gebhart/patrepeval huggingface dataset:
Enhanced Transfection of a Bacterial Plasmid into Hybridoma Cells by Electroporation: Application for the Selection of Hybrid Hybridoma (Quadroma) Cell Lines (1992)

A procedure was investigated to transduce a bacterial plasmid containing a specific drug resistance marker (pSV2-neo), into a hybridoma cell line using electroporation. The effect of several buffers and the form of plasmid DNA (circular or linearized) on the stable transfection frequency were examined. When complete cell culture medium (DMEM) was used as electroporation buffer, we observed a two-fold increase in post-pulse viability and a ten- to thirty-fold increase in the transfection frequency of pSV2-neo, as compared with HEPES buffered 0.15 M sodium chloride. Supplementing DMEM with fetal bovine serum (DMEM + FBS) had some beneficial effect on post-pulse viability of the cells after electroporation, but did not markedly increase stable transfection frequency as compared with DMEM alone. Furthermore, with DMEM + FBS, the intact plasmid was transfected as effectively as linearized PSV2-neo. However, when using HEPES buffered saline, the transfection frequency of pSV2-neo increased two-fold after linearization as compared with intact plasmid. The drug resistance was used successfully as a marker for the selection of hybrid hybridoma (quadroma) cell lines after fusing two different hybridoma cell lines, producing anti-fibrin and anti-plasminogen activator antibodies respectively. The quadroma cells produced bispecific antibodies that are capable of accumulating plasminogen activator on a fibrin surface.
Adaptive Multi-Column Deep Neural Networks with Application to Robust Image Denoising (2013)

Stacked sparse denoising autoencoders (SSDAs) have recently been shown to be successful at removing noise from corrupted images. However, like most denoising techniques, the SSDA is not robust to variation in noise types beyond what it has seen during training. To address this limitation, we present the adaptive multi-column stacked sparse denoising autoencoder (AMC-SSDA), a novel technique of combining multiple SSDAs by (1) computing optimal column weights via solving a nonlinear optimization program and (2) training a separate network to predict the optimal weights. We eliminate the need to determine the type of noise, let alone its statistics, at test time and even show that the system can be robust to noise not seen in the training set. We show that state-of-the-art denoising performance can be achieved with a single system on a variety of different noise types. Additionally, we demonstrate the efficacy of AMC-SSDA as a preprocessing (denoising) algorithm by achieving strong classification performance on corrupted MNIST digits. 1
Fast iterative alignment of pose graphs with poor initial estimates (2006)

A robot exploring an environment can estimate its own motion and the relative positions of features in the environment. Simultaneous localization and mapping (SLAM) algorithms attempt to fuse these estimates to produce a map and a robot trajectory. The constraints are generally non-linear, thus SLAM can be viewed as a non-linear optimization problem. The optimization can be difficult, due to poor initial estimates arising from odometry data, and due to the size of the state space. We present a fast non-linear optimization algorithm that rapidly recovers the robot trajectory, even when given a poor initial estimate. Our approach uses a variant of stochastic gradient descent on an alternative state-space representation that has good stability and computational properties. We compare our algorithm to several others, using both real and synthetic data sets
Oncogenic H-ras stimulates tumor angiogenesis by two distinct pathways (1997)

The switch from a quiescent tumor to an invasive tumor is accompanied by the acquisition of angiogenic properties. This phenotypic change likely requires a change in the balance of angiogenic stimulators and angiogenic inhibitors. The nature of the angiogenic switch is not known. Here, we show that introduction of activated H-ras into immortalized endothelial cells is capable of activating the angiogenic switch. Angiogenic switching is accompanied by up-regulation of vascular endothelial growth factor and matrix metalloproteinase (MMP) bioactivity and downregulation of tissue inhibitor of MMP. Furthermore, we show that inhibition of phosphatidylinositol-3-kinase leads to partial inhibition of tumor angiogenesis, thus demonstrating that activated H-ras activates tumor angiogenesis through two distinct pathways. Finally, we show evidence for two forms of tumor dormancy.
Experimental evidence of ferroelectric negative capacitance in nanoscale heterostructures (2011)

We report a proof-of-concept demonstration of negative capacitance effect in a nanoscale ferroelectric-dielectric heterostructure. In a bilayer of ferroelectric Pb(Zr0.2Ti0.8)O3 and dielectric SrTiO3, the composite capacitance was observed to be larger than the constituent SrTiO3 capacitance, indicating an effective negative capacitance of the constituent Pb(Zr0.2Ti0.8)O3 layer. Temperature is shown to be an effective tuning parameter for the ferroelectric negative capacitance and the degree of capacitance enhancement in the heterostructure. Landau’s mean field theory based calculations show qualitative agreement with observed effects. This work underpins the possibility that by replacing gate oxides by ferroelectrics in nanoscale transistors, the sub threshold slope can be lowered below the classical limit (60 mV/decade).
Low cholesterol in erythrocyte membranes and high lipoperoxides in erythrocytes are the potential risk factors for cerebral hemorrhagic stroke in human. (2001)

The findings of the present study suggest that marked low RBC cholesterol and marked high RBC lipoperoxides may constitute the potential main risk factors for human cerebral hemorrhage, and that the oxidative and lipoperoxidative stress in the CHP bodies is pathologically aggravated, leading to the oxidative and lipoperoxidative damages in the CHP.
KINETICS OF MEMORY CONSOLIDATION: ROLE OF AMNESIC TREATMENT PARAMETERS (1969)

The consolidation theory states that with the passage of time the engram of a recent learning experience grows increasingly resistant to disruption by amnesic treatment. The time required to reach complete resistance ("consolidation time") is a controversial issue; current estimates range from 10(1) to 10(5) seconds. The present study suggests a parsimonious interpretation of the divergence, namely, that weak amnesic treatments fail to block memory consolidation but do slow its rate, so that post-treatment consolidation inflates the retention scores measured 24 hours later and leads to variably shortened "consolidation times."This study utilized 2880 neonate chicks trained in a one-trial avoidance paradigm. Retrograde amnesia was induced by treatment with flurothyl (CF(3)CH(2)-OCH(2)CF(3)) vapor. Apparent "consolidation times" determined by conventional data analysis varied widely as a function of flurothyl concentration and exposure time, ranging from 4 minutes under weak amnesic conditions (0.85% flurothyl; 1-min exposure) to 24 hours under strong conditions (1.7% flurothyl; 8-min exposure). With 1.7% flurothyl, the consolidation half-time was found to be 9.8 hours.
Functional Synthetic DNA Nanostructures (2014)

This thesis reports the use of molecular self-assembly with DNA to create custom tools for single molecule techniques. Explored tools include DNA gatekeepers for solid-state nanopores, a DNA based synthetic transmembrane channel and a DNA support for single-particle electron microscopy. It was possible to demonstrated the immense potential of DNA nanotechnology for single-molecule studies and lay the foundation for the structure evaluation of DNA nanostructures with near atomic resolution.
Genetic fusions with viral chemokines target delivery of nonimmunogenic antigen to trigger antitumor immunity independent of chemotaxis (2004)

The ideal vaccine carrier should be able to target antigen delivery and possibly recruit antigen-presenting cells (APC) and deliver an activation signal to promote adaptive immune responses. Ligands for chemokine receptors expressed on APC may be attractive candidates, as they can both target and attract APC. To investigate the requirement for APC recruitment, we used a pair of viral chemokines, agonist herpes simplex virus 8-derived macrophage inflammatory protein-I (vMIP-I) and antagonist MC148, which induce and suppress chemotaxis, respectively. Chemokine-antigen fusions efficiently delivered a model nonimmunogenic tumor antigen to APC for processing and presentation to antigen-specific T cells in vitro. Physical linkage of chemokine and antigen and specific binding of chemokine receptor by the fusion protein were required. Mice immunized with vMIP-I or MC148 fusion DNA vaccines elicited protection against tumor challenge. Therefore, vaccine efficacy depends primarily on the ability of the carrier to target antigen delivery to APC for subsequent processing and presentation, and chemotaxis directly induced by the chemokine moiety in the fusion may not be necessary.
Genetic algorithm based selective neural network ensemble (2001)

Neural network ensemble is a learning paradigm where several neural networks are jointly used to solve a problem. In this paper, the relationship between the generalization ability of the neural network ensemble and the correlation of the individual neural networks is analyzed, which reveals that ensembling a selective subset of individual networks is superior to ensembling all the individual networks in some cases. Therefore an approach named GASEN is proposed, which trains several individual neural networks and then employs genetic algorithm to select an optimum subset of individual networks to constitute an ensemble. Experimental results show that, comparing with a popular ensemble approach, i.e. averaging all, and a theoretically optimum selective ensemble approach, i.e. enumerating, GASEN has preferable performance in generating ensembles with strong generalization ability in relatively small computational cost. 1
Tracheobronchial mucin receptor for Pseudomonas aeruginosa: predominance of amino sugars in binding sites (1985)

Pseudomonas aeruginosa, a common respiratory tract colonizer and pathogen, adheres to injured tracheal cells and to tracheobronchial mucin. These phenomena suggest that there are specific receptors for this organism in the respiratory tract. The receptor on injured tracheal cells contains n-acetylneuraminic acid as the principal sugar, but the structure of the receptor in mucin has not been described. Using a microtiter plate assay to study bacterial adherence to mucin, we have partially characterized the mucin receptor for P. aeruginosa. The receptor for both nonmucoid and mucoid strains is sensitive to periodate oxidation, suggesting that it is carbohydrate in nature, and the amino sugars n-acetylglucosamine and n-acetylneuraminic acid inhibited the adherence of both types of strains. Nonmucoid strains were more sensitive to inhibition by n-acetylneuraminic acid than to inhibition by n-acetylglucosamine, but the mucoid strains varied in their sensitivities to inhibition by each amino sugar. Preincubation of mucin with heat-inactivated influenza A virus (which binds to neuraminic acid) significantly reduced the adherence of P. aeruginosa. Treatment of mucin with Clostridium perfringens neuraminidase also reduced bacterial adherence significantly. Treatment of mucin with pronase did not affect adherence. Our results suggest that n-acetylglucosamine and n-acetylneuraminic acid are important constituents of the binding sites for P. aeruginosa on human tracheobronchial mucin.
Adsorption equilibrium in immuno‐affinity chromatography with polyclonal and monoclonal antibodies (1986)

Abstract The effects of pH, ionic strength, anion species, and antibody concentration on the adsorption equilibrium between immobilized antibodies and antigens were studied by use of anti‐BSA, anti‐HSA, anti‐BlgG, and monoclonal anti‐HSA coupled to Sepharose 4B. The polyclonal antibodies possessed average binding affinities of the order of 10 8 M −1 , and the heterogeneity was accounted for by assuming a normal distribution of the free energy of antibody–antigen combination. The monoclonal antibody, on the other hand, showed a homogeneous affinity of the Langmuir type. Bound antigens could be eluted by lowering pH or adding a chaotropic anion, and their purity was very high. The antibody ligand was sufficiently stable for repeated use.
Inhibition of human endothelial cell proliferation by gold compounds. (1987)

Neovascularization has a role in the propagation of rheumatoid synovitis because the spread of mononuclear cell infiltration and the growth of pannus are dependent on the growth of new blood vessels. Growth of such vessels requires local endothelial cell (EC) proliferation. Inhibition of synovial EC proliferation, therefore, would have the potential to diminish rheumatoid inflammation. We have, therefore, studied the effects of gold sodium thiomalate (GST), auranofin, and gold chloride on the proliferation of human umbilical vein EC. GST suppressed both basal and EC growth factor-induced tritiated thymidine incorporation into EC in a dose-dependent fashion. Inhibition was observed with concentrations as low as 1 microgram/ml GST, 5 micrograms/ml gold chloride, and 0.1 microgram/ml auranofin, levels attainable in blood and synovium of patients. These results suggest that gold compounds have an antiangiogenic effect. The low concentrations inhibiting EC proliferation suggest that gold compounds may suppress rheumatoid synovitis by reducing the number of small blood vessels available for mononuclear cell infiltration and synovial tissue proliferation.
Stress enhancement and fatigue susceptibility of porous coated Ti‐6Al‐4V implants: An elastic analysis (1990)

An elastic stress analysis of porous-coated implant surfaces was performed using the finite element method. Three-hundred-microns-diameter metal beads sinter bonded onto an implant surface were modeled with sinter neck radii of 5, 10, 20, and 50 microns. Smooth-surface, single-bead, single-layer, and double-layer systems were analyzed. The finite element models were loaded to simulate bone-bead contact forces and lateral hip implant tensile forces. Results showed that, for a single bead sinter-bonded onto an implant surface, concentration of stress occurs either at the base of the sinter neck or within the neck itself, depending on the type of load applied. Under lateral hip implant tensile loads, a maximum stress concentration factor of 1.97 was obtained for a single bead sinter-bonded onto a implant surface. Addition of a single layer of beads onto the implant surface resulted in a significant increase in stress at the most proximal and distal ends of the porous layer, with a maximum stress concentration factor of 4.3. Addition of a second layer of beads did not significantly increase the magnitude of the stress concentration occurring at the ends of the porous layer. The results of this study provide stress concentration factors for porous coatings with sinter necks of known dimensions under loading conditions similar to those present along the lateral surface of a hip prosthesis.
Engineering Aggregation-Resistant Antibodies (2012)

The ability of antibodies to bind to target molecules with high affinity and specificity has led to their widespread use in diagnostic and therapeutic applications. Nevertheless, a limitation of antibodies is their propensity to self-associate and aggregate at high concentrations and elevated temperatures. The large size and multidomain architecture of full-length monoclonal antibodies have frustrated systematic analysis of how antibody sequence and structure regulate antibody solubility. In contrast, analysis of single and multidomain antibody fragments that retain the binding activity of mono-clonal antibodies has provided valuable insights into the determinants of antibody aggregation. Here we review advances in engineering antibody frameworks, domain interfaces, and antigen-binding loops to prevent aggregation of natively and nonnatively folded antibody fragments. We also highlight advances and unmet challenges in developing robust strategies for engineering large, multidomain antibodies to resist aggregation.
From Hydrogenases to Noble Metal–Free Catalytic Nanomaterials for H 2 Production and Uptake (2009)

Interconversion of water and hydrogen in unitized regenerative fuel cells is a promising energy storage framework for smoothing out the temporal fluctuations of solar and wind power. However, replacement of presently available platinum catalysts by lower-cost and more abundant materials is a requisite for this technology to become economically viable. Here, we show that the covalent attachment of a nickel bisdiphosphine-based mimic of the active site of hydrogenase enzymes onto multiwalled carbon nanotubes results in a high-surface area cathode material with high catalytic activity under the strongly acidic conditions required in proton exchange membrane technology. Hydrogen evolves from aqueous sulfuric acid solution with very low overvoltages (20 millivolts), and the catalyst exhibits exceptional stability (more than 100,000 turnovers). The same catalyst is also very efficient for hydrogen oxidation in this environment, exhibiting current densities similar to those observed for hydrogenase-based materials.
Multilevel Measurement of Acetabular Version Using 3-D CT-generated Models: Implications for Hip Preservation Surgery (2010)

These data are relevant for surgeons in providing targets for normal positioning of the acetabulum during periacetabular osteotomies and acetabular recontouring procedures.
High SMAD4 levels appear in microsatellite instability and hypermethylated colon cancers, and indicate a better prognosis (2011)

Colorectal cancer (CRC) is one of the most common causes of cancer-related deaths in western countries. CRC are commonly divided in cancers showing microsatellite stability (MSS) or microsatellite instability (MSI). A more novel classification is dependent on promoter hypermethylation of CpG islands (the CpG island methylator phenotype, CIMP), where cancers show high, low or negative methylation status. SMAD4, located on chromosome 18q, has been thoroughly investigated during the last years. Loss of SMAD4 expression has been reported to correlate with poor CRC patient prognosis. In this study, we analyze the impact of SMAD4 expression on prognosis in relation to MSI screening status and CIMP status. Four hundred and seventy-nine paraffin-embedded specimens of CRC were examined for nuclear SMAD4 expression using immunohistochemistry. The tumors were scored loss (-), moderate (+) and high (++) expressing tumors. Loss of SMAD4 correlated significantly with decreased survival in all colon cancer patients. High SMAD4 expression, however, was significantly associated with increased survival, especially in colon cancer patients, which has undergone potential curative surgery. In addition, in MSI tumors and CIMP-high tumors, high SMAD4 expression was significantly related to increase in survival, while loss of SMAD4 resulted in a significantly poorer prognosis. SMAD4 expression was not correlated to prognosis in rectal cancer cases. We conclude, loss of SMAD4 indicates a poor prognosis in colon cancer patients. The novel findings that high SMAD4 expression predicts a better prognosis suggests that SMAD4 immunohistochemistry could constitute a prognostic marker in combination with CIMP and MSI screening status.
The Rep Protein of Adeno-Associated Virus Type 2 Interacts with Single-Stranded DNA-Binding Proteins That Enhance Viral Replication (2003)

Adeno-associated virus (AAV) type 2 is a human parvovirus whose replication is dependent upon cellular proteins as well as functions supplied by helper viruses. The minimal herpes simplex virus type 1 (HSV-1) proteins that support AAV replication in cell culture are the helicase-primase complex of UL5, UL8, and UL52, together with the UL29 gene product ICP8. We show that AAV and HSV-1 replication proteins colocalize at discrete intranuclear sites. Transfections with mutant genes demonstrate that enzymatic functions of the helicase-primase are not essential. The ICP8 protein alone enhances AAV replication in an in vitro assay. We also show localization of the cellular replication protein A (RPA) at AAV centers under a variety of conditions that support replication. In vitro assays demonstrate that the AAV Rep68 and Rep78 proteins interact with the single-stranded DNA-binding proteins (ssDBPs) of Ad (Ad-DBP), HSV-1 (ICP8), and the cell (RPA) and that these proteins enhance binding and nicking of Rep proteins at the origin. These results highlight the importance of intranuclear localization and suggest that Rep interaction with multiple ssDBPs allows AAV to replicate under a diverse set of conditions.
Plasma-induced-damage of GaN (1996)

Plasma-induced-damage often degrades the electrical and optical properties of compound semiconductor devices. Despite the fact that the binding energy of GaN is larger than that for more conventional III--V compounds, etch damage is still a concern. Photoluminescence measurements and atomic force microscopy have been used to determine the damage induced in GaN by exposure to both electron cyclotron resonance (ECR) and inductively coupled plasmas (ICP) generated Ar plasmas.
Gamma delta T cell recognition of tumor Ig peptide. (1995)

Although gamma delta T cells have been postulated to act as a surveillance mechanism that eliminates transformed or otherwise damaged cells, little is known about tumor recognition by gamma delta T cells, including the Ags that are recognized and the molecules that present them. Previously, we described human gamma delta CTL that recognize the autologous B cell lymphoma. Here we report that these gamma delta CTL lyse heterologous cells transfected with the tumor Ig lambda chain gene. Furthermore, the lambda chain is recognized as processed peptide in an Id-specific manner. T cell recognition does not involve classical MHC molecules, but it could be blocked by Abs directed against the heat shock protein grp75. These findings show a specific gamma delta T cell response to a highly polymorphic Ag such as tumor Id and implicate heat shock protein as a molecule required for recognition.
Pharmacy Compounding Quality Control and Pharmaceutical Development Strategies for Seventeen alpha Hydroxyprogesterone Caproate in Prevention of Preterm Delivery (2014)

Seventeen alpha hydroxyprogesterone caproate (17-OHPC) is the only FDA-approved drug labeled for prevention of preterm delivery. This drug is also available as a compounded product from licensed compounding pharmacies. This article reviews the FDA approval history and pharmacy compounding quality control data of 17-OHPC, as well as briefly discusses possible future pharmaceutical development strategies for 17-OHPC.