gebhart/patrepeval huggingface dataset:
Structural basis for the recognition of LDL-receptor family members by VSV glycoprotein (2018)

Vesicular stomatitis virus (VSV) is an oncolytic rhabdovirus and its glycoprotein G is widely used to pseudotype other viruses for gene therapy. Low-density lipoprotein receptor (LDL-R) serves as a major entry receptor for VSV. Here we report two crystal structures of VSV G in complex with two distinct cysteine-rich domains (CR2 and CR3) of LDL-R, showing that their binding sites on G are identical. We identify two basic residues on G, which are essential for its interaction with CR2 and CR3. Mutating these residues abolishes VSV infectivity even though VSV can use alternative receptors, indicating that all VSV receptors are members of the LDL-R family. Collectively, our data suggest that VSV G has specifically evolved to interact with receptor CR domains. These structural insights into the interaction between VSV G and host cell receptors provide a basis for the design of recombinant viruses with an altered tropism.
Autoproteolysis in hedgehog protein biogenesis (1994)

Extracellular signaling proteins encoded by the hedgehog (hh) multigene family are responsible for the patterning of a variety of embryonic structures in vertebrates and invertebrates. The Drosophila hh gene has now been shown to generate two predominant protein species that are derived by an internal autoproteolytic cleavage of a larger precursor. Mutations that reduced the efficiency of autoproteolysis in vitro diminished precursor cleavage in vivo and also impaired the signaling and patterning activities of the HH protein. The two HH protein species exhibited distinctive biochemical properties and tissue distribution, and these differences suggest a mechanism that could account for the long- and short-range signaling activities of HH in vivo.
Subtle differences in antibody responses and hypermutation of λ light chains in mice with a disrupted χ constant region (1995)

Analysis of lambda light chain use in normal mice is made difficult by the dominant chi light chain repertoire. We produced mice rendered deficient in chi light chain expression by gene targeting and focused on questions concerned with the generation of lambda light chain diversity. Whilst these mice compensate the chi deficiency with increased lambda liters, and their Ig level is therefore not significantly reduced, they show major differences in immunization titers, germinal center (GC) development and somatic hypermutation. After immunization, using antigens that elicit a restricted IgL response in normal mice, we obtained in the chi-/- mice elevated primary antibody titers but a subsequent lack in titer increase after repeated antigen challenge. Analysis of the Peyer's patches (PP) revealed a dramatically reduced cell content with rather small but highly active GC. Flow cytometric analysis showed different cell populations in the PP with enriched peanut agglutinin (PNA)hi/CD45R(B220)+ B cells, implying that the apparent compensation for the lack of lambda light chain expression involves the GC microenvironment in cell selection, the initiation of hypermutation and high affinity expansion. The three V lambda genes, V1, V2 and Vx, are mutated in the GC B cells, but show no junctional diversity. In contrast, a reduced rate of V lambda hypermutation is found in the hybridoma antibodies, which appears to reflect a selection bias rather than structural constraints. However, mechanisms of somatic mutation and specificity selection can operate with equal efficiency on the few V lambda genes.
Dielectrophoretic isolation and detection of cancer‐related circulating cell‐free DNA biomarkers from blood and plasma (2014)

Conventional methods for the isolation of cancer-related circulating cell-free (ccf) DNA from patient blood (plasma) are time consuming and laborious. A DEP approach utilizing a microarray device now allows rapid isolation of ccf-DNA directly from a small volume of unprocessed blood. In this study, the DEP device is used to compare the ccf-DNA isolated directly from whole blood and plasma from 11 chronic lymphocytic leukemia (CLL) patients and one normal individual. Ccf-DNA from both blood and plasma samples was separated into DEP high-field regions, after which cells (blood), proteins, and other biomolecules were removed by a fluidic wash. The concentrated ccf-DNA was detected on-chip by fluorescence, and then eluted for PCR and DNA sequencing. The complete process from blood to PCR required less than 10 min; an additional 15 min was required to obtain plasma from whole blood. Ccf-DNA from the equivalent of 5 μL of CLL blood and 5 μL of plasma was amplified by PCR using Ig heavy-chain variable (IGHV) specific primers to identify the unique IGHV gene expressed by the leukemic B-cell clone. The PCR and DNA sequencing results obtained by DEP from all 11 CLL blood samples and from 8 of the 11 CLL plasma samples were exactly comparable to the DNA sequencing results obtained from genomic DNA isolated from CLL patient leukemic B cells (gold standard).
Low complexity algorithm for robust video frame rate up-conversion (FRUC) technique (2009)

Two challenging situations for video frame rate up-conversion (FRUC) are first identified and analyzed; namely, when the input video has abrupt illumination change and/or a low frame rate. Then, a low-complexity processing technique and robust FRUC algorithm are proposed to address these two issues. The proposed algorithm utilizes a translational motion vector model of the first- and the second-order and detects the continuity of these motion vectors. Additionally, in order to improve perceptual quality of interpolated frame, spatial smoothness criterion is employed. The superior performance of the proposed algorithm has been tested extensively and representative examples are given in this work.
Kenaf Dry Matter Production, Chemical Composition, and In Situ Disappearance When Harvested at Different Intervals (1999)

Kenaf (Hibiscus cannabinus L.) is a tropical plant that has potential as a forage crop. However, data on the amount and quality of forage produced by kenaf is scarce. The objectives of this research were to determine 1) the DM yield, proportions of leaf and stalk, and chemical composition and 2) the in situ OM and N disappearance of kenaf harvested throughout the growing season. Kenaf (‘Everglades 41’) was planted in June of 1990, 1991, and 1993. The seeding rate was 5.6 kg/ha and 100 kg of N /ha was applied shortly before or after planting. Harvesting began 40 d after planting (DAP) with additional harvests at 10-d (1991 and 1993) or 20-d (1990) intervals. Daily whole plant DM accumulation ranged from 12.6 to 17.2 g/m2. At 101 DAP, 726 to 974 g of DM were harvested/m2. As kenaf matured, the proportion of the total plant DM represented in leaves decreased (P<0.01) from 68% at 40 DAP to 44% at 101 DAP. Leaf DM contained more (P<0.01) than twice the CP as stalk DM at all harvests. Delaying harvest decreased (P<0.01) whole plant CP concentration from 22% at 40 DP to 15% at 101 DAP, because the stalks made up a larger proportion of the total biomass. The OM in the leaves was twice as digestible (P<0.01) as the OM in the stalks (89.3 vs 44.8%). The N in the leaves was more (P<0.01) digestible than the N in the stalks (93.2 vs 61.5%). Kenaf can be grown during the summer season and harvested as high quality forage as early as 40 DAP. Whole plants harvested at 80 DAP produced from 426 to 729 g/m2 of DM and had a CP content of 14 to 19%. Harvesting later than 80 DAP will increase DM yield, but CP content and in situ OM and N disappearance will decrease.
Phase II trial of single-agent ganetespib (STA-9090), a heat shock protein 90 (Hsp90) inhibitor in heavily pretreated patients with metastatic castration-resistant prostate cancer (mCRPC) post docetaxel-based chemotherapy: Results of a Prostate Cancer Clinical Trials Consortium (PCCTC) study. (2013)

5085 Background: Hsp90 is a molecular chaperone required for the proper folding and activation of numerous client proteins and is critical to cell survival and proliferation. Ganetespib (G), a synthetic small molecule that binds to the ATP pocket in the N-terminus of Hsp90 causes the degradation of cellular proteins and ultimately death of cancer cells dependent on these proteins. G displays potent anticancer activity in prostate cancer cells. Methods: Eligible patients were ≥ 18 yrs old with ECOG performance status ≤ 2. Adequate hepatic, renal, and bone marrow function was required. Patients were treated with G 200 mg/m 2 intravenously once weekly for 3 consecutive weeks followed by 1 off-week. The primary objective was to evaluate the 6-month progression-free survival (PFS). Secondary endpoints included overall safety and tolerability of G and overall survival. Exploratory markers including maspin, cytokeratins 8 and 18, and HDAC1 were obtained pre, during, and post G treatment. We sought ≥ 4 patients with ≥ 6 months PFS (a success) in Stage 1 of a 2-stage near-optimal Simon design. Results: 18 patients were enrolled at 4 institutions. The patients’ median age was 68 (range 51-82), 13 were Caucasian, 4 were African American, and 1 was Asian. Median PSA was 210.7 ng/mL (range 25.9 – 3,489 ng/mL). One patient never started therapy. Among the 17 treated patients, the median number of cycles was 2 (range 1-5). The most frequent Grade 3 toxicities were diarrhea (3 patients), fatigue (3), and dehydration (3). Prior therapy included abiraterone (8), sipuleucel-T (4), and other targeted therapy (4). With &lt; 4 successes in Stage 1, the trial was terminated early. Median PFS was 1.9 months (90% CI: 1.7 – 2.7 months); median OS was 10.2 months (90% CI: 2.3 – 18.3 months). Exploratory markers have been evaluated and will be presented. Conclusions: Our study represents the first clinical trial of G in treating mCRPC patients. As a single agent therapy, G did not prolong PFS. Combination therapy is a consideration to improve therapeutic efficacy. Clinical trial information: NCT01270880.
Quantitation of silanol in silicones by FTIR spectroscopy (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTQuantitation of silanol in silicones by FTIR spectroscopyGreg W. GriffithCite this: Ind. Eng. Chem. Prod. Res. Dev. 1984, 23, 4, 590–593Publication Date (Print):December 1, 1984Publication History Published online1 May 2002Published inissue 1 December 1984https://pubs.acs.org/doi/10.1021/i300016a015https://doi.org/10.1021/i300016a015research-articleACS PublicationsRequest reuse permissionsArticle Views1195Altmetric-Citations24LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Kinetics of Gag-specific cytotoxic T lymphocyte responses during the clinical course of HIV-1 infection: a longitudinal analysis of rapid progressors and long-term asymptomatics. (1995)

To gain more insight into the role of HIV-1-specific cytotoxic T lymphocytes (CTL) in the pathogenesis of AIDS, we investigated temporal relations between HIV-1 Gag-specific precursor CTL (CTLp), HIV-1 viral load, CD4+ T cell counts, and T cell function. Six HIV-1-infected subjects, who were asymptomatic for more than 8 yr with CD4+ counts > 500 cells/mm3, were compared with six subjects who progressed to AIDS within 5 yr after HIV-1 seroconversion. In the long-term asymptomatics, persistent HIV-1 Gag-specific CTL responses and very low numbers of HIV-1-infected CD4+ T cells coincided with normal and stable CD4+ counts and preserved CD3 mAb-induced T cell reactivity for more than 8 yr. In five out of six rapid progressors Gag-specific CTLp were also detected. However, early in infection the number of circulating HIV-1-infected CD4+ T cells increased despite strong and mounting Gag-specific CTL responses. During subsequent clinical progression to AIDS, loss of Gag-specific CTLp coincided with precipitating CD4+ counts and severe deterioration of T cell function. The possible relationships of HIV-1 Gag-specific CTLp to disease progression are discussed.
Droplets for Ultrasmall-Volume Analysis (2009)

By using methods that permit the generation and manipulation of ultrasmall-volume droplets, researchers are pushing the boundaries of ultrasensitive chemical analyses. (To listen to a podcast about this feature, please go to the Analytical Chemistry Web site at pubs.acs.org/ancham.).
Hypoxic Stabilization of Vascular Endothelial Growth Factor mRNA by the RNA-binding Protein HuR (1998)

Vascular endothelial growth factor (VEGF) is a potent angiogenic factor whose expression is dramatically induced by hypoxia due in large part to an increase in the stability of its mRNA. Here we show that HuR binds with high affinity and specificity to the element that regulates VEGF mRNA stability by hypoxia. Inhibition of HuR expression abrogates the hypoxia-mediated increase in VEGF mRNA stability. Overexpression of HuR increases the stability of VEGF mRNA. However, this only occurs efficiently in hypoxic cells. We further show that the stabilization of VEGF mRNA can be recapitulated in vitro. Using an S-100 extract, we show that the addition of recombinant HuR stabilizes VEGF mRNA markedly. These data support the critical role of HuR in mediating the hypoxic stabilization of VEGF mRNA by hypoxia.
Annealing of GaN under high pressure of nitrogen (2002)

Gallium nitride, aluminum nitride and indium nitride are basic materials for blue optoelectronic devices. The essential part of the technology of these devices is annealing at high temperatures. Thermodynamic properties of the Ga–N system and their consequences to application of high nitrogen pressure for the annealing of GaN based materials are summarized.
Phononic Band Gap Width Control through Structural and Material Parameters in Two-Dimensional Phononic Crystals (2005)

The phononic band structures of two-dimensional solid phononic crystals with different lattice and scatterer symmetry are studied numerically, with three types of lattice (square, triangular, and rectangular) and four different scatterer shapes (circle, hexagon, square, and rectangle) considered. XY and Z vibration modes are investigated separately. Two types of phononic crystal are considered: one composed of high-density rods embedded in a low-density matrix, the other of low-density rods in a high-density matrix. In the former case, lattice type and polarization being fixed, the broadest gaps are obtained when the symmetry of the rods corresponds to that of the lattice (the shape of a rod is identical with that of the first Brillouin zone); the largest gap width values are observed in triangular lattice--based crystals (compared to those based on the square and rectangular lattices), the shape of the corresponding first Brillouin zone being closest to a circle. These rules do not apply to structures in which the density of the rod material is lower than that of the matrix. In this case, when the symmetry of the rods corresponds to that of the lattice, gaps either fail to appear at all, or are much narrower than in other configurations. The effect of other material parameter values (such as the longitudinal and transversal velocity values) on the relation between the energy gap width and the scatterer symmetry is found to be much lesser.
Isotonic Nebulized Disodium Cromoglycate Provides Better Protection against Methacholine- and Exercise-induced Bronchoconstriction (1988)

In 21 asthmatic subjects we determined whether inhalation of an isotonic solution of disodium cromoglycate (DSCG) would result in better protection against bronchial provocation with methacholine or exercise than the standard hypotonic solution of DSCG. Pretreatment with isotonic DSCG resulted in significantly greater reduction in exercise-induced bronchospasm (10 patients) than with hypotonic DSCG. In addition, the dose of methacholine required to induce a decrease greater than 20% in FEV1 was significantly higher following pretreatment with isotonic DSCG compared with placebo or hypotonic solution of the drug (11 patients). We conclude that nebulized isotonic DSCG provides better protection against exercise- and methacholine-induced bronchoconstriction than does the standard solution. Our findings suggest that the use of an isotonic solution of DSCG would be beneficial in the management of asthmatic patients.
Tyrosine phosphorylation of the alpha and beta subunits of the type I interferon receptor. Interferon-beta selectively induces tyrosine phosphorylation of an alpha subunit-associated protein. (1994)

We studied the phosphorylation of the alpha and beta subunits of the Type I interferon (IFN) receptor induced by Type I IFNs in the human U-266 and MOLT-4 cell lines. Both IFN-alpha and IFN-beta induced tyrosine phosphorylation of the beta subunit of the receptor. The Type I IFN-induced tyrosine phosphorylation of the beta subunit was rapid and transient, being detectable within 1 min of Type I IFN treatment and gradually diminishing to almost base-line levels by 60 min. All Type I IFNs studied were found to induce tyrosine phosphorylation of the alpha subunit of the Type I IFN receptor, the p135tyk2 and JAK-1 tyrosine kinases, and the ISGF3 alpha components. Interestingly, IFN-beta, but not IFN-alpha or IFN-omega, induced tyrosine phosphorylation of an alpha subunit-associated protein with an apparent molecular mass of approximately 100 kDa (p100). These data suggest the existence of a common signaling pathway(s) for Type I IFNs involving the alpha and beta subunits of the receptor, the tyrosine kinases p135tyk2 and JAK-1, and the ISGF3 alpha components. However, differences between the signaling pathways of different Type I IFNs exist, as suggested by tyrosine phosphorylation of an alpha subunit-associated protein only in response to IFN-beta.
Off-Line Bangla Signature Verification (2012)

In the field of information security, biometric systems play an important role. Within biometrics, automatic signature identification and verification has been a strong research area because of the social and legal acceptance and extensive use of the written signature as an individual authentication. Signature verification is a process in which the questioned signature is examined in detail in order to determine whether it belongs to the claimed person or not. Despite substantial research in the field of signature verification involving Western signatures, very few works have been dedicated to non-Western signatures such as Chinese, Japanese, Arabic, or Persian etc. In this paper, the performance of an off-line signature verification system involving Bangla signatures, whose style is distinct from Western scripts, was investigated. The Gaussian Grid feature extraction technique was employed for feature extraction and Support Vector Machines (SVMs) were considered for classification. The Bangla signature database employed in the experiments consisted of 3000 forgeries and 2400 genuine signatures. An encouraging accuracy of 90.4% was obtained from the experiments.
Synthesis of Pulcherriminic Acid by Bacillus subtilis (1972)

The pathway of pulcherriminic acid synthesis in Bacillus subtilis strains AM and AM-L11 (a leucine-requiring auxotroph) was investigated. Determinations of radioactivity in pulcherriminic acid synthesized by cells growing in media containing (14)C-labeled amino acids indicated that B. subtilis produced pulcherriminic acid from l-leucine. The organism utilized the carbon skeletons of two l-leucine molecules to synthesize one molecule of pulcherriminic acid. Similar results were obtained with starved cell suspensions. Growing cells formed significant amounts of pulcherriminic acid only in media including a carbohydrate such as starch. However, carbohydrate carbon was not required for the synthesis of pulcherriminic acid molecules. Data obtained with cell suspensions supported the hypothesis that cyclo-l-leucyl-l-leucyl is an intermediate in pulcherriminic acid biosynthesis and indicated that molecular oxygen is required for the conversion of cyclo-l-leucyl-l-leucyl to pulcherriminic acid. A pathway for the synthesis of pulcherrimin from l-leucine in B. subtilis is proposed.
Correlation between OPC model accuracy and image parameters (2006)

Performing MBOPC (model based Optical Proximity Correction) on layouts is an essential part of patterning advanced integrated circuits. With constantly shrinking CD tolerance and tighter ACLV budgets, the model has to be accurate within a few nanometers. The accuracy of a model in predicting wafer behavior dictates the success of the patterning process. Model calibration is a critical procedure to provide an accurate correlation between design and wafer features. The model calibration process consists of arriving at a variable threshold polynomial as a function of aerial image parameters -intensity maximum (I<sub>max</sub>), intensity minimum (I<sub>min</sub>), Slope, curvature etc.. In this paper, a strong correlation between the accuracy of the model and the image parameters is demonstrated. Data from model calibration of two different layers in 65nm technology node will be shown to demonstrate the dependence of model accuracy on aerial image parameters. Data show that accuracy of the model degrades a function of resolution, i.e. features with low I<sub>max</sub>, low slope and low contrast are difficult to model than higher resolution features. During calibration of the model, some parameters can be adjusted to obtain a balance between the model accuracy of weak and stronger resolution features. Suggestions for improving the accuracy of the weaker features based on an analysis of the image parameters are shown. The correlation between accuracy of the model and image parameters will be useful in limiting OPC corrections on features with poor aerial image quality.
Distortion-invariant target detection using shifted-reference joint transform correlator (2008)

A new pattern recognition system is proposed using multiple phase-shifted-reference fringe-adjusted joint transform correlation technique. The algorithm involves four different phase-shifted versions of the reference image, which eliminates all unwanted correlation terms and produces a single cross-correlation signal corresponding to each potential target. A fringe-adjusted filter is designed to generate a delta-like correlation peak with high discrimination between the signal and the noise. In addition, the detection performance is made invariant to different spatial distortions by incorporating a synthetic discriminant function, which is created from a set of training images of the reference object. The target detection system is also designed for recognition of multiple targets belonging to multiple reference objects simultaneously in the given input scene and hence provides a real-time class-associative decision on the presence of any target. The proposed technique is investigated using computer simulation with binary as well as gray images in various complex environments where it performs excellent in every case.
A Simple and Efficient Iodination of Alcohols on Polymer-Supported Triphenylphosphine (2002)

A simple, mild, and high-yielding procedure for the iodination of allylic, benzylic, and other primary alcohols using a combination of iodine and imidazole on polymer-supported triphenyl phosphine is described.