gebhart/patrepeval huggingface dataset:
Remote Manipulation of Ligand Nano-Oscillations Regulates Adhesion and Polarization of Macrophages in Vivo (2017)

Macrophages play crucial roles in various immune-related responses, such as host defense, wound healing, disease progression, and tissue regeneration. Macrophages perform distinct and dynamic functions in vivo, depending on their polarization states, such as the pro-inflammatory M1 phenotype and pro-healing M2 phenotype. Remote manipulation of the adhesion of host macrophages to the implants and their subsequent polarization in vivo can be an attractive strategy to control macrophage polarization-specific functions but has rarely been achieved. In this study, we grafted RGD ligand-bearing superparamagnetic iron oxide nanoparticles (SPIONs) to a planar matrix via a long flexible linker. We characterized the nanoscale motion of the RGD-bearing SPIONs grafted to the matrix, in real time by in situ magnetic scanning transmission electron microscopy (STEM) and in situ atomic force microscopy. The magnetic field was applied at various oscillation frequencies to manipulate the frequency-dependent ligand nano-oscillation speeds of the RGD-bearing SPIONs. We demonstrate that a low oscillation frequency of the magnetic field stimulated the adhesion and M2 polarization of macrophages, whereas a high oscillation frequency suppressed the adhesion of macrophages but promoted their M1 polarization, both in vitro and in vivo. Macrophage adhesion was also temporally regulated by switching between the low and high frequencies of the oscillating magnetic field. To the best of our knowledge, this is the first demonstration of the remote manipulation of the adhesion and polarization phenotype of macrophages, both in vitro and in vivo. Our system offers the promising potential to manipulate host immune responses to implanted biomaterials, including inflammation or tissue reparative processes, by regulating macrophage adhesion and polarization.
Wavelength Multiplexed Computer Generated Volume Holography (1993)

We demonstrate the first experiment of multiple-storage of computer generated holograms (CGHs) in a volume holographic storage medium.
Environment representations for automated on-road vehicles (2018)

Abstract One of the key challenges of any Automated Driving (AD) system lies in the perception and representation of the driving environment. Data from a multitude of different information sources such as various vehicle environment sensors, external communication interfaces, and digital maps must be adequately combined to one consistent Comprehensive Environment Model (CEM) that acts as a generic abstraction layer for the driving functions. This overview article summarizes and discusses different approaches in this area with a focus on metric representations of static and dynamic driving environments for on-road AD systems. Feature maps, parametric free space maps, interval maps, occupancy grid maps, elevation maps, the stixel world, multi-level surface maps, voxel grids, meshes, and raw sensor data models are presented and compared in this regard.
InfoScale 2008: The Third International ICST Conference on Scalable Information Systems (2008)

Scalability is the key word for today's modern software architectures. As data and knowledge volume keep increasing while global means for information dissemination continue to diversify, new methods, modeling paradigms, and structures are needed to efficiently support the mounting scalability requi
Self-Organizing Materials with Low Surface Energy:  The Synthesis and Solid-State Properties of Semifluorinated Side-Chain Ionenes (1997)

The synthesis of new semifluorinated alkyl side-chain ionenes (SFASI) is reported and involves reaction of semifluorinated 1-bromoalkanes with poly(N,N ‘-dimethyl-1,6-hexanediamine) (PDHD) which was prepared by reduction of poly(N,N‘-dimethylhexamethyleneadipamide). The quaternization efficiency of the polyamine is 80−85% when carried out using a solvent mixture of DMF/ethanol (1/2 volume ratio) at 65 °C over long reaction times. The structure of SFASI consists of a 10 Å charged layer resulting from quarternary ammonium groups with strong coulombic interactions and a smectic B-like packing of the semifluorinated side-chain layer. The perfluorocarbon segments favor self-organization in a hexagonal array to form a head-to-head bilayer between the charged layers. These ionenes exhibit a smectic to isotropic transition, with the transition temperature dominated by the length of the fluorocarbon side chain. The surface energy of a spin-coated SFASI film, as estimated from the critical surface tension, was as low as 8 dyn/cm at 20 °C. This result indicates that the surface of the as-spun cast film consists largely of CF3 end groups even though hydrophilic ammonium groups are present in the polymer. The surface segregation and orientation of the low surface energy mesogenic semiflorinated side groups were confirmed by X-ray photoelectron spectroscopy (XPS) and near-edge X-ray fine structure (NEXAFS) analysis. Surface reconstruction was observed due to polymer chain defects and surface mobility.
Toward the Establishment of Standardizedin VitroTests for Lipid-Based Formulations. 2. The Effect of Bile Salt Concentration and Drug Loading on the Performance of Type I, II, IIIA, IIIB, and IV Formulations duringin VitroDigestion (2012)

The LFCS Consortium was established to develop standardized in vitro tests for lipid-based formulations (LBFs) and to examine the utility of these tests to probe the fundamental mechanisms that underlie LBF performance. In this publication, the impact of bile salt (sodium taurodeoxycholate, NaTDC) concentration and drug loading on the ability of a range of representative LBFs to generate and sustain drug solubilization and supersaturation during in vitro digestion testing has been explored and a common driver of the potential for drug precipitation identified. Danazol was used as a model poorly water-soluble drug throughout. In general, increasing NaTDC concentrations increased the digestion of the most lipophilic LBFs and promoted lipid (and drug) trafficking from poorly dispersed oil phases to the aqueous colloidal phase (AP(DIGEST)). High NaTDC concentrations showed some capacity to reduce drug precipitation, although, at NaTDC concentrations ≥3 mM, NaTDC effects on either digestion or drug solubilization were modest. In contrast, increasing drug load had a marked impact on drug solubilization. For LBFs containing long-chain lipids, drug precipitation was limited even at drug loads approaching saturation in the formulation and concentrations of solubilized drug in AP(DIGEST) increased with increased drug load. For LBFs containing medium-chain lipids, however, significant precipitation was evident, especially at higher drug loads. Across all formulations a remarkably consistent trend emerged such that the likelihood of precipitation was almost entirely dependent on the maximum supersaturation ratio (SR(M)) attained on initiation of digestion. SR(M) defines the supersaturation "pressure" in the system and is calculated from the maximum attainable concentration in the AP(DIGEST) (assuming zero precipitation), divided by the solubility of the drug in the colloidal phases formed post digestion. For LBFs where phase separation of oil phases did not occur, a threshold value for SR(M) was evident, regardless of formulation composition and drug solubilization reduced markedly above SR(M) > 2.5. The threshold SR(M) may prove to be an effective tool in discriminating between LBFs based on performance.
Multiple Forms of Human Tumor Calcitonin Demonstrated by Denaturing Polyacrylamide Gel Electrophoresis and Lectin Affinity Chromatography* (1981)

The molecular weight forms of immunoreactive calcitonin in human tumors have been studied using two sodium dodecyl sulfate polyacrylamide gel electrophoretic systems. Under denaturing conditions, which produce monomer peptides, it has been possible to document further the size heterogeneity of this immunoreactivity. Small molecular weight forms (native size human calcitonin of 3,600 daltons and immunoreactive peptides of 4,000–6,000 daltons) predominated in extracts of four medullary thyroid carcinomas. Smaller amounts of larger molecular weight forms (8,000–22,000 daltons) were detected. In one medullary thyroid carcinoma and in an extract of small (oat) cell lung carcinoma, the higher molecular weight forms predominated, with the greatest amount of immunoreactivity found in 12,000–and 10,000-dalton peptides. Evidence has been obtained that all of the tumors studied contain a component of immunoreactive calcitonin that binds to lectins immobilized on agarose. Five to 20% of the total immunoreactive material from the medullary thyroid carcinomas and from human small (oat) cell lung carcinoma bound to columns of agarose-bound Concanavalin A and/or wheat germ agglutinin. The conditions of binding and elution with specific sugars strongly suggest that this lectinbound immunoreactive calcitonin may contain mannose and Nacetylglucosamine residues. Gel electrophoresis of the carbohydrate-eluted material showed that the lectin-bound forms comprise a portion of each of the several molecular weight classes of immunoreactive calcitonin moieties identified. These studies indicate further that human tumors contain different sizes of calcitonin immunoreactivity and that the ratios among these forms may vary among different neoplasms. The fact that some calcitonin forms may contain carbohydrate moieties is another potential determinant for the heterogeneity of the circulating immunoreactive calcitonin in patients with medullary thyroid carcinoma or small (oat) cell lung cancer.
Sphingosine mediates FTY720-induced apoptosis in LLC-PK1 cells (2004)

FTY720, a synthetic sphingoid base analog, was examined as a new sphingosine kinase inhibitor, which converts endogenous sphingosine into its phosphate form. With 20 microM of FTY720, sphingosine accumulated in the LLC-PK(1) cells in a time- and dose-dependent manner. The FTY720 treated cells showed a high concentration of fragmented DNA, a high caspase-3 like activity and TUNEL staining cells. It was also found that the sphingosine and sphinganine level increased in a time- and dose-dependent manner within 12 h after the FTY720 treatment. The sphingosine kinase activity was reduced by FTY720 as much as other sphingosine kinase inhibitors, N, N-dimethylsphingosine (DMS), dl-threo-dihydrosphingosine (DHS). The fragmented DNA content as a result of the 20 microM of FTY720 treatment and by 5 microM of the exogenously added BSA-sphingosine complex indicated typical apoptosis. Under similar conditions, the accumulated sphingosine concentration in all the cells was almost identical even though the sphingosine distribution inside the cells was somewhat different. These results indicate that the FTY720 induced apoptosis is associated with the inhibition of the sphingosine kinase activity and is strongly associated with the successive accumulation of sphingosine.
Vpx requires active cellular dNTP biosynthesis to effectively counteract the anti-lentivirus activity of SAMHD1 in macrophages (2023)

HIV-1 replication in primary monocyte-derived macrophages (MDMs) is kinetically restricted at the reverse transcription step due to the low deoxynucleoside triphosphates (dNTP) pools established by host dNTPase, SAM and HD domain containing protein 1 (SAMHD1). Lentiviruses such as HIV-2 and some Simian immunodeficiency virus counteract this restriction using viral protein X (Vpx), which proteosomally degrades SAMHD1 and elevates intracellular dNTP pools. However, how dNTP pools increase after Vpx degrades SAMHD1 in nondividing MDMs where no active dNTP biosynthesis is expected to exists remains unclear. In this study, we monitored known dNTP biosynthesis machinery during primary human monocyte differentiation to MDMs and unexpectedly found MDMs actively express dNTP biosynthesis enzymes such as ribonucleotide reductase, thymidine kinase 1, and nucleoside-diphosphate kinase. During differentiation from monocytes the expression levels of several biosynthesis enzymes are upregulated, while there is an increase in inactivating SAMHD1 phosphorylation. Correspondingly, we observed significantly lower levels of dNTPs in monocytes compared to MDMs. Without dNTP biosynthesis availability, Vpx failed to elevate dNTPs in monocytes, despite SAMHD1 degradation. These extremely low monocyte dNTP concentrations, which cannot be elevated by Vpx, impaired HIV-1 reverse transcription in a biochemical simulation. Furthermore, Vpx failed to rescue the transduction efficiency of a HIV-1 GFP vector in monocytes. Collectively, these data suggest that MDMs harbor active dNTP biosynthesis and Vpx requires this dNTP biosynthesis to elevate dNTP levels to effectively counteract SAMHD1 and relieve the kinetic block to HIV-1 reverse transcription in MDMs.
Unsupervised Learning for Nonlinear PieceWise Smooth Hybrid Systems (2017)

This paper introduces a novel system identification and tracking method for PieceWise Smooth (PWS) nonlinear stochastic hybrid systems. We are able to correctly identify and track challenging problems with diverse dynamics and low dimensional transitions. We exploit the composite structure system to learn a simpler model on each component/mode. We use Gaussian Process Regression techniques to learn smooth, nonlinear manifolds across mode transitions, guard-regions, and make multi-step ahead predictions on each mode dynamics. We combine a PWS non-linear model with a particle filter to effectively track multi-modal transitions. We further use synthetic oversampling techniques to address the challenge of detecting mode transition which is sparse compared to mode dynamics. This work provides an effective form of model learning in a complex hybrid system, which can be useful for future integration in a reinforcement learning setting. We compare multi-step prediction and tracking performance against traditional dynamical system tracking methods, such as EKF and Switching Gaussian Processes, and show that this framework performs significantly better, being able to correctly track complex dynamics with sparse transitions.
Electrospun Conjugated Polymer/Fullerene Hybrid Fibers: Photoactive Blends, Conductivity through Tunneling-AFM, Light Scattering, and Perspective for Their Use in Bulk-Heterojunction Organic Solar Cells (2018)

Hybrid conjugated polymer/fullerene filaments based on MEH-PPV/PVP/PCBM were prepared by electrospinning, and their properties were assessed by scanning electron, atomic and lateral-force, tunneling, and confocal microscopies, as well as by attenuated-total-reflection Fourier transform infrared spectroscopy, photoluminescence quantum yield, and spatially resolved fluorescence. Highlighted features include the ribbon shape of the realized fibers and the persistence of a network serving as a template for heterogeneous active layers in solar cell devices. A set of favorable characteristics is evidenced in this way in terms of homogeneous charge-transport behavior and formation of effective interfaces for diffusion and dissociation of photogenerated excitons. The interaction of the organic filaments with light, exhibiting specific light-scattering properties of the nanofibrous mat, might also contribute to spreading incident radiation across the active layers, thus potentially enhancing photovoltaic performance. This method might be applied to other electron donor-electron acceptor material systems for the fabrication of solar cell devices enhanced by nanofibrillar morphologies embedding conjugated polymers and fullerene compounds.
Heparan Sulfate Facilitates Rift Valley Fever Virus Entry into the Cell (2012)

Rift Valley fever virus (RVFV), an emerging arthropod-borne pathogen, has a broad host and cell tropism. Here we report that the glycosaminoglycan heparan sulfate, abundantly present on the surface of most animal cells, is required for efficient entry of RVFV. Entry was significantly reduced by preincubating the virus inoculum with highly sulfated heparin, by enzymatic removal of heparan sulfate from cells and in cells genetically deficient in heparan sulfate synthesis.
Stark erhöhte Affinität modifizierter Oligonucleotide mit in ihrer Konformation eingeschränkten Furanose‐Ringen für komplementäre RNA‐Stränge (1996)

Eine erhöhte Stabilität von Duplices zwischen amidmodifizierten Oligonucleotiden (siehe rechts) und RNA wird durch Einführen von 2′‐OMe‐Gruppen erreicht. Da die modifizierten Oligonucleotide eine sehr hohe Affinität zur komplementären RNA aufweisen und erheblich stabiler gegenüber Nucleasen sind, konnten sie als Antisense‐Reagentien verwendet werden. × = H, OH, OMe; Y = H, OMe. magnified image
In vivo imaging reveals that pregabalin inhibits cortical spreading depression and propagation to subcortical brain structures (2017)

Migraine is characterized by severe headaches that can be preceded by an aura likely caused by cortical spreading depression (SD). The antiepileptic pregabalin (Lyrica) shows clinical promise for migraine therapy, although its efficacy and mechanism of action are unclear. As detected by diffusion-weighted MRI (DW-MRI) in wild-type (WT) mice, the acute systemic administration of pregabalin increased the threshold for SD initiation in vivo. In familial hemiplegic migraine type 1 mutant mice expressing human mutations (R192Q and S218L) in the Ca<sub>V</sub>2.1 (P/Q-type) calcium channel subunit, pregabalin slowed the speed of SD propagation in vivo. Acute systemic administration of pregabalin in vivo also selectively prevented the migration of SD into subcortical striatal and hippocampal regions in the R192Q strain that exhibits a milder phenotype and gain of Ca<sub>V</sub>2.1 channel function. At the cellular level, pregabalin inhibited glutamatergic synaptic transmission differentially in WT, R192Q, and S218L mice. The study describes a DW-MRI analysis method for tracking the progression of SD and provides support and a mechanism of action for pregabalin as a possible effective therapy in the treatment of migraine.
Rippled-Field Magnetron with a Transparent Cathode (2018)

The rippled field magnetron is a source of millimeter-wave radiation theoretically described and experimentally verified by Bekefi [1]. It uses an array of azimuthally periodic permanent magnets to modulate electrons and allow them to become synchronous with a fast TM or TE electromagnetic mode in a smooth interaction space. The azimuthally periodic permanent magnets create an azimuthally periodic magnetic field (wiggler). Due to the radial component of the wiggler B <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">r</inf> , electrons undergoing an azimuthal <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$\text{ve}=\mathrm{E}_{\mathrm{r}}\text{xH}$</tex> , drift will experience an extra force <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$\mathrm{v}\theta\text{xB}_{\mathrm{r}},$</tex> causing them to oscillate in the axial direction and bunching them in the azimuthal direction.
Generation of Large Insert YAC Libraries (2003)

The introduction of yeast artificial chromosomes (YACs) as cloning vectors in 1987 has significantly advanced the analysis of complex genomes (1). The capability of cloning large DNA (100–2000 kb) as YACs has accelerated the construction of physical maps and contig building (a contiguous set of overlapping clones). YAC contigs now cover entire human chromosomes (i.e., Y and 21) (2,3) and small genomes (i.e., Schizo-saccharomyces pombe) (4), and large YAC contigs cover much of the human genome (5). The main advantages of YACs over prokaryotic-based cloning systems are their large insert capacity and ability to maintain sequences that are unstable or not well represented in bacteriophage or cosmid genomic libraries (6). Therefore, YACs complement existing cloning vectors (cosmids, bacteriophage) and new cloning vectors (PI bacteriophage [PI], bacterial artificial chromosomes [BACs], and PI-derived artificial chromosomes [PACs]; for review, see ref. 7) in mapping and chromosome walking projects (6,8).
Choosing the Device Generator and Leads (2021)

This chapter provides a brief summary of the algorithm generally used for deciding which pulse generator, mode selection, and leads are to be used. It points out specific issues relevant to physiological conduction system pacing and cardiac resynchronization devices. The chapter also provides direction in choosing the most appropriate pulse generator – pacemaker, internal cardioverter-defibrillator or cardiac resynchronization therapy – and leads for a given patient. The chapter aims to provide practical considerations and a generic approach to determine the type of hardware most appropriate for the patient who is receiving an implantable cardiac device. If a patient requires pacing for neurocardiogenic syncope, whether the vasovagal variety or carotid sinus hypersensitivity, dual-chamber pacing is necessary for several reasons. Using a dual-chamber pacemaker with rate-adaptive capabilities in all patients provides the greatest long-term flexibility, and most patients with symptomatic bradycardia often have associated chronotropic incompetence, or at least the potential for this to occur.
Improving Pointing in Graphical User Interfaces for People with Motor Impairments Through Ability-Based Design (2013)

Pointing to targets in graphical user interfaces remains a frequent and fundamental necessity in modern computing systems. Yet for millions of people with motor impairments, children, and older users, pointing—whether with a mouse cursor, a stylus, or a finger on a touch screen—remains a major access barrier because of the fine-motor skills required. In a series of projects inspired by and contributing to ability-based design, we have reconsidered the nature and assumptions behind pointing, resulting in changes to how mouse cursors work, the types of targets used, the way interfaces are designed and laid out, and even how input devices are used. The results from these explorations show that people with motor difficulties can acquire targets in graphical user interfaces when interfaces are designed to better match the abilities of their users. Ability-based design, as both a design philosophy and a design approach, provides a route to realizing a future in which people can utilize whatever abilities they have to express themselves not only to machines, but to the world.
Extracorporeal Membrane Oxygenation and the Kidney (2015)

AKI is frequently observed in patients supported with ECMO. The pathophysiology of the associated AKI is chiefly related to a reduction in renal oxygen delivery and/or to inflammatory damage. Risk factors for AKI are associated with a patient's underlying disease and ECMO-related conditions.
Lassa Fever in Post-Conflict Sierra Leone (2014)

Lassa fever remains a major public health threat in Sierra Leone. Outreach activities should expand because LF may be more widespread in Sierra Leone than previously recognized. Enhanced case finding to ensure rapid diagnosis and treatment is imperative to reduce mortality. Even with ribavirin treatment, there was a high rate of fatalities underscoring the need to develop more effective and/or supplemental treatments for LF.