gebhart/patrepeval huggingface dataset:
Multi-branched peptides based on the HIV-1 V3 loop consensus motif inhibit HIV-1 and HIV-2 infection in CD4+ and CD4- cells. (1993)

The V3 loop is an hypervariable region of the HIV-1 surface envelope glycoprotein gp120 that is able to generate neutralizing antibodies. These antibodies are generally type-specific. They inhibit the interaction between the V3 loop and the membrane molecules involved in virus-cell and cell-cell fusion. Synthetic peptides based on the V3 loop sequence have been tentatively used to block the fusion process, but the results were unsuccessful. In this report, we confirm that monomeric V3 peptides are devoid of any anti-HIV activity. However, we found that, when assembled in a synthetic polymeric construction (SPC), these peptides have been able to inhibit the infection of human CD4+ lymphocytes and macrophages as well as CD4- epithelial intestinal cells by distantly related isolates of HIV-1 and HIV-2. V3 SPCs, based on the consensus HIV-1 sequence, may therefore represent a new class of therapeutically useful anti-HIV agents able to neutralize a wide range of viral isolates in both CD4+ and CD4- susceptible cells.
Method Of Packaging And Assembling Electro-Microfluidic Devices (2023)

A new architecture for packaging surface micromachined electro-microfluidic devices is presented. This architecture relies on two scales of packaging to bring fluid to the device scale (picoliters) from the macro-scale (microliters). The architecture emulates and utilizes electronics packaging technology. The larger package consists of a circuit board with embedded fluidic channels and standard fluidic connectors (e.g. Fluidic Printed Wiring Board). The embedded channels connect to the smaller package, an Electro-Microfluidic Dual-Inline-Package (EMDIP) that takes fluid to the microfluidic integrated circuit (MIC). The fluidic connection is made to the back of the MIC through Bosch-etched holes that take fluid to surface micromachined channels on the front of the MIC. Electrical connection is made to bond pads on the front of the MIC.
Predicting Cloud-to-Ground Lightning with Neural Networks (1991)

A neural network is being trained to predict lightning at Cape Canaveral for periods up to two hours in advance. Inputs consist of ground based field mill data, meteorological tower data, lightning location data, and radiosonde data. High values of the field mill data and rapid changes in the field mill data, offset in time, provide the forecasts or desired output values used to train the neural network through backpropagation. Examples of input data are shown and an example of data compression using a hidden layer in the neural network is discussed.
Inkjet Alchemy - Inkjet-printing of Thin Metal Oxide Films with Metallic Appearance (2016)

In this paper, we describe a new way of producing digital prints with high reflectivity and dichroic or metallic appearance. The special visual effect is achieved using conventional office class inkjet printers and jetting inks containing metal oxide nano-particles onto surface of nanoporous substrates, such as inkjet photo papers. A thin metal oxide layer of uniform thickness in ~10-1000μm range may be produced almost instantly by ambient drying of the print. The formation of metal oxide layer of highly uniform thickness is a result of interaction of metal oxide ink with surface of inkjet media of certain pore structure and high volume porosity. Capillary forces drain liquid phase of the ink into the substrate, while retaining the nanoparticles on the surface. These forces also help to flatten jetted metal oxide particles into optically uniform and continuous layer with high optical reflectivity. The appearance of the films produced is highly dependent on refractive index, native coloration and printed layer thickness of the metal oxide used. Inks based on magnetite (Fe3O4, refractive index ~2.5) printed into layers with ~ 50-100-nm thickness produce prints with visual appearance of metallic gold. Inkjet printing may also be used for stacking high refractive index metal oxide films with layers of conventional colorants (organic pigment particles) and produce prints with metallic color appearance.
Colonization of the Human Oral Cavity by a Strain of Streptococcus mutans (1985)

Streptococcus mutans strain JH1001 produces a bacteriocin that can kill virtually all other strains of this micro-organism. The ability of JH1001 to colonize the human oral cavity was tested in a study involving five subjects and three different infection regimens, all of which involved multiple exposures to large numbers of organisms. Two and one-half years after infection, JH1001 was found to have persistently colonized three of the subjects. The indigenous S. mutans in one subject were reduced below the level of detection. Levels of (total) S. mutans and S. sanguis were not affected in persistently colonized subjects. Mutants of indigenous S. mutans resistant to the bacteriocin were not observed. The results indicate the importance of host variability and infection regimen for superinfection by this strain of S. mutans. The efficient replacement of indigenous S. mutans by JH1001 in one subject lends support to the eventual application of replacement therapy to the prevention of dental caries.
Isolation and Characterization of a Novel IgD-Binding Protein from <i>Moraxella catarrhalis</i> (2001)

A novel surface protein of the bacterial species Moraxella catarrhalis that displays a high affinity for IgD (MID) was solubilized in Empigen and isolated by ion exchange chromatography and gel filtration. The apparent molecular mass of monomeric MID was estimated to approximately 200 kDa by SDS-PAGE. The mid gene was cloned and expressed in Escherichia coli. The complete mid nucleotide gene sequence was determined, and the deduced amino acid sequence consists of 2123 residues. The sequence of MID has no similarity to other Ig-binding proteins and differs from all previously described outer membrane proteins of M. catarrhalis. MID was found to exhibit unique Ig-binding properties. Thus, in ELISA, dot blots, and Western blots, MID bound two purified IgD myeloma proteins, four IgD myeloma sera, and finally one IgD standard serum. No binding of MID was detected to IgG, IgM, IgA, or IgE myeloma proteins. MID also bound to the surface-expressed B cell receptor IgD, but not to other membrane molecules on human PBLs. This novel Ig-binding reagent promises to be of theoretical and practical interest in immunological research.
Toward Improved Optical Transparency of Polyimide Aerogels (2020)

Highly translucent polyimide aerogels were prepared by combining equimolar amounts of pyromellitic dianhydride, 4,4'-hexafluoroisopropylidene di(phthalic anhydride) (6FDA), and 2,2'-dimethylbenzidine and cross-linking with 1,3,5-benzenetricarbonyl trichloride. A multivariable statistical design of experiments was used to perform a comparison study between three variables used to fabricate the aerogels: formulated repeat unit (<i>n</i>) of polyimide oligomers, 6FDA fraction of total dianhydride (0-50 mol %), and total polymer concentration in solution (7-10 wt %). Polymers with 25 mol % 6FDA in the backbone structure were found to produce polyimide aerogels with high optical transmission and low haze. These aerogels also possessed higher surface areas and very narrow nanoscale pore size distribution. Because of the decreased thermal conductivity with increasing amount of 6FDA in the backbone, these aerogels may find use where the combination of high optical transparency and thermal impedance is desired, such as insulated window panes. To this end, future efforts will focus on reducing the yellow color of the polyimide aerogels.
Current technologies to endotoxin detection and removal for biopharmaceutical purification (2020)

Endotoxins are the major contributors to the pyrogenic response caused by contaminated pharmaceutical products, formulation ingredients, and medical devices. Recombinant biopharmaceutical products are manufactured using living organisms, including Gram-negative bacteria. Upon the death of a Gram-negative bacterium, endotoxins (also known as lipopolysaccharides) in the outer cell membrane are released into the lysate where they can interact with and form bonds with biomolecules, including target therapeutic compounds. Endotoxin contamination of biologic products may also occur through water, raw materials such as excipients, media, additives, sera, equipment, containers closure systems, and expression systems used in manufacturing. The manufacturing process is, therefore, in critical need of methods to reduce and remove endotoxins by monitoring raw materials and in-process intermediates at critical steps, in addition to final drug product release testing. This review paper highlights a discussion on three major topics about endotoxin detection techniques, upstream processes for the production of therapeutic molecules, and downstream processes to eliminate endotoxins during product purification. Finally, we have evaluated the effectiveness of endotoxin removal processes from a perspective of high purity and low cost.
Preproinsulin mRNA engineering and its application to the regulation of insulin secretion from human hepatomas (2003)

Cell-based therapies for treating insulin-dependent diabetes (IDD) can provide a more physiologic regulation of blood glucose levels in a less invasive fashion than daily insulin injections. Promising cells include non-beta cells genetically engineered to secrete insulin in response to physiologic cues; responsiveness can be introduced at the transcriptional level to regulate preproinsulin (PPI) mRNA biosynthesis. However, these cells exhibit sluggish secretion dynamics, which is not appropriate for achieving euglycemia in higher animals and, eventually, humans. In this work, we have engineered the PPI mRNA so as to destabilize it through nonsense-mediated mRNA decay (NMD). When expressed under transcriptional regulation in HepG2 hepatomas, the engineered PPI mRNA level and of the insulin secretion rate declined faster upon switching off transcription, compared to the one-copy non-engineered control. Our work provides a simple and straightforward method to improve the dynamics of transcriptionally regulated insulin secretion, which can be a useful tool in developing cell-based therapies for IDD.
Integrated CMOS Compatible Low Power 10Gbps Silicon Photonic Heater-Modulator (2012)

We quantify bit-error performance of a heater-modulator that uses CMOS compatible heater and modulator voltages, occupies 50µm2, is compatible with differential signaling and shows consistent extinction ratio under tuning while consuming only 7µW /GHz.
Measurement and characterization of ultra-precision freeform surfaces using an intrinsic surface feature-based method (2010)

Ultra-precision freeform surfaces are complex surfaces that possess non-rotational symmetry and are widely used in advanced optics applications. Due to the geometrical complexity of optical freeform surfaces, there is, as yet, a lack of generalized surface characterization methods which measure various types of ultra-precision freeform surfaces with sub-micrometer form accuracy and surface finish in the nanometer range. To make good this deficiency, a generalized approach for the measurement and characterization of ultra-precision freeform surfaces, named the intrinsic surface feature-based method (ISFM), is presented in this paper. The ISFM makes use of intrinsic surface properties (e.g. curvatures, normal vectors, torsion and intrinsic frames) to conduct data matching or uses some algorithms to search for correspondences such as correlation functions. The method is experimentally verified through a series of measurement experiments. The results show that the proposed ISFM is capable of addressing the deficiencies and limitations of traditional freeform surface characterization methods which are susceptible to outliers and to uncertainty due to the geometry of the freeform surfaces. ISFM is a generalized methodology which is not dependent on the type of freeform surface being characterized.
Therapeutic Activity of an Engineered Synthetic Killer Antiidiotypic Antibody Fragment against Experimental Mucosal and Systemic Candidiasis (2003)

Peptides derived from the sequence of a single-chain, recombinant, antiidiotypic antibody (IdAb; KT-scFv) acting as a functional internal image of a microbicidal, wide-spectrum yeast killer toxin (KT) were synthesized and studied for their antimicrobial activity by using the KT-susceptible Candida albicans as model organism. A decapeptide containing the first three amino acids (SAS) of the light chain CDR1 was selected and optimized by alanine replacement of a single residue. This peptide exerted a strong candidacidal activity in vitro, with a 50% inhibitory concentration of 0.056 microM, and was therefore designated killer peptide (KP). Its activity was neutralized by laminarin, a beta1-3 glucan molecule, but not by pustulan, a beta1-6 glucan molecule. KP also competed with the binding of a KT-like monoclonal IdAb to germinating cells of the fungus. In a rat model of vaginal candidiasis, local, postchallenge administration of KP was efficacious in rapidly abating infections caused by fluconazole-susceptible or -resistant C. albicans strains. In systemic infection of BALB/c or SCID mice preinfected intravenously with a lethal fungal load, KP caused a highly significant prolongation of the median survival time, with >80% of the animals still surviving after >60 days, whereas >90% of control mice died within 3 to 5 days. KP is therefore the first engineered peptide derived from a recombinant IdAb retaining KT microbicidal activity, probably through the interaction with the beta-glucan KT receptor on target microbial cells.
Single-Chain Semiconducting Polymer Dots (2014)

This work describes the preparation and validation of single-chain semiconducting polymer dots (sPdots), which were generated using a method based on surface immobilization, washing, and cleavage. The sPdots have an ultrasmall size of ∼3.0 nm as determined by atomic force microscopy, a size that is consistent with the anticipated diameter calculated from the molecular weight of the single-chain semiconducting polymer. sPdots should find use in biology and medicine as a new class of fluorescent probes. The FRET assay this work presents is a simple and rapid test to ensure methods developed for preparing sPdot indeed produced single-chain Pdots as designed.
Monte Carlo Model of Spatially Offset Raman Spectroscopy for Breast Tumor Margin Analysis (2010)

We have previously demonstrated the discrimination of two layers of soft tissue, specifically normal breast tissue overlying breast tumor, using spatially offset Raman spectroscopy (SORS). In this report, a Monte Carlo code for evaluating SORS in soft tissues has been developed and compared to experimental results. The model was employed to investigate the effects of tissue and probe geometry on SORS measurements and therefore to develop the design strategies of applying SORS for breast tumor surgical margin evaluation. The model was used to predict SORS signals for different tissue geometries difficult to precisely control experimentally, such as varying normal and tumor layer sizes and the addition of a third layer. The results from the model suggest that, using source-detector separations of up to 3.75 mm, SORS can detect sub-millimeter-thick tumors under a 1 mm normal layer, and tumors at least 1 mm thick can be detected under a 2 mm normal layer.
White-light interferometry with reference signal (2002)

White light interferometer (WLI) has become a common tool for measuring surfaces with large height range and/or roughness. Typically, the object is scanned through focus, thus varying the optical path difference (OPD) between the object and reference beams. The rate of the OPD change affects the quality and accuracy of the surface measurement. For high quality measurements a scanning device is often enhanced by a closed loop feedback while the scanning speed is assumed to be known and constant. In this paper we describe a white light interferometer that yields excellent results without requiring a high-end scanner. These results are achieved by embedding an additional interferometer with a long coherence length source that provides an interferometric reference signal that is used to monitor the motion of the scanner during each measurement in real time. The information about the scanner motion is then used in a WLI algorithm. This yields significant improvements in both the accuracy and repeatability of topography measurements.
Multi-Kernel Construction of Polar Codes (2016)

We propose a generalized construction for binary polar codes based on mixing multiple kernels of different sizes in order to construct polar codes of block lengths that are not only powers of integers. This results in a multi kernel polar code with very good performance while the encoding complexity remains low and the decoding follows the same general structure as for the original Arikan polar codes. The construction provides numerous practical advantages as more code lengths can be achieved without puncturing or shortening. We observe numerically that the error-rate performance of our construction outperforms stateof the-art constructions using puncturing methods.
Inhibition of preS1-hepatocyte interaction by an array of recombinant human antibodies from naturally recovered individuals (2016)

Neutralizing monoclonal antibodies are being found to be increasingly useful in viral infections. In hepatitis B infection, antibodies are proven to be useful for passive prophylaxis. The preS1 region (21-47a.a.) of HBV contains the viral hepatocyte-binding domain crucial for its attachment and infection of hepatocytes. Antibodies against this region are neutralizing and are best suited for immune-based neutralization of HBV, especially in view of their not recognizing decoy particles. Anti-preS1 (21-47a.a.) antibodies are present in serum of spontaneously recovered individuals. We generated a phage-displayed scFv library using circulating lymphocytes from these individuals and selected four preS1-peptide specific scFvs with markedly distinct sequences from this library. All the antibodies recognized the blood-derived and recombinant preS1 containing antigens. Each scFv showed a discrete binding signature, interacting with different amino acids within the preS1-peptide region. Ability to prevent binding of the preS1 protein (N-terminus 60a.a.) to HepG2 cells stably expressing hNTCP (HepG2-hNTCP-C4 cells), the HBV receptor on human hepatocytes was taken as a surrogate marker for neutralizing capacity. These antibodies inhibited preS1-hepatocyte interaction individually and even better in combination. Such a combination of potentially neutralizing recombinant antibodies with defined specificities could be used for preventing/managing HBV infections, including those by possible escape mutants.
High refractive-index resists composed of anionic photoacid generator (PAG) bound polymers for 193 nm immersion lithography (2008)

The objective of to develop high refractive index (HRI) chemical amplified resists (CAR), which are composed of HRI photoacid generator (PAG) bound polymer resists, and incorporate HRI nanoparticles into the polymer matrix. Therefore, this new series of nanocomposite resists should be effective for 193 nm immersion lithography with high RI, to obtain feature sizes down to 32 nm or lower.
Identification of Mycobacterial Species by Comparative Sequence Analysis of the RNA Polymerase Gene ( <i>rpoB</i> ) (1999)

For the differentiation and identification of mycobacterial species, the rpoB gene, encoding the beta subunit of RNA polymerase, was investigated. rpoB DNAs (342 bp) were amplified from 44 reference strains of mycobacteria and clinical isolates (107 strains) by PCR. The nucleotide sequences were directly determined (306 bp) and aligned by using the multiple alignment algorithm in the MegAlign package (DNASTAR) and the MEGA program. A phylogenetic tree was constructed by the neighbor-joining method. Comparative sequence analysis of rpoB DNAs provided the basis for species differentiation within the genus Mycobacterium. Slowly and rapidly growing groups of mycobacteria were clearly separated, and each mycobacterial species was differentiated as a distinct entity in the phylogenetic tree. Pathogenic Mycobacterium kansasii was easily differentiated from nonpathogenic M. gastri; this differentiation cannot be achieved by using 16S rRNA gene (rDNA) sequences. By being grouped into species-specific clusters with low-level sequence divergence among strains of the same species, all of the clinical isolates could be easily identified. These results suggest that comparative sequence analysis of amplified rpoB DNAs can be used efficiently to identify clinical isolates of mycobacteria in parallel with traditional culture methods and as a supplement to 16S rDNA gene analysis. Furthermore, in the case of M. tuberculosis, rifampin resistance can be simultaneously determined.
Detection of single and multiple polymorphic loci by synthetic tandem repeats of short oligonucleotides (1991)

Loci containing tandem repeats of short sequences are sometimes associated with a high level of polymorphism due to variations in the number of repeats. The different variants can be easily characterized by Southern blotting when the repeats span a range from a few hundred bases to a few kilobases, and probes derived from such tandem repeats constitute convenient genetic markers. These structures, usually called minisatellites, are best documented in the human genome, where their number has been estimated to be at least 1500. However, their role and mode of evolution are poorly understood. We are developing tools to evaluate the number of such redundant sequences in a genome and to gain access to new polymorphic loci. Our strategy is based on the use of polymers of oligonucleotides as DNA probes for hybridization on Southern blots. In a previous report, we made polymers with random units of 14 bp and showed that they detect multiple polymorphic loci on human genomic DNA. At present, we are testing the effect of an increase in the complexity of the polymer, as obtained by the use of a longer random unit, and the effect of slight sequence modifications to a particular tandem repeat sequence. In addition, some of these synthetic probes can detect a single polymorphic locus and directly provide new genetic markers.