gebhart/patrepeval huggingface dataset:
Protein Coating of DNA Nanostructures for Enhanced Stability and Immunocompatibility (2017)

Fully addressable DNA nanostructures, especially DNA origami, possess huge potential to serve as inherently biocompatible and versatile molecular platforms. However, their use as delivery vehicles in therapeutics is compromised by their low stability and poor transfection rates. This study shows that DNA origami can be coated by precisely defined one-to-one protein-dendron conjugates to tackle the aforementioned issues. The dendron part of the conjugate serves as a cationic binding domain that attaches to the negatively charged DNA origami surface via electrostatic interactions. The protein is attached to dendron through cysteine-maleimide bond, making the modular approach highly versatile. This work demonstrates the coating using two different proteins: bovine serum albumin (BSA) and class II hydrophobin (HFBI). The results reveal that BSA-coating significantly improves the origami stability against endonucleases (DNase I) and enhances the transfection into human embryonic kidney (HEK293) cells. Importantly, it is observed that BSA-coating attenuates the activation of immune response in mouse primary splenocytes. Serum albumin is the most abundant protein in the blood with a long circulation half-life and has already found clinically approved applications in drug delivery. It is therefore envisioned that the proposed system can open up further opportunities to tune the properties of DNA nanostructures in biological environment, and enable their use in various delivery applications.
Processing and mechanical properties of organic filler–polypropylene composites (2005)

Abstract The addition of organic fillers into thermoplastic polymers is an interesting issue, which has had growing consideration and experimentation during the last years. It can give rise to several advantages. First, the cost of these fillers is usually very low. Also, the organic fillers are biodegradable (thus contributing to an improved environmental impact), and finally, some mechanical and thermomechanical properties can be enhanced. In this study, the effect of the addition of different organic fillers on the mechanical properties and processability of an extrusion‐grade polypropylene were investigated. The organic fillers came from natural sources (wood, kenaf, and sago) and were compared to short glass fibers, a widely used inorganic filler. The organic fillers caused enhancements in the rigidity and thermomechanical resistance of the matrix in a way that was rather similar to the one observed for the inorganic filler. A reduction in impact strength was observed for both types of fillers. The use of an adhesion promoter could improve their behavior. © 2005 Wiley Periodicals, Inc. J Appl Polym Sci 96: 1906–1913, 2005
Finding a needle in a haystack: detection of a small protein (the 12-kDa VP26) in a large complex (the 200-MDa capsid of herpes simplex virus). (1994)

Macromolecular complexes that consist of homopolymeric protein frameworks with additional proteins attached at strategic sites for a variety of structural and functional purposes are widespread in subcellular biology. One such complex is the capsid of herpes simplex virus type 1 whose basic framework consists of 960 copies of the viral protein, VP5 (149 kDa), arranged in an icosahedrally symmetric shell. This shell also contains major amounts of three other proteins, including VP26 (12 kDa), a small protein that is approximately equimolar with VP5 and accounts for approximately 6% of the capsid mass. With a view to inferring the role of VP26 in capsid assembly, we have localized it by quantitative difference imaging based on three-dimensional reconstructions calculated from cryo-electron micrographs. Purified capsids from which VP26 had been removed in vitro by treatment with guanidine hydrochloride were compared with preparations of the same depleted capsids to which purified VP26 had been rebound and with native (undepleted) capsids. The resulting three-dimensional density maps indicate that six VP26 subunits are distributed symmetrically around the outer tip of each hexon protrusion on VP26-containing capsids. Because VP26 may be readily dissociated from and reattached to the capsid, it does not appear to contribute significantly to structural stabilization. Rather, its exposed location suggests that VP26 may be involved in linking the capsid to the surrounding tegument and envelope at a later stage of viral assembly.
<scp>L</scp>‐<i>o</i>‐Carboranylalanine, a Boron Analogue of Phenylalanine (1976)

Abstract The synthesis of a new, boron‐containing analogue of phenylalanine is described. Carboranylalanine (Car) carries a 1,2‐carborane cage in place of the benzene ring of phenylalanine. It is obtained by the reaction of derivatives of propargylglycine with decaborane. Possibilities of practical application derive from the facile neutron activation of boron nuclei with mass number 10.
Learning object-specific grasp affordance densities (2009)

This paper addresses the issue of learning and representing object grasp affordances, i.e. object-gripper relative configurations that lead to successful grasps. The purpose of grasp affordances is to organize and store the whole knowledge that an agent has about the grasping of an object, in order to facilitate reasoning on grasping solutions and their achievability. The affordance representation consists in a continuous probability density function defined on the 6D gripper pose space - 3D position and orientation -, within an object-relative reference frame. Grasp affordances are initially learned from various sources, e.g. from imitation or from visual cues, leading to grasp hypothesis densities. Grasp densities are attached to a learned 3D visual object model, and pose estimation of the visual model allows a robotic agent to execute samples from a grasp hypothesis density under various object poses. Grasp outcomes are used to learn grasp empirical densities, i.e. grasps that have been confirmed through experience. We show the result of learning grasp hypothesis densities from both imitation and visual cues, and present grasp empirical densities learned from physical experience by a robot.
Photometric Properties of Retroreflective Materials in Dependence on their Structure and Angle of Illumination (2019)

The purpose of high visibility products is to reflect light at a low angle towards the source, such as vehicle headlights. The article presents measurements of the photometric properties of selected retroreflective materials made either of microlenses on a textile base or microprisms on a polymer base. The effects of the structure of the textile and polymer layers on the photometric properties of high visibility materials is analysed and the test methods applied are described.
Major Histocompatibility Complex Class I Viral Antigen Processing in the Secretory Pathway Defined by the <i>trans</i>-Golgi Network Protease Furin (1998)

Classical antigen presentation by major histocompatibility complex class I molecules involves cytosolic processing of endogenously synthesized antigens by proteasomes and translocation of processed peptides into the endoplasmic reticulum (ER) by transporters associated with antigen presentation (TAP). Alternative pathways for processing of endogenous antigens, generally involving the ER, have been suggested but not fully proved. We analyzed the potential for class I presentation of proteolytic maturation of secretory antigens in the exocytic pathway. We found that hepatitis B (HB) virus secretory core protein HBe can efficiently deliver COOH-terminally located antigenic peptides for endogenous class I loading in the absence of TAP. Antigen presentation to specific cytotoxic T lymphocytes correlates with protein maturation at the COOH terminus, since modification of maturation and transport of HBe through the secretory pathway alters antigen presentation. Both maturation and a necessary processing step occur in the Golgi or post-Golgi compartment. Antigen presentation is independent of proteasome activity, but inhibitors of the trans-Golgi network resident protease furin inhibit both HBe maturation and antigen presentation. These results define a new antigen processing pathway located in the secretory route, with a central role for proteolytic maturation mediated by the subtilisin protease family member furin as an efficient source for antigen presentation.
Application of Multi-agent System in a Microgrid (2008)

In order to improve the efficiency and reliability of the microgrid,a multi-agent based control framework is presented.Then,a three-layer multi-agent control system,including main grid agents,microgrid agents and component agents,is established.Accordingly,the special functions and control strategies of each agent are discussed in detail.A simulation example of a particular microgrid based on the multi-agent system(MAS) is performed to demonstrate that the efficiency and reliability of the microgrid can be improved by using MAS.
[Kinetic characteristics of Cd2+ desorption in minerals and soils under simulated acid rain]. (2004)

The kinetic characteristics of Cd2+ desorption in minerals and soils under simulated acid rain were studied by using the flow-stirred method. It showed that Cd2+ desorption could be described by first-order kinetics. Percents of desorption amounts of Cd2+ calculated were 70%-100% in red soil and goethite, and 25%-50% in latosols and kaolinite. Parabolic diffusion could describe Cd2+ desorption kinetics in latosols and not suitable for red soil and goethite and kaolinite. Cd2+ desorption, regarded as a heterogeneous diffusion in minerals and soils, could be fitted by Elovich equation more than Parabolic diffusion and two-constant equation. Cd2+ desorption could be divided into fast reaction and slow reaction. Except for latosols, fast reaction would be over during 60 min and be close to quasi-equilibrium. Adsorption forms of Cd2+ in soil surface could be exchangeable and specific. Fast reaction was relative to easily desorbed Cd2+. The affinity of edge hydroxyl to Cd2+ would lead to the difference of Cd2+ desorption rate and amounts. Increase of pH value in effluent indicated H+ consumption in the processes of Cd2+ desorption.
Automatic generation of efficient array redistribution routines for distributed memory multicomputers (2002)

Appropriate data distribution has been found to be critical for obtaining good performance on Distributed Memory Multicomputers like the CM-5, Intel Paragon and IBM SP-1. It has also been found that some programs need to change their distributions during execution for better performance (redistribution). This work focuses on automatically generating efficient routines for redistribution. We present a new mathematical representation for regular distributions called PITFALLS and then discuss algorithms for redistribution based on this representation. A significant contribution of this work is the ability to handle arbitrary source and target processor sets while performing redistribution; another is the ability to handle arbitrary dimensionality for the array being redistributed in a sealable manner. The results presented show low overheads for our redistribution algorithm as compared to naive runtime methods.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Convergence of isoprene and polyketide biosynthetic machinery: Isoprenyl- <i>S</i> -carrier proteins in the <i>pksX</i> pathway of <i>Bacillus subtilis</i> (2006)

The pksX gene cluster from Bacillus subtilis is predicted to encode the biosynthesis of an as yet uncharacterized hybrid nonribosomal peptide/polyketide secondary metabolite. We used a combination of biochemical and mass spectrometric techniques to assign functional roles to the proteins AcpK, PksC, PksL, PksF, PksG, PksH, and PksI, and we conclude that they act to incorporate an acetate-derived beta-methyl branch on an acetoacetyl-S-carrier protein and ultimately generate a Delta(2)-isoprenyl-S-carrier protein. This work highlights the power of mass spectrometry to elucidate the functions of orphan biosynthetic enzymes, and it details a mechanism by which single-carbon beta-branches can be inserted into polyketide-like structures. This pathway represents a noncanonical route to the construction of prenyl units and serves as a prototype for the intersection of isoprenoid and polyketide biosynthetic manifolds in other natural product biosynthetic pathways.
Determination of the spatial distribution of a physical parameter from the distribution of another physical variable— a differential inverse problem (1996)

We propose a new type of inverse problem, in which the spatial distribution of the relative value of a physical parameter can be determined only from the distribution of another physical variable in the region of interest if there is no source in that region. The inverse problem proposed here has two features different from conventional remote probing type problems. One is that the physical variable data are given throughout the region of interest although the number of data variables is insufficient to determine directly the physical parameter of interest, while only remote data are given in a conventional problem. The other is the mathematical structure of the inverse problem: this new inverse problem yields a spatial differential equation on the target parameter, while the conventional problem becomes an integral equation on the target parameter. To show the nature of the problem, we formulated an illustrative inverse problem on the steady-state electric current field, in which the spatial distribution of the relative conductivity can be determined from the distribution of either the potential or the current density. We give examples of computational results obtained when using the simulated potential data and the current density data. This proposed formalism for a new type of inverse problem could provide a new approach and open up new measurement schemes in many fields of science and engineering.
New Software for Processing of LWD Extradeep Resistivity and Azimuthal Resistivity Data (2014)

Summary In petroleum exploration, reservoir navigation is used for reaching a productive reservoir and placing the borehole optimally inside the reservoir to maximize production. For proper well placement, it is necessary to calculate in real-time the parameters of the formation we are drilling in and the parameters of formations we are approaching. On the basis of these results, a decision to change the direction of drilling could be made. Modern logging-while-drilling (LWD) extra-deep and azimuthal resistivity tools acquire multicomponent, multispacing, and multifrequency data that provide sufficient information for resolving the surrounding formation parameters. These tools are generally used for reservoir navigation and real-time formation evaluation. However, real-time interpretation software is very often based on simplified resistivity models that can be inadequate and lead to incorrect geosteering decisions. The core of the newly developed software is an inversion algorithm based on transversely isotropic layered Earth with an arbitrary number of layers. The following model parameters are determined in real time: horizontal and vertical resistivities and thickness of each layer, formation dip, and azimuth. The inversion algorithm is based on the method of the most-probable parameter combination. The algorithm has good performance and excellent convergence because of its enhanced capability of avoiding local minima. This capability enables interpretation of real-time resistivity data, including azimuthal and extra-deep measurements. A graphical user interface (GUI) was developed to provide an interactive environment for each stage of the resistivity data interpretation process: preview of input resistivity logs, initial preprocessing and filtering of raw data, creation of initial guess, running inversion and viewing inversion results, and quality-control indicators. Applications of the developed software will be shown on a series of synthetic examples and field data from the North Sea and Gulf of Mexico (GOM). This newly developed software is currently in use for real-time reservoir navigation and post-well analysis.
A classical experiment revisited: The bounce of balls and superballs in three dimensions (2004)

A description of the inelastic collision of a ball when it bounces on a rigid horizontal surface with arbitrary initial spin conditions is presented. I consider cases where rebound occurs with and without sliding, and when the ball grips the surface. Two rebound models are discussed in which friction is described in terms of the static and dynamic coefficients of friction and the friction is expressed in terms of horizontal coefficients of restitution. The azimuthal and vertical deviation angles of the ball after impact are predicted as a function of the incident angle. We present data from an experiment in which a ball is launched horizontally from the edge of the laboratory bench and then rebounds on a horizontal surface. Ordinary balls exhibit two rebound regimes, with and without sliding, and can be satisfactorily described by the first model. Superballs exhibit a grip behavior whose description requires the use of the second model.
Transforming growth factor‐β induces loss of epithelial character and smooth muscle cell differentiation in epicardial cells (2005)

During embryogenesis, epicardial cells undergo epithelial-mesenchymal transformation (EMT), invade the myocardium, and differentiate into components of the coronary vasculature, including smooth muscle cells. We tested the hypothesis that transforming growth factor-beta (TGFbeta) stimulates EMT and smooth muscle differentiation of epicardial cells. In epicardial explants, TGFbeta1 and TGFbeta2 induce loss of epithelial morphology, cytokeratin, and membrane-associated Zonula Occludens-1 and increase the smooth muscle markers calponin and caldesmon. Inhibition of activin receptor-like kinase (ALK) 5 blocks these effects, whereas constitutively active (ca) ALK5 increases cell invasion by 42%. Overexpression of Smad 3 did not mimic the effects of caALK5. Inhibition of p160 rho kinase or p38 MAP kinase prevented the loss of epithelial morphology in response to TGFbeta, whereas only inhibition of p160 rho kinase blocked TGFbeta-stimulated caldesmon expression. These data demonstrate that TGFbeta stimulates loss of epithelial character and smooth muscle differentiation in epicardial cells by means of a mechanism that requires ALK5 and p160 rho kinase.
Myeloid Cells and Related Chronic Inflammatory Factors as Novel Predictive Markers in Melanoma Treatment with Ipilimumab (2015)

These findings highlight additional mechanisms of ipilimumab effects and suggest levels of eosinophils, MDSCs, as well as related inflammatory factors S100A8/A9 and HMGB1 as novel complex predictive markers for patients who may benefit from the ipilimumab therapy. Clin Cancer Res; 21(24); 5453-9. ©2015 AACR.
Strategies for the management of haemorrhage following pelvic fractures and associated trauma-induced coagulopathy (2014)

Exsanguination is the second most common cause of death in patients who suffer severe trauma. The management of haemodynamically unstable high-energy pelvic injuries remains controversial, as there are no universally accepted guidelines to direct surgeons on the ideal use of pelvic packing or early angio-embolisation. Additionally, the optimal resuscitation strategy, which prevents or halts the progression of the trauma-induced coagulopathy, remains unknown. Although early and aggressive use of blood products in these patients appears to improve survival, over-enthusiastic resuscitative measures may not be the safest strategy. This paper provides an overview of the classification of pelvic injuries and the current evidence on best-practice management of high-energy pelvic fractures, including resuscitation, transfusion of blood components, monitoring of coagulopathy, and procedural interventions including pre-peritoneal pelvic packing, external fixation and angiographic embolisation.
Microfabrication of Interdigitated Polyaniline/Polymethylene Patterns on a Gold Surface (1998)

Micrometer scale patterns of polymethylene film was prepared by selective formation of polymethylene on a gold surface patterned with an organothiol monolayer as the resist. The monolayer effectively retarded the gold-catalyzed polymerization reaction from diazomethane. The polymethylene film, in the thickness range of 300−400 Å, in turn serves as a stable resist in preventing electrochemical polymerization of polyaniline on the covered area. Selective deposition was thus achieved to give interdigitated patterns of conducting and insulating polymer films.
Damage to Skeletal Muscle from Eccentric Exercise (2005)

Evidence is provided for a mechanical event as the first step in the process leading to muscle damage after a series of eccentric contractions. Aspects discussed include the decline in active tension, increase in passive tension, shift in length-tension relation, soreness, swelling, and disturbed proprioception.
Vacuolar transport of nicotine is mediated by a multidrug and toxic compound extrusion (MATE) transporter in <i>Nicotiana tabacum</i> (2009)

Alkaloids play a key role in plant defense mechanisms against pathogens and herbivores, but the plants themselves need to cope with their toxicity as well. The major alkaloid of the Nicotiana species, nicotine, is translocated via xylem transport from the root tissues where it is biosynthesized to the accumulation sites, the vacuoles of leaves. To unravel the molecular mechanisms behind this membrane transport, we characterized one transporter, the tobacco (Nicotiana tabacum) jasmonate-inducible alkaloid transporter 1 (Nt-JAT1), whose expression was coregulated with that of nicotine biosynthetic genes in methyl jasmonate-treated tobacco cells. Nt-JAT1, belonging to the family of multidrug and toxic compound extrusion transporters, was expressed in roots, stems, and leaves, and localized in the tonoplast of leaf cells. When produced in yeast cells, Nt-JAT1 occurred mainly in the plasma membrane and showed nicotine efflux activity. Biochemical analysis with proteoliposomes reconstituted with purified Nt-JAT1 and bacterial F(0)F(1)-ATPase revealed that Nt-JAT1 functioned as a proton antiporter and recognized endogenous tobacco alkaloids, such as nicotine and anabasine, and other alkaloids, such as hyoscyamine and berberine, but not flavonoids. These findings strongly suggest that Nt-JAT1 plays an important role in the nicotine translocation by acting as a secondary transporter responsible for unloading of alkaloids in the aerial parts and deposition in the vacuoles.
Expression of nuclear factor-kB and COX-2 and their role in experimental allergic encephalomyelitis in rabbits (2008)

Objective To study the expression of nuclear factor-κB （NF-KB） and COX-2 and their relationship in experimental allergic encephalomyelitis （EAE）, and investigate their role in the pathogenesis of EAE. Methods All rabbits were classified three groups in according to making models by different immunogens： group A is immuned without immunogen, group B is immuned with R-SCH, group C is immuned with C-SCH. Immunofluorescence and imrnunohistochemistry were performed for morphological observations of the brain tissues in all animals, and then the activity of NF-κBp65 was detected using enzyme-linked immunosorbent assay. Results The expressions of NF-κBp65 and COX-2 were observed in brain issues with EAE. Significant differences were found in the number of cells positive for NF-κBp65 and COX-2 between EAE groups and the control group. NF-KBp65 and COX-2 expressions were associated with the symptoms of EAE. In addition, significantly increased activity of NF-κBp65 was noted in EAE, which is immuned with R-SCH. Conclusion NF-KB and COX-2 are expressed in rabbits with EAE and play important roles in the pathogenesis of EAE.

Key words: 
Experimental allergic encephalomyelitis;  Nucleus transfer factor;  Cyclooxygenase-2