gebhart/patrepeval huggingface dataset:
Low-dose rectal inoculation of rhesus macaques by SIVsmE660 or SIVmac251 recapitulates human mucosal infection by HIV-1 (2009)

We recently developed a novel strategy to identify transmitted HIV-1 genomes in acutely infected humans using single-genome amplification and a model of random virus evolution. Here, we used this approach to determine the molecular features of simian immunodeficiency virus (SIV) transmission in 18 experimentally infected Indian rhesus macaques. Animals were inoculated intrarectally (i.r.) or intravenously (i.v.) with stocks of SIVmac251 or SIVsmE660 that exhibited sequence diversity typical of early-chronic HIV-1 infection. 987 full-length SIV env sequences (median of 48 per animal) were determined from plasma virion RNA 1-5 wk after infection. i.r. inoculation was followed by productive infection by one or a few viruses (median 1; range 1-5) that diversified randomly with near starlike phylogeny and a Poisson distribution of mutations. Consensus viral sequences from ramp-up and peak viremia were identical to viruses found in the inocula or differed from them by only one or a few nucleotides, providing direct evidence that early plasma viral sequences coalesce to transmitted/founder viruses. i.v. infection was >2,000-fold more efficient than i.r. infection, and viruses transmitted by either route represented the full genetic spectra of the inocula. These findings identify key similarities in mucosal transmission and early diversification between SIV and HIV-1, and thus validate the SIV-macaque mucosal infection model for HIV-1 vaccine and microbicide research.
The effect of nedocromil on weal reactions in human skin. (1987)

1. Nedocromil 2% iontophoresed into human skin had no effect on wealing produced by intradermal histamine, 48/80 or house dust mite antigen. 2. Iontophoresis of 0.002-2% nedocromil itself resulted in dose-related wealing. 3. This wealing was reduced by 62 +/- 8% s.e. mean by the H1-receptor antagonist terfenadine which decreased histamine wealing by 68 +/- 2% s.e. mean. 4. Nedocromil may therefore act as a weak agonist on a skin mast cell receptor concerned with histamine release.
Transurethral ultrasound array for prostate thermal therapy: initial studies (1996)

This study presents the initial evaluation of an applicator designed for transurethral ultrasound thermotherapy (TUST) of prostate tissue in the treatment of benign prostatic hyperplasia (BPH) and cancer. A tubular multitransducer applicator, consisting of four piezoceramic tubes (2.5 mm diameter, 6 mm long, 6.8 MHz) under separate power control, was designed to fit within a semiflexible water-cooled temperature-regulated delivery catheter to be placed within the prostatic urethra during therapy. Sonication patterns were tailored to produce power depositions which avoid nontargeted tissues, such as the rectum. Computer simulations have demonstrated that 1.4-2.0 cm radial therapeutic zones (temperatures /spl ges/50-55/spl deg/C, thermal doses >300 EM/sub 43/) with concurrent sparing of the urethral mucosa can be produced within prostate tissue having blood perfusion as high as 10 kg m/sup -3/ s/sup -1/ within 15-30 min. Acoustic distributions and power output measurements of a prototype applicator have demonstrated acoustic power levels approaching 10 W per each sectored transducer segment are attainable, with beam profiles collimated within the transducer length and with desired circumferential distributions. In vivo thermal dosimetry characterizations of these transurethral applicators have indicated that therapeutic temperatures between 50 and 90/spl deg/C are attainable, controllable in the longitudinal and circumferential directions, and have effective radial heating. These results clearly indicate that transurethral ultrasound applicators have potential to provide improved spatial localization and control of the heating distribution over existing transurethral thermal therapy techniques for both hyperthermia and thermal coagulative therapy of the prostate.
Chemoenzymatic synthesis of glycoconjugate polymers: greening the synthesis of biomaterials (2003)

Glycoconjugate polymers with biodegradable poly(vinyl alcohol) (PVA) were synthesized via lipase-catalyzed transesterification of sugar alcohols (maltitol and lactitol) with divinyl dicarboxylates and subsequent radical polymerization. The conversion and chemoselectivity in transesterification were dependent on the lipases, the sugar alcohols, and the alkyl chain length of the dicarboxylates. Chemoselective esterification was attained in the presence of lipase from Candida antarctica (lipase CA) to give maltitol 6-vinyl sebacate, lactitol 6-vinyl sebacate, and lactitol 6-vinyl adipate in high yields. Polymerization of these vinyl esters with hydrogen peroxide/ascorbic acid as initiator gave glycoconjugate polymers. These polymers were suggested to take micellar conformations in water and to bind strongly to specific lectins (concanavalin A or RCA120). The biodegradabilities of these polymers were modest but higher than PVA. This simple synthesis will be useful to develop various glycoconjugate polymers with high biological activities due to the multivalent glyco-cluster effect and biodegradability due to their PVA backbone and ester linkage.
Skin Permeation Enhancement of Diclofenac by Fatty Acids (2008)

This study systematically investigated the enhancing effect of fatty acids on the skin permeation of diclofenac. The fatty acids were evaluated in terms of their carbon-chain length, the degree of unsaturation, and their functional groups. The rat-skin permeation rates of diclofenac, saturated in propylene glycol (PG) containing 1% (w/v) fatty acid, were determined using the Keshary-Chien diffusion cells at 37 degrees C. The effect of fatty acids on the saturated solubility of diclofenac in PG was also determined at 37 degrees C using high-performance liquid chromatography. Among the saturated fatty acids tested, palmitic acid (C16:0) showed the most potent skin permeation-enhancing effect. A parabolic correlation was observed between the enhancement effect and the fatty acid carbon-chain length among these saturated fatty acids of C12-C20 units. For the monounsaturated fatty acid series, an increase in permeation was observed as the carbon-chain length increased, and oleic acid (C18:1) showed the highest permeation-enhancing effect. Increasing the number of double bonds in the octadecanoic acids resulted in a parabolic effect in the permeation of diclofenac, revealing oleic acid as the most effective enhancer used in this study. When the carboxylic acid moiety of oleic acid was changed to an amide (oleamide) or hydroxyl (oleyl alcohol) group, a decrease in permeation activity was observed. These results, therefore, suggest that the cis-monounsaturated configuration and the carboxylic acid moiety of an 18-carbon unit fatty acid in PG are the optimum requirements for the effective skin permeation of diclofenac.
A new generation of Ca2+ indicators with greatly improved fluorescence properties. (1985)

A new family of highly fluorescent indicators has been synthesized for biochemical studies of the physiological role of cytosolic free Ca2+. The compounds combine an 8-coordinate tetracarboxylate chelating site with stilbene chromophores. Incorporation of the ethylenic linkage of the stilbene into a heterocyclic ring enhances the quantum efficiency and photochemical stability of the fluorophore. Compared to their widely used predecessor, "quin2", the new dyes offer up to 30-fold brighter fluorescence, major changes in wavelength not just intensity upon Ca2+ binding, slightly lower affinities for Ca2+, slightly longer wavelengths of excitation, and considerably improved selectivity for Ca2+ over other divalent cations. These properties, particularly the wavelength sensitivity to Ca2+, should make these dyes the preferred fluorescent indicators for many intracellular applications, especially in single cells, adherent cell layers, or bulk tissues.
Dietary supplementation with n-3 polyunsaturated fatty acids and vitamin E after myocardial infarction: results of the GISSI-Prevenzione trial. Gruppo Italiano per lo Studio della Sopravvivenza nell'Infarto miocardico. (1999)

Dietary supplementation with n-3 PUFA led to a clinically important and statistically significant benefit. Vitamin E had no benefit. Its effects on fatal cardiovascular events require further exploration.
Leveraging BERT for Extractive Text Summarization on Lectures (2019)

In the last two decades, automatic extractive text summarization on lectures has demonstrated to be a useful tool for collecting key phrases and sentences that best represent the content. However, many current approaches utilize dated approaches, producing sub-par outputs or requiring several hours of manual tuning to produce meaningful results. Recently, new machine learning architectures have provided mechanisms for extractive summarization through the clustering of output embeddings from deep learning models. This paper reports on the project called Lecture Summarization Service, a python based RESTful service that utilizes the BERT model for text embeddings and KMeans clustering to identify sentences closes to the centroid for summary selection. The purpose of the service was to provide students a utility that could summarize lecture content, based on their desired number of sentences. On top of the summary work, the service also includes lecture and summary management, storing content on the cloud which can be used for collaboration. While the results of utilizing BERT for extractive summarization were promising, there were still areas where the model struggled, providing feature research opportunities for further improvement.
Ultra-Fast Bloom Filters using SIMD Techniques (2018)

The network link speed is growing at an ever-increasing rate, which requires all network functions on routers/switches to keep pace. Bloom filter is a widely-used membership check data structure in networking applications. Correspondingly, it also faces the urgent demand of improving the performance in membership check speed. To this end, this paper proposes a new Bloom filter variant called Ultra-Fast Bloom Filters (UFBF), by leveraging the Single Instruction Multiple Data (SIMD) techniques. We make three improvements for UFBF to accelerate the membership check speed. First, we develop a novel hash computation algorithm which can compute multiple hash functions in parallel with the use of SIMD instructions. Second, we elaborate a Bloom filter's bit-test process from sequential to parallel, enabling more bit-tests per unit time. Third, we improve the cache efficiency of membership check by encoding an element's information to a small block so that it can fit into a cache-line. We further generalize UFBF, called c-UFBF, to make UFBF supporting large number of hash functions. Both theoretical analysis and extensive evaluations show that the UFBF greatly outperforms the state-of-the-art Bloom filter variants on membership check speed.
MEMS vacuum packaging technology and applications (2004)

Vacuum packaging is essential for various kinds of microelectromechanical system (MEMS) devices for enhancing the performance and reliability. This paper presents our works on research on vacuum packaging of MEMS devices. A hermetical sealing technique has been developed, which involves the processes of anodic bonding for silicon and glass wafers with imperfect interface, adhesive bonding, glass frit bonding and silicon-to-gold eutectic bonding. Vacuum maintenance has been achieved by applying evaporable and nonevaporable getter films in the packaging process. A specific helium leak detector with bombing system is introduced, which can monitor the deformation of micro diaphragms and conduct leak detection for MEMS structures.
Lipid-Dependent Membrane Protein Topogenesis (2009)

The topology of polytopic membrane proteins is determined by topogenic sequences in the protein, protein-translocon interactions, and interactions during folding within the protein and between the protein and the lipid environment. Orientation of transmembrane domains is dependent on membrane phospholipid composition during initial assembly as well as on changes in lipid composition postassembly. The membrane translocation potential of negative amino acids working in opposition to the positive-inside rule is largely dampened by the normal presence of phosphatidylethanolamine, thus explaining the dominance of positive residues as retention signals. Phosphatidylethanolamine provides the appropriate charge density that permits the membrane surface to maintain a charge balance between membrane translocation and retention signals and also allows the presence of negative residues in the cytoplasmic face of proteins for other purposes.
Temperature dependent magnetic properties of highly chemically ordered Fe55−xNixPt45L1 films (2002)

Magnetic media using materials with high uniaxial magneto-crystalline anisotropy, KU, combined with a thermal assist to overcome write field limitations have been proposed as one of the potential technologies to extend the areal density of magnetic disk recording beyond the limitations of current technology. Here we present an investigation on structural and temperature dependent magnetic properties of chemically ordered epitaxial Fe55−xNixPt45 thin films. Increasing Ni additions result in a steady reduction of magneto-crystalline anisotropy, saturation magnetization, and Curie temperature. The ability to control thermomagnetic properties over a wide range makes Fe55−xNixPt45 and similar FePt-based pseudo-binary alloys attractive base materials for media applications in thermally assisted magnetic recording.
TiO2 Surface Active Sites for Water Splitting (2006)

The mechanism of photoreactivity between the TiO(2) surface and H(2)O, and the related charge transfer, is considered in terms of both collective and local properties. It is shown that the effective charge transfer between TiO(2) and water requires the presence of surface active sites that are able to provide electron holes to adsorbed water molecules. Titanium vacancies located at or near the surface are identified as the active sites for water adsorption leading to the formation of an active complex and resulting, in consequence, in water splitting. A model of the photoreactivity between the TiO(2) surface and water is proposed. This model indicates that the photoreactivity of the TiO(2)-based photoelectrode may be enhanced through imposition of the surface active sites (Ti vacancies) in a controlled manner by surface engineering.
Characterization of self-limitingSiH2Cl2chemisorption and photon-stimulated desorption as elementary steps for Si atomic-layer epitaxy (1996)

The reactive sticking of ${\mathrm{SiH}}_{2}$${\mathrm{Cl}}_{2}$ and the photon-stimulated desorption (PSD) of H and Cl atoms passivating the resulting surface have been investigated as elementary steps in the synchrotron-radiation-excited atomic layer epitaxy (SR-ALE) of Si crystals. The temperature dependence of the amount of Si adatoms delivered to a Ge(100) surface exhibits bistable self-limiting features. Two plateau regimes are observed: (I) below 260 \ifmmode^\circ\else\textdegree\fi{}C, and (II) between 430 and 500 \ifmmode^\circ\else\textdegree\fi{}C. In regime (I) all H and Cl atoms bound to the ${\mathrm{SiH}}_{2}$${\mathrm{Cl}}_{2}$ gas molecules are left on the surface. In regime (II), ${\mathrm{H}}_{2}$ and HCl desorption, Si adatom migration and rearrangement promote increasing Si coverage. Time-of-flight mass spectroscopy detected the PSD of ${\mathrm{Cl}}^{+}$ and ${\mathrm{HCl}}^{+}$ species, and the kinetics of the Cl removal process were found to be first order. More than 90% of the initially present Cl atoms can be removed by PSD, while H atoms are only partially removed. The temperature dependence of the SR-ALE growth rate shows two plateaus corresponding to the two regimes seen in the temperature dependence of Si uptake on a Ge(100) surface. \textcopyright{} 1996 The American Physical Society.
Relocalization of the Mre11-Rad50-Nbs1 Complex by the Adenovirus E4 ORF3 Protein Is Required for Viral Replication (2005)

Adenovirus replication is controlled by the relocalization or modification of nuclear protein complexes, including promyelocytic leukemia protein (PML) nuclear domains and the Mre11-Rad50-Nbs1 (MRN) DNA damage machinery. In this study, we demonstrated that the E4 ORF3 protein effects the relocalization of both PML and MRN proteins to similar structures within the nucleus at early times after infection. These proteins colocalize with E4 ORF3. Through the analysis of specific viral mutants, we found a direct correlation between MRN reorganization at early times after infection and the establishment of viral DNA replication domains. Further, the reorganization of MRN components may be uncoupled from the ability of E4 ORF3 to rearrange PML. At later stages of infection, components of the MRN complex disperse within the nucleus, Nbs1 is found within viral replication centers, Rad50 remains localized with E4 ORF3, and Mre11 is degraded. The importance of viral regulation of the MRN complex is underscored by the complementation of E4 mutant viruses in cells that lack Mre11 or Nbs1 activity. These results illustrate the importance of nuclear organization in virus growth and suggest that E4 ORF3 regulates activities in both PML nuclear bodies and the MRN complex to stimulate the viral replication program.
Examination of Bcl‐2, Bcl‐X and bax protein expression in psoriasis (2003)

These findings indicate a discordant expression of bcl-2 and bax/bcl-x in psoriatic epidermis. Increased bcl-x expression might contribute to the antiapoptotic response in psoriatic keratinocytes. The presence of strong bax expression with a concomitant decrease in bcl-2 expression suggests either a functional defect in bax protein or an inherent/acquired resistance to bax-mediated apoptosis in psoriatic keratinocytes.
Understanding Geographical Markets of Online Firms Using Spatial Models of Customer Choice (2005)

As the online channel matures, many firms are finding that an understanding of how their online customers' preferences and choices vary across geographical markets can be very useful. In this paper, we propose a spatial multinomial model of customer choice and illustrate how spatial modeling of choices of online customers across geographical markets provides useful insights in the context of a product mix and pricing decision of an online book publisher. The spatial multinomial model specifically accounts for the spatial correlations among customer choices among different product forms—print and PDF. The estimation results obtained using data generated from an online experiment show that the spatial model accounts for the geographical variation in many of the unobserved effects possibly due to locational differences and price sensitivities. The resultant spatial decision maps provide useful predictions as to how purchase rates vary across geographical markets as a function of the price differential between product forms, with implications for targeting customers through local market advertising, direct marketing, and cross-channel promotion.
A binary matrix of 2,5‐dihydroxybenzoic acid and glycerol produces homogenous sample preparations for matrix‐assisted laser desorption/ionization mass spectrometry (2007)

We introduce a two-component matrix for ultraviolet matrix-assisted laser desorption/ionization mass spectrometry (UV-MALDI-MS) that consists of 2,5-dihydroxybenzoic acid (DHB) and glycerol. Upon slow evaporation of residual water/methanol solvents in a pre-vacuum chamber sample preparations are obtained that exhibit a homogeneous morphology with analyte-matrix crystals evenly distributed over the whole sample spot. At a molar DHB/glycerol ratio of approximately 1:5, the crystals range in length from approximately 100 to 300 microm and are about 15-30 microm wide. Mass spectra of peptides, proteins, and an oligosaccharide are presented and compared with those recorded from standard dried-droplet DHB matrix. The ion signals show a reproducibility of the order of 10-15% when scanning the surface of an individual sample or even different samples that contain the same amount of peptide, A close to linear relationship between peptide concentration and the corresponding peptide ion signal is found over three orders of magnitude of sample prepared. However, when a fixed position is irradiated with a large number of laser pulses, a monotonous decay of peptide ion signal with time is observed. Potentially, the binary matrix will be especially useful for the analysis of samples that are stabilized in buffered aqueous glycerol solution and preliminary results addressing this aspect are shown.
The cobra venom factor-dependent C3 convertase of human complement. A kinetic and thermodynamic analysis of a protease acting on its natural high molecular weight substrate. (1982)

Enzymes of the complement system exhibit, unlike most other proteases, a high substrate specificity, hydrolyzing only a single peptide bond in their protein substrates.This property allowed the performance of a detailed analysis of the enzymatic activity of a protease acting on its natural high molecular weight substrate.The enzyme investigated was the cobra venom factor-dependent C3 convertase (EC 3.4.21.47) of human complement.The enzyme constitutes a bimolecular complex of cobra venom factor and the catalytic site bearing fragment Bb of human Factor B. It hydrolyzes peptide bond 77 (Arg-Ser) of the a-chain of the human complement protein C3, thereby producing the fragments C3a and C3b.The enzyme was generated from isolated proteins.It exhibited spontaneous decaydissociation into its subunits with a half-life of 7 h at 37 "C.The following kinetic parameters for C3 hydrolysis were determined: the Michaelis constant, K,, the catalytic constant, kc,,, the turnover number, the catalytic cycle time, the specific activity, the apparent second order rate constant, k,,,/K,, and the apparent first order rate constant for the low substrate concentration range.The encounter of enzyme and substrate proceeded under rapid equilibrium conditions.For the formation of the enzyme-substrate complex, the equilibrium constant, K, the standard enthalpy, AH", standard entropy, AS", and standard Gibbs energy, AG", were determined.For the rate-limiting step of the overall reaction, the activation energy, E,, activation enthalpy, AH*, activation entropy, AS*, and Gibbs energy of activation, AG*, were derived.The results demonstrate that action of a protease of high molecular weight (Mr = 210,000) on its substrate of high molecular weight (Mr = 185,000) can be described in terms of Michaelis-Menten kinetics.The data are consistent with a double intermediate catalytic mechanism and a kinetic mechanism of a Tetra Uni Ping Pang Bi Bi reaction reduced to a Uni Bi reaction and therefore support the serine protease concept of Factor B-derived enzymes.