gebhart/patrepeval huggingface dataset:
In Vivo Safety Evaluation of Polyarginine Coated Magnetic Nanovectors (2013)

Safety and efficacy are of critical importance to any nanomaterial-based diagnostic and therapy. The innocuity and functionality of a nanomaterial in vivo is largely dependent on the physicochemical properties of the material, particularly its surface coating. Here, we evaluated the influence of polycationic coating on the efficacy, clearance organ uptake, and safety of magnetic nanovectors designed for siRNA delivery. Polyethylene glycol (PEG) coated superparamagnetic iron oxide nanoparticles (NPs) of 12 nm in core diameter were modified with a polycationic coating of either poly-l-arginine (pArg) or polyethylenimine (PEI) and further covalently functionalized with siRNA oligonucleotides. The produced NP-pArg-siRNA and NP-PEI-siRNA nanovectors were similar in hydrodynamic size (21 and 22 nm, respectively) but significantly differed in zeta potentials (+2.1 mV and +29.8 mV, respectively). Fluorescence quantification assays revealed that the NP-pArg-siRNA nanovector was 3-fold more potent than NP-PEI-siRNA in delivering siRNA and 1.8-fold more effective in gene silencing when tested in rat C6 glioblastoma cells. In vivo, both nanovector formulations were similarly taken up by the spleen and liver as determined by histopathological and hemopathological assays. However, PEI coated nanovectors elicited severe hemoincompatibility and damage to the liver and spleen, while pArg coated nanovectors were found to be safe and tolerable. Combined, our findings suggest that polycationic coatings of pArg were more effective and safer than commonly used PEI coatings for preparation of nanovectors. The NP-pArg-siRNA nanovector formulation developed here shows great potential for in vivo based biomedical applications.
Generation of high harmonics from silicon (2016)

We generate high-order harmonics of a mid-infrared laser from a silicon single crystal and find their origin in the recollision of coherently accelerated electrons with their holes, analogously to the atomic and molecular case, and to ZnO [Vampa et al., Nature 522, 462-464 (2015)], a direct bandgap material. Therefore indirect bandgap materials are shown to sustain the recollision process as well as direct bandgap materials. Furthermore, we find that the generation is perturbed with electric fields as low as 30 V/$μ$m, equal to the DC damage threshold. Our results extend high-harmonic spectroscopy to the most technologically relevant material, and open the possibility to integrate high harmonics with conventional electronics.
Immunostimulating Substances from Human Casein (1981)

Delipidated human casein was digested with trypsin and the enzymatic digest was fractionated on Sephadex G-50. The peptidic fractions were assayed for immunomodulating activity in two in vitro models. Fractions corresponding to molecular weights in the range of 2,000 +/- 600 were found to possess stimulating activity in these models.
Differences in Impact Performance of Bicycle Helmets During Oblique Impacts (2018)

Cycling is a leading cause of sport-related head injuries in the U.S. Although bicycle helmets must comply with standards limiting head acceleration in severe impacts, helmets are not evaluated under more common, concussive-level impacts, and limited data are available indicating which helmets offer superior protection. Further, standards evaluate normal impacts, while real-world cyclist head impacts are oblique-involving normal and tangential velocities. The objective of this study was to investigate differences in protective capabilities of ten helmet models under common real-world accident conditions. Oblique impacts were evaluated through drop tests onto an angled anvil at common cyclist head impact velocities and locations. Linear and rotational accelerations were evaluated and related to concussion risk, which was then correlated with design parameters. Significant differences were observed in linear and rotational accelerations between models, producing concussion risks spanning >50% within single impact configurations. Risk differences were more attributable to linear acceleration, as rotational varied less between models. At the temporal location, shell thickness, vent configuration, and radius of curvature were found to influence helmet effective stiffness. This should be optimized to reduce impact kinematics. At the frontal, helmet rim location, liner thickness tapered off for some helmets, likely due to lack of standards testing at this location. This is a frequently impacted location for cyclists, suggesting that the standards testable area should be expanded to include the rim. These results can inform manufacturers, standards bodies, and consumers alike, aiding the development of improved bicycle helmet safety.
Hyaluronan Mediates Ozone-induced Airway Hyperresponsiveness in Mice (2009)

Ozone is a common urban environmental air pollutant and significantly contributes to hospitalizations for respiratory illness. The mechanisms, which regulate ozone-induced bronchoconstriction, remain poorly understood. Hyaluronan was recently shown to play a central role in the response to noninfectious lung injury. Therefore, we hypothesized that hyaluronan contributes to airway hyperreactivity (AHR) after exposure to ambient ozone. Using an established model of ozone-induced airways disease, we characterized the role of hyaluronan in airway hyperresponsiveness. The role of hyaluronan in response to ozone was determined by using therapeutic blockade, genetically modified animals, and direct challenge to hyaluronan. Ozone-exposed mice demonstrate enhanced AHR associated with elevated hyaluronan levels in the lavage fluid. Mice deficient in either CD44 (the major receptor for hyaluronan) or inter-alpha-trypsin inhibitor (molecule that facilitates hyaluronan binding) show similar elevations in hyaluronan but are protected from ozone-induced AHR. Mice pretreated with hyaluronan-binding peptide are protected from the development of ozone-induced AHR. Overexpression of hyaluronan enhances the airway response to ozone. Intratracheal instillation of endotoxin-free low molecular weight hyaluronan induces AHR dependent on CD44, whereas instillation of high molecular weight hyaluronan protects against ozone-induced AHR. In conclusion, we demonstrate that hyaluronan mediates ozone-induced AHR, which is dependent on the fragment size and both CD44 and inter-alpha-trypsin inhibitor. These data support the conclusion that pulmonary matrix can contribute to the development of airway hyperresponsiveness.
A Slow Release CO2 for Enhanced Oil Recovery in Carbonate Reservoirs (2015)

Abstract CO2 is used to swell the oil and increase its mobility by reducing the viscosity and reducing the IFT between the rock and oil. The problem of CO2 during the EOR process is the gravity override and the displacement efficiency. Foamed CO2 was introduced to overcome the displacement efficiency problem. The foam can be generated using different types of surfactants. The surfactants will not from a stable foam at HPHT conditions and the reservoir water salinity will impact the foam quality in addition to the surfactant adsorption to the carbonate rocks will reduce the surfactant concentration and will affect the generated foam. In this study we will investigate the use of slow release CO2 concept. The CO2 can be slowly released in the carbonate reservoir by injecting low reaction rate fluids (in this case citric acid) that will react with the rock after placement and this will generate CO2. Coreflooding test will be performed using carbonate core at 100°C saturated with crude oil. CMG will be used to simulate the process of CO2 generation by injecting the CO2 in an aquifer underlying the carbonate formation and after that allow the CO2 to release to the oil zone. The slow released CO2 from the aquifer will swell the oil and then the oil can be displaced by sea water. Coreflooding results showed that the slow release CO2 technique gave up to 42 % extra oil recovery from the oil in place after sea water flooding into the carbonate core at 100°C and 1100 psi back pressure. The extra oil recovery was due to the slow resealed CO2 and oil swelling and also due to the rock dissolution and IFT reduction. The simulation results by CMG showed that the slow release CO2 technique gave 70% oil recovery from the residual oil more than the sea water injection which confirmed the efficiency of the slow release technique in large scale.
Addition of the keto functional group to the genetic code of <i>Escherichia</i> <i>coli</i> (2002)

Although the keto group is the most versatile of the functional groups in organic chemistry, it is absent in the genetically encoded amino acids. To overcome this natural limitation on protein biosynthesis, we have evolved an orthogonal tRNA-synthetase pair that makes possible the efficient incorporation of a keto amino acid, p-acetyl-l-phenylalanine, into proteins in E. coli with high translational fidelity in response to the amber nonsense codon. To demonstrate the utility of this keto amino acid, we have used it to modify a protein selectively with a small molecule fluorophore and biotin derivative. This additional genetically encoded amino acid should greatly expand our ability to manipulate protein structure and function both in vitro and in living cells.
Structure Formation in Electromagnetically Driven Granular Media (2005)

We report structure formation in submonolayers of magnetic microparticles subjected to periodic electrostatic and magnetic excitations. Depending on the excitation parameters, we observe the formation of a rich variety of structures: clusters, rings, chains, and networks. The dynamics and shapes of the structures are strongly dependent on the amplitude and frequency of the external magnetic field. We find that for pure ac magnetic driving the low-frequency magnetic excitation favors compact clusters, whereas high frequency driving favors chains and netlike structures. An abrupt phase transition from chains to a network phase was observed for a high density of particles.
A torque controller suitable for electric vehicles (1997)

A torque controller suitable for electric vehicles is studied. The controller ensures that an induction motor generates motor torque efficiently, stably and accurately. The torque control system feeds back an assumed motor torque calculated using the secondary magnetic flux and the torque current detected from current sensors of the primary currents. The motor torque is controlled by using the torque current reference determined from the generated secondary magnetic flux and the magnetizing current reference. The magnetizing current reference is determined on the basis of the torque current reference so that motor torque generation efficiency is always optimal. The magnetizing current regulator is operated according to the magnetizing current reference. This ensures the motor generates the motor torque stably even in transient states. Fundamental performance characteristics, such as response, accuracy and efficiency of the motor torque are verified by simulation and experiments. The torque controller is judged suitable for the drive system of electric vehicles.
Dissecting Therapeutic Resistance to RAF Inhibition in Melanoma by Tumor Genomic Profiling (2011)

A detailed understanding of the mechanisms by which tumors acquire resistance to targeted anticancer agents should speed the development of treatment strategies with lasting clinical efficacy. RAF inhibition in BRAF-mutant melanoma exemplifies the promise and challenge of many targeted drugs; although response rates are high, resistance invariably develops. Here, we articulate overarching principles of resistance to kinase inhibitors, as well as a translational approach to characterize resistance in the clinical setting through tumor mutation profiling. As a proof of principle, we performed targeted, massively parallel sequencing of 138 cancer genes in a tumor obtained from a patient with melanoma who developed resistance to PLX4032 after an initial dramatic response. The resulting profile identified an activating mutation at codon 121 in the downstream kinase MEK1 that was absent in the corresponding pretreatment tumor. The MEK1(C121S) mutation was shown to increase kinase activity and confer robust resistance to both RAF and MEK inhibition in vitro. Thus, MEK1(C121S) or functionally similar mutations are predicted to confer resistance to combined MEK/RAF inhibition. These results provide an instructive framework for assessing mechanisms of acquired resistance to kinase inhibition and illustrate the use of emerging technologies in a manner that may accelerate personalized cancer medicine.
Demonstration of Nonpolar GaN-Based Vertical-Cavity Surface-Emitting Lasers (2012)

Electrically injected, single-longitudinal-mode nonpolar m-plane vertical-cavity surface-emitting lasers (VCSELs) are reported with a room-temperature lasing wavelength of 411.9 nm, a full width at half maximum (FWHM) of 0.25 nm, and a peak output power of 19.5 µW under pulsed conditions. The polarization direction of the VCSELs is consistently oriented along the [1210] a-direction. The degree of polarization increases from 0.13 below threshold to 0.72 above threshold. A process is demonstrated that utilizes bandgap-selective photoelectrochemical (PEC) undercut etching of an intracavity-embedded In0.12Ga0.88N sacrificial layer to achieve precise cavity length control and allow for top and bottom dielectric distributed Bragg reflector (DBR) mirrors.
Pressure Waves as a Noninvasive Tool for Artery Stiffness Estimation (2008)

In hypertension and aging, central elastic arteries become stiffer and hence the central pulse pressure is augmented due to the increase in the pulse wave velocity and the early return of reflected waves to the heart from the periphery. Valuable information on arterial properties, such as stiffness, can be obtained from both central (aortic) and peripheral (radial) pressure wave forms. A feasibility study for the noninvasive estimation of arterial stiffness using pressure waves detected by a pneumatic cuff wrapped around the upper arm is presented. The propagation and reflection of arterial pressure waves (generated by the heart) in the central elastic arteries are simulated using a simplified water hammer acoustic model. Furthermore, a lumped parameter model is used to describe the transmission of the pressure waves from the brachial artery to the cuff external wall. By combining the two models, we were able to simulate the pressure contours in the brachial artery and illustrate how these pressures transmit to the cuff’s external wall. The effects of aortic stiffness are investigated by simulating the model at different values of aortic elastic moduli and observing the pressure augmentation and the timing of feature points. This work was done as part of the development of a noninvasive diagnostic device by Pulsecor Ltd. The model results obtained in this work are in agreement with published experimental results and the device output; hence, the model can be used to develop the device’s stiffness estimation algorithm.
Comparison of Protection in Rabbits against Host-Adapted and Cultivated<i>Borrelia burgdorferi</i>following Infection-Derived Immunity or Immunization with Outer Membrane Vesicles or Outer Surface Protein A (2000)

In this study, infection-derived immunity in the rabbit model of Lyme disease was compared to immunity following immunization with purified outer membrane vesicles (OMV) isolated from Borrelia burgdorferi and recombinant outer surface protein A (OspA). Immunization of rabbits with OMV isolated from virulent strain B31 and its avirulent derivative B313 (lacking OspA and DbpA) conferred highly significant protection against intradermal injection with 6 x 10(4) in vitro-cultivated virulent B. burgdorferi. This is the first demonstration of protective immunogenicity induced by OMV. While immunization with OspA and avirulent B31 OMV provided far less protection against this challenge, rabbits with infection-derived immunity were completely protected. Protection against host-adapted B. burgdorferi was assessed by implantation of skin biopsies taken from rabbit erythema migrans (a uniquely rich source of B. burgdorferi in vertebrate tissue) containing up to 10(8) spirochetes. While all of the OMV- and OspA-immunized rabbits were fully susceptible to skin and disseminated infection, rabbits with infection-derived immunity were completely protected. Analysis of the antibody responses to outer membrane proteins, including DbpA, OspA, and OspC, suggests that the remarkable protection exhibited by the infection-immune rabbits is due to antibodies directed at antigens unique to or markedly up-regulated in host-adapted B. burgdorferi.
Compact Catadioptric Imaging Spectrometer Designs Utilizing Immersed Gratings (2023)

An imaging spectrometer comprising an entrance slit for directing light, a lens that receives said light and reflects said light, a grating that defracts said light back onto said lens which focuses said light, and a detector array that receives said focused light. In one embodiment the grating has rulings immersed into a germanium surface.
Flux-Feedback Magnetic-Suspension Actuator (1990)

Flux-feedback magnetic-suspension actuator provides magnetic suspension and control forces having linear transfer characteristics between force command and force output over large range of gaps. Hall-effect devices used as sensors for electronic feedback circuit controlling currents flowing in electromagnetic windings to maintain flux linking suspended element at substantially constant value independent of changes in length of gap. Technique provides effective method for maintenance of constant flux density in gap and simpler than previous methods. Applications include magnetic actuators for control of shapes and figures of antennas and of precise segmented reflectors, magnetic suspensions in devices for storage of angular momentum and/or kinetic energy, and systems for control, pointing, and isolation of instruments.
Use of Alcohol as Initiator for Reversible Chain Transfer Catalyzed Polymerization (2010)

Abstract A novel initiation system, using a hydroxyl group as an initiating moiety, was developed for reversible chain transfer catalyzed polymerization (RTCP), a living radical polymerization. The hydroxyl (alcohol) group was reacted with an iodinating agent and a monomer (M), giving a dormant species RO–M–I (I = iodine). It was prepared in the polymerization medium (monomer) and used in the polymerization without the purification, leading to a one‐pot RTCP from a hydroxyl group (an alcohol). magnified image
Crystal structure, catalytic mechanism, and mitogenic properties of <i>Trypanosoma cruzi</i> proline racemase (2006)

Amino acid racemases catalyze the stereoinversion of the chiral C alpha to produce the d-enantiomers that participate in biological processes, such as cell wall construction in prokaryotes. Within this large protein family, bacterial proline racemases have been extensively studied as a model of enzymes acting with a pyridoxal-phosphate-independent mechanism. Here we report the crystal structure of the proline racemase from the human parasite Trypanosoma cruzi (TcPRACA), a secreted enzyme that triggers host B cell polyclonal activation, which prevents specific humoral immune responses and is crucial for parasite evasion and fate. The enzyme is a homodimer, with each monomer folded in two symmetric alpha/beta subunits separated by a deep crevice. The structure of TcPRACA in complex with a transition-state analog, pyrrole-2-carboxylic acid, reveals the presence of one reaction center per monomer, with two Cys residues optimally located to perform acid/base catalysis through a carbanion stabilization mechanism. Mutation of the catalytic Cys residues abolishes the enzymatic activity but preserves the mitogenic properties of the protein. In contrast, inhibitor binding promotes the closure of the interdomain crevice and completely abrogates B cell proliferation, suggesting that the mitogenic properties of TcPRACA depend on the exposure of transient epitopes in the ligand-free enzyme.
Three-dimensional optical tomography of fluorescent proteins in the visible (2004)

We present a new modality for tomographic imaging of fluorescence activity in the visible light range. The tomographic method employed a multi-angle, multi-projection illumination scheme from an Ar+ laser emitting at 488nm, while detection was achieved using a highly sensitive CCD camera. Reconstruction is based on novel photon propagation models developed specifically for visible light. We show that the technique can quantitatively detect fluorescence with sub millimeter spatial resolution. We also show that the detection of gene expression (using GFP) is possible in deep tissues quantitatively.
High-power vertical-cavity surface-emitting lasers for solid-state laser pumping (2012)

Vertical-cavity surface-emitting lasers (VCSELs) have emerged as a promising candidate for pumping of solid-state lasers, as they can be configured into high-power two-dimensional arrays and modules of arrays. VCSELs emit in a circular, uniform beam which can greatly reduce the complexity and cost of coupling optics. Their narrow and stable emission spectrum is well suited to the narrow absorption spectrum generally observed for solid-state gain media. The superior reliability of VCSELs greatly enhances the robustness of solid-state laser systems and enables high-temperature operation. In this work, we discuss recent developments on kW-class VCSEL pumps for solid-state lasers. Results on VCSEL modules designed for end-pumping and for side-pumping are presented. More than 4kW in CW operation is demonstrated from a multi-array VCSEL module. We also present results on solid-state lasers using VCSEL modules as pumps. In an end-pumping configuration, more than 250W peak power at 1064nm is demonstrated, and in a sidepumping Q-switched configuration, more than 21mJ at 946nm is demonstrated for an Nd:YAG solid-state laser.
Feasibility Study on Negative Capacitance SIS Phase Shifter for Low-Power Optical Phase Modulation (2018)

We investigate a negative capacitance SIS phase shifter with ferroelectric materials for low-power optical switching. Negative capacitance can realize comparable charge with lower voltage owing to the charge polarization of ferroelectric materials. We discuss the charge enhancement, modulation efficiency and switching characteristic of this device.
Helicobacter hepaticus sp. nov., a microaerophilic bacterium isolated from livers and intestinal mucosal scrapings from mice (1994)

A bacterium with a spiral shape and bipolar, single, sheathed flagella was isolated from the livers of mice with active, chronic hepatitis. The bacteria also colonized the cecal and colonic mucosae of mice. The bacterium grew at 37 degrees C under microaerophilic and anaerobic conditions, rapidly hydrolyzed urea, was catalase and oxidase positive, reduced nitrate to nitrite, and was resistant to cephalothin metronidazole. On the basis of 16S rRNA gene sequence analysis, the organism was classified as a novel helicobacter, Helicobacter hepaticus. This new helicobacter, like two other murine Helicobacter species, H. muridarum and "H. rappini," is an efficient colonizer of the gastrointestinal tract, but in addition, it has the pathogenic potential to elicit persistent hepatitis in mice.
Molecular combing reveals allelic combinations in facioscapulohumeral dystrophy (2011)

MC enables the detailed exploration of the FSHD locus and accurate diagnosis of FSHD, the first Mendelian disease to benefit from this technique. MC is also likely to be applicable to other copy number-variant or repeat expansion-associated human diseases.
Aromatase Inhibitors for Ovulation Induction (2006)

Preliminary evidence suggests that AIs may replace CC in the future because of similar efficacy with a reduced side effect profile. Although worldwide experience with AIs for ovulation induction is increasing, at present, definitive studies in the form of randomized controlled trials comparing CC with AIs are lacking.