gebhart/patrepeval huggingface dataset:
Peptides Corresponding to the Heptad Repeat Motifs in the Transmembrane Protein (gp41) of Human Immunodeficiency Virus Type 1 Elicit Antibodies to Receptor-Activated Conformations of the Envelope Glycoprotein (2001)

Two heptad repeat regions in the ectodomain of the human immunodeficiency virus type 1 (HIV-1) transmembrane subunit (gp41) self-assemble into a six-helix bundle structure that is critical for virus entry. Immunizations with peptides corresponding to these regions generated antibodies specific to the receptor-activated conformations of gp41.
Antihypertensive 5,6-diarylpyridazin-3-ones (1980)

The synthesis of a series of 5,6-diarylpyridazinones is described. Some members of this series display an antihypertensive effect in both the spontaneously hypertensive rat (SHR) model and the deoxycorticosteroid (DOCA) model of hypertension. The most potent compounds in the series have halogen substituents on the 5,6-diphenyl rings, a beta-substituted alkyl group at the 2 position of the ring, and acetyl or cyano substituent at the 4 position.
Testing the Significance of Microorganism Identification by Mass Spectrometry and Proteome Database Search (2000)

We derive and validate a simple statistical model that predicts the distribution of false matches between peaks in matrix-assisted laser desorption/ionization mass spectrometry data and proteins in proteome databases. The model allows us to calculate the significance of previously reported microorganism identification results. In particular, for deltam = +/-1.5 Da, we find that the computed significance levels are sufficient to demonstrate the ability to identify microorganisms, provided the number of candidate microorganisms is limited to roughly three Escherichia coli-like or roughly 10 Bacillus subtilis-like microorganisms (in the sense of having roughly the same number of proteins per unit-mass interval). We conclude that, given the cluttered and incomplete nature of the data, it is likely that neither simple ranking nor simple hypothesis testing will be sufficient for truly robust microorganism identification over a large number of candidate microorganisms.
Development of a Probiotic Cheddar Cheese Containing Human-Derived <i>Lactobacillus paracasei</i> Strains (1998)

Cheddar cheese was manufactured with either Lactobacillus salivarius NFBC 310, NFBC 321, or NFBC 348 or L. paracasei NFBC 338 or NFBC 364 as the dairy starter adjunct. These five strains had previously been isolated from the human small intestine and have been characterized extensively with respect to their probiotic potential. Enumeration of these strains in mature Cheddar cheese, however, was complicated by the presence of high numbers (>10(7) CFU/g of cheese) of nonstarter lactic acid bacteria, principally composed of lactobacilli which proliferate as the cheese ripens. Attempts to differentiate the adjunct lactobacilli from the nonstarter lactobacilli based on bile tolerance and growth temperature were unsuccessful. In contrast, the randomly amplified polymorphic DNA method allowed the generation of discrete DNA fingerprints for each strain which were clearly distinguishable from those generated from the natural flora of the cheeses. Using this approach, it was found that both L. paracasei strains grew and sustained high viability in cheese during ripening, while each of the L. salivarius species declined over the ripening period. These data demonstrate that Cheddar cheese can be an effective vehicle for delivery of some probiotic organisms to the consumer.
Recruitment of the <i>mecA</i> Gene Homologue of <i>Staphylococcus sciuri</i> into a Resistance Determinant and Expression of the Resistant Phenotype in <i>Staphylococcus aureus</i> (2001)

Strains of methicillin-resistant Staphylococcus aureus (MRSA) have become the most important causative agents of hospital-acquired diseases worldwide. The genetic determinant of resistance, mecA, is not a gene native to S. aureus but was acquired from an extraspecies source by an unknown mechanism. We recently identified a close homologue of this gene in isolates of Staphylococcus sciuri, a taxonomically primitive staphylococcal species recovered most frequently from rodents and primitive mammals. In spite of the close sequence similarity between the mecA homologue of S. sciuri and the antibiotic resistance determinant mecA of S. aureus, S. sciuri strains were found to be uniformly susceptible to beta-lactam antibiotics. In an attempt to activate the apparently "silent" mecA gene of S. sciuri, a methicillin-resistant derivative, K1M200 (for which the MIC of methicillin is 200 microg/ml), was obtained through stepwise exposure of the parental strain S. sciuri K1 (methicillin MIC of 4 microg/ml) to increasing concentrations of methicillin. DNA sequencing of the mecA homologue from K1M200 revealed the introduction of a point mutation into the -10 consensus of the promoter: the replacement of a thymine residue at nucleotide 1577 in the susceptible strain K1 by adenine in the resistant strain K1M200, which was accompanied by a drastic increase in transcription rate and the appearance of a new protein that reacted with monoclonal antibody prepared against the penicillin-binding protein 2A (PBP2A), i.e., the gene product of S. aureus mecA. Transduction of mecA from K1M200 (cloned into a plasmid vector) into a methicillin-susceptible S. aureus mutant resulted in a significant increase of methicillin resistance (from a methicillin MIC of 4 micro/ml to 12 and up to 50 microg/ml), the appearance of a low-affinity PBP detectable by the fluorographic assay, and the production of a protein that reacted in a Western blot with monoclonal antibody to PBP2A. Antibiotic resistance and the protein products disappeared upon removal of the plasmid-borne mecA homologue. The observations support the proposition that the mecA homologue ubiquitous in the antibiotic-susceptible animal species S. sciuri may be an evolutionary precursor of the methicillin resistance gene mecA of the pathogenic strains of MRSA.
Photochromism of Diarylnaphthopyrans (1994)

Abstract A series of 3,3-diaryl-3H-naphtho[2,1-b]pyrans were prepared and their photochromic properties measured in plastic matrix. The influence of a variety of substituents on color, intensity, and fade were studied.
Highly reflective fiber Bragg gratings written through a vinyl ether fiber coating (1999)

Highly reflective fiber Bragg gratings (reflectivity >99.99%, -45 dB in transmission) have been written through a 55-μm-thick novel polymer fiber coating in a low (5 mole%) germania-doped optical fiber. The coating is based on vinyl ether chemistry using a cationic photoinitiator."
Pulsed Oscillating Mass Spectrometer:  A Miniaturized Type of Time-of-Flight Mass Spectrometer (2005)

We report the development, characterization, and performance of a new type of time-of-flight mass analyzer that employs an oscillatory ion flight path and uses secondary electrons to record the mass spectrum. The analyzer is simple in concept and design and inexpensive to build and has been made as small as 6-cm total length. The oscillating ions produce a periodic secondary electron signal whose frequency is mass dependent in mathematically the same way as a conventional time-of-flight analyzer. Because of the oscillating nature of the ions, we have called the analyzer the pulsed oscillating mass spectrometer.
Exact simplification of support vector solutions (2002)

This paper demonstrates that standard algorithms for training support vector machines generally produce solutions with a greater number of support vectors than are strictly necessary. An algorithm is presented that allows unnecessary support vectors to be recognized and eliminated while leaving the solution otherwise unchanged. The algorithm is applied to a variety of benchmark data sets (for both classification and regression) and in most cases the procedure leads to a reduction in the number of support vectors. In some cases the reduction is substantial.
Analysis of Steady State Detection of Resistive Bridging Faults in BiCMOS Digital ICs (1992)

This paper analyzes the effects induced on the electrical behavior of BiCMOS digital circuits by bridging faults, whose instrinsic resistance value is shown to have a strong impact on the static behavior of faulty gates and of their fan-out gates. The problem of fault detection is then addressed considering two different testing techniques (current monitoring and functional testing). Simulations of the electrical behavior of faulty BiCMOS circuits have enlightened the main differences with respect to the CMOS technology: the larger driving capability of BJTs with respect to MOSFETs makes the detection of bridging faults much more difficult in BiCMOS circuits when functional testing is considered, but more effective when current monitoring is used.
Epstein-Barr virus latent infection membrane protein increases vimentin expression in human B-cell lines (1989)

Latent Epstein-Barr virus (EBV) infection activates B-lymphocyte proliferation through mechanisms which are partially known. One approach to further delineate these mechanisms is to identify cellular genes whose expression is augmented in cells latently infected with EBV. Since EBV-negative Burkitt's lymphoma cells can be grown in continuous culture and EBV can establish growth-altering latent infection in these cells, some effects of EBV on B-lymphocyte gene expression can be studied by using this in vitro system. Pursuing this latter approach, we have used cDNA cloning and subtractive hybridization to identify a gene whose expression is increased after EBV infection. This gene encodes the cytoskeletal protein vimentin. Latent infection of established EBV-negative Burkitt's lymphoma cell lines with the transforming EBV strain, B95-8, resulted in dramatic increases in vimentin mRNA and protein levels, while infection with the nontransforming P3HR1 strain failed to do so. Vimentin induction was reproduced by the expression of the single EBV gene which encodes the latent infection membrane protein (LMP). An amino-terminal LMP deletion mutant did not induce vimentin. These results are of particular interest in light of the transforming potential of LMP, as demonstrated in rodent fibroblasts, and the interaction between vimentin and LMP observed in immunofluorescent colocalization and cell fractionation studies.
Quantitative methods for reconstructing tissue biomechanical properties in optical coherence elastography: a comparison study (2015)

We present a systematic analysis of the accuracy of five different methods for extracting the biomechanical properties of soft samples using optical coherence elastography (OCE). OCE is an emerging noninvasive technique, which allows assessment of biomechanical properties of tissues with micrometer spatial resolution. However, in order to accurately extract biomechanical properties from OCE measurements, application of a proper mechanical model is required. In this study, we utilize tissue-mimicking phantoms with controlled elastic properties and investigate the feasibilities of four available methods for reconstructing elasticity (Young's modulus) based on OCE measurements of an air-pulse induced elastic wave. The approaches are based on the shear wave equation (SWE), the surface wave equation (SuWE), Rayleigh-Lamb frequency equation (RLFE), and finite element method (FEM), Elasticity values were compared with uniaxial mechanical testing. The results show that the RLFE and the FEM are more robust in quantitatively assessing elasticity than the other simplified models. This study provides a foundation and reference for reconstructing the biomechanical properties of tissues from OCE data, which is important for the further development of noninvasive elastography methods.
Synthesis and Biological Evaluation of a Focused Mixture Library of Analogues of the Antimitotic Marine Natural Product Curacin A (2000)

The marine natural product curacin A served as the lead compound for the combinatorial synthesis of 6-compound mixture libraries. Fluorous trapping with a vinyl ether tag was used to streamline purification of the heterogeneous multicomponent reaction products and provide chemically clearly defined mixtures. The screening profile of one mixture library, 17mix, was attractive enough to warrant the re-synthesis of the individual compounds, and an evaluation of their biological effects validated the composite data previously obtained on the product mixture. The most active of these compounds inhibited tubulin polymerization with an IC50 of ca. 1 μM, showed an average growth inhibition activity GI50 of ca. 250 nM, inhibited [3H]colchicine binding to tubulin, and blocked mitotic progression at nanomolar concentrations. These compounds represent some of the most potent synthetic curacin A analogues identified to date but have simplified structures, greater water solubility, and increased chemical stability.
A pressure/oxygen/temperature sensing SoC for multimodality intracranial neuromonitoring (2013)

A fully integrated SoC for multimodality intracranial neuromonitoring is presented. This SoC includes a capacitive MEMS pressure sensor, an electrochemical oxygen sensor, a solid-state temperature sensor and sensor interface circuits in a single chip. Chopper stabilization and dynamic element matching techniques are applied in sensor interface circuits to reduce circuit noise and offset. On-chip calibration is implemented for each sensor to compensate process variations. Measured accuracies of the pressure, oxygen, and temperature sensors are ±1 mmHg, ±1 mmHg, and ±0.2 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">o</sup> C, respectively. Implemented in 0.18-μm CMOS, the SoC occupies an area of 1.4 mm × 4mm and consumes 188-μW DC power.
Tree detection from aerial imagery (2009)

We propose an automatic approach to tree detection from aerial imagery. First a pixel-level classifier is trained to assign a {tree, non-tree} label to each pixel in an aerial image. The pixel-level classification is then refined by a partitioning algorithm to a clean image segmentation of tree and non-tree regions. Based on the refined segmentation results, we adopt template matching followed by greedy selection to locate individual tree crowns.
Diagnostic Potential of Serum VEGF-D for Lymphangioleiomyomatosis (2008)

rate of recurrence, particularly distant recurrence, by approximately 50 percent" 1 and "The addition of trastuzumab to paclitaxel after a regimen of doxorubicin and cyclophosphamide reduced the rates of recurrence by half among women with HER2-positive breast cancer." 2 Dr. Nash's letter calls attention to the importance of understanding the difference between absolute and relative risks in analyzing the results of clinical trials.
Oligonucleotide-Polyamide Conjugate Probes with Multiple Non-Radioactive Labels: Applications and Comparison to Radiolabelled Probes (1991)

Abstract Oligonucleotide-polyamide conjugate molecules containing multiple biotin labelled polyamide have been used as non-radioactive probes. We found that these probes have similar sensitivity to 32p labelled probes. Chemiluminescent detection is the method of choice.
A Novel Design of Static Electrostatic Generator for High Voltage Low Power Applications Based on Electric Field Manipulation by Area Geometric Difference (2019)

An electrostatic generator is an electromechanical device that produces static charges at high voltage and low current. This technology is mature enough, as it has existed for many centuries. Nevertheless, the working principle of most of the commonly used electrostatic generators is still based on typical mechanical methods, which consequently makes them bulky and limits their controllability on the generated charges, e.g., Van de Graaff generator that uses the friction between two different materials to generate electrostatic charges. In this paper, a novel design of a static electrostatic generator (SEG) is presented based on a completely different idea compared to existing electrostatic generators, which offers several potential benefits. The idea originates from the study of a parallel plates capacitor—for instance, if a voltage is applied to two plates of a capacitor, then according to Gauss’s law, both of the plates must have an equal and opposite charge. Suppose one of the plates has a different geometry, with a shorter length than the other, then the number of the charges on both plates will not be equal. Thus, by manipulating the geometrical area of the device, a different number of charges will be generated on both metal conductors. Therefore, a different number of charges are generated on both conductors; hence, by connecting both conductor plates of the capacitance, excess charges will remain on the device. The proposed idea was assessed with computer simulations using finite element and finite difference methods for a variety of different scenarios to determine the optimal design of the proposed device. The device offers several advantages over traditional electrostatic generators, such as that it can generate either positive or negative charges by merely reversing the polarity of the DC source; additionally, it is very simple, lightweight, and easy to manufacture. In particular, the principal advantage of the proposed device is that it is a static one, and no mechanical movement is required to produce charges. Further, the design is general enough and scalable. The simulation results demonstrate the performance of the proposed device.
Implementation and Validation of a New Combined Model for Outdoor to Indoor Radio Coverage Predictions (2010)

A new model used to compute the outdoor to indoor signal strength emitted from an outdoor base station is presented. This model is based on the combination of 2 existing models: IRLA (Intelligent Ray Launching), a 3D Ray Optical model especially optimized for outdoor predictions, and MR-FDPF (Multiresolution Frequency Domain ParFlow), a 2D Finite Difference model initially implemented for indoor propagation. The combination of these models implies the conversion of the ray launching paths on the border of the buildings, into virtual source flows that will be used as input for the indoor model. The performance of the new combined model is evaluated via measurements at 2 frequencies (WiMAX and WiFi). This solution appears to be efficient for radio network planning, in term of both accuracy and computational cost.
Identifying regional sensitive queries in web search (2008)

In Web search ranking, the expected results for some queries could vary greatly depending upon location of the user. We name such queries regional sensitive queries. Identifying regional sensitivity of queries is important to meet users' needs. The objective of this work is to identify whether a user expects only regional results for a query. We present three novel features generated from search logs and build a meta query classifier to identify regional sensitive query. Experimental results show that the proposed method achieves high accuracy in identifying regional sensitive queries.
Molecular Cloning of the Gene for Mouse Leukotriene‐C<sub>4</sub> Synthase (1997)

Leukotriene C4 (LTC4) synthase (LTC4S), an integral membrane protein, catalyzes the conjugation of leukotriene A4 with reduced glutathione to form LTC4, the biosynthetic parent of the additional cysteinyl leukotriene metabolites. An XmnI-digested fragment of a P1 clone from a 129 mouse ES library contained the full-length gene of 2.01 kb for mouse LTC4S. The mouse LTC4S gene is comprised of 5 exons of 122, 100, 71, 82 and 241 nucleotides, with intron sizes that range from 76 nucleotides to 937 nucleotides. The intron/exon boundaries are identical to those of the human genes for LTC4S and 5-lipoxygenase-activating protein (FLAP). Primer extension demonstrated a single transcription-initiation site 64 bp 5' of the ATG translation-start site. Nucleotide sequencing of 1.2 kb of the 5' flanking region revealed multiple putative sites for activating protein-2, CCAAT/enhancer-binding protein, and polyoma virus enhancer-3. Fluorescent in situ hybridization mapped the mouse LTC4S gene to mouse chromosome 11, in a region containing the genes for interleukin 13 and granulocyte/macrophage-colony-stimulating factor, and orthologous to the chromosomal location of 5q35 for the human LTC4S gene. Thus, the mouse LTC4S gene is similar in size, intron/exon organization and chromosomal localization to the human LTC4S gene. Recent mutagenic analysis of the conjugation function of human LTC4S has identified R51 and Y93 as critical for acid and base catalysis of LTA4 and reduced glutathione, respectively. A comparison across species for proteins that possess LTC4S activity reveals conservation of both of these residues, whereas R51 is absent in the FLAP molecules. Thus, within the glutathione S-transferase superfamily of genes, alignment of specific residues allows the separation of LTC4S family members from their most structurally similar counterparts, the FLAP molecules.
Erbium-doped and Raman microlasers on a silicon chip fabricated by the sol–gel process (2005)

We report high-Q sol–gel microresonators on silicon chips, fabricated directly from a sol–gel layer deposited onto a silicon substrate. Quality factors as high as 2.5×107 at 1561nm were obtained in toroidal microcavities formed of silica sol–gel, which allowed Raman lasing at absorbed pump powers below 1mW. Additionally, Er3+-doped microlasers were fabricated from Er3+-doped sol–gel layers with control of the laser dynamics possible by varying the erbium concentration of the starting sol–gel material. Continuous lasing with a threshold of 660nW for erbium-doped microlaser was also obtained.
PSP94: Evaluation of Prognostic Utility in Patients Treated with Radiotherapy for Nonmetastatic Prostate Cancer (2000)

ABSTRACT Objectives: Conflicting reports exist as to the utility of PSP94 in the diagnosis and management of prostate cancer. We have identified serum‐bound forms of PSP94 in prostate cancer patients. To further evaluate the usefulness of this finding, we measured bound and free serum PSP94 levels in patients with nonmetastatic prostate cancer before radiotherapy. Materials and Methods: Pretreatment levels of free PSP94 in 42 patients were measured in serum via a competitive enzyme‐linked immunosorbent assay. Levels of bound PSP94 were measured by a semiquantitative assay after fractionation of total serum proteins by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis and Western blot analysis. Pretreatment levels of prostate specific antigen (PSA) were measured by a commercially available assay. Archival sera from 42 patients and a subgroup of 27 patients with “favorable” pretreatment PSA values (i.e., < 10 ng/ml) were statistically analyzed. Pretreatment levels of PSP94 (free and bound) and PSA, as well as tumor stage and grade, were correlated with treatment outcome (biochemical relapse‐free survival) postradiotherapy. Results: Pretreatment PSA and the ratio of bound to free PSP94 were significant predictors of relapse postradiotherapy on univariate analysis. An elevated ratio of bound to free PSP94 was a stronger predictor ( p = 0.0074) of relapse postradiotherapy compared with PSA level ( p = 0.070) in a subgroup of prostate cancer patients with “favorable” pretreatment PSA levels. Conclusions: The results presented here indicate that serum PSP94‐bound complexes must be considered in evaluating the clinical utility of PSP94 as a prostate cancer marker. A higher ratio of bound to free PSP94 may indicate worse outcome postradiotherapy. Differential testing of serum PSP94 has shown that it, in addition to PSA, may be of prognostic value for patients receiving radiotherapy for nonmetastatic prostate cancer.