gebhart/patrepeval huggingface dataset:
P-C3 Targeting the epitopes in the C1-C2 region of HIV-1 gp120 for effective Fc-mediated effector function (2016)

Accumulating evidence indicates a role for Fc receptor (FcR)-mediated effector functions of antibodies, including antibody-dependent cell- mediated cytotoxicity (ADCC), in prevention of HIV-1 acquisition and in post-infection control of viremia. Consequently, an understanding of the molecular basis for Env epitopes that constitute effective ADCC targets is of fundamental interest for humoral anti-HIV-1 immunity and for HIV-1 vaccine design. A substantial portion of FcR-effector function of potentially protective anti-HIV-1 antibodies is directed toward non-neutralizing, transitional, CD4-induceable (CD4i) epitopes associated with the gp41 reactive region of gp120 (Cluster A epitopes). Our previous studies defined two highly conserved epitope sub-groups within the Cluster A region; the A32-like epitope which maps to the mobile layers 1 and 2 within C1- C2 regions of gp120 and a hybrid A32-C11-like epitope which maps to elements of both the A32-like sub-region and the 7 layered β-sheet of the gp41-interactive region of gp120. Here we elucidate the structural basis for antigen engagement into an effective immune-complex that leads to potent ADCC function to the Cluster A region. We also present the structure based design of an independent inner domain molecule, ID, an immunogen candidate stably expressing the Cluster A epitopes involved in potent FcR-effector function to HIV-1 within a minimal structural unit of gp120.
Synthetic Applications of Azolium Ylides to a Traceless Solid-Phase Synthesis of 2-Substituted Azoles (2002)

A new approach for the preparation of 2-substituted azole libraries using a polystyrene-carbamyl chloride resin in a traceless fashion is described. Azole substrates II are assembled in a one-pot condensation reaction of azoles and aldehydes with a resin-bound carbamyl chloride. Treatment of the azolyl-carbamate II with boron trifluoride etherate under thermal or microwave-assisted solvolysis conditions afforded 2-substituted azoles. [reaction: see text]
Wettability Alteration of Polymer Surfaces Produced by Scraping (2008)

In this paper, we present a simple, yet novel, method, utilizing scraping to obtain continuous rough microstructures over large areas, leading to a tunable wettability conversion from hydrophilicity to superhydrophobicity on polymer surfaces. A series of polymers ranging from hydrophobic to hydrophilic were used, and we found that the wettability of these polymer surfaces could be modified by the scraping process, irrespective of their hydrophobicity or hydrophilicity. More importantly, those polymers with contact angle ranging from 65° to 90° on their smooth surfaces also exhibit enhanced hydrophobicity after scraping. Our results indicate that 65° is the critical value which is more suitable to define hydrophobicity and hydrophilicity for polymer materials.
Low‐Dimensional Organic Tin Bromide Perovskites and Their Photoinduced Structural Transformation (2017)

Hybrid organic-inorganic metal halide perovskites possess exceptional structural tunability, with three- (3D), two- (2D), one- (1D), and zero-dimensional (0D) structures on the molecular level all possible. While remarkable progress has been realized in perovskite research in recent years, the focus has been mainly on 3D and 2D structures, with 1D and 0D structures significantly underexplored. The synthesis and characterization of a series of low-dimensional organic tin bromide perovskites with 1D and 0D structures is reported. Using the same organic and inorganic components, but at different ratios and reaction conditions, both 1D (C<sub>4</sub> N<sub>2</sub> H<sub>14</sub> )SnBr<sub>4</sub> and 0D (C<sub>4</sub> N<sub>2</sub> H<sub>14</sub> Br)<sub>4</sub> SnBr<sub>6</sub> can be prepared in high yields. Moreover, photoinduced structural transformation from 1D to 0D was investigated experimentally and theoretically in which photodissociation of 1D metal halide chains followed by structural reorganization leads to the formation of a more thermodynamically stable 0D structure.
Single-Step Conversion of Cells to Retrovirus Vector Producers with Herpes Simplex Virus–Epstein-Barr Virus Hybrid Amplicons (1999)

We report here on the development and characterization of a novel herpes simplex virus type 1 (HSV-1) amplicon-based vector system which takes advantage of the host range and retention properties of HSV-Epstein-Barr virus (EBV) hybrid amplicons to efficiently convert cells to retrovirus vector producer cells after single-step transduction. The retrovirus genes gag-pol and env (GPE) and retroviral vector sequences were modified to minimize sequence overlap and cloned into an HSV-EBV hybrid amplicon. Retrovirus expression cassettes were used to generate the HSV-EBV-retrovirus hybrid vectors, HERE and HERA, which code for the ecotropic and the amphotropic envelopes, respectively. Retrovirus vector sequences encoding lacZ were cloned downstream from the GPE expression unit. Transfection of 293T/17 cells with amplicon plasmids yielded retrovirus titers between 10(6) and 10(7) transducing units/ml, while infection of the same cells with amplicon vectors generated maximum titers 1 order of magnitude lower. Retrovirus titers were dependent on the extent of transduction by amplicon vectors for the same cell line, but different cell lines displayed varying capacities to produce retrovirus vectors even at the same transduction efficiencies. Infection of human and dog primary gliomas with this system resulted in the production of retrovirus vectors for more than 1 week and the long-term retention and increase in transgene activity over time in these cell populations. Although the efficiency of this system still has to be determined in vivo, many applications are foreseeable for this approach to gene delivery.
Material synthesis routes for thin film bonding interfaces in reworkable and bumpless nano-interconnects (2004)

This work explores novel material synthesis routes towards reworkable nano-dimensional interfaces for IC-package assembly, leading to bumpless and nano interconnections. Reworkability is addressed by a thin interface of lead-free high-strength solders. Two approaches, sol-gel process and electroless plating, were used to achieve these nano-dimensional bonding interfaces. In the sol-gel process, metal-organic polymer solutions were heat-treated in a reducing atmosphere at 400/spl deg/C to form lead-free solders (Sn-Ag-Cu). In the electroless plating approach, lead-free alloy films were deposited from aqueous plating solutions consisting of suitable metal salts and reducing agents. This process was done at a temperature of 45/spl deg/C. The lead-free solder composition was controlled by altering the plating bath formulation. Solder films formed from both the above approaches were demonstrated to bond copper pads. Solution-derived nano-solder technology is an attractive low-cost method for bumpless nano-interconnects and other applications such as MEMS hermetic packaging and compliant interconnect bonding.
Quantum-Size-Controlled Photoelectrochemical Fabrication of Epitaxial InGaN Quantum Dots (2014)

We demonstrate a new route to the precision fabrication of epitaxial semiconductor nanostructures in the sub-10 nm size regime: quantum-size-controlled photoelectrochemical (QSC-PEC) etching. We show that quantum dots (QDs) can be QSC-PEC-etched from epitaxial InGaN thin films using narrowband laser photoexcitation, and that the QD sizes (and hence bandgaps and photoluminescence wavelengths) are determined by the photoexcitation wavelength. Low-temperature photoluminescence from ensembles of such QDs have peak wavelengths that can be tunably blue shifted by 35 nm (from 440 to 405 nm) and have line widths that narrow by 3 times (from 19 to 6 nm).
The Angiogenic and Lymphangiogenic Factor Vascular Endothelial Growth Factor-D Exhibits a Paracrine Mode of Action in Cancer (2002)

Vascular endothelial growth factor-D (VEGF-D) promotes angiogenesis, lymphangiogenesis and metastatic spread via the lymphatics, however, the mode of VEGF-D action (e.g. paracrine vs. autocrine) was unknown. We analyzed VEGF-D action in human tumors and a mouse model of metastasis. VEGF-D was localized in tumor cells and endothelium in human non-small cell lung carcinoma and breast ductal carcinoma in situ. Tumor vessels positive for VEGF-D were also positive for its receptors, VEGF receptor-2 (VEGFR-2) and/or VEGFR-3 but negative for VEGF-D mRNA, indicating that VEGF-D is secreted by tumor cells and subsequently associates with endothelium via receptor-mediated uptake. The mature form of VEGF-D was detected in tumors demonstrating that VEGF-D is proteolytically processed and bioactive. In a mouse model of metastasis, VEGF-D synthesized in tumor cells became localized on the endothelium and thereby promoted metastatic spread. These data indicate that VEGF-D promotes tumor angiogenesis, lymphangiogenesis and metastatic spread by a paracrine mechanism.
Measuring Traces Of Oxygen By Resonant Electron Attachment (1995)

Method of detecting trace amounts of oxygen based on dissociative attachment of electrons to oxygen molecules followed by measurement of resulting flux of negative oxygen ions in mass spectrometer. High sensitivity achieved in method by exploiting resonance in dissociative attachment of electrons to oxygen molecules: electron-attachment cross section rises to high peak at incident electron kinetic energy of 6.2 eV. Relative concentrations below 1 ppb detected. Devised to increase sensitivity of detection of oxygen in processing chambers in which oxygen regarded as contaminant; for example, chambers used in making semiconductor devices and in growing high-purity crystals.
Self-Assembly of Short Linear Chains to A- and B-Type Starch Spherulites and Their Enzymatic Digestibility (2013)

A novel process combining enzymatic debranching, melting, and crystallization was developed to produce spherulites from short linear α-1,4-linked glucans (short-chain amylose, SCA) with controlled enzyme digestibility. SCA was obtained by completely debranching waxy maize starch at 50 °C and 25% solids in 0.01 M sodium acetate buffer. The mixture was then heated to 180 °C followed by cooling and crystallization to form well-developed spherulites. Multiple analytical techniques including light microscopy, scanning electron microscopy, differential scanning calorimetry, wide-angle X-ray diffraction, and synchrotron small-angle X-ray scattering (SAXS) covered over 5 orders of length scale and were applied to study the morphology and structure of the spherulites. Spherulites crystallized at low temperatures (4 and 25 °C) had a large size (5-10 μm), a B-type starch X-ray diffraction pattern, a lower melting temperature (70-110 °C), and a higher digestibility (Englyst method) compared to the spherulites crystallized at 50 °C, which had a small size (1-5 μm), an A-type diffraction pattern, a higher melting temperature (100-140 °C), and a lower digestibility. Intact spherulites along with small fragments were observed after digestion with a mixture of α-amyase and amyloglucosidase, indicating that digestion was not homogeneous and preferentially occurred in weak spherulites. A second exposure of the undigested residues to the amylases showed a similar digestive pattern as with the parent spherulites, suggesting that the spherulites were hydrolyzed by enzymes at essentially a constant digestion rate between 20 min and 3 h.
Maize Ribosome-Inactivating Protein (b-32) (Homologs in Related Species, Effects on Maize Ribosomes, and Modulation of Activity by Pro-Peptide Deletions) (1995)

The ribosome-inactivating protein (RIP) from maize (Zea mays L.) is unusual in that it is produced in the endosperm as an inactive pro-form, also known as b-32, which can be converted by limited proteolysis to a two-chain active form, alpha beta RIP. Immunological analysis of seed extracts from a variety of species related to maize showed that pro/alpha beta forms of RIP are not unique to maize but are also found in other members of the Panicoideae, including Tripsacum and sorghum. Ribosomes isolated from maize were quite resistant to both purified pro- and alpha beta maize RIPs, whereas they were highly susceptible to the RIP from pokeweed. This suggests that the production of an inactive pro-RIP is not a mechanism to protect the plant's own ribosomes from deleterious action of the alpha beta RIP. RIP derivatives with various pro-segments removed were expressed at high levels in Escherichia coli. Measurement of their activity before and after treatment with subtilisin Carlsberg clearly identified the 25-amino acid intradomain insertion, rather than the N- or C-terminal extensions, as the major element responsible for suppression of enzymatic activity. A RIP with all three processed regions deleted had activity close to that of the native alpha beta form.
Photophysics and Electrochemiluminescence of Bright Cyclometalated Ir(III) Complexes in Aqueous Solutions (2016)

A family of neutral bis-cyclometalated iridium complexes [Ir(C^N)2(LX)] has been investigated as ECL labels under immunoassay conditions. Among them, the complex based on phenylphenanthridine (pphent) as the C^N ligand, exhibits outstanding performance and it is a candidate to substitute the commercially available Ru-based label in diagnostics.
61.5L: <i>Late‐News Paper</i> : Extremely Long Lived White Phosphorescent Organic Light Emitting Device with Minimum Organic Materials (2008)

Abstract A non‐stacked white phosphorescent organic light emitting device with 6 organic materials is demonstrated with extremely long lifetime of LT50 >200,000 hrs from 1,000 nits initial luminance. At 1,000 nits without enhanced outcoupling, EQE = 15.3% (32.4 cd/A), operating voltage = 6.3 V, power efficacy = 16.1 lm/W (30 lm/W with outcoupling enhancement), and CIE (0.45, 0.46).
Continuous-Flow Process for the Purification and Fractionation of Alkali and Organosolv Lignins (2016)

Hot acetic acid–water mixtures can be used to purify and fractionate alkali (kraft) and organosolv lignins via the Aqueous Lignin Purification with Hot Acids (ALPHA) process. However, condensation polymerization reactions can occur in the solvated, lignin-rich liquid fraction at the elevated temperatures (e.g., 60–100 °C) of operation, significantly increasing the lignin molecular weight. Thus, conversion of ALPHA to continuous-flow operation was investigated in order to determine the effect of reduced residence times on both the above reactions and on the extraction of metals from the solvated lignin to the solvent phase. All four lignins investigated could be converted to a homogeneous lignin–water slurry at ambient temperatures, facilitating continuous operation. When a static mixer is used for the mixing and equilibration device, reducing residence times to 20–30 s, condensation polymerization reactions are essentially eliminated. For example, the molecular weight of the lignin fraction remained unchanged with continuous processing but increased from 7900 to 13200 when batch processing was used for the same ALPHA conditions. Furthermore, the 10-fold reduction in metals content (e.g., sodium content reduced from 1400 to <100 ppm) was equal to or better than that obtained by single-stage batch processing. Thus, continuous ALPHA can be used to obtain an ultrapure, metals-free lignin of well-defined and controllable molecular weight.
Hydroxylated boron nitride nanotube‐reinforced polyvinyl alcohol nanocomposite films with simultaneous improvement of mechanical and thermal properties (2020)

Abstract Stable dispersion of boron nitride nanotube (BNNT) in a solvent is a critical challenge that has restricted the development of potential applications. In this study, stable BNNT aqueous dispersions are obtained by direct tip sonication in water without any surfactant and organic solvent. BNNTs are functionalized with hydroxyl groups (OH) as a result of the tip sonication‐assisted hydrolysis. The energy from tip sonication results in the disentanglement of the as‐received BNNT clusters and partial B‐N bond cleavage to unzip nanotubes. Using the BNNT aqueous dispersion, a transparent, strong, and ductile OH‐BNNT‐reinforced polyvinyl alcohol (PVA) multifunctional nanocomposite film is prepared. Tensile fracture strength, Young's modulus, and elongation at failure of 1.0 wt% OH‐BNNT/PVA nanocomposite film increased by 46%, 55%, and 45%, respectively, in comparison with pure PVA film. The addition of a mere 1.0 wt% BNNT contributed to a significant (25%) improvement in thermal conductivity. Simultaneous improvement in mechanical and thermal properties is attributed to the superior intrinsic properties of homogenously dispersed BNNTs and strong interfacial interactions between OH‐BNNT and PVA chains.
A Comparison Between Bass Management Parameter Selection Techniques for Multichannel and Multi-position Room Equalization (2006)

Traditionally, room acoustic equalization is performed to improve sound quality. In a multi-channel audio system, employing simultaneous multi-position room equalization, the selection of the bass management parameter(s) between the subwoofer and a satellite is important for accurate reproduction of sound at the listening positions. Presently, many systems, such as home-theater receivers, have selectable crossover frequencies with fixed decay rates. Furthermore, the crossover frequency is selected by the user through informal listening tests. However, a choice of a single bass management parameter (viz., the crossover frequency) can limit equalization performance in the crossover region at all listening positions as shown in this paper. Such limitations arise from interactions, due to complex addition (i.e., phase and amplitude) of the subwoofer and satellite response, and manifest as large spectral deviations in the crossover region. In this paper, we present a comparison in the equalization performance resulting from the automatic optimization of a single bass management parameter (viz., the crossover frequency) with an all-parameter optimization (viz., the crossover frequency and the decay rates) using the spectral deviation measure. As expected, the results indicate that the all-parameter optimization provides a significant improvement over the standard single parameter optimization
[WT1 peptide-based immunotherapy]. (2005)

The Wilms' tumor gene WT1 is overexpressed in leukemia and various types of solid cancers and its product is a tumor rejection antigen. A phase I clinical trials of WT1 peptide-based cancer immunotherapy were performed with good clinical response but with only skin reaction at the injection sites of WT1 vaccine. Thus, WT1-targeting immunotherapy should be promissing.
A genetic algorithm for video segmentation and summarization (2002)

We describe a genetic segmentation algorithm for video. This algorithm operates on segments of a string representation. It is similar to both classical genetic algorithms that operate on bits of a string and genetic grouping algorithms that operate on subsets of a set. For evaluating segmentations, we define similarity adjacency functions, which are extremely expensive to optimize with traditional methods. The evolutionary nature of genetic algorithms offers a further advantage by enabling incremental segmentation. Applications include video summarization and indexing for browsing, plus adapting to user access patterns.
Lossless and near-lossless source coding for multiple access networks (2003)

A multiple access source code (MASC) is a source code designed for the following network configuration: a pair of correlated information sequences {X/sub i/}/sub i=1//sup /spl infin// and {Y/sub i/}/sub i=1//sup /spl infin// is drawn independent and identically distributed (i.i.d.) according to joint probability mass function (p.m.f.) p(x,y); the encoder for each source operates without knowledge of the other source; the decoder jointly decodes the encoded bit streams from both sources. The work of Slepian and Wolf describes all rates achievable by MASCs of infinite coding dimension (n/spl rarr//spl infin/) and asymptotically negligible error probabilities (P/sub e//sup (n)//spl rarr/0). In this paper, we consider the properties of optimal instantaneous MASCs with finite coding dimension (n</spl infin/) and both lossless (P/sub e//sup (n)/=0) and nearlossless (P/sub e//sup (n)//spl rarr/0) performance. The interest in near-lossless codes is inspired by the discontinuity in the limiting rate region at P/sub e//sup (n)/=0 and the resulting performance benefits achievable by using near-lossless MASCs as entropy codes within lossy MASCs. Our central results include generalizations of Huffman and arithmetic codes to the MASC framework for arbitrary p(x,y), n, and P/sub e//sup (n)/ and polynomial-time design algorithms that approximate these optimal solutions.
Tyrosylprotein sulfotransferase: Purification and molecular cloning of an enzyme that catalyzes tyrosine <i>O</i> -sulfation, a common posttranslational modification of eukaryotic proteins (1998)

Tyrosine O-sulfation is a common posttranslational modification of proteins in all multicellular organisms. This reaction is mediated by a Golgi enzyme activity called tyrosylprotein sulfotransferase (TPST) that catalyzes the transfer of sulfate from 3'-phosphoadenosine 5'-phosphosulfate to tyrosine residues within acidic motifs of polypeptides. Tyrosine O-sulfation has been shown to be important in protein-protein interactions in several systems. For example, sulfation of tyrosine residues in the leukocyte adhesion molecule P-selectin glycoprotein ligand 1 (PSGL-1) is required for binding to P-selectin on activated endothelium. In this report we describe the purification of TPST from rat liver microsomes based on its affinity for the N-terminal 15 amino acids of PSGL-1. We have isolated human and mouse TPST cDNAs that predict type II transmembrane proteins of 370 amino acid residues with almost identical primary structure. The human cDNA encodes a fully functional N-glycosylated enzyme with an apparent molecular mass of approximately 54 kDa when expressed in mammalian cells. This enzyme defines a new class of Golgi sulfotransferases that may catalyze tyrosine O-sulfation of PSGL-1 and other protein substrates involved in diverse physiologic functions including inflammation and hemostasis.
The influence of conjugation variables on the design and immunogenicity of a glycoconjugate vaccine against Salmonella Typhi (2017)

In recent years there have been major efforts to develop glycoconjugate vaccines based on the Vi polysaccharide that will protect against Salmonella enterica Typhi infections, particularly typhoid fever, which remains a major public health concern in low-income countries. The design of glycoconjugate vaccines influences the immune responses they elicit. Here we systematically test the response in mice to Vi glycoconjugates that differ in Vi chain length (full-length and fragmented), carrier protein, conjugation chemistry, saccharide to protein ratio and size. We show that the length of Vi chains, but not the ultimate size of the conjugate, has an impact on the anti-Vi IgG immune response induced. Full-length Vi conjugates, independent of the carrier protein, induce peak IgG responses rapidly after just one immunization, and secondary immunization does not enhance the magnitude of these responses. Fragmented Vi linked to CRM197 and diphtheria toxoid, but not to tetanus toxoid, gives lower anti-Vi antibody responses after the first immunization than full-length Vi conjugates, but antibody titres are similar to those induced by full-length Vi conjugates following a second dose. The chemistry to conjugate Vi to the carrier protein, the linker used, and the saccharide to protein ratio do not significantly alter the response. We conclude that Vi length and carrier protein are the variables that influence the anti-Vi IgG response to immunization the most, while other parameters are of lesser importance.