gebhart/patrepeval huggingface dataset:
536. The Viral Transduction Enhancer Vectofusin-1 Is a Nanofibrillar Peptide Capable of Increasing the Contact between Viral Vectors and Target Cells (2016)

Gene transfer into hCD34+ hematopoietic stem/progenitor cells (HSPCs) using HIV-1-based lentiviral vectors (LVs) has several therapeutic applications ranging from monogenic diseases, infectious diseases and cancer. In such therapeutic context, the gene therapy could be improved by enhancing transduction levels of target cells and by reducing the amount of LVs used on the cells for greater safety and reduced costs. We recently identified a new cationic amphipathic peptide, Vectofusin-1, with viral transduction enhancing capacity, enabling higher transduction levels with low amounts of LV. Vectofusin-1 promotes the entry of several retroviral pseudotypes into target cells when added to the culture medium and is not toxic to HSPCs. Here, we present the first insights into the mechanism of action of this new transduction enhancer. First, a viral pull down assay showed that viral particles were easily pelleted by low speed centrifugation in presence of Vectofusin-1, suggesting that this latter may form unsoluble nanofibrils, trapping lentiviral particles. Atomic force (AFM) and electron microscopy (EM) of Vectofusin-1 confirmed that this peptide is rapidly forming annular aggregates and nanofibres in culture medium. Furthermore, these fibres were shown to be auto-fluorescent in medium with high-protein content (X-Vivo20), allowing the observation of a nanofibrillar network of Vectofusin-1 using confocal microscopy. Next, Vectofusin-1 was shown to strongly interact with Congo Red, especially in presence of lentiviral particles, but labeling with Thioflavin T was inefficient, suggesting that Vectofusin-1 fibres are not amyloid-type fibrils. Structural studies by circular dichroism confirmed this result. The capacity to form nanofibrils appears to be essential for the mechanism of action of Vectofusin-1 since a defective mutant called LAH2-A4, unable to promote lentiviral transduction (Majdoul S. et al (2016) J. Biol. Chem.), was also unable to form nanofibrils. In conclusion, biophysical, nanoscopic and microscopic observations have helped us to define Vectofusin-1 as a new nanofibrillar peptide capable of enhancing lentiviral transduction of target cells in conditions well-adapted to cGMP and scalable gene therapy protocols.
Tunable electronic lens using a gradient polymer network liquid crystal (2003)

Tunable electronic lenses using gradient polymer network liquid crystal (PNLC) cells were demonstrated. By changing the photomask pattern, both positive and negative lenses were fabricated. The advantages of such a PNLC lens are low operation voltage, large aperture size, and simple electrode design. To overcome the polarization dependence, stacking two orthogonal homogeneous PNLC cells is considered.
A Novel Immunoassay for the Quantitation of Human C4 Gene Products (1990)

Utilizing mouse monoclonal antibodies which recognize Rodgers 1 and Chido 1 epitopes carried on the C4A and C4B molecules, and heat-aggregated IgG to activate C1, an immunoassay was developed for the quantitation of total C4 as well as C4A and C4B. Interassay variation was 12.4, 11.5 and 10.8%, respectively. The immunoassay was compared to the quantitation of total C4 by radial immunodiffusion by testing 103 random white controls and gave a Pearson's product-moment correlation coefficient of 0.81. Three genetic total-C4-deficient individuals were nonreactive in all three assays. This activated assay is specific, reproducible, and superior to existing methods for the quantitation of C4A and C4B and detection of the heterozygous C4 null state.
Anti-Fouling Control of Plug-Flow Crystallization via Heating and Cooling Cycle (2015)

Plug-fow crystallization (PFC) is a promising continuous pharmaceutical crystal- lization process but is prone to fouling due to uncontrolled crystallization on the reactor surface (encrustation). This results in operational issues such as (1) fow blockage, (2) increased thermal resistance, and (3) reduced supersaturation, and in turn leads to limited continuous operation and reduced crystal quality and yield. In this work, we introduce a model-based anti-fouling control (AFC) via spatial and temporal heating and cooling cycle.
Controlled burnout of fires in abandoned coal mines and waste banks by in situ combustion (1981)

Technical data from the burning of tonnage quantities of coal and coal refuse under simulated in situ conditions are discussed in terms of burnout control. Based on these data a field trial of the concept is being prepared at an existing abandoned coal mine fire site at Bruceton, Pa. (Calamity Hollow mine fire project). The field burnout ventilation system has been designed to handle exhaust gas temperatures of approximately 1,400/degree/C (approximately 2,600/degree/F) and thermal power output levels of approximately 5 MW. 11 refs.
Network flow based datapath bit slicing (2013)

In deep sub-micro designs, more functions are integrated into one chip, and datapath has become a critical part of the design. Typical datapath consists an array of bit slices. The inherent high degree regularity of datapaths is especially attractive to the placement and routing to achieve regular layout with high density and high performance. However, the current design methodology may generate inferior datapath designs because the datapath regularity cannot be well understood by the traditional design tools. In previous works, several techniques are proposed to preserve/re-identify datapath structures. However, they either restrict the datapath optimization or have little tolerance on bit slice difference.
Recording characteristics of electrical impedance myography needle electrodes (2017)

The results presented show the feasibility of measuring muscle impedivity in vivo using a needle electrode from 10 kHz to 1 MHz. The development of needle EIM technology can open up a new field of study in electrodiagnostic medicine, with potential applications to both disease diagnosis and biomarker assessment of therapy.
Image processing for super-resolution localization in fluorescence microscopy (2013)

Localization of a single fluorescent particle with sub-diffraction limit accuracy is a key merit in fluorescence microscopy. Implementation of nonlinear filtering algorithms prior the localization process can improve the localization accuracy of standard existing methods and also enable the localization of overlapping particles, allowing the use of increased fluorophore activation density, and thereby increased data collection speed. In this paper we present the use of an image decomposition algorithm termed K-factor which reduces an image into a nonlinear set of contrast-ordered decompositions whose joint product reassembles the original image. The K-factor technique is implemented on the images, prior to the localization of the fluorescent probes. Numerical simulations of fluorescence data with random probe positions, and especially at high densities of activated fluorophores demonstrated an improvement in the localization precision with compare to single fitting techniques. Implanting the proposed concept also on experimental data of cellular structures yielded the theoretically predicted resolution enhancement.
Process for the production of hydrogen and oxygen from water. [iron and chlorine compounds] (1979)

A multi-phase thermochemical circulating process for producing hydrogen and oxygen from water is described, using the system of iron and chlorine compounds. Hydrogen is released by the reaction of iron(II)-oxide with water vapor and the oxygen by the reaction of chlorine with water vapor, iron(II)-oxide or iron (II, III)-oxide. Intermediately-formed iron (II)-chloride is hydrolyzed with water vapor to iron(II)-oxide in a multi-stage reaction at a gradually raised temperature, whereby in the hydrolysis the formation of metallic iron or of iron(II, III)-oxide is avoided.
Quantitative evaluation of magnetic immunoassay with remanence measurement (2006)

Magnetic immunoassays utilizing magnetic markers and a high -Tc SQUID have been performed. The marker was designed so as to generate remanence, and its remanence field was measured with the SQUID. The SQUID system was developed so as to measure 12 samples in one measurement sequence. We first conducted a detection of antigen called human IgE using IgE standard solution, and showed the detection of IgE down to 2 attomol. The binding process between IgE and the marker could be semi-quantitatively explained with the Langmuir-type adsorption model. We also measured IgE in human serums, and demonstrated the usefulness of the present method for practical diagnosis.
A Static Analysis-based Cross-Architecture Performance Prediction Using Machine Learning (2019)

Porting code from CPU to GPU is costly and time-consuming; Unless much time is invested in development and optimization, it is not obvious, a priori, how much speed-up is achievable or how much room is left for improvement. Knowing the potential speed-up a priori can be very useful: It can save hundreds of engineering hours, help programmers with prioritization and algorithm selection. We aim to address this problem using machine learning in a supervised setting, using solely the single-threaded source code of the program, without having to run or profile the code. We propose a static analysis-based cross-architecture performance prediction framework (Static XAPP) which relies solely on program properties collected using static analysis of the CPU source code and predicts whether the potential speed-up is above or below a given threshold. We offer preliminary results that show we can achieve 94% accuracy in binary classification, in average, across different thresholds
Automated IMRT planning with regional optimization using planning scripts (2013)

Intensity‐modulated radiation therapy (IMRT) has become a standard technique in radiation therapy for treating different types of cancers. Various class solutions have been developed for simple cases (e.g., localized prostate, whole breast) to generate IMRT plans efficiently. However, for more complex cases (e.g., head and neck, pelvic nodes), it can be time‐consuming for a planner to generate optimized IMRT plans. To generate optimal plans in these more complex cases which generally have multiple target volumes and organs at risk, it is often required to have additional IMRT optimization structures such as dose limiting ring structures, adjust beam geometry, select inverse planning objectives and associated weights, and additional IMRT objectives to reduce cold and hot spots in the dose distribution. These parameters are generally manually adjusted with a repeated trial and error approach during the optimization process. To improve IMRT planning efficiency in these more complex cases, an iterative method that incorporates some of these adjustment processes automatically in a planning script is designed, implemented, and validated. In particular, regional optimization has been implemented in an iterative way to reduce various hot or cold spots during the optimization process that begins with defining and automatic segmentation of hot and cold spots, introducing new objectives and their relative weights into inverse planning, and turn this into an iterative process with termination criteria. The method has been applied to three clinical sites: prostate with pelvic nodes, head and neck, and anal canal cancers, and has shown to reduce IMRT planning time significantly for clinical applications with improved plan quality. The IMRT planning scripts have been used for more than 500 clinical cases. PACS numbers: 87.55.D, 87.55.de
Iterative deblurring for CT metal artifact reduction (1996)

Iterative deblurring methods using the expectation maximization (EM) formulation and the algebraic reconstruction technique (ART), respectively, are adapted for metal artifact reduction in medical computed tomography (CT). In experiments with synthetic noise-free and additive noisy projection data of dental phantoms, it is found that both simultaneous iterative algorithms produce superior image quality as compared to filtered backprojection after linearly fitting projection gaps. Furthermore, the EM-type algorithm converges faster than the ART-type algorithm in terms of either the I-divergence or Euclidean distance between ideal and reprojected data in the authors' simulation. Also, for a given iteration number, the EM-type deblurring method produces better image clarity but stronger noise than the ART-type reconstruction. The computational complexity of EM- and ART-based iterative deblurring is essentially the same, dominated by reprojection and backprojection. Relevant practical and theoretical issues are discussed.
Calcium Channel Blockers: Potential Antimetastatic Agents (1983)

The calcium channel blocker nifedipine (Bay A 1040) was examined for its effects on tumor cell-platelet interactions. In vitro, nifedipine inhibited tumor cell-induced platelet aggregation and platelet enhanced tumor cell adhesion to confluent endothelial cell monolayers and in vivo nifedipine inhibited pulmonary tumor colony formation ("experimental metastasis") by intravenously injected tumor cells. This evidence suggests that calcium channel blockers may be a new class of antimetastatic agents.
Autonomously designed free-form 2D DNA origami (2019)

Scaffolded DNA origami offers the unique ability to organize molecules in nearly arbitrary spatial patterns at the nanometer scale, with wireframe designs further enabling complex 2D and 3D geometries with irregular boundaries and internal structures. The sequence design of the DNA staple strands needed to fold the long scaffold strand to the target geometry is typically performed manually, limiting the broad application of this materials design paradigm. Here, we present a fully autonomous procedure to design all DNA staple sequences needed to fold any free-form 2D scaffolded DNA origami wireframe object. Our algorithm uses wireframe edges consisting of two parallel DNA duplexes and enables the full autonomy of scaffold routing and staple sequence design with arbitrary network edge lengths and vertex angles. The application of our procedure to geometries with both regular and irregular external boundaries and variable internal structures demonstrates its broad utility for nanoscale materials science and nanotechnology.
Evaluation of Two Transgenes for Aluminum Tolerance in Alfalfa (2013)

ABSTRACT Alfalfa ( Medicago sativa L.) production is dramatically reduced in acidic, Al‐rich soil. Transgenic plants of several species overexpressing organic acid synthesis and/or organic acid transporter genes have shown enhanced tolerance to Al. The objective of this research was to evaluate the effect of the citrate synthase (CS) and the Daucus carota L. plasma membrane H + ‐transporting adenosine triphosphatase (H + ATPase) (DcPA1) transgenes on Al tolerance in alfalfa. Stem cuttings from a full‐sib T 2 population including four isogenic groups (plants with neither transgene, CS only, DcPA1 only, and both transgenes) together with nontransformed check genotypes were evaluated for Al and acid soil tolerance in a greenhouse assay in limed and unlimed soil. Aluminum and acid soil tolerance was assessed by measuring the ratios of root and shoot dry weight in unlimed soil compared to limed soil. The three transgenic populations, CS, DcPA1, and CS plus DcPA1, all showed higher Al and acid soil tolerance and lower levels of Al in shoot tissue than the nontransgenic isogenic population or the nontransgenic parental genotypes. This suggests that an Al‐exclusion mechanism could be driving Al and acid soil tolerance in this study. We observed no advantage of combining both transgenes in the same genetic background. These transgenes offer an efficient method to achieve enhanced Al and acid soil tolerant alfalfa cultivars, but more information is needed on their stability across generations and genetic backgrounds and their performance under field conditions.
Mechanical Property Characterization of a Polymeric Nanocomposite Reinforced by Graphitic Nanofibers with Reactive Linkers (2004)

Mechanical property characterization including bending, tensile, and fracture properties for a new functionalized nanofiber/epoxy composite were conducted. Results show that there was only very little increase in mechanical properties of nanocomposites although we used GCNF-ODA reactive linkers to improve the interface. The interfacial stress level of nanocomposites should be much higher than that of traditional composites because of high property mismatch between the nanoscale reinforcement and the matrix. In order to design strong and stiff nanocomposite materials, one should use aligned nanofibers with a relatively large volume or weight fraction. Also, the length of the nanofiber should be long enough and its diameter not very small in order to facilitate the interfacial load transfer mechanism.
Reactivities of HIV-1 <i>gag</i> -Derived Peptides with Antibodies of HIV-1-Infected and Uninfected Humans (1992)

A group of 41 peptides, each 24 amino acids long and overlapping with each other by 12 residues spanning the total gag open reading frame (orf) of HIV-1 (HTLV-IIIBH 10 isolate) were synthesized using Fmoc chemistry. The purified compounds were used in ELISA assays and tested for antibody reactivities in sera of human HIV-1-infected and noninfected individuals. Sera of HIV- humans showed reactivity against four defined regions, two in p17, one in p24, and one in p15. The values of these reactivities were elevated especially in serum samples of HIV- individuals showing cross-reaction with gag proteins on Western blot. Amino acid sequence comparison of HIV-1 gag proteins with those of human endogenous retroviruses (ERV K10, ERV 3) revealed significant similarities predominantly in the domains showing elevated antibody cross-reactions. The majority of sera from HIV-1+ individuals showed strong reactivities to the cross-reactive regions and to various other peptide sequences, a sequential epitope recognized by all HIV-1+ sera could, however, not be identified. The results suggest that human individuals may have immune reactions to endogenous retroviral protein sequences, which are enhanced by infections with HIV-1. Specific antibodies to HIV-1 gag proteins are probably mainly directed to tertiary structure defined epitopes formed by particle formation of the p24 monomers to the nucleocapsid.
[Augmentation of antitumor activity of Lactobacillus casei YIT 8018 (LC 9018) in combination with various antitumor drugs]. (1984)

Augmentation of antitumor activity of Lactobacillus casei YIT 9018 (LC 9018), which strongly inhibits the growth of transplantable allogeneic and syngeneic mouse tumors, in combination with antitumor drugs was investigated. Antitumor drugs used in this study were cyclophosphamide (CY), mitomycin C (MMC), 5-fluorouracil (5-FU) and bleomycin (BLM). The antitumor activity of LC 9018 was augmented by combining 5-FU, MMC or BLM against subcutaneously implanted Meth A and BLM, 5-FU or CY against subcutaneously implanted Sarcoma 180 respectively. Furthermore, combinations with BLM, CY, MMC or 5-FU, BLM, CY, MMC significantly inhibited the growth of intraperitoneally inoculated Meth A or Sarcoma 180, respectively. The combination therapy of LC 9018 with CY significantly prolonged the life span of L 1210-inoculated mouse, while the treatment with LC 9018 alone had no inhibitory effect on L 1210. It was suggested that augmentation of antitumor activity of LC 9018 in combination with CY was due to the inhibition of decrease in the number of peritoneal exudate cells caused by CY injection.
Compact Eye Safe Lidar Systems. (1995)

New technology for compact, eye safe lidar is surveyed. Advances with solid state lasers and detectors permit efficient lidar designs that meet requirements for full time atmospheric monitoring. Micro pulse lidar is an approach that employs kHz pulse rate Nd:YLF lasers and micro Joule pulse energies at visible wavelengths. Eye safety is an essential factor and is obtained by beam expansion. High performance is realized by solid state Geiger mode avalanche photodiode photon counting signal acquisition. The capability to monitor all significant cloud and aerosol scattering by a compact instrument has been demonstrated. Pseudorandom modulation CW lidar is under development. CW diode lasers are used directly as transmitters with the advantage of wavelength tunability for water vapor and other differential absorption measurements. Background photon noise and dynamic range are problems for CW lidar. Advanced conventional pulsed diode laser lidar and near infrared lidar at fundamentally eye safe wavelengths are in development for some applications.
Enhancing the Accuracy of Subcutaneous Glucose Sensors: A Real-Time Deconvolution-Based Approach (2012)

Minimally invasive continuous glucose monitoring (CGM) sensors can greatly help diabetes management. Most of these sensors consist of a needle electrode, placed in the subcutaneous tissue, which measures an electrical current exploiting the glucose-oxidase principle. This current is then transformed to glucose levels after calibrating the sensor on the basis of one, or more, self-monitoring blood glucose (SMBG) samples. In this study, we design and test a real-time signal-enhancement module that, cascaded to the CGM device, improves the quality of its output by a proper postprocessing of the CGM signal. In fact, CGM sensors measure glucose in the interstitium rather than in the blood compartment. We show that this distortion can be compensated by means of a regularized deconvolution procedure relying on a linear regression model that can be updated whenever a pair of suitably sampled SMBG references is collected. Tests performed both on simulated and real data demonstrate a significant accuracy improvement of the CGM signal. Simulation studies also demonstrate the robustness of the method against departures from nominal conditions, such as temporal misplacement of the SMBG samples and uncertainty in the blood-to-interstitium glucose kinetic model. Thanks to its online capabilities, the proposed signal-enhancement algorithm can be used to improve the performance of CGM-based real-time systems such as the hypo/hyper glycemic alert generators or the artificial pancreas.
Study on Schottky barrier modulation of NiGe/Ge by ion-implantation after Germanidation technique (2012)

In this letter, the As <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> implantation after Germanidation technique is comprehensively studied to modulate the Schottky barrier height of NiGe/Ge contact. With the optimized drive-in annealing temperature, ion-implantation energy and dose, the current characteristics of NiGe/p-Ge diode changes from Ohmic to well rectifying with I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">on</sub> /I <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">off</sub> ratio over 10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</sup> , and the corresponding hole barrier height increases to 0.52eV, which indicates a low electron barrier of 0.14eV has been achieved by this technique. In addition, an Ohmic behavior is obtained on n-Ge substrate, verifying the effective modulation of the electron Schottky barrier. The results may provide the guideline for improvement the performance of Ge-based Schottky barrier nMOSFETs.