feedback linearisation of a non-smooth nonlinear system by the method of receptances (2018)

Input–output partial feedback linearisation is experimentally implemented on a non-smooth nonlinear system without the necessity of a conventional system matrix model for the first time. The experimental rig consists of three lumped masses connected and supported by springs with low damping. The input and output are at the first degree of freedom with a non-smooth clearance-type nonlinearity at the third degree of freedom. Feedback linearisation has the effect of separating the system into two parts: one linear and controllable and the other nonlinear and uncontrollable. When control is applied to the former, the latter must be shown to be stable if the complete system is to be stable with the desired dynamic behaviour.
Mathematical modeling for the scientific method (2011)

Part of the International Series in Mathematics Mathematical Modeling for the Scientific Method is intended for the sophomore/junior-level student seeking to be well-grounded in mathematical modeling for their studies in biology, the physical sciences, engineering, and/or medicine. It clarifies the connection between deductive and inductive reasoning as used in Mathematics and Science and urges students to think critically about concepts and applications. The authors' goal is to be introductory in level while covering a broad range of techniques. They unite topics in statistics, linear algebra, calculus, and differential equations, while discussing how these subjects are interrelated and utilized. Mathematical Modeling for the Scientific Method leaves students with a clearer perspective of the role of mathematics within the sciences and the understanding of how to rationally work through even rigorous applications with ease.