gebhart/patrepeval huggingface dataset:
Synthesis and Antimicrobial Evaluation of Amphiphilic Neamine Derivatives (2009)

The aminoglycoside antibiotics bind to the 16S bacterial rRNA and disturb the protein synthesis. One to four hydroxyl functions of the small aminoglycoside neamine were capped with phenyl, naphthyl, pyridyl, or quinolyl rings. The 3′,4′- (6), 3′,6- (7a), and the 3′,4′,6- (10a) 2-naphthylmethylene derivatives appeared to be active against sensitive and resistant Staphylococcus aureus strains. 10a also showed marked antibacterial activities against Gram (−) bacteria, including strains expressing enzymes modifying aminoglycosides, efflux pumps, or rRNA methylases. 7a and 10a revealed a weak and aspecific binding to a model bacterial 16S rRNA. Moreover, as compared to neomycin B, 10a showed a lower ability to decrease 3H leucine incorporation into proteins in Pseudomonas aeruginosa. All together, our results suggest that the 3′,4′,6-tri-2-naphthylmethylene neamine derivative 10a should act against Gram (−) bacteria through a mechanism different from inhibition of protein synthesis, probably by membrane destabilization.
Design of bacteriophage T4-based artificial viral vectors for human genome remodeling (2023)

Designing artificial viral vectors (AVVs) programmed with biomolecules that can enter human cells and carry out molecular repairs will have broad applications. Here, we describe an assembly-line approach to build AVVs by engineering the well-characterized structural components of bacteriophage T4. Starting with a 120 × 86 nm capsid shell that can accommodate 171-Kbp DNA and thousands of protein copies, various combinations of biomolecules, including DNAs, proteins, RNAs, and ribonucleoproteins, are externally and internally incorporated. The nanoparticles are then coated with cationic lipid to enable efficient entry into human cells. As proof of concept, we assemble a series of AVVs designed to deliver full-length dystrophin gene or perform various molecular operations to remodel human genome, including genome editing, gene recombination, gene replacement, gene expression, and gene silencing. These large capacity, customizable, multiplex, and all-in-one phage-based AVVs represent an additional category of nanomaterial that could potentially transform gene therapies and personalized medicine.
Implementation and evaluation of a comprehensive system to deliver pediatric continuous infusion medications with standardized concentrations (2009)

A technology-based, scientific, comprehensive yet simplified solution to attain the Joint Commission mandate concerning standardized concentrations was developed, implemented, and evaluated. The system successfully determined a limited number of concentrations for each continuous infusion medication for pediatrics and improved safety by eliminating medication errors when delivering these medications.
Reactor fuel assemblies. [BWR; PWR] (1976)

A description is given of an improved spacer grid for a nuclear fuel assembly comprising fuel rods in a matrix wherein each rod is adapted to be enclosed by a spacer ''cell'' for positioning thereof relative to adjacent rods in the fuel assembly. 7 claims, 12 drawing figures.
Multispectral metamaterial absorber (2014)

We present the simulation, implementation, and measurement of a multispectral metamaterial absorber (MSMMA) and show that we can realize a simple absorber structure that operates in the mid-IR and terahertz (THz) bands. By embedding an IR metamaterial absorber layer into a standard THz metamaterial absorber stack, a narrowband resonance is induced at a wavelength of 4.3 μm. This resonance is in addition to the THz metamaterial absorption resonance at 109 μm (2.75 THz). We demonstrate the inherent scalability and versatility of our MSMMA by describing a second device whereby the MM-induced IR absorption peak frequency is tuned by varying the IR absorber geometry. Such a MSMMA could be coupled with a suitable sensor and formed into a focal plane array, enabling multispectral imaging.
Tunneling nanoelectromechanical switches (2015)

Nanoelectromechanical (NEM) switches have emerged as a promising competing technology to the conventional metal-oxide semiconductor (MOS) transistors. NEM switches exhibit abrupt switching behavior with large on-off current ratios, near-zero off-state leakage currents and sub-threshold slopes below the 60 mV/decade theoretical limit of conventional MOS devices [1]. However, current NEM switches commonly operate at relatively high actuation voltages exceeding 1 V and suffer from failure due to stiction [1]. Reducing the switching gap is a common approach utilized to lower the operating voltage. However, the decrease in the gap size further increases the surface adhesion forces and consequently the possibility of stiction-induced failure.
Citrus Tristeza Virus: Molecular Approaches to Cross Protection (1994)

Citrus tristeza virus (CTV) has the largest genomes among RNA viruses of plants. The 19,296-nt CTV genome codes for eleven open reading frames (ORFs) and can produce at least 19 protein products ranging in size from 6 to 401 kDa. The complex biology of CTV results in an unusual composition of CTV-specific RNAs in infected plants which includes multiple defective RNAs and mixed infections. The complex structure of CTV populations poses special problems for diagnosis, strain differentiation, and studies of pathogenesis. A manipulatable genetic system with the full-length cDNA copy of the CTV genome has been created which allows direct studies of various aspects of the CTV biology and pathology. This genetic system is being used to identify determinants of the decline and stem-pitting disease syndromes, as well as determinants responsible for aphid transmission.
Development of a Dichotomous-Flow Quantitative Fit Test for Half-Mask and Full-Facepiece Respirators (1994)

Abstract A new method to quantitate the fit of elastomeric half-mask and full-facepiece air-purifying respirators was developed. In this method the two flows, cartridge flow and leak flow, are separate. The air-purifying cartridges of the respirator are attached to a reference respirator. A selected flow equivalent to the inhalation flow of the wearer is drawn through the cartridge pair: A feedback system consisting of a pressure controller and a control valve is used to set the pressure drop in the mask on the subject's face equal to the pressure drop in the reference mask. The faceseal leak flow is measured while the subject holds his or her breath for a short period of time. The ratio of total flow (cartridge flow+leak flow) to leak flow is a measure of fit and is defined as the flow fit factor. Aerosol fit factors and flow fit factors were determined using sampling probes in three mask locations: top, center, and bottom. A Kruskal-Wallis test showed that aerosol fit factors obtained from the three locations were significantly different from each other (p=0.0001) while the corresponding flow fit factors were not. Aerosol fit factors obtained with the center probe had the least variability. The coefficient of variation in aerosol fit factors ranged from 5.4% for the center probe to 19% for the bottom probe; the coefficient of variation in flow fit factors was much lower, ranging from 1.7% for the top probe to 2.2% for the center and bottom probes.
Small molecule GS-nitroxide ameliorates ionizing irradiation-induced delay in bone wound healing in a novel murine model. (2010)

We studied radioprotection and mitigation by mitochondrial-targeted Tempol (GS-nitroxide, JP4-039), in a mouse injury/irradiation model of combined injury (fracture/irradiation). Right hind legs of control C57BL/6NHsd female mice, mice pretreated with MnSOD-PL, JP4-039, or with amifostine were irradiated with single and fractionated doses of 0 to 20 Gy. Twenty-four hours later, unicortical holes were drilled into the tibiae of both hind legs; at intervals, tibias were excised, radiographed, and processed for histology. Bone wounds irradiated to 20 or 30 Gy showed delayed healing at 21 to 28 days. Treatment with JP4-039 MnSOD-PL or amifostine, before or after single fraction 20 Gy or during fractionated irradiation followed by drilling accelerated wound healing at days 21 and 28. Orthotopic 3LL tumors were not protected by JP4-039 or amifostine. In nonirradiated mice, pretreatment with JP4-039 accelerated bone wound healing. This test system should be useful for the development of new small molecule radioprotectors.
Rôle of DNA damage in local suppression of contact hypersensitivity in mice by UV radiation (1996)

Exposure of mice to UVB radiation down-regulates the induction of contact hypersensitivity (CHS) responses to haptens applied to the site of irradiation. Concomittantly, the activity of antigen-presenting cells (APC) in the draining lymph nodes is decreased, and T lymphocytes that suppress the induction of CHS are induced. We assessed the rôle of DNA damage in modulation of the CHS response by UV irradiation by applying liposomes containing T4 endonuclease V (T4N5) to the UV-irradiated skin. Liposomal T4N5, which increases the rate of repair of cyclobutyl pyrimidine dimers (CPD) in DNA, prevented the reduction in the CHS response, the impairement in APC function, and the induction of transferrable immune suppression. Liposomes containing heat-inactivated T4N5 did not restore immune responsiveness. In this model, hapten-bearing APC from unirradiated mice also fail to induce CHS upon injection into UV-irradiated recipients. This systemic effect of UV irradiation on APC function was also prevented by application of liposomes containing active, but not inactive, T4N5. These studies support the hypothesis that DNA damage is an essential initiator of one or more steps leading to impaired immune responsiveness after UV irradiation. They further imply that the release of cytokines that modulate APC function after UV irradiation is triggered by DNA damage.
A functional genomic model for predicting prognosis in idiopathic pulmonary fibrosis (2015)

Using supervised and unsupervised analyses, we identified a set of IPF prognostic predictor genes and derived a functional genomic model that predicted high and low-risk IPF patients with high accuracy. This genomic model may complement current prognostic tools to deliver more personalized care for IPF patients.
Ion Source Design for Industrial Applications (1982)

The design of broad-beam industrial ion sources is described. The approach used emphasizes refractory metal cathodes and permanent-magnet multipole discharge chambers. Design procedures and sample calculations are given for the discharge chamber, ion optics, cathodes, and magnetic circuit. Hardware designs are included for the isolator, cathode supports, anode supports, pole-piece assembly, and ion-optics supports. There are other ways of designing most ion source components, but the designs presented are representative of current technology and adaptable to a wide range of configurations.
Robust and efficient upwind finite-difference traveltime calculations in three dimensions (1995)

Abstract First-arrival traveltimes in complicated 3-D geologic media may be computed robustly and efficiently using an upwind finite-difference solution of the 3-D eikonal equation. An important application of this technique is computing traveltimes for imaging seismic data with 3-D prestack Kirchhoff depth migration. The method performs radial extrapolation of the three components of the slowness vector in spherical coordinates. Traveltimes are computed by numerically integrating the radial component of the slowness vector. The original finite-difference equations are recast into unitless forms that are more stable to numerical errors. A stability condition adaptively determines the radial steps that are used to extrapolate. Computations are done in a rotated spherical coordinate system that places the small arc-length regions of the spherical grid at the earth's surface (z = 0 plane). This improves efficiency by placing large grid cells in the central regions of the grid where wavefields are complicated, thereby maximizing the radial steps. Adaptive gridding allows the angular grid spacings to vary with radius. The computation grid is also adaptively truncated so that it does not extend beyond the predefined Cartesian traveltime grid. This grid handling improves efficiency. The method cannot compute traveltimes corresponding to wavefronts that have 'turned' so that they propagate in the negative radial direction. Such wavefronts usually represent headwaves and are not needed to image seismic data. An adaptive angular normalization prevents this turning, while allowing lower-angle wavefront components to accurately propagate.This upwind finite-difference method is optimal for vector-parallel supercomputers, such as the CRAY Y-MP. A complicated velocity model that generates turned wavefronts is used to demonstrate the method's accuracy by comparing with results that were generated by 3-D ray tracing and by an alternate traveltime calculation method. This upwind method has also proven successful in the 3-D prestack Kirchhoff depth migration of field data.
Nonlinear WEC Optimized Geometric Buoy Design for Efficient Reactive Power Requirements (2019)

This paper presents a nonlinear geometric buoy design for Wave Energy Converters (WECs). A nonlinear dynamic model is presented for an hour glass (HG) configured WEC. The HG buoy operates in heave motion or as a single Degree-of-Freedom (DOF). The unique formulation of the interaction between the buoy and the waves produces a nonlinear stiffening effect that provides the actual energy storage or reactive power during operation. A Complex Conjugate Control (C3) with a practical Proportional-Derivative (PD) controller is employed to optimize power absorption for off-resonance conditions and applied to a linear right circular cylinder (RCC) WEC. For a single frequency the PDC3 RCC buoy is compared with the HG buoy design. A Bretschneider spectrum of wave excitation input conditions are reviewed and evaluated for the HG buoy. Numerical simulations demonstrate power and energy capture for the HG geometric buoy design which incorporates and capitalizes on the nonlinear geometry to provide reactive power for the single DOF WEC. By exploiting the nonlinear physics in the HG design simplified operational performance is observed when compared to an optimized linear cylindrical WEC. The HG steepness angle <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">$\alpha$</tex> with respect to the wave is varied and initially optimized for improved energy capture.
A noise suppression system for FM radio receiver (1993)

A noise suppression algorithm using the digital signal processing technique incorporated with the spectral subtraction technology in the audio frequency band has been developed in order to improve the SNR (signal-to-noise ratio) of the audio output of the FM radio receiver. By using a single DSP (digital signal processor) in which the algorithm is implemented, a prototype system has been constructed. Experimental results are presented. SNR improvements of up to 6 dB are consistently obtained in the range from weak to strong antenna input signal strengths. The levels of distortion and process noise generated by the introduction of the noise suppression system are lower than the detection threshold of the measuring equipment used.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
NFC Reader Antenna Design and Considerations for Automotive Applications (2021)

This paper presents antenna design and packaging consideration for near field communication (NFC) system that is being used in automotive security systems, and, more specifically, to an NFC reader for obtaining access to, and controlling activation of, a transportation vehicle such as a motor vehicle. Various important studies for automotive applications were performed in this work such as a magnetic wall method. This magnetic wall method can prevent the reduction in NFC reading range caused by proximity to body sheet metal. It provides a unique and superior magnetic shielding effect as compared to ferrite sheets because it is not temperature dependent and can be implemented with minimal cost and complexity. The proposed design can be easily fabricated on the back face of the NFC reader antenna PCB using conventional PCB techniques.
Multiple hit readout of a microchannel plate detector with a three-layer delay-line anode (2002)

We have developed a delay-line readout technique for microchannel plate detectors with an increased acceptance for multiple hit events compared to standard two-layer delay-line anodes. This technique allows unambiguous determination of arrival time and position of at least two simultaneously detected particles, and/or to detect an even larger number of particles in a shower, as long as any two particles do not arrive both at the same time and at the same position within certain limits. We demonstrate and discuss the abilities and limitations of this technique and the relevance for certain experimental tasks.
Properties of magnetic tunnel junctions with a MgO/CoFeB/Ta/CoFeB/MgO recording structure down to junction diameter of 11 nm (2014)

We investigate properties of perpendicular anisotropy magnetic tunnel junctions (MTJs) with a recording structure of MgO/CoFeB/Ta/CoFeB/MgO down to junction diameter (D) of 11 nm from 56 nm. Thermal stability factor (Δ) of MTJ with the structure starts to decrease at D = 30 nm. D dependence of Δ agrees well with that expected from magnetic properties of blanket film taking into account the change in demagnetizing factors of MTJs. Intrinsic critical current (IC0) reduces with decrease of D in the entire investigated D range. A ratio of Δ to IC0 shows continuous increase with decrease of D down to 11 nm.
Stem Cell-derived Neural Stem/Progenitor Cell Supporting Factor Is an Autocrine/Paracrine Survival Factor for Adult Neural Stem/Progenitor Cells (2003)

Recent evidence suggests that adult neural stem/progenitor cells (ANSCs) secrete autocrine/paracrine factors and that these intrinsic factors are involved in the maintenance of adult neurogenesis. We identified a novel secretory molecule, stem cell-derived neural stem/progenitor cell supporting factor (SDNSF), from adult hippocampal neural stem/progenitor cells by using the signal sequence trap method. The expression of SDNSF in adult central nervous system was localized to hippocampus including dentate gyrus, where the neurogenesis persists throughout life. In induced neurogenesis status seen in ischemically treated hippocampus, the expression of SDNSF was up-regulated. As functional aspects, SDNSF protein provided a dose-dependent survival effect for ANSC following basic fibroblast growth factor 2 (FGF-2) withdrawal. ANSCs treated by SDNSF also retain self-renewal potential and multipotency in the absence of FGF-2. However, SDNSF did not have mitogenic activity, nor was it a cofactor that promoted the mitogenic effects of FGF-2. These data suggested an important role of SDNSF as an autocrine/paracrine factor in maintaining stem cell potential and lifelong neurogenesis in adult central nervous system.
Glioma cells release excitotoxic concentrations of glutamate. (1999)

Elevated levels of extracellular glutamate ([Glu]o) cause uncontrolled Ca2+ increases in most neurons and are believed to mediate excitotoxic brain injury following stroke and other nervous system insults. In the normal brain, [Glu]o is tightly controlled by uptake into astrocytes. Because the vast majority of primary brain tumors (gliomas) are derived from astrocytes, we investigated glutamate uptake in glioma cells surgically isolated from glioma patients (glioblastoma multiforme) and in seven established human glioma cell lines, including STTG-1, D-54 MG, D-65 MG, U-373 MG, U-138 MG, U-251 MG, and CH-235 MG. All glioma cells studied showed impaired glutamate uptake, with a Vmax < 10% that of normal astrocytes. Moreover, rather than removing glutamate from the extracellular fluid, glioma cells release large amounts of glutamate, resulting in elevations of [Glu]o in excess of 100 microM within hours in a space that is 1000-fold larger than the cellular volume. Exposure of cultured hippocampal neurons to glioma-conditioned medium elicited sustained [Ca2+]i elevations that were followed by widespread neuronal death. Similarly, coculturing of hippocampal neurons and glioma cells, either with or without direct contact, resulted in neuronal death. Glioma-induced neuronal death could be completely prevented by treating neurons with the N-methyl-D-aspartate receptor antagonists MK-801/D(-)-2-amino-5-phosphonopentanoic acid or by depletion of glutamate from the medium. Interestingly, several phenylglycine derivatives including the metabotropic glutamate receptor agonist/antagonist (S)-4-carboxyphenylglycine (S-4CPG) potently and selectively inhibited glutamate release from glioma cells and prevented neurotoxicity. These data suggest that growing glioma tumors may actively kill surrounding neuronal cells through the release of glutamate. This glutamate release may also be responsible in part for tumor-associated seizures that occur frequently in conjunction with glioma. These data also suggest that neurotoxic release of glutamate by gliomas may be prevented by phenylglycine derivatives, which may thus be useful as an adjuvant treatment for brain tumors.
Analytical motion blur rasterization with compression (2010)

We present a rasterizer, based on time-dependent edge equations, that computes analytical visibility in order to render accurate motion blur. The theory for doing the computations in a rasterization framework is derived in detail, and then implemented. To keep the frame buffer requirements low, we also present a new oracle-based compression algorithm for the time intervals. Our results are promising in that high quality motion blurred scenes can be rendered using a rasterizer with rather low memory requirements. Our resulting images contain motion blur for both opaque and transparent objects.
A multilayer element for determining hemoglobin in whole blood: principles and analytical performance. (1986)

We described the structure and analytical performance of a thin-film element for determining total hemoglobin in whole blood. The element can be used with the Kodak Ektachem DT60 analyzer. The method, analogous to the standard Drabkin's method, provides accurate and precise results on 10-microL samples of undiluted whole blood. Dynamic range is linear from 0 to 200 g/L, and the method is relatively free from interference.
Advances in the development of farnesyltransferase inhibitors: substrate recognition by protein farnesyltransferase. (1997)

A variety of compounds that show promise in cancer chemotherapy and chemoprevention have been identified as farnesyltransferase inhibitors. These can be classified into mainly two different types of inhibitors, farnesyl diphosphate competitors and CAAX peptidomimetics. The former type acts by competitively inhibiting farnesyltransferase with respect to one of the substrates, farnesyl diphosphate, whereas the latter type acts by mimicking the other substrate, the C-terminal CAAX motif of Ras protein. One example of a farnesyl diphosphate competitor is manumycin, an antibiotic detected in the culture media of a Streptomyces strain. The CAAX peptidomimetics were developed based on the unique property of farnesyltransferase to recognize the CAAX motif at the C-terminus of the protein substrate. Our recent studies have focused on understanding the structural basis of this CAAX recognition. By using in vitro mutagenesis, residues of yeast farnesyltransferase important for the recognition of the CAAX motif have been identified. Two of these residues are closely located at the C-terminal region of the beta-subunit of farnesyltransferase. These and other results on the structural basis of the CAAX recognition may provide information valuable for structure-based design of farnesyltransferase inhibitors.